A POPULATION VIABILITY ANALYSIS OF THE LAYSAN FINCH

(TELESPIZA CANTANS)

A DISSERTATION SUBMITTED TO THE GRADUATE DIVISION OF THE

UNIVERSITY OF HAWAI‘I IN PARTIAL FULFILLMENT OF THE
REQUIREMENTS FOR THE DEGREE OF

DOCTOR OF PHILOSOPHY

IN

ZOOLOGY
(ECOLOGY, EVOLUTION, AND CONSERVATION BIOLOGY)

AUGUST 2005

By
Andrew McClung

Dissertation Committee:

Sheila Conant, Chairperson

Leonard Freed
Robert Kinzie
Miriam Stark
Andrew Taylor
We certify that we have read this dissertation and that, in our opinion, it is satisfactory in

scope and quality as a dissertation for the degree of Doctor of Philosophy in Zoology

(Ecology, Evolution, and Conservation Biology).

DISSERTATION COMMITTEE

____________________________
Chairperson

____________________________

____________________________

____________________________

____________________________

ii
 ACKNOWLEDGEMENTS

I wish to thank my committee, Sheila Conant, Leonard Freed, Bob Kinzie, Miriam

Stark, and Andy Taylor, for their help, guidance, and patience. I am particularly grateful

to Sheila for being such a great friend and mentor for these many years, and to Andy for

helping me learn multivariate statistics and aspects of population modeling that would

otherwise have remained opaque. The UH EECB program funded my initial three-year

fellowship and research grants that made most of my data collection possible. I am also

indebted to Dan Doak at the University of California at Santa Cruz, for illuminating

many of the fundamental concepts of population viability analysis, both practical and

theoretical. Chad Yoshinaga and Bud Antonelis of the NOAA National Marine Fisheries

Service, along with Phil Johnson and Beth Flint of the US Fish and Wildlife Service, and

a host of co-workers affiliated with both agencies, made field work in the Northwest

Hawaiian Islands both feasible and a great pleasure. George Roderick, Rosie Gillespie,

Leo Shapiro, Andy Bohonak, and other post-doctoral researchers and graduate students in

the Roderick-Gillespie laboratory at UC-Berkeley helped me get my early bearings on

PCR and basic genetics. Rob Fleischer, Carl Macintosh, Lori Eggert, Stacey Lance, and

many other researchers at the Genetics Laboratory of the National Zoo (now part of the

Smithsonian Institution Museum of Natural History) helped guide me through the

challenges of genetics research, and Sarah Burgess and Rob Toonen helped immensely

with the analytical aspects of that discipline once the data had been collected. Finally, I

wish to thank my parents, Ann Merritt and Nelson McClung, and friends in both

California and Hawaii for their years of unwavering support, generosity, and compassion.

iii
 ABSTRACT

Species diversity has been shown to enhance ecosystem resilience, and human

dependence on ecosystem functions creates incentives to maintain diversity and minimize

human contributions to extinction. Population viability analysis (PVA) provides a way to

assess both the extinction risk of threatened populations and the relative value of

management actions. This set of studies applies three PVA methodologies to native and

translocated populations of the Laysan finch (Telespiza cantans), a federally listed

endangered endemic passerine. Historically restricted to Laysan, the finches went nearly

extinct when rabbits devegetated the island in the early 20th century. The 1967

translocation of 108 finches to Southeast Island at Pearl and Hermes Reef (PHR),

intended to reduce global extinction risk, had by 1985 grown to four populations

comprising over 900 individuals. However, by 1998 two of those populations had gone

extinct, raising questions about the viability of the remaining populations.

Count-based PVA, stochastic demographic matrix (SDM) simulations, and VORTEX

all project low levels of intrinsic extinction risk among the three populations. Precision of

specific extinction risk estimates is limited by the amount and quality of time series and

demographic data, making it difficult to resolve a change in extinction risk associated

with a weed invasion at Southeast Island. However, sea level rise scenarios substantially

increase extinction risk over 100-year time horizons.

SDM and VORTEX models roughly agree on the mean stochastic growth rate for the

Southeast Island population, although the effect of genetic parameters in VORTEX

appears to inflate extinction risk estimates. Microsatellite genotypes of families at PHR-

Southeast yield an extra-pair paternity estimate of 19%, high for a tropical island

iv
passerine but, based on VORTEX simulations, not likely to increase extinction risk due

to increased inbreeding depression.

Both VORTEX and a modified count-based PVA indicate that management actions

such as supplementation of individuals from Laysan to the higher-risk populations, along

with translocation to establish an additional population, could substantially reduce

extinction risk for the species. These scenarios also indicate that translocation may be

more cost-effective in reducing extinction risk. However, translocation options are

limited, so there remain questions about the long-term viability of this species.

v
 TABLE OF CONTENTS

Acknowledgements............................................................................................................iii
Abstract...............................................................................................................................iv
List of Tables.....................................................................................................................vii
List of Figures...................................................................................................................viii
List of Abbreviations..........................................................................................................ix
Chapter 1: Introduction......................................................................................................10
Macroevolution and Biodiversity....................................................................................10
Population Viability Analysis (PVA)..............................................................................16
Purpose and Content of Chapters....................................................................................20
Chapter 2: A Count-Based PVA for Three Populations of the Laysan Finch...................22
Introduction.....................................................................................................................22
Methods...........................................................................................................................26
Results.............................................................................................................................32
Discussion.......................................................................................................................53
Chapter 3: Laysan Finch PVA: Individual-Based and Stochastic Demographic
Matrix Models...............................................................................................................58
Introduction.....................................................................................................................58
Methods...........................................................................................................................62
Results.............................................................................................................................75
Discussion.......................................................................................................................86
Chapter 4: The Laysan Finch Genetic Mating System: Estimating the Rate of
Extra-Pair Paternity and Its Impact on Extinction Risk................................................91
Introduction.....................................................................................................................91
Methods...........................................................................................................................95
Results...........................................................................................................................100
Discussion......................................................................................................................104
Chapter 5: Conclusions and Future Work........................................................................109
Risk and the Costs and Benefits of Management Action..............................................112
Appendix A: Laysan Finch Time Series Data.................................................................121
Appendix B: MATLAB Program for Count-Based PVA................................................122
Appendix C: Regression Coefficients (Sensitivities) for Count-Based PVA Model......125
Appendix D:: MATLAB Program for Stochastic Demographic Matrix Model..............126
Appendix E: MATLAB Program for Extinction Risk Cost-Benefit Model....................129
Literature Cited................................................................................................................136

vi
 LIST OF TABLES

2.1. Model selection results for three Laysan finch populations.......................................32

2.2. Environmental autocorrelation in growth rates...........................................................35

2.3. Volumes under risk surfaces shown in Figure 2.8......................................................52

3.1. Nonlinear regression results: logistic model fitted to time series data.......................64

3.2. Summary of encounter histories used to estimate survival.........................................67

3.3. Parameter values used in VORTEX simulations .......................................................71

3.4. Sensitivities of the stochastic demographic matrix model.........................................82

3.5. Supplementation and translocation parameter sensitivities in VORTEX..................84

4.1. Mark-recapture and tissue-sample sizes at Pearl and Hermes Reef and Laysan........96

4.2. Microsatellite locus characterization and tests for Hardy-Weinberg equilibrium....101

5.1. Relative risk volumes defined by extinction probability surfaces............................112

5.2. Extrinsic catastrophe probabilities and expected survival impacts...........................113

5.3. Cost structure for the two forms of management intervention.................................113

5.4. Effects of supplementation and translocation...........................................................115

vii
 LIST OF FIGURES

2.1. Extinction behavior of the logistic simulation model.................................................38

2.2. Effect of adding catastrophes to the simulation model for the Laysan population.....40

2.3. Median extinction probability CDFs for three Laysan finch populations..................40

2.4 Median extinction probability CDFs with overlapping confidence envelopes............42

2.5. Apparent effect of the Verbesina invasion on Laysan finch extinction risk...............45

2.6. The effect of the missed 2001 count on parameter estimates.....................................48

2.7. Asymptotic decline in relative uncertainty in population parameter estimates..........49

2.8. Extinction risk surfaces...............................................................................................51

3.1. Mortality values by stage and sex for Laysan finches at Southeast Island (PHR).....69

3.2. Log stochastic growth rates for three Laysan finch populations................................77

3.3. VORTEX projections of intrinsic extinction risk.......................................................78

3.4. Projected population sizes for SDM simulation models.............................................78

3.5. VORTEX projections of inbreeding effects...............................................................80

3.6. VORTEX parameter sensitivities...............................................................................82

4.1. Distribution of LOD scores for Laysan finch paternity tests....................................102

viii
 LIST OF ABBREVIATIONS

AIC..........................................................................................Akaike information criterion

ANOVA.................................................................................................analysis of variance
ASY............................................................................................................after second year
CDF....................................................................................cumulative distribution function
CE.........................................................................................................confidence envelope
CI.............................................................................................................confidence interval
EPF.....................................................................................................extra-pair fertilization
EPP..........................................................................................................extra-pair paternity
HY.........................................................................................................................hatch year
MLE.......................................................................................maximum likelihood estimate
NWHI.......................................................................................Northwest Hawaiian Islands
PHR...................................................................................................Pearl and Hermes Reef
PVA..........................................................................................population viability analysis
QE................................................................................................................quasi-extinction
SLR....................................................................................................................sea level rise
SY.......................................................................................................................second year

ix
 CHAPTER 1

INTRODUCTION

Macroevolution and Biodiversity

Macroevolution involves two interdependent stochastic processes, speciation and

extinction (Ridley 1996), and can be viewed as a species-scale analog of similar,

individual-scale stochastic processes, such as population fluctuations. As population sizes

rise and fall with changes in rates of births and deaths, aggregate numbers of species

similarly rise and fall with changes in speciation and extinction rates. Fossil evidence

shows that some speciation processes, such as adaptive radiation, accelerate in the wake

of extinctions (Raup 1991a, Jablonski 2001), making extinctions facilitators of those

types of speciation. As interspecific competition at a given trophic level is reduced,

ecological resources at lower trophic levels go underexploited, opening up opportunities

for adaptation. Other species processes such as phyletic evolution are less tightly coupled

to extinctions. However, phyletic change typically occurs at much slower rates than the

punctuational evolutionary bursts of radiations (Ridley 1996), so the tempo of evolution

depends more sensitively on extinction and radiation rates than on rates of phyletic

transformation. Radiations, then, while not historically common, contribute significantly

to the structure and distribution of higher taxa (families, orders, and classes), while

phyletic transitions are most significant at the level of individual species.

The impact of extinctions on speciation rates is most obvious when the extinction event

is large, affecting a disproportionate number of taxa. A small number of mass extinctions

inferred from the fossil record, killed large fractions of the extant species (on average

10
about half) over a time period quite short (about 1-5%) compared to the preceding period

of relative stability (Raup 1991b). These mass extinctions' short durations are obscured

by imprecision in the fossil record; their actual durations may have been shorter, and

there is evidence that transition times of about 1-10 thousand years are typical (Raup

1991a, Ridley 1996). Thus, mass extinctions can be characterized by extinction rates on

the order of 0.1 –1% of extant species per millennium. Paleontological estimates give

average species lifetimes on the order of 1-10 million years, and a background extinction

rate of roughly one species per year, or 0.001 per millennium. Therefore, averaged across

the slowly growing taxonomic diversity reflected in the fossil record, mass extinctions

represent an acceleration of extinction over the background rate by four to six orders of

magnitude (Raup 1991b, Ridley 1996).

Both mass extinctions and extinctions of individual species during periods of relative

biotic stability are two extremes of a continuous, strongly right-skewed distribution of

extinction event magnitudes (Raup 1991b). Between the extremes are regional-scale

extinctions that affect intermediate numbers of taxa. Over the last billion years, during

the most significant evolution of eukaryotic life, paleontological evidence suggests that

most extinction events at global and regional scales were due to climatic changes, and

therefore took place over one or several millennia (Ridley 1996). The most famous

exception is not really an exception: the mass extinction at the end of the Cretaceous, for

which there is strong evidence of meteoric impact initiating particularly rapid climate

change, can therefore still be considered climate-driven even though the pace of change

was between two and three orders of magnitude faster than endogenous climate changes

(Raup 1991b).

11
 Assessments of background versus mass extinction rates are of interest because species

losses due to human activity have been estimated at between 1,000 and 10,000 times the

background extinction rate (Myers 1988, Wilson1998). With evidence for extensive

mammal extinctions during the late Pleistocene invasions of Australia and the Americas,

the advent of Homo sapiens may be driving a mass extinction of its own (Martin and

Klein 1984, Diamond 1984). Comparable anthropogenic extinctions involving not only

mammals, but also birds, arthropods, mollusks, and plants, have been documented

throughout the archipelagoes of the Pacific, and most recently, within the last half

millennium, have been further extended to include most higher taxa of animals and plants

across most of the planet. Universality and causation are key distinctions: mass

extinctions in fossil history are attributable to major climatic changes, and they often

affected the most ecologically vulnerable taxa, while the current extinction spasm is not

only more pervasive taxonomically (including plants and arthropods much more

extensively than before) but also causally linked to the activity of a particular species.

The recent increase in extinction rates has been particularly dramatic in geographic

centers of biotic endemism (Myers 1988, Wilson 1998). This fact makes intuitive sense

on probabilistic grounds: in more species-rich areas, more species will have a limited

range and small population size, and are therefore more likely to go extinct than very

widespread, populous species. However, in addition to the probabilistic argument,

geographically constrained endemics have also proven to be more extinction-prone in

island ecosystems, where isolation typically alleviates certain selective pressures on

colonizing species, which therefore evolve a reduced ability to resist those pressures. The

extreme example of this scenario is the Hawaiian archipelago, the most isolated in the

12
world, whose biota is predominantly comprised of species evolved in situ, so that prior to

human colonization more than 90% of the birds, arthropods, mollusks, and plants were

endemic species (Carson and Clague, 1995). Land bird species, for which the

paleontological evidence is best-documented, declined by half after the advent of

Polynesian and European colonists, and the remaining native species are with few

exceptions formally listed as endangered or at least threatened (Olson and James 1982,

1984). This situation does, however, make Hawaii a good place to study extinction

processes. Like tropical wet forests in South America, Madagascar, Indonesia, and

Africa, Hawaii is undergoing rapid anthropogenic change (Martin 1984), with the

advantage to extinction studies that the small geographic scale and extreme isolation of

the islands, most especially the Northwestern Hawaiian Islands (NWHI) throws into

relief aspects of extinction processes that can remain obscure elsewhere.

The modern avifauna of the Northwestern Hawaiian Islands (NWHI) is now comprised

primarily of seabirds. Several million years ago, however, the islands now visible only as

coral atolls were more topographically varied, much as the main Hawaiian Islands are

today (Carson and Clague, 1995). Fossil and historical records of the main islands

indicate that the Hawaiian biota was more diverse even in the recent past, and the

ancestral avifauna contained numerous passerine species. Between three and five million

years ago, a single vagrant flock of finches established a stable population and

eventually began to colonize new adaptive zones created by the geographic and

ecological diversity of the island environment, leading to the radiation of the Hawaiian

honeycreepers (Tarr and Fleischer, 1995). Today, a single generalist finch species persists

on Laysan Island. This bird, the Laysan Finch (Telespiza cantans), is one of only three

13
remaining passerines in the NWHI, and the only one remaining on Laysan. Unlike the

more derived honeycreepers, the Laysan species is an omnivorous ground-finch, feeding

on a variety of seeds, leaves, flowers, insects, and the eggs of seabirds and conspecifics

(Ely and Clapp 1973, Morin and Conant 2002). Such behavioral flexibility has enabled

the finch to survive not only the harsh environment of Laysan, but also the introduction

of rabbits, a catastrophe that devegetated Laysan and nearly extinguished the finch

population by 1924 (Morin and Conant 2002). Having declined between 1915 and 1923

from aabout 4,000 to about 100 individuals, the finch population rebounded to over 1,000

individuals by 1936 (Ely and Clapp 1973). However, the catastrophic nature of the rabbit

introduction, coupled with the high environmental stochasticity of Laysan, led the US

Fish & Wildlife Service to translocate 108 finches 640 kilometers to the northwest, to

Pearl and Hermes Reef (PHR) in 1967. The agency's goal in creating a second population

was reduce the risk of species extinction in the event of a population-level extinction at

Laysan, which might occur if, for example, a shipwreck resulted in the establishment of

rats on Laysan.

At the time of the translocation, the vegetation at PHR was similar to that of Laysan.

Thus, despite of the difference in habitat area (approximately 200 vegetated hectares at

Laysan, versus a total of 27 vegetated hectares at PHR, distributed across four islets), the

habitat quality at PHR appeared to be comparable to that of Laysan. The apparent

suitability of PHR as a translocation site was supported by the rapid growth of the

founder population at Southeast Island. After a bout of winter mortality, the Southeast

Island population rose from approximately 50 to over 700 individuals by 1973 (Sincock

and Kridler 1977). By that time, two finches had spontaneously colonized Grass Island,

14
about eight kilometers west of Southeast, and these were supplemented by the

translocation of six more Southeast Island birds in 1970. With the Southeast Island

population peak in 1973, another spontaneous colonization was detected, at North Island,

about 16 kilometers north of Southeast. By the mid-1980s, the North Island population

grew to more than 300 individuals (Morin and Conant 2002), so that the total population

across all four islets at PHR (Seal-Kittery Island was also spontaneously colonized by the

mid-1970s) was estimated at around 900 birds through much of the 1980s.

However, in the intervening years, both the Seal-Kittery and North Island populations

have gone extinct, and at Southeast Island, the flora has changed dramatically (Amerson,

et al, 1974). In particular, the bunchgrass Eragrostis variabilis, the dominant nesting and

food substrate for finches on Laysan (Morin and Conant 1990, Morin and Conant 2002),

has declined at PHR from being one of the dominant species to one of the most rare,

especially at the largest PHR islet, Southeast Island. The vegetation diversity in general

has also declined, from 22 species recorded in the early 1970s to the 12 in evidence

today. One result is that the finches have changed their nesting behavior, particularly nest

substrate choice (Morin and Conant 1990), which has shifted from nearly 100% of nests

being constructed within tussocks of E. variabilis at Laysan to only 3% of nests at PHR

(Morin and Conant 1990), with most (53%) located in the introduced weed Setaria

verticillata, and 11% in plastic debris washed ashore from the ocean. Comparable shifts

in feeding behavior accompany the nesting behavior change, with the primary food

source at PHR having become the hard-shelled seeds of Tribulus cistoides (Conant 1988).

Other researchers (Tarr, et al. 1998; and Fleischer, et al. 1991) have found evidence of

genetic drift among nine microsatellite loci, with the PHR populations showing

15
significant genetic divergence in allele frequencies (allozyme studies were less

conclusive; see Fleischer, et al. 1991), including fixation of one allele in the Grass Island

population at PHR. These changes in allele frequency are taken to indicate drift because

the microsatellite loci are not expected to be under selection. These circumstances have

led to questions about further behavioral changes that might result from either drift or

selection, or both, and also about the long-term prognosis for the translocated Laysan

finch populations at PHR. Specifically, Tarr, et al. (1998) raised the question of whether

the translocated populations can be considered, from a management perspective, to

provide adequate reserves of demographic and genetic variability to serve as robust

insurance against the risk of extinction at Laysan.

Population Viability Analysis

The continued development of conservation biology comprises continuing efforts to

make conservation practice more thoroughly grounded in, and justified by, robust

quantitative analysis (NRC 1995, Soulé and Wilcox 1980, Soulé 1987, Meffe and Carroll

1997, Hunter 2002, Morris and Doak 2002, Beissinger and McCullough 2002). A key

component of such analysis is the projection of population size trajectories over time, and

the effect of management actions on such trajectories for endangered or threatened

populations (Dennis, et al. 1991). In the United States, the Endangered Species Act gives

some conservation efforts the force of law, and the legal, political, and economic stakes

of management activity can therefore be quite high (Carroll et al. 1996). Efforts to base

management actions on analyses of population viability has led to controversy about both

16
the techniques employed in particular instances of population viability analysis (PVA),

and also about the inferences drawn regarding management responses to population risk.

Much PVA controversy has arisen from the use of diffusion approximations to model

population trajectories. Diffusion models, the continuous-time analogs of discrete

stochastic processes such as Brownian motion, had been developed substantially in the

1970's (Richter-Dyn and Goel 1972, Goel and Richter-Dyn 1974; Capocelli and Ricciardi

1974; Ricciardi 1977; Turelli 1977). The appeal of the diffusion approximation (DA) for

population modeling is that it conveniently yields explicit analytical formulas for

extinction-related quantities such as the mean time to extinction and the cumulative

distribution function (CDF) of the extinction time (Dennis, et al. 1991; Pollett 2001).

Questions about whether this convenience came at a cost of unrealistically simplifying

the dynamics of populations with age-structured demography were addressed by Lande

and Orzack (1988), who showed that diffusion models could accurately approximate the

long-term behavior of age-structured matrix models of population growth.

Dennis, et al. (1991), made diffusion modeling substantially more accessible by

presenting a linear regression method that greatly simplified estimation of the two

fundamental parameters of diffusion models, the drift parameter µ and variance

parameter σ2. These two parameters, along with the current population size, are the only

information required for calculating the extinction time CDF for an exponential-growth

diffusion process. Dennis, et al., acknowledged that the omission of density dependence

from the model (as well as the impermissibility under the diffusion approximation of

strongly non-normal, negative growth rates, or catastrophes) was unrealistic for many

natural populations. Furthermore, for populations with certain growth characteristics

17
(long term growth rates near zero, and relatively high variability in growth), the

uncertainties in parameter estimation would lead to wide confidence envelopes around

the CDF curves. However, they argued that the model could still "provide useful

supplemental information" about population dynamics and appropriate management

actions.

Unfortunately, exponential growth models give rise to extinction time distributions that

are strongly positively skewed (Dennis, et al. 1991), with some trajectories persisting for

extremely long times, so that the mean (expected) time to extinction is not well correlated

with the most likely (modal) or median times (Ludwig 1996a). Analytical expressions for

potentially less misleading metrics such as the median extinction time are mathematically

more cumbersome. Other researchers, such as Ludwig (1996a, 1996b, 1999), found fault

with projected extinction time distributions that lacked precision and predictive power to

an extent that made them unreliable for management decision-making. Ludwig's

conclusions that diffusion models would do a poor job of predicting the behavior of small

or strongly fluctuating populations (Ludwig 1996a) and that maximum likelihood

methods for count-based PVA would severely underestimate extinction risk (Ludwig

1996b) resulted in counterarguments by Dennis (1996) that Bayesian approaches like that

presented by Ludwig were tantamount to abandoning the scientific method.

The controversy intensified when Coulson, et al. (2001, but see also Burgman and

Possingham 2000) disputed the claim by Brook, et al. (2000) that PVA was, in general,

sufficiently accurate to be useful in management. This assertion followed the work of

Fieberg and Ellner (2000), which built upon Ludwig's earlier studies and showed that the

predictive accuracy of PVAs based on time series data (and relying on density-

18
independent population models and diffusion approximations) was limited to extinction

risk assessments projected no farther into the future than 20% of the time series length.

However, Elderd, et al. (2003), countered that the predictive accuracy of count-based

PVA depends on growth rates contained in the time series. Specifically, if the mean

growth rate is much greater or less than zero, and the variance is relatively low, then

predictive power is much better than if the mean is small (near zero) and the variance is

relatively large. Confirmation of this assertion (which is essentially a reiteration of the

diffusion approximation requirement that jumps around the long-term mean growth rate

be small and fit a normal distribution – see Methods below) is found in a recent study of

gray whales: Gerber, et al. (1999) found that the California Gray Whale (Eschrichtius

robustus) could have been removed from the Endangered Species List on the basis of

population projections made with arbitrarily-selected 11-year subsets of the 19 year time

series that had accrued by 1996. Similarly, McCarthy, et al. (2003) concluded that

ranking relative risk is reasonably accurate and that count-based PVA methods are

suitable for management purposes as long as investigators do not insist on precise

estimates of extinction times. Similar forms of this controversy have arisen regarding

other PVA methodologies such as stochastic demographic matrix models (Pascual et al.

1997, Beissinger and Westphal 1998, Mills et al 1999, Reed et al. 2002) and PVA

software programs such as VORTEX (Miller and Lacy 2003, Brook et al. 1997, 2000,

2002), both of which require increasing quantities of data across a broader spectrum of

parameters than do PVAs based on diffusion models.

This dissertation focuses on comparing current PVA methods, given their various

strengths and weaknesses, and applying them to the three extant Laysan finch

19
populations. The goal is to assess whether they produce congruent results, and what

management recommendations can be derived from their use.

Purpose and Content of Chapters

Chapter 2 applies a count-based PVA methodology, projecting population trajectories

using parameter estimates obtained from analysis of time series of population counts.

Annual counts are transformed to estimates of the logarithms of growth rates, and the

form of density dependence is assessed by information criteria statistics, with the null

case (no density dependence in growth) being the diffusion approximation model. Tests

to detect growth rate autocorrelation and outliers are performed, and variance in growth

rates is adjusted to compensate for observer error. Simulated populations with the

resulting parameter values are then projected fifty years into the future, and the

cumulative distribution function for the extinction probability is computed, and the

baseline CDFs of the three populations are compared. The effect of a weed invasion on

one of the populations is examined, and the number of years of population counts

required to detect meaningful differences in extinction risk is estimated. Finally, a

modified simulation is performed which varies carrying capacity to simulate the effect of

reduced land area due to projected global sea level rise.

Chapter 3 uses the VORTEX PVA program and a stochastic demographic matrix

(SDM) model to examine extinction risk among the extant Laysan finch populations.

Survival estimates for both models are obtained via Program MARK, using banding data

obtained from four field seasons at PHR, and with stochasticity implemented by sampling

randomly from a normal distribution centered on the maximum-likelihood estimates.

20
Fertility estimates are based on over 70 nests surveyed during the 1999 and 2000 field

seasons at PHR-Southeast Island. Sensitivities of both models to uncertainty in parameter

estimates are studied, and both are modified to simulate a climate change effect on

carrying capacity (specifically, a linear reduction due to sea level rise).

Chapter 4 studies the Laysan finch genetic mating system, specifically the frequency of

extra-pair paternity (EPP) and the extent to which it could influence effective population

size, which in turn is expected to influence extinction risk. Although the Laysan finch

(Telespiza cantans) mating system has been considered monogamous, the species is

sexually dimorphic in both size and plumage coloration, suggesting some frequency of

polygyny or extra-pair mating. DNA was extracted from the feathers of more than 600

finches representing about 30 PHR-Southeast families, 35 individuals at PHR-Grass

Island, and almost 100 birds at Laysan. Microsatellite alleles were amplified and sized at

eight loci, and genotypes were compared using CERVUS parentage analysis software to

detect mismatches, adjusted for allele frequencies throughout the population, between

behaviorally-assigned parents and the most likely genetic assignments.

Finally, Chapter 5 summarizes the findings of this research and discusses their

implications for management of the Laysan finch populations. The congruency of the

results obtained from different population projection techniques is reviewed, and the cost-

effectiveness of different management actions is assessed.

21
 CHAPTER 2

A COUNT-BASED POPULATION VIABILITY ANALYSIS

FOR THREE POPULATIONS OF THE LAYSAN FINCH

INTRODUCTION

The evolution of conservation biology comprises continuing efforts to make

conservation practice more thoroughly grounded in robust quantitative analysis (Soulé

and Wilcox 1980; Soulé 1987; Boyce 1992; Lande 1993; Foley 1994; Mangel and Tier

1993; Lacy, et al. 1995; NRC 1995; Beissinger and McCullough 2002; Morris and Doak

2002). A key component of such analysis is the projection of population size trajectories

over time, and the effect of management actions on such trajectories for endangered or

threatened populations (Dennis, et al. 1991). Efforts to base management actions on

analyses of population viability has led to controversy about both the techniques

employed in particular instances of population viability analysis (PVA), and also about

the inferences drawn regarding management responses to population risk.

Much of the controversy about PVA has arisen from the use of diffusion

approximations to model population trajectories. Diffusion models, the continuous-time

versions of Brownian motion, were developed substantially in the 1970's for population

modeling (Richter-Dyn and Goel 1972, Goel and Richter-Dyn 1974, Capocelli and

Ricciardi 1974, May 1974, Ricciardi 1977, Turelli 1977). A decade later, Lande and

Orzack (1988) showed that such models could accurately approximate the long-term

behavior of age-structured matrix models of population growth. The appeal of the

diffusion model is that it conveniently yields explicit analytical formulas for extinction-

22
related quantities such as the mean time to extinction and the cumulative distribution

function (CDF) of the extinction time (Dennis, et al. 1991; Pollett 2001). Dennis, et al.

(1991), made the use of diffusion models substantially more tractable by presenting a

linear regression method that greatly simplified estimation of the drift parameter µ and

variance parameter σ2. However, the use of diffusion models requires making several

assumptions about the data that are often violated by natural populations (Dennis, et al.

1991; Morris and Doak 2002). The assumptions are that the growth rate and its variance

are constant (no temporal or density dependence, implying no demographic stochasticity

at small population sizes), that deviations from the linear model are normally distributed

(no catastrophes) and serially uncorrelated (no temporal autocorrelation), and that

variance inflation due to observation error is negligible (Dennis, et al. 1991; Morris and

Doak 2002). Although Dennis, et al., described a suite of mechanisms to test for

deviations from these assumptions, techniques to compensate for them were lacking.

Furthermore, the authors acknowledged that the omission of density dependence from the

model was unrealistic for many natural populations, and that, for short time series or

populations with µ near zero, the uncertainties in parameter estimation would lead to

wide confidence envelopes around the CDF curves. Nevertheless, they argued that the

model could still "provide useful supplemental information" about population dynamics

and appropriate management actions.

Ludwig (1996a, 1996b, 1999), applying a similar population growth model to several of

the time series datasets analyzed by Dennis, et al. found fault with projected extinction

time distributions that lacked precision and predictive power to an extent that made them

unreliable for management decision-making. Ludwig's conclusions that diffusion models

23
would do a poor job of predicting the behavior of small or strongly fluctuating

populations (Ludwig 1996a) and that maximum likelihood methods for count-based PVA

would severely underestimate extinction risk (Ludwig 1996b) resulted in

counterarguments by Dennis (1996) that Bayesian approaches like that presented by

Ludwig were tantamount to abandoning the scientific method. Controversy continued as

Fieberg and Ellner (2000) estimated the length (in annual counts) of time series data

needed for a PVA to correctly predict the extinction risk of a population to within a

tolerance of +/-20%. Their result that adequate prediction could only be made for periods

of time not exceeding 20% of the duration of the time series data supported neither the

pessimistic view of Ludwig nor the optimism of Dennis, et al., but rather suggested that

PVA could usefully inform management actions only for well-studied species with long

time series, and then only for short prediction horizons (Fieberg and Ellner 2000, Elderd

et al. 2003).

In these analyses, neither the time series data nor the projection methods were adjusted

to compensate for violations of the assumptions of the diffusion model, assumptions that

are valid only for exponential growth processes. However, recent work (see Morris and

Doak 2002, chapter 4, for a review) on simulation-based methods and parameter

modifications permit PVAs based on time series data to be adjusted in ways that purport

to compensate for violations of the assumptions of diffusion models. The time series for

one species in particular, the Laysan finch (Telespiza cantans), was analyzed by both

Dennis, et al. (1991), and by Ludwig (1996a, 1999), but without testing or compensation

for density dependence, autocorrelation, or observer error effects (although observer error

was treated in one part of Ludwig's 1999 analysis). The present study re-analyzes the

24
Laysan finch time series, including not only the Laysan population studied previously but

also the two extant translocated populations at Pearl and Hermes Reef (PHR). Model

selection based on the Akaike Information Criterion (AIC) was used to assess the form of

density dependent population growth. Other deviations from the density independent

exponential growth model, such as outlying growth rates (catastrophes), autocorrelation,

and observer error are also tested and compensated for. The fit of the exponential growth

model to the time series data is compared both to the fit of a simple Ricker logistic model

(similar to that used in Saether et al. 2000), and also to a generalized form of the logistic,

the theta logistic (Gilpin and Ayala 1974, Morris and Doak 2002) in which the change in

per capita growth rate with population size is allowed to be nonlinear. Additional model

adjustments include testing for (and, where significant, incorporating) catastrophes,

environmental autocorrelation, and adjustments for observer error. Effects of time series

length on parameter uncertainty are explored, along with their consequent effects on the

width of CDF confidence envelopes. This part of the study focuses on whether the

adjustments reduce uncertainty sufficiently to enable discrimination of different degrees

of risk between different populations, or, for populations subject to particular

disturbances or management actions, discrimination of changes in risk as a result of

disturbance or management. Along these lines, there is an assessment of the effects of a

recent (1998) weed invasion at PHR, to gauge limits on the speed with which changes in

extinction risk can be evaluated using count-based techniques. Finally, because the mean

elevation of the land area available to the extant finch populations is less than five meters,

the study investigates the projected effects on extinction risk of global sea level rise and

commensurate reduction of atoll land area.

25
METHODS

Population size time series for the three Laysan finch populations (see Appendix A)

were taken from USFWS trip reports and transect data sheets, which were checked

against the numbers given in the Birds of North America (BNA) account for the Laysan

finch (Morin and Conant 2002). In the one situation where a discrepancy was detected

between the published account and the trip reports (for the PHR-Southeast time series in

1987), the data used were those obtained directly from the trip reports. At Laysan, since

the mid-1980's, transect counts have consisted of 120 100-yard strip transects, 16.5 feet

wide, walked along haphazardly-chosen edges of pre-selected randomized grid squares

placed over the island's 400 hectares of vegetated area. Prior to 1986, there was more

variability in the timing and spatial regularity of the transect counts. The data set for the

Laysan Island population consists of 28 population size estimates made between 1966

and 1998, with an interruption from 1978 to 1982. At PHR, the Southeast Island

population was estimated on the basis of 100-115 100-yard strip transects, also 16.5 feet

wide, across the island's 12 vegetated hectares; however, in contrast to Laysan's grid

array for transect placement, Southeast Island transects were haphazardly placed, subject

to the condition that they not overlap. Temporal variability in performing transect counts

at PHR-Southeast was comparable to that at Laysan (less that +/-10% of a year in year-

to-year sampling intervals). Also, in contrast to the two relatively long continuous

sampling periods at Laysan, PHR-Southeast, because of its greater remoteness and lack

of year-round field staff presence, afforded only 18 population size estimates comprising

three continuous monitoring periods (1967-1973, 1984-1991, and 1997-2000). Transect

sampling at PHR-Grass Island was conducted differently from the sampling of the other

26
two island populations: because the total vegetated area of Grass Island is less than three

hectares, only 30-35 transects of 30 yards by 16.5 feet were surveyed, with only one

continuous segment of 10 years actually obtained during the 32 years between the initial

discover of finches at Grass Island and the population estimate in 2000.

The analytical methods applied to these time series adhered as closely as possible to the

methods described in chapters one through five of Morris and Doak (2002). Because of

the importance of using the biologically appropriate model structure to making accurate

assessments of extinction risk (Pascual et al. 1997), the three time series were tested for

evidence of density dependent population growth. In addition, tests for environmental

autocorrelation among growth rates, outliers relative to model predictions (catastrophes),

and an adjustment for the effect of observation error were also applied (White 2000,

Morris and Doak 2002).

For detecting density dependent population growth, simple linear regressions of log

growth rates versus population size may be unreliable (Case 2000), so an AIC-based

model-selection method was used instead (Burnham and Anderson 1998, Morris and

Doak 2002). For each time series, a nonlinear regression1 of log growth rates versus

population size was used to fit three models to the data: zero density dependence

(exponential growth model), linear density dependence (logistic model), and nonlinear

density dependence (theta logistic model). The error sum of squares resulting from each

model fit was then divided by the total number of transitions in the time series, with the

resulting average variance V leading to a log-likelihood given by -(q/2)(ln(2πV)+1),

where q is the number of transitions (Morris and Doak 2002). From these likelihoods, for

each population and each model, the AIC statistic was calculated as

27
-2ln(Lmax) + 2pq/(q-p-1), where p is the number of parameters in the model, including the

variance estimate (this is the "corrected" AIC statistic, AICc, appropriate for small sample

sizes, described in Burnham and Anderson 1998 and Morris and Doak 2002). AIC

weights were also calculated, using the formula given in Morris and Doak (2002, p. 118),

to determine the relative degree of support for each model, given the data, for each

population time series. Finally, because the three models are nested, differing in structure

by only one additional parameter for each increase in complexity, likelihood ratio tests

were also performed and compared to the AIC results.

In density-independent models, temporal autocorrelation in log growth rates has been

shown to increase extinction risk (Foley 1994, Morris and Doak 2002). For density-

dependent cases, the effect of growth rate autocorrelation on extinction risk is more

complex, with the effect on extinction risk dependent on the sign of the correlation.

Detection of significant autocorrelation in a time series would argue for designing a

simulation model so as to accurately reflect that correlation, whether positive or negative.

In this study, autocorrelations among deviations of observed growth rates from those

predicted by the best-fit population growth model were assessed using the method given

in Morris and Doak (2002). Time series of predicted log growth rates were generated

using the maximum likelihood parameter estimates for the best-fit model (as determined

by AIC statistics and likelihood ratio tests); predicted values were subtracted from the

observed log growth rates, and Pearson correlation coefficients were calculated for

offsets of one to four years.

Density-independent models also provide a straightforward way to test for the presence

of catastrophes, according to the linear regression method of Dennis, et al. (1991): they

28
are typically taken to be any transition whose externally studentized residual is more than

two standard deviations from the fitted line (Dennis et al. 1991). This criterion is

essentially the same as that used by Ludwig (1999) in assessing extinction risk for the

Mandarte Island population of song sparrows (Melospiza melodia). For density-

dependent (nonlinear) models, it is reasonable to apply the same approach, treating as a

catastrophe any transition for which the externally studentized residual is less than -2.

The proportion of process variance (σ2) attributable to observer error was estimated

using White's (2000) method, which uses the variability among transect counts to

estimate the proportion of the variance in the log growth rates that results from

undercounts and overcounts of the actual population (Morris and Doak 2002). This

spurious variance was then subtracted from the raw value of σ 2 to estimate the true

variation in population growth rates due to environmental fluctuations. White's method

has the advantage of accommodating different levels of observation error in different

years, whereas a simpler method presented by Morris and Doak (2002) assumes constant

variance across years. USFWS records for the Pacific/Remote Islands National Wildlife

Refuge Complex include Laysan finch strip transect data for 10 years (1985-1995) at

Laysan Island, and 8 years (1984-1991) at Southeast Island. Since larger values of σ 2

increase estimates of extinction risk, population simulations were performed using

adjusted σ 2 values.

Having identified the most likely form of density dependence (among the models

tested), parameter estimates were obtained from the nonlinear regression output and used

to simulate 50 groups of 1,000 replicate populations (the program code for the Laysan

population model is listed in Appendix B), projected over 100-year time horizons. For all
29
three time series, neither the log growth rates nor their deviations from predicted values

(according to the best-fit model; see below) showed evidence of significant non-

normality (Anderson-Darling test, n = 28, 15, and 9, and p = 0.71, 0.49, and 0.98, for the

Laysan, Southeast, and Grass Island populations, respectively). Therefore, environmental

stochasticity was modeled by a normally-distributed noise term, added to the growth rate

parameter in the population growth model (May 1974, Turelli 1977). Thus, for each

simulated population trajectory, deviations from the maximum likelihood estimate (MLE)

of the growth rate were normally distributed and scaled to σ, the square root of the

growth rate process error. In addition, to account for parameter uncertainty in estimating

extinction risk, each simulated trajectory was based on parameter values randomly

chosen from normal distributions, centered on the parameter MLEs and bounded by the

confidence intervals obtained from the nonlinear regression. To simulate the effects of

catastrophes, population trajectories included a randomly-drawn growth rate from among

the observed set of outlier transitions (for those populations with non-normal growth rates

detected within their time series), supplied at the same relative frequency as the outliers

(Morris and Doak 2002). The omission of explicit accounting of demographic

stochasticity and genetic factors in the model was compensated by setting quasi-

extinction thresholds high enough that those factors would not be expected to have a

significant effect on extinction probability. For Laysan finches, that threshold density at

which Allee effects or inbreeding depression might become significant is not known.

However, given their social and vocal behavior, their tendency to forage in loose

aggregations (not flocks per se — as island endemics without predators, flocking would

not be expected to develop for migration or predator avoidance; see Gill 1995), and their

30
record of surviving a population crash (at Laysan in the early 1920s) that reduced their

number to about 100 (Ely and Clapp 1973), the Allee threshold is likely to be a low

density (roughly 0.1 individuals per hectare). In addition, for the Grass Island

simulations, because the population is not known to have risen above 50 individuals at

any time, population numbers were rounded at each time step of the simulation. This

modification was intended to reduce the possibility that non-integer population numbers

could permit simulated Grass Island populations to stay above the quasi-extinction

threshold for unrealistically long times.

To rank the relative risk of the three populations, comparisons were also made between

extinction risk levels at specific numerical quasi-extinction thresholds. Examining

particular median CDF curves and their confidence envelopes permitted an assessment of

the uncertainty in extinction risk estimates due to parameter uncertainty. For these

analyses, and particularly for the weed invasion component of the study, I chose quasi-

extinction thresholds of 50 at Laysan, 20 at Southeast, and 8 at Grass. These values were

somewhat arbitrary: although the Laysan population is known to have rebounded from

about 100 individuals and the Grass Island population at PHR has survived 35 years from

an initial founding number of 8, the Southeast Island threshold is very uncertain. To gain

a broader sense of the comparative risk faced by the different populations, and to

accommodate the uncertainty associated with identifying a single "best" quasi-extinction

threshold, for each population, 1,000 replicate simulations were projected for 100 years

each, and the extinction CDF at each value of the quasi-extinction threshold was

appended as a successive row of an extinction risk matrix. The risk matrix was then

plotted three-dimensionally as a surface, with estimated risk being a function of both time

31
and the quasi-extinction threshold. Differences in the elevation of population risk

surfaces were then used to rank relative risk between populations (Groom and Pascual

1998, Van Dyke 2003), in accordance with the findings of recent studies (McCarthy, et.

al., 2003) that have shown rankings of relative risk among populations to be substantially

more reliable than estimates of absolute risk..

RESULTS

Density Dependence: Model Selection

Fitting density-independent, logistic, and theta-logistic models to the Laysan and PHR-

Southeast time series results in the logistic model being identified as the best predictor of

the observed population sizes, by both AIC-weight and likelihood ratio test.

Parameter Estimates AIC

Population Data Set Model r K theta resid. SS p q σ2 AIC weight LRT p
Laysan 1966-98 DI -0.0174 - - 4.964 2 28 0.184 35.50 0.003
Logistic 0.7546 11636 - 3.079 3 28 0.114 24.65 0.767 DI-R < 0.001
Theta 0.3243 11956 2.344 3.043 4 28 0.113 27.06 0.229 R-Th 0.569
Southeast 1967-98 DI 0.0111 - - 4.124 2 15 0.295 28.20 0.367
Logistic 0.4215 321.2 - 3.174 3 15 0.227 27.45 0.533 DI-R 0.048
Theta 2 274.6 0.205 3.078 4 15 0.220 30.81 0.099 R-Th 0.497
PHR-Grass 1984-2000 DI 0.0259 - - 1.356 2 9 0.170 14.51 0.619
Logistic 0.6367 32.4 - 0.892 3 9 0.111 15.53 0.370 DI-R 0.052
Theta 2 31.0 0.332 0.874 4 9 0.109 22.55 0.011 R-Th 0.671
pooled DI 10.444 2 52 0.205 68.34 0.000
Ricker 7.144 3 52 0.140 50.85 0.652 DI-R < 0.001
Theta 6.995 4 52 0.137 52.11 0.348 R-Th 0.295
Nihoa 1967-1996 DI -0.0632 - - 7.540 2 19 0.419 41.11 0.125
Logistic 0.6700 2972 - 5.544 3 19 0.308 38.12 0.556 DI-R 0.016
Theta 2 2773 0.358 4.952 4 19 0.275 39.23 0.319 R-Th 0.143

Table 2.1. Model selection results for three Laysan finch populations. Candidate models are the
density-independent, exponential growth model (DI), the Ricker logistic (R), and the theta logistic
(Th). AIC weights are largest for the best-supported model. For each population, the rightmost
column gives the p-values for the likelihood ratio test between the model in that row of the table
and the next-simpler model in the row above. Pooled results are shown for all three Laysan finch
populations, and are comparable to results for the congeneric Nihoa finch (Telespiza ultima).

32
The Laysan time series, with almost twice as much data as the PHR-Southeast series,

supports the Ricker logistic model more than three times as well as the next-best model,

the theta logistic, as measured by AIC weights. Both AIC weight and LRT results

indicate that the DI model is a poor descriptor of the Laysan population dynamics. The

theta logistic model provides a slight reduction in overall error, but the improvement in

fit does not offset the AIC penalty for the additional parameter, nor does it yield a

significant result in the likelihood ratio test. Since the Laysan population is the largest,

and best-documented (both in terms of the length of the time series and the consistency

and power of the transect sampling method used), the Ricker logistic model should

probably be considered to reflect the typical form of density-dependent population

growth for the species. The BNA time series for the congeneric population of finches

(Telespiza ultima) endemic to Nihoa Island corroborates the choice of the Ricker logistic

model (AIC weight = 0.556, versus 0.125 for the DI and 0.319 for the theta models; p =

0.016 for Ricker/DI and 0.143 for theta/Ricker).

The PHR results are somewhat different. The growth rate (r) values shown for the PHR

theta model results are arbitrarily bounded at 2, because when the nonlinear regression

routine was given a sufficiently large number of iterations to converge (100 or more),

biologically implausible growth rate values of 60 or greater were ultimately reached.

Likelihood surfaces for the theta models appeared unimodal but nearly flat, so that

maxima could be attained only at very large parameter values, particularly for the growth

rate, yet the reduction in the error sum of squares obtained by letting the fitting algorithm

proceed to such unrealistic parameter values was less than one percent. The penalty

assessed by the AIC for the extra parameter was about 3% of the absolute AIC value, so

33
the improvement in fit was outweighed by the penalty for the additional parameter.

Moreover, small differences in AIC values are amplified by the AIC weight formula, so

the penalty was large relative to the improvement in fit obtained by letting the

nonlinearity exponent deviate from one. Therefore, the AIC weights characterize the

theta logistic as being a poor descriptor of the Laysan time series data.

A key difference between the Laysan and PHR time series is that, due to gaps in the

record of population size estimates, there are fewer growth rate data to work with at PHR

than at Laysan. Thus there are fewer degrees of freedom available, and therefore the

power to discriminate between more complex models is lower. At Southeast Island,

therefore, the Ricker logistic model is afforded only 45% more support than the DI

model, compared to the factor-of-three margin at Laysan, and the LRT result is just

significant at the 0.05 level. At Grass, there are only nine observations in the time series,

so the situation is more pronounced: 67% more support for the DI model relative to the

Ricker logistic by AIC weight. However, the Grass LRT result is nearly significant at the

α = 0.05 level, so the greater AIC-based support for the density-independent model is

probably not a robust result for that population. Rather, it is probably an artifact of the

limited data available for fitting models with more than three parameters. This conclusion

is supported by the fact that, when the data for all three populations of the species are

pooled, the Ricker logistic model (hereafter referred to more simply as the "logistic")

again provides the best description of the three time series overall, and with df = 52 the

data are more than sufficient to fit the four-parameter model.

34
Environmental Autocorrelation

For all three populations, no evidence was found for significant autocorrelation among

either the growth rates themselves or the deviations between the observed and predicted

growth rates.

Population lag (years) r df p

Laysan 1 -0.088 27 0.663
2 -0.168 26 0.413
3 -0.019 25 0.928
4 0.110 24 0.610
PHR-Southeast 1 -0.066 13 0.815
2 0.280 12 0.332
3 -0.091 11 0.767
4 -0.524 10 0.080
PHR-Grass 1 -0.128 6 0.762
2 0.060 5 0.899
3 -0.157 4 0.766
4 -0.479 3 0.415

Table 2.2. Correlations among deviations between observed and predicted growth rates for the
three extant Laysan finch populations. None was significant at the α = 0.05 level.

Correlations among the growth rates themselves would be relevant only if population

growth were density-independent (Morris and Doak 2002); since the logistic model was

identified as the most appropriate for these populations, it is the correlation among the

deviations between the observed and predicted growth rates that are of interest. Although

both PHR time series provide few degrees of freedom to detect significant temporal

correlation in growth rates, the Laysan time series is more complete and therefore should

provide the most resolution if growth rates are actually correlated. Autocorrelation in

Laysan finch growth rates may not be detectable for genuine biological reasons, such as

the species' high fecundity, vagility, and omnivory, combined with the extreme climatic

variability typical of small tropical oceanic islands and the concomitant variability of the

plant community. The high coefficients of variation in the time series (0.34 and 0.61 at

Laysan and PHR-Southeast, respectively) could reflect a highly variable environment

35
being tracked closely and rapidly by a very adaptable population. Rapidity of adaptive

change in the morphology and behavior of this species has already been documented

(Conant 1988; Morin and Conant 1990), as has rapid genetic divergence between

populations (Tarr et al. 1998).

Catastrophes

Although fitting a density-independent model to the Laysan time series data yields two

transitions (for the years 1976 and 1983) with studentized residuals less than –2,

suggesting they be treated as catastrophes, the better fit of the logistic model results in

only one outlying residual, that for the 1987 growth rate. As mentioned earlier, the

overall distribution of these residuals was not significantly different from normal.

However, because 1987 was known to be a drought year with low ensuing recruitment

leading to a much smaller population count in 1988 (Morin 1992a), it seemed reasonable

to modify simulations of the Laysan population to randomly apply a log growth rate of

that magnitude (-0.97), at a frequency of 0.036 (approximately one twenty-eighth of the

time), as discussed in more detail below. In contrast to the putative catastrophe at Laysan,

no outliers were detected for either of the two PHR time series.

Adjustment for Observation Error

Using White's (2000) method, the ten years of transect data at Laysan led to an estimate

of 12% of the process variance (σ 2) being attributable to observer error, a modest amount

that accords well with the 11% estimate obtained from a simpler variance adjustment

using a delta method approximation to express the variance of the log growth rates in

terms of the variance of the population sizes (Morris and Doak 2002). In contrast to

White's variance adjustment, the latter method employs a simplifying assumption that the

36
mean variance across years is an adequate approximation to the exact, fluctuating sample

variance in different years (Morris and Doak 2002). For both methods, in contrast to the

relatively modest adjustment of the Laysan variance, the eight years of PHR-Southeast

transect counts led to a much larger adjustment of 63%, which also accords well with the

59% estimated by the simpler method. The PHR adjustment estimates are surprisingly

large, especially given the small area of Southeast Island (about 13 hectares) relative to

the sample area, and may represent further evidence that the differences in plant

community structure between Laysan and PHR-Southeast have contributed to behavioral

differences between the two finch populations (Morin and Conant 1990;

Tarr, et al. 2000).

Simulation Results

To assess the general behavior of the model, simulations were run across a range of two

parameter ratios in a factorial design. Exploration of model sensitivities focused on

relationships between parameters rather than specific parameter values because it seemed

likely that extinction risk would be sensitive to the distance between the carrying capacity

K and the quasi-extinction threshold Nx, rather than to specific values of either parameter.

Likewise, the growth rate estimate by itself is not expected to predict extinction risk well,

but should require complementary information about its variability. For a range of

parameter value ratios (0 ≤ σ 2/r, N/K ≤ 0.5), these expectations appear to be born out. A

summary of regression results for a second-order linear model is given in Appendix C. In

general, for a given ratio of σ 2/r and Nx/K, the extinction probability (P(E)) rises quickly,

attaining within five years about 80% of the risk at 50 years. This "shouldering" behavior

is consistent with results for ceiling models described by Lande (1993) and Foley (1994).

37
As shown by the significance of model terms in Appendix C, extinction risk appears to be

more strongly influenced by the Nx/K ratio than by σ 2/r, particularly for any Nx/K ratio

greater than 0.1 (which is large for K > 500), and for σ 2/r values less than 0.5. Increasing

r while holding σ 2/r to the same range depresses the extinction risk surface while

increasing the slope of the CDFs. For simulations in which both the σ 2/r and Nx/K ratios

are less than 0.1, median CDF curves are quite linear, with R2 values for fitted lines

greater than 0.8.

(a) P(E) Surface for Nx/K = 0.1 and r = 0.5 Slope of Median CDF with Parameter Variability (b)

0.0016

0.0012
0.3

0.25

0.2 0.0008

0.15 50
45
40
0.1 35 0.0004
30
0.05 25 Year
20
0 15
10 0.0000
0.5
5
0.25 s2-r-K r-K s2-K s2-r K r s2 -
σ2/r 00

Figure 2.1. Extinction trends for the logistic simulation model with fixed parameter values (left)
and with parameters allowed to vary within their confidence intervals. Graph (a) is a surface of the
median extinction risk for 10 replicate simulations of 10,000 iterations each for a population with
K = 1000, Nx = 100, r = 0.5 and 0 < σ 2/r < 0.5. The coefficient of variation between replicates was
less than 2%, so the median surface is representative of the general behavior of the model. Graph
(b) shows how the median CDF slope increases as additional parameter variation is incorporated
into the simulation. The slopes shown are based on 20 replicates of 50,000 iterations each with
parameter values and their CIs taken from the estimates for the PHR-Southeast population.

Graph (b) in Figure 2.1 makes use of this linearity by condensing the information in the

median CDFs, representing them by their estimated slopes, equivalent to the rate of

change in extinction risk after the first ten years of the simulation. It can be seen that the

increase in estimated extinction risk is faster for simulations in which more parameters
38
are allowed to vary. Thus inferences drawn about the extinction risk faced by different

populations, or imposed by different environmental changes, could be quite different for

models incorporating different schemes of parameter variability.

Another important general aspect of this simulation model is the effect of adding

catastrophes. As mentioned earlier, outlying growth rate transitions are treated as random

shocks to the population. Figure 2.2 below shows the frequency and magnitude of these

shocks required to appreciably increase extinction risk. For very low (less than 0.01) Nx/K

ratios, fairly high frequencies (greater than 1/6) of relatively large catastrophes

(r < -1) are required to produce a substantial change. The effect of catastrophes scales

quickly with further increases in frequency or magnitude, but the catastrophe frequency

(0.036) and intensity (-0.97) found in the Laysan time series are about one-fourth, and

two-thirds, respectively, of the levels that would be required to substantially raise the

projected extinction risk. Similarly, raising the quasi-extinction threshold relative to the

carrying capacity makes the model much more sensitive to catastrophes, but for r, K, σ2

values like those estimated for the Laysan population, Nx has to be relatively large (about

four times the historic nadir of the early 1920s, a crash which, obviously, proved

survivable) to effect a substantial extinction risk.

39
 (a) (b)
Median CDF Slope as a Function of Slopes of Median Extinction Risk CDFs as a Function of
Catastrophe Magnitude and Frequency Quasi-Extinction Threshold
6.E-07

0.001
5.E-07

0.0008
4.E-07

0.0006
Median
CDF 3.E-07
Slope y = 2E-09x - 8E-07
0.0004 R2 = 0.7333
2.E-07

0.0002 -1.6
1.E-07
-1.3

0 -1
0.E+00
0.02 Magnitude
0.06 -0.7 0 100 200 300 400 500 600
0.1
0.14
0.18
Frequency Quasi-Extinction Threshold

Figure 2.2. The effect of adding catastrophes to the simulation model for the Laysan population. Graph
(a) shows the frequency and intensity of catastrophes required to increase the CDF slope, based on
median values of 10 groups of 10,000 replicate trajectories, across a 10x10 array of frequency and
intensity values. Graph (b) shows the effect of raising the quasi-extinction threshold, given a single
outlying growth rate of r = -0.97); the median CDF slope isnot greater than zero until Nx > 350.

With these general considerations in mind, the median extinction probabilities s are

graphed in Figure 2.3 (below) for the three populations. These curves represent the

estimated cumulative distribution functions for extinction risk.

Ext inct io n Prob abilit y M edian CDFs f o r Three Ext ant Laysan Finch Pop ulat io ns
0 .05

Grass
0.0 4

0.0 3

P(E) SE

0.0 2

0.0 1
Laysan

0
0 10 20 30 40 50 60 70 80 90 10 0
Y ears Int o The Fut ure

Figure 2.3. Median extinction probability CDFs for three Laysan finch populations. Points
represent the median extinction probability across the 50 groups of 1,000 replicate trajectories at
each time step (year). Quasi-extinction thresholds were 50, 20, and 8 individuals, respectively, for
the Laysan, PHR-Southeast, and PHR-Grass populations.

40
 A noteworthy result is that the projected extinction risk at Laysan is zero across the

entire time horizon. This result is consistent with theoretical expectations given by May

(1974) that large average population sizes should give rise to very small extinction

probabilities. In an effort to estimate such a low probability more accurately, the number

of iterations for the Laysan simulation was increased to 1000 groups of one million

replicate trajectories each. However, the increase yielded no detectable improvement in

the ability to resolve a finite median extinction risk for the Laysan population. This result

suggests that, given the large population size typical at Laysan over the last 35 years, plus

the high intrinsic growth rate of the species, the intrinsic dynamics of the population

create a near-zero risk of extinction. By contrast, the risk estimates for the PHR

populations are finite. The PHR-Southeast risk estimate grows approximately linearly to

just over 2% after 100 years. The PHR-Grass Island estimate averages about twice the

PHR-Southeast estimate across the same time horizon, but, at 4% after 100 years, still

seems relatively low for a small (n = 30) population founded by 8 individuals over 35

years ago.

Confidence envelopes around the CDFs, based on the CIs for the parameter estimates,

were constructed from the minima and maxima of the simulated extinction probabilities

(Morris and Doak 2002). However, this method is not without difficulties. Foremost

among them, from a pragmatic perspective, is that the high variability of Laysan finch

growth rates leads to relatively large uncertainties (CIs) around the parameter estimates

for the moded fitted to the time series. In addition, treating the parameters as independent

random variables permits low-probability combinations of parameter values (very low

growth rates with very low carrying capacities, and vice versa) to arise during the

41
simulation. Values of r and K near their CI lower bounds raise extinction risk, while

values near the upper bounds permit populations to persist far into the future. In the

aggregate, these chance combinations of extreme parameter values inflate the width of

the confidence envelope around the extinction CDF, making it difficult to resolve

differences in extinction risk between populations or with respect to environmental

perturbations or management actions. This is especially true for situations like this one, in

which the extinction risk estimates for all three populations are low. The result of

sampling across large parameter CIs during the simulation is that confidence regions for

both of the PHR populations' extinction CDFs overlap across the entire time horizon.

Thus the relative risk of the translocated populations cannot be unambiguously ranked via

this method.

Ext inct io n Prob abilit y M edian CDFs f o r Three Ext ant Laysan Finch Pop ulat io ns

0.0 5

Grass
0 .04

0 .03

P(E) SE

0 .02

0 .01
Laysan

0
0 10 20 30 40 50 60 70 80 90 100
Y ears Int o The Fut ure

Figure 2.4. Median extinction probability CDFs for three Laysan finch populations. Points
represent the median extinction probability across the 50 groups of 1,000 replicate trajectories at
each time step (year), and are bounded by curves representing the maximum and minimum
extinction probability for each set of 50 groups. Quasi-extinction thresholds were 50, 20, and 8
individuals, respectively, for the Laysan, PHR-Southeast (SE), and PHR-Grass populations.

42
 The inability to discern statistically significant differences in extinction risk between

populations using median CDFs for specific quasi-extinction thresholds occurs despite

the fact that the confidence envelopes obtained using the logistic model are roughly an

order of magnitude narrower than CEs constructed in a similar fashion for the density

independent model. However, while the logistic model does reduce CE width, there is a

concomitant reduction in the median risk estimates: for each population, the range of

CDF curves drops toward the x-axis by about two orders of magnitude. Why this should

be so has to do with the change in parameter estimates associated with fitting a different

population growth model to the data. Fitting the logistic model yields growth rate

parameter estimates whose MLEs are more than an order of magnitude larger, and whose

CIs are less negative, than those for growth rates estimated with the density-independent

model. For highly variable populations like those of the Laysan finch, the long-term

mean growth rate, estimated under the DI model, is near zero (as shown in Table 2.1, and

similarly in Dennis, et al. 1991, for the Laysan population). Furthermore, parameter CIs

obtained via the linear regression method are almost symmetrically distributed across

positive and negative values. For the DI model, therefore, there is a nearly even chance of

a simulated population being assigned a negative growth rate at any time step of the

simulation. In contrast, for the logistic model, only about 10% of the growth rate

parameter CIs (rather than half) extend below zero. Since the simulation is sampling from

a normal distribution in choosing randomized growth rate values, only the left tail of the

distribution extends into the negative range, and therefore there is less than a 10% chance

of choosing a negative growth rate. The result of this positive bias in the range of growth

43
rates under the logistic model is a more than 90% reduction in estimated extinction risk,

which offsets the narrowing of the CEs such that they overlap.

The lack of distinction between baseline extinction risk estimates for the three

populations may impede prioritization of conservation efforts, and when assessing the

effects of environmental disturbances, such as alien species invasions, it may inhibit

formal detection of changes in extinction risk. For example, at PHR, a non-native

herbaceous annual, Verbesina encelioides, was detected at Southeast Island in the

summer of 1998. Despite immediate extirpation of the mature plants, the Verbesina

population approximately quadrupled its range each year, until by 2001 it had formed

dense monotypic stands over most of the island (Wegmann 2001). In so doing, Verbesina

appeared to displace the existing vegetation, much of which was also non-native, but

which had sustained the Laysan finch population within a range of about 100-700 birds.

Although nest density was not specifically estimated during the years 2001-2004,

anecdotally it was reported that finch nests were profuse within the Verbesina (Wegmann

and Kropidlowski 2002, Sprague 2003). By September of 2002, transect surveys

estimated the finch population to be 1908, almost three times its previous recorded peak

at Southeast, and more than four times the 1998 estimate (Sprague 2003). Within a year,

however, successive annual diebacks of Verbesina, combined with the apparent

displacement of other plant species, were reported to leave the finches with little forage

except the existing seed bank, and the finch population dropped to less than 600.

However, the effect on extinction risk is difficult to resolve by examining extinction risk

CDFs derived from time series data. Breaking the time series into two parts, one pre-

invasion (from the founding year of 1967 through 1998) and the other post-invasion

44
(1998 through 2003) permits treatment of the pre- and post-invasion time series

separately (Morris and Doak 2002, chapter 3). As shown in Figure 4 below, there is

apparently a substantial increase in the median estimated extinction risk (more than five

orders of magnitude, from just over one one-hundredth of a percent to over 50% at 30

years). The upper bound of the confidence envelope for the post-invasion curve suggests

that extremely low parameter values consistently lead to extinction within just a few

years, while at the other extreme, the lower bound of the post-invasion CE is nearly zero

for over 45 years.

( a)
(b)
Change in Ext inct ion Risk wit h Whit e's Correct ion t o Var iance Term
Change in Extinction Risk for 1998-2003 (Post -Invasion)
( Sigma-Squared) f or PHR-SE 1967-98 (Pr e-Invasion) vs 1998-2003 ( Post -
PHR-SE Population wit h Int erpolated Year for 2001
Invasion) Populat ions
1.0
1.0

0.8 Observed
0.8 P o st

0.6 Interpo lated

0.6 P re

0.4 0.4

0.2 0.2

0.0 0.0
0 5 10 15 20 25 30 35 40 45 50 0 5 10 15 20 25 30 35 40 45 50
Years Int o The Fut ur e Years Int o The Fut ure

Figure 2.5. Apparent effect of the Verbesina encelioides invasion on Laysan finch extinction risk at
PHR-Southeast Island. Graph (a) shows the projected extinction probability CDFs for simulations
using parameter values derived from the PHR-Southeast pre-invasion and post-invasion time series.
Graph (b) shows how the post-invasion risk estimate is reduced by about half if an interpolated
population size (n = 827) is added in place of the missed 2001 population estimate. The confidence
envelopes (thin lines) in both graphs overlap almost completely, with the upper bounds rising to 1.0
within two years and the lower bounds becoming greater than zero only after 37 years.

The PHR-Southeast time series data suggest the finch population responded energetically

to the increased availability of nesting habitat, only to overconsume the food supply and

suffer a population crash. However, because only six years have elapsed since the
45
invasion began, there are few degrees of freedom available for making precise estimates

of parameter values and quantifying a change in the risk of extinction. In fact, because

the finch population size was not estimated in 2001, instead of five growth rate

transitions, only three were observed during the post-invasion period. In general for every

gap of m years, m+1 transitions are lost, so the cost of missing one population estimate

within a time series is information about two growth rate transitions. The result, as shown

in Figure 2.6 below, is that confidence intervals for the post-invasion parameter estimates

average 20 times the width of the CIs for the pre-invasion parameter estimates. This large

disparity in proportional uncertainty is due both to the increased variability in population

sizes since the invasion — the post-invasion population sizes have a coefficient of

variation of 0.96, versus 0.61 for the pre-invasion time series — and also to the inability

of three transitions to adequately parameterize a three-parameter model.

Were that parameter uncertainty to be ignored, the PHR-Southeast simulation model

could be run without allowing the parameters to vary within their confidence intervals. A

model fit to just the post-invasion time series would then feature a further 20% reduction

in the variance estimate, a result of fitting the logistic model to only three data points.

There would also be a concomitant increase in the estimate of K, from 321 to 467, due to

the higher average population size during the first post-invasion years. Those differences,

in turn, would give an extinction risk estimate about 90% lower than the CDF based on

pre-invasion data. This surprising result relates to the inference problem mentioned

above, in which the incorporation of parameter variability into the simulation, in principle

to enable construction of confidence envelopes around the CDFs, appears to change the

behavior of the model. Clearly, it is counterintuitive that a weed invasion that seems to

46
dramatically boost population size and then allow it to plummet should reduce projected

extinction risk. On the contrary, increased growth rate variance typically increases

extinction risk rather than reduces it. Therefore it seems possible that the standard

stochastic differential model, with environmental variability incorporated only in the

form of the white noise parameter σ, may underrepresent the variability of some

populations. It may also be the case that the fully-variable simulation approach

overrepresents that variability, by treating the parameters as independent random

variables, and thereby losing the correlation structure inherent in the time series data.

To assess the effect of the missing transition, I refitted the logistic model to a set of

interpolated time series, with the missing 2001 population size estimate replaced by a

range of values from 550 to 950 in increments of 100. I then fitted a second-degree

polynomial function to the series with the lowest error sum of squares value. The

minimum of the curve at N = 827 was taken to be a reasonable proxy for a 2001

population size estimate. It was then possible to treat the ratio of the confidence interval

width for each parameter to the parameter estimates themselves as a measure of relative

uncertainty. As shown in Figure 2.6 (below), the short time series since the invasion,

compounded by the increased variability in population sizes and the missed population

size estimate in 2001, substantially increases the chance that the simulation model will

choose unfavorable values for all three parameters, leading to projected population sizes

below the quasi-extinction threshold.

47
 Ratio of Confidence Interval Width to Maximum Likelihood Estimates
for Logistic Growth Model Parameters

Growth Rate (r) Carrying Capacity (K) Variance Parameter (s2)

40

35

30

25

20

15

10

0
Pre-Invasion (1967-98) Post-Invasion (1998-2003) Post-Invastion with Interpolated
2001 Count
Time Series

Figure 2.6. The effect of the missed 2001 count on parameter estimates. The ratio of the CI width to
the ML values for r, K, and σ2, based on the three observed transitions measured since the invasion,
are about 20 times larger than the pre-invasion ratios. Interpolating a value of 827 for the missed
estimate recovers the two lost transitions, reducing the proportional uncertainty in the parameter
estimates to only about 2.5 times the pre-invasion ratios.

Because the missed size estimate seems to have such a large impact given the brevity of

the time series since the invasion, and because the median extinction risk drops by about

half (see Figure 2.5 above) when the parameters are re-estimated with an interpolated

time series, it is natural to ask how much farther the median CDF would drop as

additional years of post-invasion size estimates are accumulated. The method of Gerber,

et al. (1999) for estimating data requirements for management decisions, although

designed for the DI model, is equally applicable to the logistic. As shown in Figure 2.7

below, taking contiguous subsets of varying lengths from the pre-invasion time series, the

ratios of the parameter CI widths to the maximum likelihood estimates of the parameters

decrease rapidly from a median of 26 to just under 5 with only two additional years of

data. To get the median CI/MLE ratio down to a level comparable to the 1.9 of the entire

pre-invasion time series, would take over twice as long, or at least 11 years. Both of these

inferences depend on the population reestablishing its pre-invasion growth dynamics

immediately, which, given the fecundity and tenacity of Verbesina, and hence the

48
difficulty of restoring a relatively normal vegetation community, seems unlikely.

Therefore it must be expected that using the count-based PVA method presented here

will not result in statistically significant discrimination of the change in extinction risk for

more than a decade. During that time, extinction risk may have increased, and estimates

of that increase can certainly be made; however, demonstrating that the difference is

significant at the α = 0.05 level will not be possible within the immediate future.

Arithmetic Averages of Logistic Model Parameter CI/MLE Ratios

vs. Number of Years in Sequence
40

1998-2003
30

20

10
1967-1998

0
0 2 4 6 8 10 12 14 16
Number of Additional Years of Data

Figure 2.7. Asymptotic decline in relative uncertainty in population parameter estimates. The graph
represents a modified version of the method of Gerber, et al. (1999) for estimating the number of
years of population counts required to meet management decision criteria. Dots represent CI/MLE
ratios averaged across r, K, and σ2 parameters for logistic model fit to contiguous subsets of all 1967-
2003 count data for the PHR-Southeast population. The line connecting groups of points is a median
trace.

An alternative method of accounting for extinction risk, which does not attempt to

construct CDF confidence envelopes, has the advantage of discriminating differences in

risk across a range of quasi-extinction thresholds, thereby alleviating to some extent the

arbitrariness associated with choosing a single threshold (Groom and Pascual 1998, Van

Dyke 2003). To implement this method, single simulation runs of 10,000 replicate

49
trajectories each were run at a series of quasi-extinction thresholds ranging from zero

(complete extinction) to approximately 0.1K for all three Laysan finch populations. Due

to the large difference in estimates of K for the three populations, however, the areas

under the extinction risk surface are not directly comparable. That is, 0.1K > 1000 for the

Laysan population, more than 30 times the recorded nadir of past population sizes, while

for the PHR-Southeast population, 0.1K is 32, and for the Grass Island population, 0.1K

is about 3. Thus the maximum threshold values range across more than two orders of

magnitude, so for the purposes of ranking risk among the three populations, a more

appropriate accounting of the relative size of the risk volume is to compare them only up

to equal thresholds. This is true even if, as might be the case at Laysan, the habitat area is

large enough that a number of individuals sufficient to avoid extinction within a smaller

area would suffer Allee effects when distributed over a larger area. Figure 2.8 below

shows the risk volumes for the three finch populations.

Because of the low elevation of the three islands, particularly PHR-Southeast, and given

published projections of global sea level rise expected by the end of the 21st century

(Titus and Narayanan 1995, Albritton and Meira Filho 2001), simulations were re-run

with three different trends applied to carrying capacity over the 100-year time horizon. In

terms of the rate of change in carrying capacity, the linear trend is the most optimistic,

assuming that habitat loss will be uniform over time. The quadratic trend function

assumes a much faster early approach to maximum habitat loss, but it imputes a conical

shape to the islands that they do not actually possess. In fact, the Northwest Hawaiian

Islands are typically table-shaped, although Laysan is somewhat bowl-shaped. However,

in the absence of detailed GIS data, the quadratic trend is a plausible first approximation

50
 Laysan Southeast Grass

1 1 1
Constant
0.5 0.5 0.5

0 0 0
30 30 30
20 100 20 100 20 100
10 50 10 50 10 50
QE 0 Y ear QE 0 Y ear QE 0 Y ear

1 1 1
Linear

0.5 0.5 0.5

0 0 0
30 30 30
20 100 20 100 20 100
10 50 10 50 10 50
QE 0 Y ear QE 0 Y ear QE 0 Y ear

1 1 1
Sigmoid

0.5 0.5 0.5

0 0 0
30 30 30
20 100 20 100 20 100
10 50 10 50 10 50
QE 0 Y ear QE 0 Y ear QE 0 Y ear

1 1 1
Quadratic

0.5 0.5 0.5

0 0 0
30 30 30
20 100 20 100 20 100
10 50 10 50 10 50
QE 0 Y ear QE 0 Y ear QE 0 Y ear

Figure 2.8. Extinction probability surfaces for three Laysan finch populations subjected to four
modes of carrying capacity reduction: constant (no change), linear, sigmoidal, and quadratic. For
all graphs, the x- and y-axes are time (year) and quasi-extinction threshold (QE), respectively,
while the probability of quasi-extinction is plotted vertically on the z-axis.

to faster-than-linear reduction in K that is expected to result from the linear rate of sea

level rise projected by both IPCC and US-EPA. A function that may more accurately

represent the most likely response of island area to linear sea level rise is a sigmoidal
51
decline. For these three functions, the areal reduction applied to the three islands by the

end of the time horizon was 90% of K. Given the projected 30-40 centimeter rise in mean

sea level by 2100, a 90% reduction in habitat is plausible for Southeast Island, but may be

excessive for Grass and Laysan Islands given their higher maximum elevations

(approximately 3 meters at Grass and 10 meters at Laysan, versus 1 meter at Southeast

Island). The modeled reduction has a pronounced effect on the extinction risk projections

for the PHR populations. As shown in Table 2.3 below, the volume under the risk

surfaces for the PHR-Southeast population nearly triples when the linear decline in K is

applied, and rises approximately ninefold when the sigmoidal or quadratic trends are

applied.

Laysan Southeast Grass

Constant 0 27 1133
Linear 0 77 1722
Sigmoidal 0 233 1930
Quadratic 0.002 254 2023

Table 2.3. Volumes under the risk surfaces shown in Figure 2.8. The maximum potential volume
for 0 < t < 100 and 0 < Nx < 30 is 3000.

These simulation results suggest that global sea level rise may thus present a major threat

to the Pearl and Hermes finch populations, if the land area reduction that results turns out

to be comparable to the 90% reduction modeled here. Additional risk might accrue from

increased storm frequency and intensity. Increases in the frequency and intensity of major

storms are supported by historical studies (Graham and Diaz 2001), but while further

intensification has been predicted by some climate modeling studies (Lambert 1995), it

has been contradicted by others (Henderson-Sellers et al. 1998, Knutson et al. 2001).

Thus the value of incorporating simulated effects of increased storm frequency or

52
intensity into population models is uncertain, particularly when data on the survival and

fecundity effects of storms are lacking.

DISCUSSION

Count-based PVAs (and PVA generally) have been criticized for sacrificing model

accuracy for ease of data acquisition and analysis (Coulson et al. 2001, Coulson 2003),

and in fact it is easier to collect population counts than the more detailed survival and

fertility data required by demographic matrix models. However, continued development

of count-based PVA methods, such as that presented by Morris and Doak (2002), has

improved the accuracy and reliability of count-based projections. This study estimated

extinction risk for three conspecific finch populations inhabiting geographic ranges

spanning nearly two orders of magnitude. At Laysan, the largest population in the largest

habitat area, intrinsic extinction risk was estimated to be effectively zero. At PHR, the

smaller Grass Island population faces twice the extinction risk of the Southeast Island

population at any given point in time, and 40 times the aggregate risk estimated over a

100-year time horizon. Time series data for different populations yielded substantially

different parameter estimates, not only for carrying capacity, but also for growth rate.

These differences may be partly due to the differing time series lengths among the

populations, and partly to differences in habitat quality, plant community structure, and

the effect of habitat size on stability.

The study also indicates that, for a simple density-dependent model, the relationship

between the quasi-extinction threshold and the carrying capacity exerts a dominant

influence on extinction risk, relative to influence of the relationship between the growth

53
rate and its variance. This situation underscores the importance of choosing quasi-

extinction thresholds carefully, if extinction risk distributions at single thresholds are to

be evaluated, or alternatively, of choosing a simulation and analysis method that

estimates risk across a range of quasi-extinction thresholds. In the latter case, uncertainty

may remain regarding the range of thresholds to use when comparing populations of very

different sizes. For example, for the Laysan population, Nx = 100 seems more realistic

than Nx = 30 as a threshold below which managers would be well advised to intervene,

but for the Grass Island population, Nx = 100 is nearly twice the largest population size

estimate recorded, so that simulated populations would be extinct from the outset. This

would obviously be a misleading result because the Grass Island population has persisted

for 35 years with a mean population size of about 30. Conversely, were the Laysan

population to drop to just 30 birds, it is possible that it would not be able to rebound as

effectively as it did when reduced to a size of about 100 birds. Thus the problems in

establishing baseline quasi-extinction thresholds for comparing risk across populations of

very different sizes apply not only when thresholds are set as fractions of carrying

capacity (as mentioned earlier), but also when thresholds are set in absolute numeric

terms. Setting different thresholds for different populations or habitats would appear to

alleviate this problem, except for the difficulties in establishing the proper threshold for

any particular population or habitat.

Another aspect of improving extinction risk assessment relates less to modeling

technique than to limitations of the data. In this study the effects of a missing census year

was shown to bias risk estimates upward by as much as 50% in simulations

parameterized from short time series. A related issue, not specifically addressed here, is

54
that of the growth rate variance inflation (analogous to that caused by observer under-

and overcounts) that is caused by deviations from exactly annual population sampling.

Preliminary analysis of simulated populations indicates that the maximum proportion of

the variance estimate that could be attributable to variability in census timing is 25%, but

this topic deserves further study. The linear regression method of Dennis, et al. (1991) for

the density-independent model automatically adjusts for variable sampling intervals, but

definitive results for density-dependent populations remain to be established. There are

too many populations that are too difficult to observe on perfectly regular schedules, and

monitoring budgets are too uncertain, for analysts to ignore this source of error.

The extensive density dependence literature has for decades asserted the importance of

accurately identifying the form of density dependent growth in natural populations. This

study was undertaken partly to determine whether model selection procedures, by making

identification of density dependent growth easier and more robust, would have the further

advantage of reducing uncertainty in parameter estimation and risk assessment. To the

extent that reductions in the size of confidence regions around extinction risk CDFs are

offset by parallel reductions in risk estimates due to improved model fit, it is not clear

that the uncertainty reduction has paid off. The answer to whether or not it has paid off

will depend on how the conservation science community defines appropriate methods of

risk assessment. If non-overlapping 95% confidence regions are required to distinguish

different risk levels between populations or treatments, then density dependence model

selection alone does not appear to solve the problem. Some studies (Elderd et al. 2003)

have suggested relaxing the α = 0.05 criterion to 80%, to accommodate the uncertainties

inherent in projecting population dynamics over time and enabling decisions to be made

55
more clearly in the face of such uncertainties. In the case of the weed invasion examined

here, for example, although the nonlinear regression procedures in most statistical

software packages report only 95% confidence intervals for parameter estimates, it would

be straightforward to use the reported standard errors to calculate 80% confidence

intervals and run simulations based on those, creating 80% confidence envelopes around

the extinction CDFs. This could be a suitable area for collaboration between conservation

scientists and economists to project the costs and benefits relaxing confidence criteria: if

it could be shown that little increase in population jeopardy would result from relaxed

criteria, while decisions of comparable reliability could be made faster and more cheaply,

that assurance should itself be quite valuable (as would, conversely, a confirmation that

stringent criteria should not be relaxed).

Thus, if ranked relative risk estimates can support acceptable social choices, then it is

possible that getting the density dependence model right will substantially improve PVA

practice. In order for that to happen, however, several additional related problems will

need to be solved. Among these will be the continued development of improved tools for

model identification. This study tested only three models, all nested, and only for the

longest time series did there appear to be sufficient data to discern whether the most

complex model did a good job of predicting the data. As suggested earlier, the stochastic

version of the simple logistic model may, in providing a better fit to the data, lead to an

underestimate of true variability in the population: outlying transitions are no longer

detectably outlying, even though the changes in population size are large relative to those

expected for a population at stochastic equilibrium. As Dennis, et al.(1991) pointed out,

catastrophes may be the rule rather than the exception for this population, but with the

56
exception of the single extreme transition at Laysan, catastrophes were not modeled in

this study. This is an issue of some import because the most likely causes of rapid and

substantial mortality to ground-nesting birds with established susceptibility to avian

malaria would be the introduction of rats or other predators, or the introduction of

malarial mosquitoes. Alien weed introductions that significantly alter the plant

community also could represent destabilizing influences at Laysan or Grass Island, as one

appears to have been at Southeast Island. Furthermore, as mentioned above, increases in

storm frequency and intensity, should they correlate with the expected rise in sea level,

could exacerbate the modeled habitat reduction, which might also happen in a more

discontinuous fashion than has been modeled here. None of these potentially catastrophic

influences on population survival can be parameterized with confidence given the

limitations of current data. Although there are data available on shipwreck frequencies in

the Northwestern Hawaiian Island, the risk of rat or mosquito introduction is uncertain.

Future work should include Bayesian risk assessments for these factors such that expert

opinion on the risk of biotic catastrophes can be integrated into a more comprehensive

risk analysis for the three populations. Such an analysis should also include projections of

the change in species viability should management actions such as translocation be

undertaken. If these factors can be taken into account, resource managers will be able to

make better-informed choices about the implications of the relative risk faced by

populations of endangered species.

57
 CHAPTER 3

LAYSAN FINCH POPULATION VIABILITY ANALYSIS: INDIVIDUAL-BASED

AND STOCHASTIC DEMOGRAPHIC MATRIX MODELS

INTRODUCTION

Recent research (Tilman 1996, Loreau et al. 2001) supports ecologists' theoretical

assertions (Elton 1958, MacArthur 1958, May 1974, Lehman and Tilman 2000) that

species diversity contributes to ecosystem resilience in the face of environmental

perturbations. Given human dependence on both direct and indirect benefits of natural

ecosystem functions (Costanza, et al, 1996), there is an incentive to maintain ecosystem

diversity, and therefore to minimize anthropogenic contributions to extinction rates.

However, extinctions are difficult to observe directly, even where they are occurring

frequently. Challenges include sampling problems such as finding rare individuals in

forbidding terrain, and the difficulty of proving non-existence. There are also analytical

problems in linking causal factors to the decline of a population, particularly given time

lags and complex interactions among many species across multiple trophic levels.

Because extinction processes are difficult to analyze by direct inspection, predictions of

population trajectories have been made by fitting mathematical models to field data, such

as time series of population sizes. Early attempts to model the dynamics of populations,

such as those of Lotka (1920) and Volterra (1926), went beyond simple description of

population growth to systems of differential equations that modeled intra- and

interspecific interactions, particularly competition. Leslie's (1946) subsequent

development of the matrix formulation, and its extension by Lefkovitch (1965) to stage-

58
based models, extended the analysis of population sizes to permit the inclusion of life

table data into the projection model. In recent years, increasing attention has been

focused on using matrices as a foundation for iterative simulations, so that stochastic

aspects of demography and environment can be modeled.

Population viability analysis (PVA) attempts a comprehensive approach to assessing the

extinction probability of populations. Typically undertaken after populations are found to

be in decline, PVA incorporates a range of factors—demographic, environmental,

genetic, behavioral—to determine which are most responsible for the population decline,

and which management actions stand the best chance of improving persistence

probability. Early PVA work focused substantial intellectual effort on developing models

that were highly specific to particular populations (Gilpin and Soulé 1987), on the

grounds that such specificity is necessary to capture potentially critical dynamics.

However, it has also been recognized that many endangered populations share similar

traits , are characterized by similar dynamics, and are declining due to the same kinds of

pressures, such as habitat loss, degradation, and fragmentation, genetic impoverishment,

overharvesting, etc. (Caughley 1994, Lacy et al 1995, Beissinger and Westphal 1998,

Beissinger and McCullough 2002). That realization has led to the creation of general-

purpose PVA software such as ALEX, RAMAS, and VORTEX (Brook et al. 1997,

Lindenmeyer et al. 1995). Some studies have cast doubt on the predictive ability of these

programs, due to inaccuracy in predictions of extinction probability, time to extinction,

and characteristics of future population size trajectories (Brook et al. 1997, Ellner et al.

2002). In response, developers of PVA software have pointed out that their greater

contribution lies in the heuristic value of assembling life history and habitat data on the

59
populations at risk, and evaluating the relative risk reduction attainable by different

management actions (Brook et al. 2000, 2002).

That assertion reflects a revised perspective on how PVAs should be carried out, and

also a revision of how they should be interpreted. Stability criteria for analyzed

populations are still subject to debate among PVA researchers. A 1000-year persistence

expectation may seem appropriate for a biological system, given that typical species

lifetimes range from 1-10 million years. However, thousand-year predictions are

unrealistic, given the uncertainty in management practices that arises from changing

governmental administrations, intra-agency politics, and contention over land use among

multiple stakeholders. In addition to such political considerations, Ludwig (1996, 1999)

has raised concerns about the predictive power of PVA models generally, showing that

uncertainties in parameter estimates and variances make confidence intervals

impractically large for useful predictions. Follow-up work by Fieberg and Ellner (2000)

indicates that, for a given time series of population sizes, successful extinction

predictions can only be valid for a period extending 10% farther into the future than the

length of the time series available. However, Fieberg and Ellner's result applies to

situations in which the only data available are a time series of population sizes. For

species about which more life history data is available, more detailed analyses can be

made, providing greater confidence not only in estimates of population trajectories, but

also in the projected outcomes of different management actions (White et al. 2002).

This study used the VORTEX population modeling program to assess the viability of a

set of Hawaiian bird populations under various conditions and future scenarios. The bird

in question, the Laysan finch (Telespiza cantans), like many Hawaiian species, is a

60
single-island endemic, and the only passerine remaining at Laysan (Conant 1988; Morin

1992a; Morin and Conant 2002). Laysan Island is the largest of the Northwest Hawaiian

Islands, providing 187 acres of vegetated habitat which supports an average of 10,000

finches, although the population has fluctuated dramatically over the last 25 years, from

2000 to over 20,000 (Morin 1992a; Morin and Conant 2002). Laysan is subject to

extremes of heat and wind, along with storms and drought, but the finches have been

shown to be physiologically adapted to heat and drought (Weathers and Van Riper 1982).

A more severe threat has been mammal introductions: rabbits imported to Laysan in 1903

devegetated the island until the finch population dropped into the low dozens (Morin

1992a). With the rabbits eliminated in the mid-1920's, the main threat that remains to

these ground-nesting birds is the possible introduction of predators or pathogen vectors

by shipwreck. In response to this threat a translocation was undertaken in 1967 as

insurance against further catastrophic events at Laysan Island. The US Fish and Wildlife

Service moved 108 birds approximately 640 kilometers northwest from Laysan to Pearl

& Hermes Reef (PHR). All 108 birds were originally placed on the largest islet,

Southeast Island, but by 1970 two birds were found at Grass Island, eight kilometers

west, and by 1973, two others were found at North Island, 10 km to the north. In addition,

FWS moved six more birds from Southeast to Grass in 1973. The value of the PHR

populations, as insurance against extinction at Laysan, is not clear. At Laysan, the finch

has the advantages of large population size and extensive habitat of generally high

quality. The birds' preferred food and nesting substrate, the native bunchgrass Eragrostis

variabilis, is plentiful, and the finches not only breed prolifically (nearly year-round in

some cases, and three clutches per year is not uncommon), but they also feed

61
omnivorously on seeds and other vegetation as well as on the eggs of both seabirds and

other finches (Morin 1992b). At PHR, however, life is not so rich: the PHR finches face

environmental stochasticity comparable to that at Laysan, but habitat patch sizes are

smaller by more than an order of magnitude and effective population sizes are smaller

still (Tarr et al. 1998). In addition, low elevation and small island size creates greater

exposure to wave action during winter storms, and shifts in the vegetation assemblage

have resulted in significant changes in feeding and nesting behavior (Conant 1988, Morin

and Conant 1990). Local population extinctions remain problematic due to low intra-atoll

migration rates and consequent lack of population replenishment, and fluctuations in the

E. variabilis population over the last 20 years appear to limit nest site availability and

correlate with changes in nesting behavior. From a conservation perspective, therefore, it

is important to assess how good the extinction insurance provided by the PHR

populations actually is. The expectation is that the PHR populations face greater

extinction risk than the parent population at Laysan, so that the PHR populations cannot

provide good long-term insurance against extinction. This study assesses the long-term

survival prospects of the populations at PHR, and attempts to determine whether, and to

what extent, additional translocations or supplementation from Laysan will be required to

maintain long-term viability of the species.

METHODS

VORTEX: Model Overview and Parameter Estimation

VORTEX is an individual-based modeling program that simulates population dynamics

to estimate extinction probability. By simulating the dynamics of an array of individual

62
animals, VORTEX implements a stage-structured projection of population growth based

on life history parameter values specified by the user. Users enter values for

approximately 15-20 life history parameters (actual numbers will depend on aspects of

the life history being modeled) in a set of five panels presented by the VORTEX

graphical user interface. These include the initial population size, whether the population

is starting from a stable age distribution (if not, a particular distribution can be specified),

the age of first reproduction for males and females (specified separately since they may

not be equal), the maximum reproductive age for the species, the maximum number of

surviving offspring produced in a year, and the sex ratio at birth. Additional life history

parameters include mean mortality rates for each sex in each age class (adults are treated

as a single age class with a single age-specific mortality rate for each sex), and the

variability (standard deviation) in mortality for each sex and age due to environmental

stochasticity. VORTEX program pseudocode and a flow diagram are provided in Lacy

(2000); see also Miller and Lacy (2003) for a detailed summary of VORTEX operation.

Density Dependence in Population Growth

Population growth in VORTEX models can be made density-dependent via two

mechanisms: a ceiling carrying capacity and density-dependence in the percentage of

females breeding. Carrying capacity estimation for VORTEX models is not a trivial

problem. The program documentation (Miller and Lacy 2003) points out that,

"Empirically, once could estimate the habitat carrying capacity for a given animal species

by caclulating the total food supply appropriate for that species that is available in the

habitat, and dividing that value by the rate of that species' consumption." However, the

Laysan finch, being omnivorous (Morin and Conant 2002), feeds on various parts of

63
many of the plant species in its habitat, in addition to insects, seabird eggs, and carrion,

and switches between plant foods on the basis of availability and other factors which

have not been well-characterized. Morever, the plant species preferred, and their relative

proportions in the plant community, differ between islands (Conant 1988, Morin and

Conant 2002). Finally, no studies of the energetics of Laysan finch feeding, or of Laysan

finch activity budgets, appear to have been carried out to date (Morin and Conant 2002),

so estimating carrying capacity from the abundance of vegetation relative to the birds'

nutritional requirements is not feasible at this time.

There are, however, relatively long (10-28 years) time series of population size

estimates for the three extant populations, so it is feasible to estimate carrying capacity

from identification of an appropriate model to account for population growth and then

fitting that model to the time series data (Morris and Doak 2002). For this study, carrying

capacity was estimated by nonlinear regression of population time series data, fitting a

logistic model to log-transformed population growth rates for the Laysan and PHR

populations. As shown in Table 3.1 below, results for the two longest time series (Laysan

and PHR-SE) indicate that the logistic model provides a better description of the data

then either a density-dependent, exponential-growth model or a more complex theta

logistic model.

Parameter Estimates AIC

Population Data Set r K q σ2 AIC weight p
Laysan 1966-1998 0.7546 11636 28 0.1140 24.65 0.767 < 0.001
PHR-SE 1967-1998 0.4215 321 15 0.2267 27.45 0.533 0.048
PHR-Grass 1984-2000 0.6367 32 9 0.1115 15.53 0.370 0.052

Table 3.1. Nonlinear regression results summaries for logistic model fitting for three Laysan
finch time series. The p-values at right represent likelihood ratio test results for the significance
of the added carrying capacity parameter (K) in the logistic model relative to the density-
independent exponential growth model.

64
The AIC weights and likelihood ratio statistics support modeling populations of this

species with a logistic form of density dependence. However, VORTEX implements

density dependent growth somewhat differently from the way in which a logistic

population model would implement it. A continuous-time logistic model would assume

instantaneous feedback from the environmental limits to population growth to the

growing population itself. Carrying capacity estimates for ceiling-based models are

different from those of logistic-based projections (Lande 1993, Foley 1994), and Foley

(1994) has suggested that a reasonable estimator for the carrying capacity in ceiling

models is the geometric mean of the populations size time series. For Laysan finches, this

approximation would result in lower estimates of K, by 9% at Laysan and PHR-

Southeast, and by 40% at PHR-Grass Island. Alternatively, a discrete-time logistic model

would provide a time-lagged version of carrying capacity feedback, in which additional

mortality levied against populations that overshoot K would not be applied until a time

step subsequent to the overshoot. VORTEX is somewhere in between, neither

instantaneous nor delayed by a specified number time steps. In VORTEX , if a

population's size is greater than K at the end of a time step, a random selection of

individuals across sexes and age classes is culled from the population with probability

proportional to (N-K)/N. Thus, once the population is detected above K, the time until it is

driven back below K is probabilistic, resulting in a discrete-time ceiling model with a

stochastic time lag. The theoretically optimal carrying capacity estimator for such a

model has not been defined, leading to the use of K estimates derived from time series

data as an approximation.

65
Density Dependence in Reproduction

If reproduction is specified to be density-dependent, the distribution of clutch sizes is

modified according to the distance between the population size and carrying capacity.

The proportion of females breeding is calculated as:

P(N ) = (P(0) − [(P(0) − P(K ))( NK ) B ])( N N+ A )

In this expression, the parameter B controls the change in reproduction near K, and A is

the Allee effect parameter, which affects reproduction at small population sizes. The

quantities P(0) and P(K) are the proportions of females breeding at N = 0 and N = K,

respectively. With A = 0 and B = 1, increasing N causes a linear decline in the proportion

of breeding females, while with A = B = 0, the proportion of breeding females is constant

for all 0 < N ≤ K. If density-dependent reproduction is disabled, then in each year of the

simulation a binomially-distributed random number determines the percent of females

producing clutches. In either case, the clutch size distribution remains constant and is

specified separately.

There is no data for density dependence in reproduction for this species. Miller and

Lacy's (2003) recommendation—using regression analysis for estimating values for the

parameters P(O), P(K), A, and B in the reproductive density dependence function shown

above—is not feasible because there is only two years' worth of data for fertility as a

function of population size. However, anecdotal evidence from the weed invasion at

PHR-SE (Wegmann 2001, Wegmann and Kropidlowski 2002, Sprague 2003) suggests

that Laysan finch fecundity at high population densities, possibly facilitated by

omnivorous feeding, may result in overshoot of the carrying capacity. Furthermore, the

finches' sociality and singing behavior, combined with the small size of their habitats,
66
make them sufficiently conspicuous that Allee effects are not expected to be significant.

Corroborative evidence comes from the rapid population rebound after the devegetation

of Laysan between 1903 and 1923: Wetmore's report from the Tanager expedition

indicates (Ely and Clapp 1973) that the Laysan population rebounded from about 100 to

about a thousand within 13 years as the plant community was reestablished after rabbits

were eradicated. Thus it is plausible that, to a good approximation, P(0) = P(K), A = 0 and

B = 0, and therefore density-dependent reproduction was not enabled for these models.

Survival and Mortality

Survival estimates were obtained from banding data for the years 1997-2000 at PHR-SE

using Program MARK (White and Burnham 1999). Summary data for the encounter

history file for 400 birds banded at Southeast Island in 1997-1999 are shown in Table 3.2

below,

EH HYM HYF SYM SYF ASYM ASYF totals

1997 1111 5 1 2 3 2 0 13
1110 2 2 1 0 1 0 6
1101 2 0 7 0 0 0 9
1100 9 5 4 0 2 0 20
1011 0 1 0 0 0 0 1
1010 0 0 0 1 0 0 1
1001 0 1 1 1 0 0 3
1000 10 7 1 3 2 2 25 78
1998 0111 12 5 7 2 11 4 41
0110 5 7 1 1 2 1 17
0101 14 9 5 3 17 5 53
0100 24 19 9 16 25 16 109 220
1999 0011 16 11 7 5 2 4 45
0010 38 9 3 5 1 1 57 102

Table 3.2. Summary information for encounter history file used with Program MARK to estimate
Laysan finch survival at PHR-Southeast Island. "HY", "SY", and "ASY" refer to hatch-year,
second-year, and after-second-year birds, respectively. Since, for Laysan finches, definitive
plumage is attained after the second year, all birds known to be older than that were treated as
members of a single stage.

67
MARK uses an AIC-based model selection algorithm to identify the survival model and

parameter estimates that best explain the observed encounter histories. Model likelihood

is adjusted by a penalty for additional parameters, so that relatively parsimonious models

tend to be identified as optimals, and survival estimates are adjusted by recapture

probabilities. The best model identified by MARK was a nine-parameter model with

survival parameters estimated for the six age-sex groups, designated {Phi(age)p(t)} in the

notation of Lebreton et al. (1992). Recapture probabilities varied across years but did not

differ significantly among age-sex groups. MARK survival estimates for hatch-year,

second-year (subadult), and after-second-year males (0.6023, 0.6991, and 0.8514) were

converted directly to mortalities (equal to one minus survival) for use in VORTEX

simulations. However, while female Laysan finches do not attain definitive plumage until

their third year, and therefore, like the males, can be identified as belonging to one of

three stages, most females attempt to breed in their second year (Morin 1992a).

VORTEX models only the breeding schedule relevant to the animal's life history, so

female finches were constrained to two age classes, with the after-second-year female

survival parameter used for all breeding females, and the second-year female survival

estimate omitted. The environmental variability in mortality was estimated by the

standard errors of the survival estimates.

68
 PHR-SE Laysan Finch Survival (19 97-20 00 ) Est imat es by A g e-Sex Gro up

1.0

0 .8

0 .6

0 .4

0 .2

0 .0
HY M HY F SY M SY F A SY M A SY F
Gro up

Figure 3.1. Survival values by stage and sex for banded Laysan finches at Southeast Island (PHR),
1997-2000. "HY", "SY", and "ASY" refer to hatch-year,second-year, and after-second-year birds,
respectively. The relatively large variability around around the SYF estimates is attributable to low
recapture rates for that group.

Other Parameters: Fertility, Genetics, and Catastrophes

Fertility parameters were estimated according to the clutch size frequencies and

proportion of females breeding observed at PHR-SE in 1999 and 2000. The percentage of

females breeding was estimated from the arithmetic mean of the fraction of females

banded in 1998-2000 that were found to be in breeding condition (determined by

noticeable development of the brood patch), with the environmental variation (EV) across

years estimated by the standard deviation. The percentage of males in the breeding pool

is not known, but the figure of 90% used is suggested by a recent estimate of extra-pair

fertilization (EPF) frequency of approximately 10% (see Chapter 4). The rationale is

based on variation in males' plumage coloration, song characteristics, and diligence in

providing nuptial feedings to females, suggesting that a small fraction of males are

cuckolded by either paired or unpaired males, while some males experience complete

reproductive failure.

69
 VORTEX simulates a simple form of genetic stochasticity based on a single-locus, two-

allele model of heterozygosity loss due to inbreeding. The rate of inbreeding depends

upon the mating system specified for the population being simulated. All individuals are

unrelated at the beginning of the simulation, but by the second generation, inbreeding can

begin based on allele frequency changes at a selectively neutral diallelic locus. VORTEX

tracks the mean heterozygosity at this locus for all simulated populations, and it is

equivalent to their respective inbreeding coefficients. Inbreeding depression is modeled

via a parallel accounting of ten alleles at five non-neutral loci, with founding individuals

having unique lethal alleles proportional to the mean number of lethal equivalents per

individual. Miller and Lacy (2003) recommend, in the absence of specific information

about the actual number of lethal equivalents per individual and genetic load, that

VORTEX default values of 3.14 and 50%, respectively, be used, per the results of

Ralls, et al. (1988) for 30 mammalian taxa. While it is expected that inbreeding effects

could become significant when simulated populations reach small sizes, in the absence of

detailed information about Laysan finch genetic and inbreeding parameters (the number

of lethal equivalents and the percentage of genetic load due to lethal alleles) were left at

their default values.

There was no evidence of catastrophes (outliers) in the residuals from the nonlinear

regression of the time series of log growth rates. Moreover, while it is possible to make

some estimate of historically known frequency of catastrophic events such as hurricanes

(Conant and Morin 2001), there is no information about the effects of such events on

survival and reproduction. Therefore, catastrophes were not modeled in these

simulations. Migration between populations was also not modeled; even though

70
spontaneous colonization events have been documented, they have been relatively rare

(on the order of once each 30 years), so it was considered more conservative from a

management perspective to assume that source-sink dynamics and rescue effects would

not occur without human intervention.

Parameter Estimate Parameter Estimate

Inbreeding Depression? Yes Fem. Mort. age 0 41%
Lethal equivalents 3.14 EV 10%
% genetic load = lethals 50 Adult Fem. Mort. 26%
EV concordance of repro & surv? Yes EV 18%
Mating System Monogamous Male Mort. age 0 40%
Female Breeding Age 1 EV 13%
Male Breeding Age 2 Male Mort. age 1 30%
Maximum Breeding Age 10 EV 6%
Sex Ratio (% males @ birth) 50 Adult Male Mort. 15%
All Males Breeders? No EV 6%
Percent Males In Breeding Pool 90 Probability Of Catastrophe 0
Density Dependent Breeding? No Severity--Reproduction 0
% Females Breeding 65 Severity--Survival 0
EV-% Females Breeding 8.34 Initial Population Size 350
% Clutch Size 1 20 K 321
% Clutch Size 2 27 EV--K 0
% Clutch Size 3 33 Trend In K? No
% Clutch Size 4 13 Harvest? No
% Clutch Size 5 7 Supplementation? No

Table 3.3. Parameter values used in VORTEX simulations for PHR-SE population.

Modeling Protocol

Simulations spanning 100-year periods were run for 10,000 iterations. To gauge the

uncertainty in extinction risk estimates resulting from parameter uncertainty (or

omission), a sensitivity analysis was performed on the VORTEX parameters shown in

Table 3.3. The goal of the sensitivity analysis was to discover which of the omitted or

most uncertain parameters had the greatest impact on extinction risk and stochastic

growth rate (λs) and extinction probability (P(E)). Stochastic growth rate is considered a

parameter of interest for characterizing population vulnerability because it condenses

71
critical life history information and the projected effects of environmental variation into a

single value which is independent of time (Caswell 2000, Kaye 2003). Stochastic growth

rate also permits the study of parameter effects without requiring or implying lethal

impacts. Extinction probability, on the other hand, may be more informative in multiple-

population scenarios where some populations' habitats are at risk, so that population

growth rate by iself cannot predict long-term viability. VORTBAT, a Visual BASIC

program compiled to run under MS-DOS (Kohlmann 2002) was used to generate

VORTEX batch files that varied one parameter across a range of values while leaving

other parameters constant. For some tests, two or three related parameters were varied

together and the shapes of response surfaces for the output parameter (stochastic growth

rate or extinction probability) were studied for evidence of interaction between model

parameters. Comparisons of relative risk between populations or management scenarios

were based on median values of the extinction probability cumulative distribution

function (CDF) across the entire simulation time horizon. Focus on median values should

minimize bias arising from the skewed distribution of survival times (or, conversely,

extinction probabilities) mentioned earlier (Dennis, et al. 1991; Ludwig 1996, 1999): the

means tend to understate risk, while modal values, even though they represent the

maximum likelihood estimate, are typically not very probable. The rationale for

presenting complete CDFs is simply to permit comparison across a continuous range of

time horizons.

To assess how well VORTEX estimated extinction risk, a comparable stochastic

demographic matrix (SDM) model was created, based on methods described in Morris

and Doak (2002). Using the same survival parameter estimates obtained from the MARK

72
{Phi(age)p(t)} model, and fertility estimates compiled from the 1999 and 2000 breeding

seasons, a five-stage demographic matrix was constructed. Three stages (one each for

second-year, fourth-year, and after-fourth-year females) were added to accommodate

more detailed fertility data for second-year females not explicitly modeled in VORTEX

and for females known to be older than their third year during either the 1999 or 2000

breeding seasons. For survival rates, the the MARK estimate for second-year females was

used, and the terminal stage (after-second-year) was expanded out to provide survival

values for the later stages (Lefkovitch 1965). Environmental variation was implemented

by randomly choosing, at each time step, growth rates and fertilities from truncated

normal distributions centered on the mean vital rate estimates and bounded by upper and

lower 95% confidence levels calculated for the MARK {Phi(age)p(t)} model. Density

dependent population growth was implemented via a carrying capacity ceiling similar to

that in VORTEX: at each time step, if a simulated population was projected to be larger

than K, the population size was adjusted downward by a factor of (N-K)/K by the next

time step (see Appendix E for MATLAB program code for the ceiling model). Stochastic

growth rate and extinction risk estimates (in the form of the extinction probability CDFs)

from this relatively simplified, single-sex, nongenetic model were then compared to

VORTEX results. Log stochastic growth rates were calculated as the arithmentic mean of

all ln(Nt+1/Nt) values, after discarding the first 500 to eliminate transient effects (Caswell

2000), while extinction probabilities were calculated as the sum across all replicates of

extinct populations at each time step, divided by the total number of replicates.

Sensitivities for the SDM model were calculated using a MATLAB program given in

Chapter 9 of Morris and Doak (2002), which estimates the effect of stochastic matrix

73
elements on λs, and these were compared to VORTEX sensitivities to permit a qualitative

comparison of the two models in terms of their general behavior. In terms of their

specific predictions for the populations of interest, the a priori expectation was that, if

differences in growth rate or extinction CDFs occur only at small population sizes, then

those differences may be attributable to features that are not implemented in the SDM

model, such inbreeding genetics and demographic stochasticity. Conversely, if significant

differences in predicted growth rate and extinction risk are detected across populations of

a wide range of sizes, then it would be more plausible that there are fundamental

differences between individual-based and matrix models. In the latter case, considerations

of parsimony and the difficulty of obtaining sufficient data to parameterize complex,

parameter-rich models like VORTEX might argue in favor of using simpler models to

inform management decision-making. Confirming that VORTEX extinction projections

are sufficiently similar to those of a simpler model could be useful to managers because

VORTEX makes it relatively easy to estimate the effects of management actions (such as

supplementation, harvest, and translocation) that are difficult to model in a stochastic

matrix context. Therefore, supplementation scenarios for the PHR-Southeast and PHR-

Grass populations were also investigated, across a range of magnitudes and frequencies,

as were translocation scenarios modeled by increasing the number of populations from

the three at Laysan and PHR to four or more of various carrying capacities.

74
RESULTS

Genetic Parameters and Determination of Quasi-Extinction Threshold

Estimates of extinction probability have been characterized as problematic for two main

reasons, one theoretical and one practical. The theoretical problem, mentioned above, is

the skewed distribution of extinction probabilities generally (Belovsky et al. 2002). The

practical problem is that predictions regarding complete extinction do not give resource

managers enough information to intervene while there is still a good probability of

success (Morris and Doak 2002). Once a population reaches a sufficiently small size, the

quasi-extinction (QE) threshold, genetic and demographic factors tend to contribute more

strongly to processes of decline already in operation (Caughley 1994). Therefore, from a

management perspective it makes sense to follow the precaution recommended by Morris

and Doak (2002) and estimate extinction parameters, not based on an absolute extinction

threshold of zero, but on a QE threshold defined by the population size at which

demographic stochasticity and genetic effects begin to significantly affect the probability

of extinction. Attempting to identify a suitable QE threshold for VORTEX reveals some

useful information about the underlying assumptions of the model. For the Laysan finch,

there is currently no reliable information about the number of lethal equivalents per

diploid genome, nor the fraction of the genetic load they represent, and undertaking

studies to acquire such information involves nontrivial costs in both dollars and human

effort. Therefore, a QE threshold was estimated by setting all forms of environmental

variation to zero, including variation in mortality and breeding parameters, and then

lowering K from a value of 500 (at which the population size stayed nearly level at K for

the duration of the simulation) down to 10 (which resulted in nearly immediate extinction

75
in all simulations). As K decreased, the variation in population size relative to the average

population size over the course of the simulation increased substantially, leading to

sharply increased probability of extinction. For the default values of lethal equivalents

and genetic load, and the initial population size of 108 for Southeast Island, variability in

population survival due strictly to genetic stochasticity raised the probability of extinction

to 10% for a K of 80, and then to 70% for a K of 70. The latter probability, especially,

seems quite high, given that the PHR-Southeast population founders numbered not much

more than 70 and subsequently grew to over 700 (Morin and Conant 2002). Furthermore,

PHR-Grass Island population was founded by only eight individuals, has declined to as

few as five, and yet has not gone extinct in almost 40 years. Thus it appears possible that,

as has been previously suggested (Morin and Conant 2001), that VORTEX tends to

emphasize genetic and demographic effects more strongly than the actual effects

experienced by some island endemic species (but see also Frankham 1998). For these

reasons, the QE thresholds used in both VORTEX and SDM simulations were set to 50,

20, and 8 at Laysan, Southeast, and Grass Islands, respectively.

Growth Rate and Extinction Risk

As shown in Figure 3.2 below, there is significant disagreement between the VORTEX

and SDM models regarding the expected stochastic growth rate of the Laysan and PHR-

Southeast Island populations. All three SDM estimates of log λs are, at less than 10-5, not

significantly different from zero, so that the VORTEX estimates, at 3%-6% annual

growth, are more than three orders of magnitude larger. The disagreement is less

pronounced for the PHR-Grass Island estimates; however in that case VORTEX estimate

is negative (although its confidence interval still includes zero).

76
 VORTEX and SDM Projected Log Stochastic Growth Rates
for Laysan Finch Populations
0.08

0.06

0.04 VORTEX
SDM
0.02

-0.02
Laysan PHR-Southeast PHR-Grass

Figure 3.2. Log stochastic growth rates (λs) for three Laysan finch populations estimated from
10,000-year popuation projections, using both VORTEX individual-based models and a stochastic
demographic matrix simulation.

With regard to extinction risk estimates, there is better agreement between the models for

one of the populations, but not for the other two. As shown in Figure 3.3 below, neither

VORTEX nor the SDM model predicted a detectable risk of extinction for the Laysan

population. In effect, both models fail to detect a significant risk of extinction at Laysan

due to the finches' intrinsic population dynamics as modeled, given the data with which

the models were parameterized. However, as with the projection of stochastic growth

rate, the two types of models differ widely on their predictions for the PHR populations.

The SDM model estimates zero risk of extinction at both Southeast and Grass Islands,

while VORTEX projects a 0.34 probability of extinction within 100 years at Southeast

Island, and certain extinction at Grass in as little as 50 years.

77
 V ORTEX Ext inct ion Pro bab ilit y CDFs f o r Laysan Finch Po pulat ions
1

Grass
0 .8

Sout heast
0 .6

P(E)
Laysan
0 .4

0 .2

0
0 10 20 30 40 50 60 70 80 90 10 0
Y ears Int o The Fut ure

Figure 3.3. VORTEX projections of intrinsic extinction risk for the three Laysan finch populations.
The CDF for the Laysan population is coicident with the x-axis across the entire time horizon.

Since the growth rate projections from the SDM model are nearly zero, with relatively

small confidence intervals bracketing them, it follows that extinction risk estimates for

populations with finite sizes would be very low. In fact, all extinction probability CDFs

obtained from SDM models for the three populations were zero across the entire time

horizon. The extent to which simulated populations did not approach their respective QE

thresholds is evident from Figure 3.4 below, which plots the median population size

across all replicate trajectories, bracketed by their maxima and minima.

70
600

60
500
50

400
40

300
30

200
20

100 10

0 0
0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80 90 100

Figure 3.4. Population sizes from PHR SDM simulations. Southeast Island population sizes are
shown on the left, and Grass Island sizes are at right. Results are based on sets of 10,000 replicate
population trajectories over 100-year time horizons. The smallest population size attained in the
Grass Island simulations was more than twice the quasi-extinction threshold of 8.
78
 Given that the structure of the SDM simulation model was designed to mimic that of

VORTEX in most respects, with the same survival estimates, fertility data, QE threshold,

and ceiling form of density dependence, the growth rate discrepancies are larger than

expected. However, while both models begin with stable age distributions and implement

ceiling-based density dependence the same way, there remain many potentially

significant differences between them. VORTEX is explicitly a two-sex model, while the

SDM projects population dynamics from female numbers only. VORTEX also conditions

breeding activity on user-supplied values for the fraction of breeding females and the

fraction of males in the breeding pool. Combined with differential mortality, those

features create more potential for simulated populations to experience significant sex-

ratio bias, which would increase extinction risk when simulated populations dropped to

very small sizes. The most salient structural difference between the two models, though,

is the explicit simulation of inbreeding genetics in VORTEX. Because VORTEX assigns

two unique alleles to each individual in the population at the start of each simulation, the

fact that the PHR-Southeast population is ten times larger than the PHR-Grass Island

population, translates directly into an order-of-magnitude faster increase in the mean

inbreeding coefficient at Grass, as well as a comparably fast decrease in the mean

expected heterozygosity, in spite of the fact that the rate of allele loss is the same for both

populations (because, although the rate of loss is the same, Grass begins each simulation

with fewer than a tenth the total number of alleles present in the Southeast Island

population). However, it seems likely that the higher extinction risk in the VORTEX

Grass Island simulations is attributable in large part to the extra mortality arising from

lethal homozygosity. Figure 3.5 below shows that simulations of the Grass Island

79
population, with and without inbreeding depression modeled, do produce similar results

for the change in allele number over time. However, significant divergence between the

inbred and non-inbred populations, in terms of heterozygosity loss, inbreeding

coefficient, and extinction risk, emerges rapidly.

(A) Allele Number (B) Heterozygosit y (C) Inbreeding (F)

60 1 1
ON
ON OFF
50
OFF 0.8 0.8

40
0.6 0.6
30
0.4 0.4
20
ON
0.2 0.2
10 OFF

0 0 0
0 20 40 60 80 100 0 20 40 60 80 100 0 20 40 60 80 100

(D) VORTEX Ext inction CDFs f or Grass Island Populat ion wit h and wit hout Inbreeding Depression Eff ects
1

0.8

ON
0.6

P(E)

0.4
OFF

0.2

0
0 10 20 30 40 50
Year s Int o The Fut ure

Figure 3.5. VORTEX projections of inbreeding effects on small (N=30) populations. Graph (A)
shows that allele number changes very similarly for inbred and non-inbred populations, while
graphs (B) and (C) show that heterozygosity levels and inbreeding coefficients diverge strogly.
Graph (D) shows that extinction risk in small populations is significantly higher with inbreeding.

Sensitivities

In contrast to the comparison of stochastic growth rates and extinction probabilities

generated by the two models, comparing their sensitivities is more complicated because

of their differing structures, with different numbers of parameters and different dynamics

80
modeled. As shown in Figure 3.6 below, the factors having the strongest positive

influence on the stochastic growth rate are fertility-related (maximum clutch size,

maximum breeding age, percent of females breeding, males in the breeding pool, and the

proportion of clutches at the largest sizes). However, they are not age-specific fertilities,

as would be used in the SDM context; conversely, the SDM fertility rates are not pure

fledgling-production terms, but the product of age-specific female offspring production

and the survival rate for female fledglings. Thus, because of the different way of

modeling the sexes, the strongest negative influence on VORTEX estimates of stochastic

growth rate (the breeding ages of males) is not an SDM parameter. However, the next-

most-influential factor, female breeding age, is a factor in the SDM model, and, as shown

in Table 3.4 below, in that context it turns out to have the largest influence on λs. Since

fertility of second-year females is linked to the age of first reproduction, the matrix is

strongly sensitive to this parameter, and taken together with comparable sensitivity to the

survival of hatch-year birds, the sensitivities characterize a fast-growing population with

a relatively r-selected life history. That assessment is supported by the generation time,

estimated by both VORTEX and the SDM as approximately 3.5 years. Such life history

traits appear to be consistent with Laysan finches' adaptations to the highly variable

environment of the coastal strand habitats of the Northwestern Hawaiian Islands

(Weathers and Van Riper 1982), and helps explain why these populations seem, for an

endangered species, relatively free of intrinsically-generated extinction risk.

81
 Vortex Parameter Sensitivities for Stochastic Growth Rate

-0.06 -0.04 -0.02 0 0.02 0.04 0.06

Maximum Clutch Size

Maximum Breeding Age

Percent of Females Breeding

Percent of Males Breeding

Percent of 5-Offspring Clutches

Percent of 4-Offspring Clutches

Std. Deviation of % Females Breeding

Percent of 3-Offspring Clutches

Environmental Variation in K

EV in Male Mortality (2nd year)

EV in Female Mortality (hatch year)

EV in Male Mortality (hatch year)

EV in Male Mortality (adult)

Percent of 2-Offspring Clutches

EV in Female Mortality (adult)

Percent of 1-Offspring Clutches

Male Mortality (hatch year)

Lethal Equivalents per Genome

Female Mortality (hatch year)

Male Mortality (2nd year)

Male Mortality (adult)

Female Mortality (adult)

Female Age of 1st Breeding

Male Age of 1st Breeding

Figure 3.6. VORTEX parameter sensitivities, estimated by the slopes of regression lines fitted to
stochastic growth rate results from 1000-iteration simulations run at each of a range of 4-10 values
of each parameter while holding all other parameter values constant (see Table 2 for baseline
parameter values). Input batch files for VORTEX were generated using VORTBAT (Kohlmann
2002). Parameters not implemented in Laysan finch simulations are not shown.

Vital Rate Sensitivity

2nd-Year Fertility 0.0974
Hatch-year Survival 0.0920
Adult (> 2nd-Year) Survival 0.0721
5th-Year Fertility 0.0599
2nd-Year Fertility 0.0488
3rd-Year Fertility 0.0353
2nd-Year Survival 0.0326

Table 3.4. Sensitivities for the stochastic demographic matrix model, calculated in MATLAB using
a modified sample program from Morris and Doak (2002).

82
Supplementation and Translocation

As mentioned above, one reason VORTEX appeals to resource managers is the ease

with which it can model the effects of management actions that would be substantially

more challenging to model via a customized simulation program. For example, should

managers wish to provide additional insurance against extinction risk, they may need to

establish whether it is more useful to create additional populations, or to supplement the

small populations with individuals from a larger, more stable population. Without

considering the corollary issues of finding suitable habitat for translocation, or of the cost

of continued intermittent supplementation efforts, this study investigated the effects of

supplementation from Laysan and the effects of translocation (creating additional

populations) on the stochastic growth rate and extinction risk faced by the PHR-Southeast

Island population. Supplementation scenarios were based on adding one to ten

individuals of either sex at intervals ranging from 6 to 34 years. Also studied were the

effects of starting and stopping the supplementation program at different points along the

simulation time horizon. Translocation scenarios were analyzed somewhat differently:

rather than study the change in stochastic growth rate and extinction risk for a particular

population caused by creating additional populations, the parameter of interest was the

overall extinction risk faced by the aggregate set of populations. This approach permits

the assessment of the relative importance, not only of the number of populations created,

but also their initial size and the carrying capacity of their habitats, to the overall

extinction risk faced by the species. A sensitivity analysis similar to that applied to the

basic life history parameters above was also applied to VORTEX supplementation and

translocation parameters. As shown in Table 4 below, the result is that, in VORTEX, the

83
magnitude of the extinction rate sensitivity to the number of additional populations

created is more than twenty times larger than the extinction rate influence of any other

parameter. That is, VORTEX predicts that translocation for a given founder population

size and habitat carrying capacity, will be a more effective conservation tactic than

supplementation.

Management VORTEX Sensitivity Sensitivity

Action Parameter log(λs) P(E)
Translocation Number of Added Populations -0.00689 -0.24420
Supplementation Number of Males Added 0.00061 -0.01401
Supplementation Number of Females Added 0.00025 -0.00811
Supplementation Interval Between Events -0.00031 0.00735
Supplementation End of Supplementation 0.00006 -0.00168
Translocation Added-Population Initial Size 0.00004 -0.00120
Translocation Added-Population Increase in K -0.00009 -0.00021
Supplementation Start of Supplementation -0.00003 0.00021

Table 3.5. Supplementation and translocation parameter sensitivities in VORTEX. Values are negative for
the start of supplementation and the interval between supplementation events because, over the time
horizon of a given simulation, a population's stochastic growth rate is reduced by increasing the delay
before the start of supplementation or increasing the interval between supplementation.

Although the sensitivity of VORTEX extinction risk projections to the creation of

additional populations seems reasonable, other sensitivity results do not accord as well

with intuitive expectations. For example, it is counter-intuitive that additional populations

should have a negative impact on the stochastic growth rates of the set of populations

overall. This circumstance is an artifact of the proximity of the lowest carrying capacity

value used (50) to the quasi-extinction threshold and affects only single-population

scenarios. With K set so low, populations that experience any decline go extinct almost

immediately, so stochastic growth rate estimates tend to be biased high. Once a second

population is being simulated, the exinction probability for the pair of populations is

lower than for a single population, and the longer average survival time allows more low-

or negative-growth years to be included in the stochastic growth rate calculation.

84
 On the other hand, it is more difficult to elucidate why the next-most-sensitive

parameter is the supplementation of males, estimated as being between two and three

times more influential than supplementation with females. It is unclear why VORTEX

would tend to project the adding of males to a population to have a greater impact than

the adding of females. However, as was the case with the single-population sensitivity

results given in Figure 3.6 above (in which the male age of first breeding is shown to

have a greater influence on stochastic growth rate than the female age of first breeding),

this relatively high sensitivity to male supplementation suggests that the genetic

stochasticity implemented in VORTEX has a strong impact on the dynamics of small

populations. This could be an artifact of having chose the default values of 3.14 lethal

allele equivalents per individual and the genetic load of 0.5, figures derived from

characteristically outbreeding continental mammal species (Ralls et al. 1988). These

default values may be high for inbred island endemic species such as the Laysan finch

(Tarr et al. 1998, Conant and Morin 2001, Frankham 1998), causing VORTEX to

exaggerate the simulated effects of inbreeding on small finch populations. To date studies

of the actual number of lethal equivalents per individual and the proportion not exposed

to selection have not been performed, so choosing justifiable alternative values would be

difficult. However, it is suggestive that the VORTEX model's response to

supplementation could be sustained with as few as five adults of each sex added to a

population every 20 years, a relatively low rate of introduction of new alleles which

indicates that, given the survival and fertility values supplied for this species, and in the

absence of catastrophes or substantial variation in carrying capacity, most of the risk to

small simulated populations is derived from genetic stochasticity. The response to

85
supplementation, however, depends on the rate of decline in the supplemented population

in the absence of immigration: if extinction risk is already projected to be very low, then

there is little or no improvement to be gained from supplementation. Likewise, if the

habitat is degraded or lost due to exogenous factors such as biotic invasions or sea level

rise, supplementation may be futile. Ultimately, the value of either supplementation or

translocation as management options will depend not only on the availability of suitable

translocation sites or the ability to continue a supplementation program for an indefinite

time period, but also on the nature of the threat necessitating the management action in

the first place. The PHR islands are less than one-third the elevation of Laysan and, in the

aggregate, have about one-tenth as much vegetated area. The fact that neither VORTEX

nor the SDM model foresee much risk of extinction from the intrinsic dynamics of the

population and a relatively short temporal sample of its environmental variability may not

reveal much about the additional risk that could accrue from factors which cannot be

parameterized in either model.

DISCUSSION:

Numerous authors (Burgman and Possingham 2000, Morris and Doak 2002, Ralls et al.

2002) have recently asserted the need for population viability analyses to incorporate

results from different models, the rationale being that, where different model structures

lead to convergent projections, management actions will be more reliably effective. This

study finds little agreement between the individual-based model implemented in

VORTEX and a stochastic demographic matrix model. Both project low intrinsic

extinction risk for the largest finch population at Laysan, but the SDM model estimates

86
zero risk for both of the much smaller PHR populations, in spite of also estimating their

growth rate as approximately zero. VORTEX projections diverge from the SDM results

both in terms of making significantly different growth rate estimates and in projecting

higher extinction risk. With regard to the PHR-Grass Island population, its small size

almost certainly contributes to the divergent predictions of the two models, especially

given the inclusion in VORTEX of genetic and demographic stochasticity. For the PHR-

Southeast Island population, the reason for the divergence is not as obvious but most

likely relates to the same factors. Given that VORTEX models seem to emphasize the

role of genetic stochasticity to a such a strong degree, a quasi-extinction threshold

assumed to be appropriate for a given population may actually be lower than what would

be appropriate in VORTEX. Clearly, setting the QE threshold as high as the transition

point obtained from a zero-stochasticity model will greatly increase estimates of

extinction risk. Frankham (1995, 1998) and Conant and Morin (2001) have suggested that

island endemics may be more resilient to inbreeding effects due to past population

bottlenecks, which may have intensified drift. Populations surviving such bottlenecks

could benefit from a reduced genetic load due to purging of lethal alleles. The VORTEX

default values of lethal equivalents and load, derived as they are from outbreeding

continental species, may be a high for some insular species, but there is no firm

justification for alternative values, and sensitivity analysis does not conclusively

demonstrate a strong effect of either parameter.

Apart from questions about the effects of the genetic parameters in VORTEX, there are

additional unresolved questions about the form of density dependence used in modeling

population growth. As mentioned earlier, ceiling-based models such as those studied by

87
Lande (1993) and Foley (1994) behave differently from logistic-based projections. It is

therefore worthwhile to investigate the behavior of individual-based models such as

VORTEX and compare their projections with those of other models. The VORTEX

ceiling model of carrying capacity has a different meaning from (and a more lethal effect

than) the K used in simulations based on the logistic model. In the latter, the maximum

likelihood estimate of K is obtained from a nonlinear regression of population growth

rates against population size, and simulated population trajectories may randomly

generate K at each time step from a normal distribution centered on the MLE and

bounded by its confidence interval. However, such a simulation would not automatically

kill all individuals exceeding K at any time, as VORTEX does. Moreover, it is not clear

that estimates of K (e.g., from nonlinear regression) that are appropriate for logistic-based

projections are comparably suitable for ceiling models. The VORTEX documentation

implicitly makes this point by suggesting studies of resource availability in the

population's habitat, energy and activity budget studies, and so on, but of course these are

not commonly carried out, or even feasible, for rare species in remote locations.

Similarly, the recommended regression analysis of clutch production and size distribution

against population size, while surely the best way to estimate the strength of density

dependent regulation of reproduction, requires numerous years of both population

censusing and nest (or den, etc.) surveys. Thus these data are mostly lacking, leading to

ongoing skepticism about the use of parameter-rich models like VORTEX which, it is

argued, entice naïve users into making unjustified estimates or projections, leading in turn

to counterproductive management efforts (Burgman and Possingham 2000, Coulson et al.

2001). It turns out, however, that modifying the SDM model used here, so that the ceiling

88
form of density dependence is replaced by a logistic form of density dependence in

fertility, survival, or both, does not significantly change the predicted outcome for the

three Laysan finch populations. The extinction risk estimate obtained from the simulation

depends more strongly on the distance between K and the quasi-extinction threshold. One

possibility that has not been investigated is that Laysan finches at PHR-Southeast Island

may experience a different tempo of density-dependent regulation than do the finches at

Laysan. Building time lags into the simulation might lead to population size trajectories

that show large fluctuations spanning several years, as observed in the Southeast Island

time series, rather than the faster annual fluctuation observed at Laysan and Grass Island.

Unfortunately, the nature of those apparently longer-term fluctuations is poorly

documented, due to sampling gaps in the PHR population records, and because there is

currently a severe alien plant infestation displacing most of the PHR-Southeast plant

community, it may not be possible, even with additional years of data, to resolve the pre-

invasion dynamics of that population's producer-consumer interactions.

The 1998 weed invasion at PHR-Southeast Island, in which Verbesina encelioides

rapidly overtook the island's vegetation, permitted a tripling of the finch population

within three years, only to die back and and leave the island bare of plant cover. The

subsequent drop in the Laysan finch population size from over 1900 to less than 600

(Wegmann 2001, Wegmann and Kropidlowski 2002, Sprague 2003), along with the

history of near-extinction at Laysan due to the introduction of rabbits, underscores the

possibility that exogenous factors are the primary source of risk to these populations. It is

possible to compile data on shipwreck rates throughout the Hawaiian archipelago to give

a rough estimate of the risk of predator or pathogen introduction. It is likewise possible to

89
model effects of projected sea-level rises as changes in the carrying capacity of these

low-elevation islands. However, the projected consequences of either of these sources of

risk, derived as they are from highly uncertain processes and rare stochastic events,

would have to be regarded skeptically.

90
 CHAPTER 4

THE LAYSAN FINCH GENETIC MATING SYSTEM:

ESTIMATING THE RATE OF EXTRA-PAIR PATERNITY AND ITS IMPACT ON

EFFECTIVE POPULATION SIZE AND EXTINCTION RISK

INTRODUCTION

Recently, increasing attention has been focused on the importance of animal behavior in

conservation biology. Despite the inherent complexity of behavior, compounded by its

interactions with the complexities of population dynamics, Reed (1999) suggested that

conservationists study behavior explicitly, because ignoring it could undermine

conservation efforts. Examples of behavioral effects on extinction risk include Allee

effects, in which growth rates drop at low population densities, typically due to difficulty

in finding mates (Roughgarden, 1998; Case, 2000). Studies of small or declining

populations have revealed other mechanisms by which behavior can contribute to decline.

The mechanisms fall into two main categories: either the animal's behavior changes at

small population sizes or densities, or the adaptive value of the behavior changes, so that

behaviors that are adaptive, or at least not selected against, at high densities may prove

maladaptive low densities. An example is the endemic Hawaiian monk seal (Monachus

schauinslandi), juvenile males of which are known to mob isolated females when female

population density is low (Starfield et al. 1995). Mobbing increases female mortality,

leading to adverse demographic effects given the species' low fecundity and long

generation time. Besides problems that arise from persistent behavior at declining

population sizes, behaviors themselves can shift, or frequencies of component behaviors

91
in mixed strategies can shift, as population size changes. Creel's (1998) studies of social

carnivores showed that extra-pair copulation frequencies could change at low densities,

strongly influencing effective population sizes (Ne). Finally, there is the additional

consideration of changes in adaptive value with translocation. Species in which some

populations are declining for one set of reasons, such as habitat fragmentation or

degradation, may be unsuited to a particular translocation site for different reasons, e.g.

behavioral ones, as was the case with translocated Turkish ibexes (Capra ibex), whose

breeding schedule proved ill-timed for the harsh winters in Slovakia (Whitehead 1960).

Despite these clear instances of behavioral contributions to extinction risk, few

population viability analysis (PVA) studies, or the general methods upon which they are

based, make explicit provision for behavior. For the most part, this is simply a practical

constraint: modeling any particular behavior explicitly can be quite complicated, but the

general modeling of any organism's spectrum of potential behaviors is typically

intractable. A practial alternative, therefore, is to assess which subset of behaviors is

expected to have the greatest impact on viability, and include those in the overall

analysis. The PVA program VORTEX does enable users to model the effects of certain

behavior-related parameters, such as Allee effects and skewed distributions of

reproductive success caused by non-monogamous mating systems. In this, VORTEX is

different from other "off-the-shelf" PVA programs, providing a means to test the long-

term projected effects of some behavioral traits.

The endangered Laysan finch (Telespiza cantans) is endemic to Laysan Island, located

in the Northwest Hawaiian Islands about 1280 kilometers northwest of Honolulu. Guano

miners introduced rodents on multiple occasions in 1903 and 1904, mostly rabbits

92
(Oryctolagus cuniculus), but also European brown hares, (Lepus europaeus), and even

guinea pigs, (Cavia porcellus; Ely and Clapp 1973). The introductions catastrophically

devegetated the island, driving several species of endemic birds, arthropods, and plants to

extinction within two decades. To reduce extinction risk, the US Fish and Wildlife

Service in 1967 translocated 108 finches 640 kilometers northwest of Laysan to Pearl and

Hermes Reef (PHR). The largest of the four main PHR islets, Southeast Island, comprises

only about 12 vegetated hectares, compared to Laysan's 187 vegetated hectares. Within a

year of the translocation, two finches were sighted at still smaller (2 ha) Grass Island ,

eight kilometers to the west of Southeast Island, and in 1973 two more birds were found

at North Island, about 16 kilometers north of Southeast Island. Eventually, due to natural

and FWS-assisted movements, finches colonized all four of the vegetated islands, but by

1998 two of those populations had gone extinct. Translocation has reduced the

vulnerability of the species to catastrophes at either atoll; however, the small (based on

USFWS estimates from 1967 to 1997) PHR census population sizes, their extreme

variability, and the even smaller effective population sizes (Tarr, et al, 1998) of the

translocated popuations have raised questions about the long-term viability of the PHR

populations as insurance against extinction.

Mating system studies are of interest in this case because the Laysan Finch, a socially

monogamous bird, is sexually dimorphic in size and plumage coloration (adult males are

a bright canary yellow about the head and breast, while females are more drab), a trait

associated with non-monogamous mating systems (Moller and Birkhead 1994, Yezerinac

and Weatherhead 1997, Birkhead and Moller 1998). However, non-monogamous mating

systems have not been documented in Hawaiian honeycreepers, and a DNA

93
fingerprinting study of the Palila (Loxioides balleui; Fleischer et al. 1994) did not detect

any evidence of extra-pair paternity or intraspecific brood parasitism. However, despite

the apparent monogamy in the honeycreepers, male Laysan finches exhibit delayed

plumage maturation, such that the juvenile plumage of second-year males closely

resembles that of second-year and adult females. In other endemic Hawaiian passerines,

specifically the 'Elepaio, the delay in plumage maturation has been shown (Vanderwerf

1999) to reduce aggressive interactions with adult males. In other bird species, delayed

plumage maturation has effects similar to the effect of different size classes among males

of some species of fish, permitting sneak matings and enhancing the reproductive success

of males which would otherwise be excluded from mating by dominance interactions

with older males (Birkhead and Moller 1993, 1998). Laysan finches, are not territorial

with regard to foraging areas, but they do defend nest sites during the breeding season, so

it is possible that the delay in plumage maturation reduces aggressive interactions with

adult males, or permits sneak matings, or both. Second-year males have only rarely been

observed to breed successfully (Morin and Conant 2002), and plumage coloration and

brightness in adult males may be related to social dominance. Therefore, establishing the

frequency and age distribution of extra-pair paternity could reveal the extent to which

second-year males might enhance lifetime reproductive success by mating with females

with whom they are unable to pair due to their subordinate social status. Either polygyny

or extra-pair mating, whether by second-year or adult males, would increase the variance

in male reproductive success and thereby create more opportunity for sexual selection

(Yezerinac et al. 1995), relative to a completely monogamous mating system, providing a

94
potential explanation for the sexual dimorphism and plumage dichromatism characteristic

of the species.

In fact, an instance of polygyny was recorded at Southeast Island in July of 1999: a

banded adult male was seen nesting with one banded female in late May, then

subsequently guarding a different banded female while she built her nest. Within several

days the male had returned to spending more time with the first female, and then

switched back again a few weeks later. This event raised the question of how much extra-

pair mating occurs, and what impact such skew in male reproductive success may have

on effective population size and inbreeding. Therefore, as part of a comprehensive PVA,

this study estimates the extra-pair fertilization frequency among Laysan finch families in

the largest population (Southeast Island) at Pearl and Hermes Reef, examines its

influence on effective population size, and assesses what effect it might have on estimates

of extinction risk.

METHODS

Field Work:

Tissue samples were collected over three summer (late May to late July) field seasons at

PHR and one spring (late March to mid-May) season at Laysan. Birds were caught in

potter traps baited with jar lids of fresh water. When more than one bird was caught at a

time, those not being immediately measured and banded were held in cotton muslin bags,

always for less than twenty minutes. Feathers were collected instead of blood because

doing so reduced handling time per bird, permitting larger sample sizes and minimizing

risk of heat stress to the birds. Taking feathers also reduced the logistical challenges of

95
maintaining tissue samples in tropical conditions without cooling equipment. Typically,

one tail feather, the rightmost remix, was taken from each bird, as specificed in the

USFWS endangered species special use permits issued prior to each field season. Tail

feathers afford a larger tissue sample than countour feathers, but at some potential short-

term cost to the flying ability of the bird sampled. Laysan finches molt after the breeding

season, which winds down in early autumn, and summers inflict lower mortality on the

population than other seasons (especially winter). Furthermore, the finches are ground-

foraging birds living in a predator-free environment, so it was reasoned that the loss of a

single tail feather would not impose undue risks to the well-being of the birds. In addition

to the tail feather taken as the primary sample, contour feathers were collected

adventitiously when left in the muslin bird bag.

Captures ------------------------------>
1998 1998 1999 1999 2000 2000 Tissue Complete Approx. %
Island New Recap New Recap New Recap Total Samples Genotyped Genotypes of Population
Southeast (PHR) 220 53 105 85 241 119 823 603 199 189 42.0
Grass (PHR) 20 0 5 7 10 4 46 35 35 31 70.0
Laysan 0 0 0 0 200 0 200 96 96 51 0.2

Table 4.1. Mark-recapture and tissue-sample sizes for three field seasons at Pearl and Hermes Reef
and one season at Laysan.

Most samples were collected as part of daily banding efforts. However, as more

breeding pairs were identified through the season, more targeted efforts were required to

obtain samples from known pair members. Laysan finch mating is generally cryptic: only

two copulations were observed during a total of six months on Southeast Island. In the

two-month 2000 season, 62 clutches initiated by 49 breeding females were detected, but

of those, only 30 females' nests produced fledglings that could be sampled. Social pairs

were identified by observation of males and females nesting together: nest construction
96
(the male guarding while the female gathered material and built the nest) or nuptial

feedings were considered diagnostic of social-pair status. For the 30 social pairs tracked

in 2000, observations of one or more nuptial feedings, or feedings of offspring in the

presence of the social mate, were obtained for 80% of the pairs studied. Of the 20% for

which feedings could not be directly observed, two pairs were identified during nest

building, two more on the basis of agitated behavior of the pair in close proximity to the

nest while fledgelings were being banded, and one on the basis of alarm calls made while

the putative social mate was being banded. One pair was identified on the weaker

evidence of being seen foraging together, but as this foraging bout was observed for more

than 20 minutes and the pair were seen together on other occasions, it was considered

worth testing. Thirteen of the 30 pair identifications were based on more than one type of

behavior, or on multiple instances of the same behavior. Although 27 breeding pairs were

identified in 1999, nuptial-feeding-based behavioral evidence of social pair status could

only be established for six of those, and of those six, tissue samples from offspring were

available for only four.

Laboratory Work:

Genotyping procedures used eight of the nine microsatellite loci identified in the Laysan

finch genome by Tarr (et al. 1998; GenBank accession numbers AF036258-AF036267,

excludingAF036265, which could not be amplifed). DNA extraction was performed

using Qiagen® DNeasy™ kits. One to four millimeters of feather shaft from the tip of the

calamus was clipped into 1-millimeter pieces, which were then incubated in a mixture of

180 µL buffer solution and 20 µL proteinase K at 55°C forat least three hours. Two

washing and centrifugation steps were followed by elution to release the DNA from the

97
filter. The extraction protocol yielded 200 µL of dilute DNA template solution for each

bird to be genotyped. To increase the amount of DNA available for allele-sizing,

polymerase chain reaction (PCR) was performed using either Applied Biosystems

GeneAmp® PCR System 9700 or MJ Research PTC-200 thermal cyclers in 0.5mL

reaction tubes. For 25 µL reaction volumes, four microliters of template solution were

mixed with approximately 12 µL of doubly-distilled, deionized water, 2.5 µL each

Applied Biosystems PCR buffer and 0.1mM dNTP mix, 1.25 µL each 10 µM forward

and reverse primers, 0.1 µL AmpliTaq DNA polymerase (Applied Biosystems, Inc.), and

1-2 µL of 1.5mM magnesium chloride solution, depending on the locus to be amplified

(Tarr et al. 1998). Primers were labeled using either 6-FAM, HEX, or TAMRA

fluorescent dyes, so that PCR products could be visualized using an automated ABI 373

sequencer at the National Zoological Park Molecular Genetics Laboratory. Gels for the

373 sequencer were 48-lane, 6% acrylamide denaturing gels, with ROX dye-labeled

DNA size standard included in each lane. Allele sizing was partially automated by ABI's

GeneScan software, which compares fluorescence emission peak locations on the gel to

peaks resulting from the ROX standard's known fragment sizes (50, 75, 100, 139, 150,

and 160 bp). However, fluorescence peaks for all PCR products were visually inspected

to confirm size results. Allele sizes for each individual at each locus were then entered

into an Excel spreadsheet and sorted into genotypes for the known parent, putative father,

and offspring. Genotypes were then analyzed using GENEPOP (Raymond and Rousset

1995), using option 1, suboption 3 to test for Hardy-Weinberg equilibrium. Genotypes

based on loci in equilibrium were then analyzed using CERVUS (Marshall et al. 1998,

Slate, et al. 2000) to calculate likelihoods that offspring genotypes could result from a

98
mating between the known parent and one or more putative sires. An advantage of

CERVUS is that its likelihood calculations go beyond simple exclusion based on parent-

offspring mismatch detection, using allele frequency data to estimate the probability that

a socially-identified parent is more or less likely than any randomly chosen member of

the population to be the actual, genetic parent. Moreover, the likelihood ratios used to

assess that probability adjust for the estimated frequency of typing errors (Marshall et al.

1998). In cases where the putative sire of a fledgling was found to be less likely than a

randomly chosen member of the population to the genetic parent, those offspring were

considered the product of extra-pair fertilizations. Effective population sizes were

calculated by the computer program Ne Estimator (Peel et al. 2004), which uses formulas

9 and 12 in Waples (1989), such that: Ne = t/2[Fc – 1/(2S0) – 1/(2St)], where t is the

generation time, Fc = 1/(K-1)[Σ{(xi-yi)2/((xi+yi)/2)}], and S0 and St are the sample sizes for

generations 0 and t, respectively. The generation time was estimated by applying the

matrix analysis routine in PopTools to the five-stage Lefkovitch matrix used as the basis

of the stochastic demographic matrix model presented in Chapter 3. Finally, the possible

impact of skew in male reproductive success due to extra-pair paternity was estimated by

modeling the PHR-Southeast Island finch population in VORTEX with either a reduced

proportion of males in the breeding pool or a skewed sex ratio at birth, and the effects of

these different parameters on VORTEX extinction risk projections are presented.

99
RESULTS

As mentioned earlier, Laysan finch mating has rarely been observed, and both of the

instances witnessed over three two-month periods were crepuscular (one at daybreak, one

at dusk). Further, during three field seasons only one instance of extra-pair courtship

activity was observed. That event also took place at dusk, so it appears likely that extra-

pair mating attempts in general are similarly crepuscular or nocturnal. Thus it was not

possible for this study to corroborate a genetic estimate of the extra-pair fertilization rate

with observations of extra-pair mating activity. However, based on the 49 pairs observed

in 1999 and 2000, social mate fidelity (re-pairing) between seasons appears to be

approximately 100%. All pairs observed in 1999 or 2000 in which one mate differed

from the previous year's mate coincided with failure to resight the missing bird. Mate-

switching between years is therefore attributable primarily to winter mortality. With the

exception of the aforementioned dually-mated male, within-year mate-switching has not

been observed (Morin 1992b, Morin and Conant 2002).

Of the eight loci used to genotype the Laysan finch families at PHR-Southeast, three

(5A5A, 11B4E, 12B5E; see Table 4.2 below) showed significant deviation from Hardy-

Weinberg Equilibrium. These were excluded from parentage analysis. Among the

remaining five loci, based on the allele sizes detected in the offspring compared to those

found in the parents, there was no evidence of non-Mendelian inheritance or mutation for

the individuals genotyped.

100
 Locus Repeat Structure PCR Lengths # Alleles p SE(p) Fis (W&C) power
3A2C (GT)11 102, 104 2 0.379 0.005 0.077 0.122
4A4E (GT)11(AT)(GT)3 104, 106 2 0.398 0.005 -0.075 0.120
5A1B (GT)14(AT)(GT)2 85, 87, 89, 91, 93 5 1 0 -0.045 0.022
5A5A (GT)14 101, 103, 105, 107 4 0 0 0.584 -
11A4D (GT)15 95, 99, 101 3 0.202 0.006 0.044 0.158
11B1C (GT)16(GCGT)2(GT) 120, 122, 126, 134 4 0.968 0.001 0.004 0.204
11B4E (GT)12 85, 87, 91, 93, 97, 103 6 0 0 0.186 -
12B5E (GT)6(GCAT)(GT)20 127, 129, 134 3 0 0 -0.21 -

Table 4.2. Microsatellite locus characterization and Fisher exact test results for Hardy-Weinberg
equilibrium at the eight microsatellite loci used in genotyping Laysan finch family groups at PHR-
Southeast Island. Power to discriminate among paternity likelihoods, shown in the rightmost
column, is not given for non-equilibrium loci, which were not used for genotyping.

The 24 breeding pairs identified were associated with 58 offspring in 31 family groups

across the two partial breeding seasons monitored. CERVUS identified allele-size

mismatches between seven of the 58 offspring and their putative fathers, indicating an

extra-pair paternity (EPP) rate of 12.1%. There were no mismatches found between

mothers and offspring, hence there was no evidence of egg dumping by females. Failure

to detect egg dumping was expected, because there had been no observations of females

loitering near other female's nests. In contrast to the EPP estimate obtained from father-

offspring mismatches, however, likelihood (LOD) scores indicate that eleven males are

less likely to be the fathers of their putative offspring than randomly-chosen males from

the Southeast Island population. This the maximum-likelihood estimate of extra-pair

paternity is 19%. However, because of the relatively low power to resolve mismatches, as

shown in Table 4.2 above (see also Hill and Post 2005), the 95% confidence interval for

that estimate is quite large: (5.2%, 72.4%). Even the less stringent 80% confidence

interval (12.1%, 41.4%) comprises a range larger than the ML estimate itself.

101
 PHR-Southeast LOD Scores f or 58 Of f spring and 24 Putative Fathers
14
Number of Offspring 12

10

0
-4.0 -3.2 -2.4 -1.6 -0.8 0.0 0.8 1.6 2.4 3.2 4.0
LOD score

Figure 4.1. Frequency distribution of LOD scores for 58 paternity tests between Laysan finch
offspring and putative fathers.

Power afforded by the loci used, estimated by CERVUS to be 0.49 appears to be

constrained by the small number of alleles per locus and the absence, among the families

studied, of the rarer alleles at certain loci (particularly 5A1B and 11B1C). The mean

number of alleles per locus, 3.2, is just over one-third of the 9.2 alleles per locus in a

recent study of Seaside Sparrows (Hill and Post 2005), in which the power to resolve

paternity was estimated to be 0.98. The relatively low power available means that

identifying the true fathers of extra-pair offspring is not feasible. Therefore, because the

actual number of males fathering extra-pair offspring is unknown, and more generally,

because there is insufficient information about reproductive success across generations,

recently-developed demographic estimators of Ne that account for overlapping

generations cannot be used. However, because the census population size at PHR-

Southeast has typically been estimated at well over 100, and because the generation time

is short at 3.2 ± 0.7 years, the actual effect of generational overlap on Ne should be small.

A relatively simple demographic estimator (Lande and Barrowclough 1987) which

102
assumes non-overlapping generations puts Ne for PHR-Southeast at 136. This estimate is

biased upward by the omission of generational overlap, and genetic estimators give much

lower values. The effective population size estimate obtained from the observed rate of

heterozygosity decay is 25 ± 4, slightly higher than the estimate of 21 obtained by Tarr, et

al. (1998). The variance effective population size (Waples 1989) is estimated to be 29.6,

with a confidence interval of (12.7, 55.3), about one-third larger than the prior estimate,

most likely because the generation time used here is about 25% shorter than that used in

the previous study.

To assess the impact of a 19% EPP rate on extinction risk, the worst-case assumption

would be that a small subset of males cuckolds the others, thereby increasing the overall

variance in reproductive success. While it is possible that all males breed with equal

success and EPFs are evenly apportioned among males, the greatest impact on the

population in terms of inbreeding depression would be for a smaller number of males to

garner all the successful matings in the population. In this scenario, the deviation from

monogamy can be treated as a special case of harem polygyny (Nunney 1993) in which h,

the number of females mated to the average successful male, is slightly greater than one.

Effectively, EPFs shrink the proportion of males in the adult breeding pool. VORTEX

was used to test the projected effects of polygynous mating and sex ratio skew on

extinction risk because it allows the modeler to specify either a reduced proportion of

males in the breeding pool, or an arbitrarily distorted sex ratio at birth, or both factors

operating simultaneously. Simulations projecting populations over 100-year time

horizons with demographic parameters based on estimates for the PHR-Southeast

population showed that extinction was largely unaffected by reproductive skew. With

103
only 10% of the males siring all chicks in the population, the extinction probability for

simulated populations with finite extinction risk increased by 10%. For the mean time to

extinction there was a small affect, such that changing the fraction of breeding males

from 70% to 10% would yield a 25% drop in projected survival time, from about 300

years to just over 200. A caveat to these results is that VORTEX estimates are based on

census population size, so very low Ne values could be more problematic for real

populations than VORTEX would estimate. Also, the VORTEX genetic model was not

developed with single-island endemics in mind, so it seems to extinguish small

populations faster, and at a higher size threshold, than the Laysan finch population

histories suggest to be realistic.

DISCUSSION

The estimated rate of extra-pair mating among Laysan finches is approximately 19%,

which is relatively high for a tropical passerine but appears to have little impact on

effective population size. The fact that the demographic estimate of Ne, while only about

a third of the census population size, is four times larger than the genetically estimated

Ne(H) suggests that the reproductive capacity of the population, assessed

demographically, may be a better indicator of population survival probability than the

genetic estimate of drift and inbreeding.This estimate accords with the range of EPF rates

observed in passerines generally (Birkhead and Moller 1993; Wink and Dyrcz 1999;

Griffiths et al. 2002) although it is much higher than the rate of zero estimated for the

Palila via DNA fingerprinting (Fleischer et al. 1994). Newman and Pilson (1997) showed

that small effective population size increased extinction risk, and in the case of these

104
small translocated finch populations, if some males were gaining most of the matings, the

resulting skew in reproductive success would be expected to reduce the effective

population size and thereby increase extinction risk. However, VORTEX simulations

suggest that even frequent polygyny, creating strong reproductive skew such that only

10% of adult males breeding, would increase extinction risk over a 50-year horizon by at

most 10%. On the other hand, effective populations sizes at PHR are so small (ranging

from 6 to 28, with two of the four populations established in the 1970's now extinct) that

any shift downward could be cause for management concern. Behavioral observations

made in this study are not consistent with a high EPC rate: the few instances of courtship

or other solicitation of paired females by paired or unpaired males have all been strongly

rebuffed. Nonetheless it is possible that EPCs occur cryptically. However, while complex

mating dynamics in socially monogamous birds are no longer regarded as uncommon in

temperate passerines (Birkhead and Moller, 1998), Fleischer (et al. 1994, 1997) showed

that tropical passerines may practice genetic monogamy more strictly than their

temperate counterparts. Therefore, it is not expected that the Laysan finch would show a

dramatic departure from monogamy, but it is of zoological and possible management

interest to affirm or falsify such expectations.

EPFs – unless they are completely random and have no sexual selection component –

suggest that some males have more mating success than others, and some males lose out

completely. Thus the effective sex ratio changes, with fewer breeding males in proportion

to EPF frequency. As the sex ratio shifts towards fewer males breeding, the sex ratio at

maximum effective population size becomes more female-biased. Concomitantly, the

maximum effective population size attainable by the population declines to about 2/3 the

105
maximum value attainable with no extra-pair mating. Therefore drift and inbreeding

effects should be more pronounced in populations with high degrees of extra-pair

paternity.

As for the reproductive success of the polygynous male mentioned earlier, his second

mate's two clutches produced 6 eggs, none of which hatched. The initial female's two

clutches fledged one chick from the first and appeared likely to fledge three more from

the second nest by the end of the field season. The production of approximately one

dozen eggs, resulting in at most 4 chicks, is a yield attained by other males maintaining

single-mate fidelity, so it is not clear that polygyny enhanced reproductive success in this

case. However, if polygyny were taking place more generally and other males

experienced greater success than did the observed male, it is possible that the adaptive

value of this behavior could be contributing to the plumage dichromatism and other

sexually dimorphic traits in this species. For this reason, further investigation of mating

behavior and courtship in Laysan finches may be of interest. A related consideration is

that the chicks with 3 and 4 mismatches turned out to be from second clutches within the

season, which might be expected given the increased opportunities for extra-pair

copulations in asynchronously mating birds later in the breeding season.

Island endemics may be resilient to inbreeding, as low allelic diversity and high

inbreeding coefficients characterize populations which have persisted for hundreds or

even thousands of generations (Frankham 1995, 1998). As is the case with other

populations known to have experienced genetic bottlenecks, such as cheetahs or elephant

seals, low genetic diversity by itself may not increase extinction risk as much as it can in

very small captive populations or in larger, recently fragmented populations. Extremely

106
small populations, however, may still face inbreeding problems. At PHR, although the

Grass Island population has persisted for about 10 generations, its colonization by two

individuals in 1968 was supplemented by the addition of six more individuals from

Southeast Island in 1970. In contrast, the North Island population, founded by two

individuals in 1973, went extinct by 1998 despite having increased to over 200 birds by

the mid-1980's. The steady decline at North Island (Morin and Conant 2002) is

suggestive of inbreeding depression, although other factors, from changes in plant

community structure to storm surge exposure during winter, were also likely at work.

With regard to the remaining Laysan finch populations, with the possible exception of

Grass Island, deviation from monogamy in the mating system seems unlikely to exert a

significant effect on extinction risk. The dominant factors expected to have the greatest

influence on risk should be those which drive the population to low enough numbers that

the genetic and demographic factors can begin to play a larger role. That quasi-extinction

threshold is difficult to estimate, particularly for endangered species, since experiments in

which numerous small populations are replicated and then permitted to go extinct are

difficult to justify to permitting agencies. In simulating Laysan finch population

dynamics, quasi-extinction thresholds of 50, 20 and eight were used for the Laysan,

Southeast, and Grass Island populations, respectively, but these numbers represent

arbitrary guesses at the effect of island size on the birds' ability to find mates. The larger

issue (sensu Caughley 1994) for all three populations is the set of factors that could push

them near the quasi-extinction threshold. Smaller islands can experience more complete

shifts in habitat quality in a given amount of time than larger islands, so alien species

invasions pose a greater threat to the PHR islands than to Laysan. Similarly, the impacts

107
of adverse weather conditions on small, low-lying islands should be proportionally

greater. The latter issue relates to the question of climate change and the extent to which

rising sea levels may reduce the carrying capacity of the islands. Thus the forces that pose

the greatest threat to Laysan finch populations do not seem likely to be related to mating

behaviors, but rather to extrinsic factors such as alien introductions and environmental

stochasticity. Because of the limited options for further translocations, it will be a

substantial challenge to find ways to head off these threats within the next several

decades.

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 CHAPTER 5

CONCLUSIONS AND FUTURE WORK

The three PVA techniques applied in the preceding chapters have been used to estimate

the intrinsic extinction risk attributable to the natural dynamics of the three Laysan finch

populations. In addition, the incremental risk associated with a loss of island carrying

capacity due to global sea level rise (SLR) has also been estimated. Two of the

techniques studied, the count-based simulation method presented in Chapter 2 and the

VORTEX simulations presented in Chapter 3, give congruent rankings of relative risk

across the three extant populations: the Laysan population is estimated to face

approximately zero intrinsic risk, the PHR-Southeast Island population an intermediate

level of risk, and the PHR-Grass Island population is estimated to face a high degree of

intrinsic risk. By comparing Figures 2.3 and 3.3, however, it can be seen that, while the

ranking of the populations is the same for the two methods, the particular values of

extinction probability calculated by the two models are quite different. These differing

risk projections may be attributable to the difference in the form of density dependence at

work in the two models. The VORTEX ceiling model may be more forgiving of fast

population growth near K than the logistic model is, because VORTEX only applies

mortality commensurate with the excess above K, whereas the logistic model, as

implemented in the simulations in Chapter 2, will choose a lower growth rate that may set

the population size at the next time step well below K. Conversely, the simulated

inbreeding dynamics in VORTEX appear to penalize populations near the quasi-

extinction threshold more aggressively than the logistic model simulations do, leading to

109
a higher extinction rate for small populations than the logistic model predicts. In contrast

to both of these, the SDM model does not apply either form of penalty, so that even

highly variable simulated populations may, on average, spend most of their time in the

vicinity of the carrying capacity. This behavior is perhaps not as conservative as one

might wish when modeling risk in endangered species.

Another aspect of the foregoing simulation models that is possibly not sufficiently

conservative is the focus on intrinsic sources of risk. While the historical record indicates

that the Laysan finch is a hardy and resilient species, and extrinsic sources of risk are

difficult to parameterize and model with confidence, failure to at least attempt to account

for the incremental risk such factors impose will itself impose additional risk. Therefore,

as a step towards better understanding such effects, the logistic simulation program used

in Chapter 2 was modified to account for extrinsic risk factors. These extrinsic factors

include not only the projected effects on extinction risk of global sea level rise and

commensurate reduction of atoll land area, but also the prospective effects of biotic

invasions.

To rank the relative risk of the three populations, comparisons were made between

extinction risk levels across a range of quasi-extinction thresholds, with the volume under

an extinction probability surface (as a fraction of the total possible volume) used as an

index of extinction risk. Relative risk volumes were used to facilitate comparisons with

studies which may choose different time horizons or ranges of quasi-extinction

thresholds. Raw risk estimates were obtained from 1,000 replicate simulations projected

for 100 years each at quasi-extinction threshold ranging from 0 to 30, with the extinction

CDF at each threshold appended as successive rows of an extinction risk matrix. The

110
relative volume was calculated by summing the risk matrix to obtain the total volume

under the extinction probability surface and dividing by the total potential volume

(100x30x1, or 3000). Differences in the relative risk volumes were then used to rank

relative risk between populations (Groom and Pascual 1998, Van Dyke 2003), in

accordance with the findings of recent studies (McCarthy, et. al., 2003) that have shown

rankings of relative risk among populations to be substantially more reliable than

estimates of absolute risk. The effect of global sea-level rise was modeled as a quadratic

decline in carrying capacity, treating the islands as cones subject to annular areal loss at

each time step. The SLR effect was augmented by an increased frequency and intensity

of catastrophic storms and three types of biotic invasions: weeds, predators, and

pathogens. The increase in risk volume due to these catastrophic processes was then

offset by modeling two types of management action. One action was supplementation of

the smaller, higher-risk PHR populations by the importation of individuals from Laysan,

in different numbers (5 to 30 birds) and frequencies (5- to 30-year intervals). The other

action was to create an additional population, starting with 30 individuals, and allowing

for different carrying capacities from 80 to 320. For simplicity, the product of the risk

volumes were used as a proxy for the aggregate risk to the entire metapopulation. Risk

reductions obtainable via these two different management tactics were then cost-adjusted

according to the amount of equipment, manpower, and days of boat operation required to

effect the action being modeled, with these costs added across the number of times the

action would be carried out over the hundred-year time horizon of the simulation. The

management actions were then compared according to the extinction risk reduction per

dollar that they were estimated to afford.

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Risk and the Costs and Benefits of Management Action
Extinction risks are summarized in Table 5.1 (below) for the three populations. As was
the case for the simulations carried out in Chapter two, a salient result is that,

Carrying Capacity Trend

Population None Linear Sigmoid Quadratic
Laysan 0 0 0.0000030 0.0000033
PHR-SE 0.009 0.025 0.077 0.083
PHR-Grass 0.379 0.574 0.643 0.675

Table 5.1. Relative risk volumes defined by extinction probability surfaces for three Laysan finch
populations, using 100-year time horizons and integer quasi-extinction thresholds ranging from 0 to
30 individuals. Baseline conditions (constant carrying capacity) are given in the column whose
carrying capacity trend is labeled "None", while the other three columns show how the risk for the
SLR-only scenario increases according to the function that describes the rate of sea level rise (or,
equivalently, its effect on habitat area).

for the baseline (constant carrying capacity) scenario, the projected extinction risk at

Laysan is zero across the entire time horizon. However, for simulations with the

quadratic trend applied to carrying capacity substantially raises extinction risk, an effect

that is exacerbated by the modeled increase in storm frequency and intensity. Increases in

the frequency and intensity of major storms are supported by historical studies (Graham

and Diaz 2001), but while further intensification has been predicted by some climate

modeling studies (Lambert 1995), it has been contradicted by others (Henderson-Sellers

et al. 1998, Knutson et al. 2001). Thus the value of incorporating simulated effects of

increased storm frequency or intensity into population models is uncertain, particularly

when data on the survival and fecundity effects of storms are lacking. Likewise, the

probabilities associated with biotic invasions are not well known, both due to lack of

historical data from which to parameterize simulations and also because of changing

circumstances such as increased visitation rates to the islands and increases in vessel

traffic associated with NWHI fishery activity. Nonetheless, through discussions with

other researchers (Conant, pers. comm.; Flint, pers. comm.), it was possible to construct a
112
table of probabilities for extrinsic catastrophes in addition to global sea level rise, based

on their best subjective estimates of the likely probabilities and impacts, as shown in

Table 5.2 below.

Population Laysan Southeast Grass

Baseline Risk 0 0.00933 0.379
Global SLR 3E-06 0.08267 0.675
Probability Impact Duration Probability Impact Duration Probability Impact Duration
Global SLR 1.00 0.30 100 1.00 0.90 100 1.00 0.50 100
Storms 0.05 0.20 1 0.05 0.20 1 0.05 0.20 1
Predators 0.01 0.99 1 0.01 0.99 1 0.01 0.99 1
Plants 0.03 0.25 100 0.03 0.25 100 0.03 0.25 100
Disease 0.01 0.40 1 0.01 0.40 1 0.01 0.40 1

Table 5.2. Extrinsic catastrophe probabilities and expected survival impacts for the three Laysan
finch populations modeled. Durations represent the number of time steps across which the impact
of the catastrophe was exerted; thus trends in carrying capacity developed to their full extent over
the entire time horizon, while storm and predation effects struck intensely for only a single year.

When this matrix of uniformly-distributed probabilities implemented in the simulation

code as shown in Appendix E, the risk volumes that result can be analyzed by fitting a

second-order linear model with interactions to them, so that the relative impact of

management actions on extinction risk can be assessed by comparing the magnitude of

the model coefficients. Prospective costs of management actions (supplementation and

translocation) were also derived from discussions with the same NWHI experts, and are

shown in Table 5.3 below. A 5% discount rate was applied to the values shown.

Action No Action Supplement Translocate

Boat Days 0 2 4
Cost/Day 0 10,000 10,000
Person-Days 0 7 21
Cost/Day 0 500 500
Materials 0 1000 1000
Pest Control 0 0 200,000
0 24,500 251,500

Table 5.3. Cost structure for the two forms of management intervention designed to reduce
extinction risk. Figures are given in US dollars.

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 In the trivial case, the best-performing treatment combinations (or "management action

models") are those that involve no action, simply because they cost no money. That is,

relative to the treatment that performs worst (whose relative risk estimate is highest),

some zero-cost models result in less extinction risk simply by chance. Thus, in this study

the 23 (of 192) treatments resulting in the greatest risk reduction per dollar, relative to the

worst performing model, turn out to be "no action" models in which neither

supplementation nor translocation were applied. This outcome suggests that the effects of

the catastrophic extrinsic risk factors, which are purely stochastic, tend to obscure the

effects of offsetting management actions, which are deterministic. This interpretation is

supported by the fact that, when ranked not by benefit/cost ratio but only on the basis of

the proportional risk reduction attained, the 8 best-performing models are those featuring

both translocation and supplementation (with half of those involving the minimum

supplementation interval of five years), and the 19 worst are "no action" models. To

resolve differences in treatment effects, a second-order linear regression model with

interactions was applied to the benefit/cost ratios, with the results shown in Table 5.4

below. The dominant effects are the first order treatment factors: translocation,

supplementation number, and supplementation interval. The number of individuals

supplemented tends affects extinction risk more than three times as strongly as either

translocation or supplementation interval, which are comparable in strength but opposite

in the direction of their influence (as expected, longer intervals increase risk, while

translocation and higher supplementation numbers decrease it).

114
 Dept. variable: RiskProd
R squared = 44.9% R squared (adjusted) = 44.5%
s = 0.0001 with 1920 - 14 = 1906 degrees of freedom
Source SS df MS F-ratio
Regression 0.000005 13 0 119
Residual 0.000006 1906 0

Variable Coefficient SE of Coeff t-ratio prob

Constant 0.000153 0 12.1 ≤ 0.0001
K 0 0 0.631 0.5278
IPS -2.00E-06 0 -6.86 ≤ 0.0001
SupNum -7.38E-06 0 -13.8 ≤ 0.0001
SupInt 2.36E-06 0 2.85 0.0045
SNxSI 5.53E-08 0 4.19 ≤ 0.0001
SNxSN 6.00E-08 0 4.77 ≤ 0.0001
SIxSI -5.35E-08 0 -2.65 0.0081
IPSxIPS 0 0 • •
KSxKS 0 0 -1.06 0.2908
IPSxKS -2.35E-09 0 -2.5 0.0125
IPSxSN 5.85E-08 0 7.8 ≤ 0.0001
IPSxSI -1.83E-08 0 -1.86 0.0625
KSxSI 0 0 -0.414 0.6787
KSxSN 2.10E-09 0 1.66 0.0961

Table 5.4. Effects of supplementation and translocation on simulated populations with all extrinsic
catastrophes modeled. First-order variables are carrying capacity ("K"), translocation ("IPS"), the
number of individuals supplemented ("SupNum"), and the interval between supplementation events
("SupInt"). Note that carrying capacity does not have a significant effect on risk, and that even for
those higher-order terms whose effects are significant, their coefficients are two to three orders of
magnitude smaller than those of the first-order variables.

Two additional points are noteworthy. When the "no action" models are removed from

consideration, the 24 best-performing models involve translocation only, and represent all

of the translocation-only scenarios. Any scenarios that involve supplementation, even at

relatively infrequent intervals, are much more costly than translocation in this analysis

because the translocation cost is assessed at the outset, in present dollars, while the 5%

discount rate applied to supplementation costs raises them into the millions by the latter

half of the time horizon. Thus the mixed translocation-supplementation models that

perform relatively well tend to be those in which supplementation is infrequent (30-year

intervals) and in which supplementation numbers are high (20-30 individuals). The other

point to note is that the regression model cannot discern a significant effect of carrying
115
capacity on extinction risk. This outcome may be an artifact of the stochastic nature of

the extrinsic risk factors mentioned above. However, it could also be the case that even a

small, relatively risky population can have a significant effect on the collective risk of a

small number of populations, such that raising K does not have a market effect. In

absolute terms, the creation of an additional population provides almost exactly the same

average risk reduction as the 24 next-best supplementation-only models do, but the six-

fold difference in cost between the two methods makes translocation that much more

cost-effective. This result, however, depends on the translocation being effective on the

first attempt, which seems plausible given the history and ecology of this species,

including the successful establishment and persistence of the two PHR populations. The

issue is not that supplementation does not provide significant risk reduction, but in the

case of islands such as those at PHR, if the projected sea level rise does diminish the land

area as much as estimated, it may be unrealistic to expect that supplementation could

keep that population going. The difference in the cost-efficiency of translocation over

supplementation indicates that translocation may be more cost-justifiable than its high

initial cost would seem to indicate. However, translocation may have other, deleterious

ecological effects not discussed here, and moreover, the apparent superiority of

translocation based on the results of this modeling approach, although concordant with

the sensitivity results obtained using VORTEX in Chapter 3, depends on the cost figures

used as well as the estimated probabilties and intensities of the extrinsic risk factors

modeled. It is quite possible, for example, that pathogen establishment is even less than

1% probable in the Northwest Hawaiian Islands, due to the lack of standing fresh water

required by their mosquito vectors. Furthermore, climate change scenarios are only as

116
good as the models used to implement them are realistic. An obvious next step for

research, therefore, is the acquisition of detailed mapping data for the Northwest

Hawaiian Islands. A GIS database with topographic resolution comparable to that

available for the main Hawaiians Islands would be invaluable for projecting the most

probable effects of the estimates 30-40cm sea level rise on plant and animal habitat. As it

happens, recent data collected by Jason Baker (pers. comm.) of the National Marine

Fisheries Service in Honolulu indicates that the 90% area reduction reduction at Souteast

Island, as well as the 50% reduction at Grass Island, may actually come to pass by the

end of this century, if the upper-bound of the IPCC sea level rise projections are attained.

Count-based PVAs (and PVA generally) have been criticized for sacrificing model

accuracy for ease of data acquisition and analysis (Coulson et al. 2001, Coulson 2003),

and in fact it is easier to collect population counts than the more detailed survival and

fertility data required by demographic matrix models. However, continued development

of count-based PVA methods, such as that presented by Morris and Doak (2002), has

improved the accuracy and reliability of count-based projections. This study estimated

extinction risk for three conspecific finch populations inhabiting geographic ranges

spanning nearly two orders of magnitude. At Laysan, the largest population in the largest

habitat, intrinsic extinction risk was estimated to be effectively zero. At PHR, the smaller

Grass Island population faces four times the extinction risk of the Southeast Island

population. Time series for different populations yielded substantially different parameter

estimates, not only for carrying capacity, but also for growth rate. These differences may

be partly due to the differing time series lengths among the populations, and partly to

117
differences in habitat quality, plant community structure, and the effect of habitat size on

stability.

It has been a well-known ecological principle that fast-growing, unregulated herbivores

can overshoot their habitat's carrying capacity and go extinct simply by overconsuming

their resources. Reindeer introduced to St. George island illustrated this principle, as did

the rabbits introduced to Laysan in the early 1900's. In the case of omnivores, however,

the overshoot effect could be even more dramatic if a biotic invasion at a lower trophic

level suddenly increased the short-term carrying capacity of the habitat. This situation

seems to have occurred at PHR-Southeast island, where the rapid invasion by a fast-

growing annual plant contributed to rapid finch population growth, well beyond previous

maximum sizes, only to leave the consumer species with essentially nothing but a seed

bank once the prior plant community had been completely displaced. It remains to be

seen how the extinction risk estimate for this population should change over time. The

risk might be significantly higher at whatever the post-invasion carrying capacity turns

out to be, and the possible management actions that could be taken to improve the

situation are not obvious. Any comprehensive weed eradication effort will result in some

harm to not only the consumer species but to co-resident seabird populations, and

eradication of the weed would have to be complemented by restoration of some facsimile

of the original PHR plant community. The VORTEX sensitivity analysis indicates that

supplementation of individuals from Laysan should have the greatest impact on long-

term population viability, especially when populations are small. However, that result

may depend on the genetic parameter values used in the model, and the VORTEX default

values may not be accurate for this species. Moreover, supplementation would likely be

118
ineffective unless the habitat were at least partly restored, but restoration of the habitat,

given the projected 30-40cm sea-level rise, may not be a worthwhile investment of

management resources. Alternatively, translocation of Laysan finches to higher-elevation

islands will become problematic because of potential interactions with species already

established at the few islands available for such a program, and because of the finches'

ground-nesting habits and extreme disease susceptibility. The only suitable translocation

options are places free of either mosquitoes, malaria, or both, as well as free of rats, feral

cats, and mongoose. Thus the Laysan finch may be at an early stage of what may become

an extremely challenging conservation situation, one in which none of the options are

particularly attractive, but are all both expensive and very risky.

119
NOTES

1. The model-fitting analysis for this paper was performed using SAS/STAT® software,

Version 8 of the SAS System for Windows. Copyright © 1999-2002, SAS Institute Inc.

SAS and all other SAS Institute Inc. product or service names are registered trademarks

or trademarks of SAS Institute Inc., Cary, NC, USA. The specific procedure for the

nonlinear regressions was SAS® PROC NLIN, as documented in Morris and Doak

(2002). Additional nonlinear regression analysis was performed with the

MATHEMATICA function NonLinearRegress, particularly for the data-requirements

studies, and was found to give congruent results, to within eight decimal places, to those

obtained with SAS software.

120
 APPENDIX A: LAYSAN FINCH TIME SERIES DATA

Laysan Month N ln(growth) Southeast Month N ln(growth) Grass N ln(growth)

1966 March 9573 -0.208
1967 September 7779 0.039 1967 March 108 0.711 1967 0
1968 September 8090 0.384 1968 March 220 -0.288 1968 2
1969 March 11882 -0.563 1969 March 165 0.098 1969
1970 August 6764 0.466 1970 April 182 0.970 1970 8
1971 September 10775 -0.124 1971 April 480 -0.252 1971
1972 September 9517 0.155 1972 June 373 0.670 1972
1973 July 11115 -0.396 1973 March 729 -0.523 1973
1974 July 7478 0.682 1974 March 432 1974
1975 August 14786 0.341 1975 1975
1976 August 20802 -0.971 1976 1976
1977 August 7881 -0.242 1977 1977
1978 August 6188 0.058 1978 June 205 1978 20
1979 May 6560 1979 1979
1980 1980 1980
1981 1981 1981
1982 1982 1982
1983 July 11047 0.503 1983 1983
1984 November 18274 -0.824 1984 July 513 0.135 1984 31 0.395
1985 April 8013 0.254 1985 June 587 -0.307 1985 46 0.197
1986 May 10333 0.054 1986 August 432 -0.870 1986 56 -0.658
1987 May 10911 -0.741 1987 August 181 -0.130 1987 29 -0.276
1988 May 5201 0.706 1988 July 159 -0.290 1988 22 0.310
1989 July 10537 0.382 1989 July 119 -0.236 1989 30 -0.511
1990 October 15432 0.025 1990 94 0.813 1990 18 0.511
1991 June 15826 -0.281 1991 August 212 1991 30
1992 July 11947 0.086 1992 1992
1993 August 13023 0.138 1993 August 153 1993 5
1994 July 14955 -0.043 1994 1994
1995 July 14331 0.125 1995 1995
1996 July 16233 -0.359 1996 1996
1997 July 11340 -0.135 1997 1997
1998 July 9911 1998 August 350 -0.336 1998 23 0.083
1999 August 250 0.588 1999 25 0.182
2000 August 450 2000 30
2001 2001
2002 September 1908 -1.172
2003 July 591

121
 APPENDIX B: MATLAB SIMULATION PROGRAMS

The code segments below comprise most of the program codes and modifications

required to generate the simulation data analyzed in this study.

% PROGRAM RiskSurfs.m
% Calculates by simulation the probability that a population
% following the RICKER logistic model and starting at Nc will fall
% below the quasi-extinction threshold Nx at or before time tmax
% REQUIRES THE FILES chi2rv.m, gammarv.m, and betarv.m
clear all;
%****************** PARAMETERS FOR ALL SIMULATIONS *************************
tmax=100; % time horizon
NumReps=1000; % number of replicate population trajectories
reduction=0.9; % proportional reduction in K over time horizon
NumSims=50; % number of "Results" CDFs to generate for each Pop. x K
combination
%**************************************************************************
% GRASS POPULATION, CONSTANT K
%****************** POPULATION-SPECIFIC PARAMETERS *************************
Gr=0.6367; % intrinsic rate of increase
GSEr=0.3413; % standard deviation for rate of increase
GCI_r=[-0.1703,1.4437]; % confidence interval for r
GK0=32.429; % carrying capacity
GSEK=6.0983; % standard deviation of carrying capacity
GCI_K=[18.009,46.85]; % confidence interval for K
Gsigma2=0.0411713; % environmental variance
GCI_sig2=[0.018784,0.1511064]; % confidence interval for sigma^2
Gq=9; % the number of transitions in the data set
GNc=30; % starting population size
GNx=8; % set QE threshold to same proportion of K for all pops
%**************************************************************************
randn('state',sum(100*clock)); % seed the normal random number generator
GCRisk=[]; %initialize vector of risk areas under CDFs
GCResults=[]; % initialize array of CDFs, 1 each at all Nx's
for z=1:NumSims
disp(z)
GCExtMat=[]; % initialize array of extinct populations across Sims
for j=1:NumReps
GCN=GNc; % population starts at Nc, future is zeroed
GCExtinct=zeros(1,tmax); % initialize counter to record extinctions
% generate a random r within its confidence interval
GCrrnd=inf;
while GCrrnd<GCI_r(1)|GCrrnd>GCI_r(2)
GCrrnd=Gr+GSEr*randn;
end;
% generate a random K within its confidence interval
GCKrnd0=inf;
while GCKrnd0<GCI_K(1)|GCKrnd0>GCI_K(2)
GCKrnd0=GK0+GSEK*randn;
end;
% generate a random sigma^2 within its confidence interval
GCsig2rnd=inf;
while GCsig2rnd<GCI_sig2(1)|GCsig2rnd>GCI_sig2(2)
GCsig2rnd=Gsigma2*chi2rv(Gq-1)/(Gq-1);
end;
GCsigma=sqrt(GCsig2rnd);
GCKrnd=GCKrnd0;
for t=1:tmax, % For each future time,
122
 % get new N from the RICKER logistic with random environmental effects.
GCN=[GCN round(GCN(t).*exp(GCrrnd*(1-(GCN(t)./GCKrnd))+GCsigma*randn))];
if GCN(t+1)<=GNx % if quasi-extinct,
GCN(t+1)=0; % zero out the population
GCExtinct(t)=GCExtinct(t)+1; % update extinction counter
end;
% keep K CONSTANT
end; % at the end of each replicate population run
GCExtMat=[GCExtMat; GCExtinct];
end; % "NumReps" loop - completes one batch of replicate trajectories
GCResults=[GCResults; sum(GCExtMat)./NumReps];
GCRisk=[GCRisk; sum(GCResults(z,:))];
end; % "NumSims" loop - completes one batch of replicate CDFs

Additional modifications to the program must be made in order to save extinction CDFs

at each quasi-extinction threshold into a matrix that represents the risk surface. The code

below implements the risk surface modifications for quasi-extinction thresholds from 0 to

30, and also implements the quadratic trend in carrying capacity used to model habitat

reduction due to global sea level rise.

% PROGRAM RiskSurfs.m
% Calculates by simulation the probability that a population
% following the RICKER logistic model and starting at Nc will fall
% below the quasi-extinction threshold Nx at or before time tmax
% REQUIRES THE FILES chi2rv.m, gammarv.m, and betarv.m
clear all;
%****************** PARAMETERS FOR ALL SIMULATIONS *************************
NxMax=30; % upper bound for quasi-extinction threshold
tmax=100; % time horizon
NumReps=1000; % number of replicate population trajectories
reduction=0.9; % proportional reduction in K over time horizon
%**************************************************************************
% GRASS POPULATION, CONSTANT K
%****************** POPULATION-SPECIFIC PARAMETERS *************************
r=0.6367; % intrinsic rate of increase
SEr=0.3413; % standard deviation for rate of increase
CI_r=[-0.1703,1.4437]; % confidence interval for r
K0=32.429; % carrying capacity
SEK=6.0983; % standard deviation of carrying capacity
CI_K=[18.009,46.85]; % confidence interval for K
sigma2=0.0411713; % environmental variance
CI_sig2=[0.018784,0.1511064]; % confidence interval for sigma^2
q=9; % the number of transitions in the data set
Nc=30; % starting population size
%**************************************************************************
randn('state',sum(100*clock)); % seed the normal random number generator
%**************************************************************************
% GRASS POPULATION, QUADRATIC K-TREND
%**************************************************************************
GQResults=[]; % initialize array of CDFs, 1 each at all Nx's
for Nx=0:NxMax % iterate simulations across range of quasi-extinction thresholds
123
 disp(Nx)
ExtMat=[]; % initialize array of extinct populations across Sims
for j=1:NumReps
N=Nc; % population starts at Nc, future is zeroed
Extinct=zeros(1,tmax); % initialize counter to record extinctions
% generate a random r within its confidence interval
rrnd=inf;
while rrnd<CI_r(1)|rrnd>CI_r(2)
rrnd=r+SEr*randn;
end;
% generate a random K within its confidence interval
Krnd0=inf;
while Krnd0<CI_K(1)|Krnd0>CI_K(2)
Krnd0=K0+SEK*randn;
end;
% generate a random sigma^2 within its confidence interval
sig2rnd=inf;
while sig2rnd<CI_sig2(1)|sig2rnd>CI_sig2(2)
sig2rnd=sigma2*chi2rv(q-1)/(q-1);
end;
sigma=sqrt(sig2rnd);
Krnd=Krnd0;
for t=1:tmax, % For each future time,
% get new N from the RICKER logistic with random environmental effects.
N=[N round(N(t).*exp(rrnd*(1-(N(t)./Krnd))+sigma*randn))];
if N(t+1)<=Nx % if quasi-extinct,
N(t+1)=0; % zero out the population
Extinct(t)=Extinct(t)+1; % update extinction counter
end;
% apply NONLINEAR (QUADRATIC) decrease to K
Klin=Krnd0*(1-(reduction*(t/tmax)));
Kquad=Krnd0*(1-(reduction*((t/tmax)^2)));
Krnd=Klin-(Kquad-Klin);
end; % at the end of each replicate population run
ExtMat=[ExtMat; Extinct];
end; % "NumReps" loop - completes one batch of replicate trajectories
PE=sum(ExtMat(:,1:(tmax-1))/NumReps);
GQResults=[GQResults; PE];
end; % "Nx" loop - completes replicate batches to get CDF change vs. Nx
GKquadRisk=sum(sum(GQResults))

124
 APPENDIX C:

COEFFICIENTS FOR LINEAR REGRESSION OF OUTPUT OF COUNT-BASED PVA MATLAB PROGRAM

(0 ≤ σ2/r, Nx/K ≤ 0.5)
Year Term Coef Stdev t-ratio p
1 Constant -0.202 0.048 -4.23 0
2 Constant -0.210 0.047 -4.46 0
3 Constant -0.213 0.047 -4.53 0
4 Constant -0.214 0.047 -4.57 0
5 Constant -0.215 0.047 -4.58 0
10 Constant -0.216 0.047 -4.61 0
20 Constant -0.218 0.047 -4.64 0
30 Constant -0.220 0.047 -4.68 0
40 Constant -0.223 0.047 -4.71 0
50 Constant -0.225 0.047 -4.75 0
1 Nx.K 5.586 0.287 19.48 0
2 Nx.K 5.682 0.283 20.05 0
3 Nx.K 5.712 0.283 20.22 0
4 Nx.K 5.726 0.282 20.29 0
5 Nx.K 5.734 0.282 20.33 0
10 Nx.K 5.757 0.282 20.40 0
20 Nx.K 5.793 0.283 20.48 0
30 Nx.K 5.826 0.284 20.54 0
40 Nx.K 5.858 0.285 20.59 0
50 Nx.K 5.887 0.285 20.63 0
1 Nx.K*Nx.K -6.220 0.508 -12.23 0
2 Nx.K*Nx.K -6.406 0.502 -12.75 0
3 Nx.K*Nx.K -6.462 0.501 -12.90 0
4 Nx.K*Nx.K -6.488 0.500 -12.97 0
5 Nx.K*Nx.K -6.504 0.500 -13.01 0
10 Nx.K*Nx.K -6.549 0.500 -13.10 0
20 Nx.K*Nx.K -6.622 0.501 -13.21 0
30 Nx.K*Nx.K -6.687 0.503 -13.30 0
40 Nx.K*Nx.K -6.748 0.504 -13.38 0
50 Nx.K*Nx.K -6.804 0.506 -13.45 0
1 Nx.K*σ2.r -0.467 0.449 -1.04 0.300
2 Nx.K* σ2.r -0.541 0.444 -1.22 0.225
3 Nx.K* σ2.r -0.568 0.442 -1.29 0.201
4 Nx.K* σ2.r -0.580 0.442 -1.31 0.192
5 Nx.K* σ2.r -0.584 0.442 -1.32 0.188
10 Nx.K* σ2.r -0.584 0.442 -1.32 0.189
20 Nx.K* σ2.r -0.578 0.443 -1.30 0.195
30 Nx.K* σ2.r -0.582 0.444 -1.31 0.192
40 Nx.K* σ2.r -0.592 0.445 -1.33 0.186
50 Nx.K* σ2.r -0.605 0.447 -1.35 0.179
1 σ2.r 0.186 0.287 0.65 0.517
2 σ2.r 0.222 0.283 0.79 0.434
3 σ2.r 0.230 0.283 0.81 0.418
4 σ2.r 0.230 0.282 0.82 0.416
5 σ2.r 0.229 0.282 0.81 0.418
10 σ2.r 0.218 0.282 0.77 0.440
20 σ2.r 0.202 0.283 0.72 0.476
30 σ2.r 0.192 0.284 0.68 0.500
40 σ2.r 0.186 0.285 0.65 0.516
50 σ2.r 0.181 0.285 0.64 0.526
1 σ2.r* σ2.r -0.226 0.508 -0.45 0.657
2 σ2.r* σ2.r -0.192 0.502 -0.38 0.702
3 σ2.r* σ2.r -0.168 0.501 -0.34 0.738
4 σ2.r* σ2.r -0.151 0.500 -0.30 0.763
5 σ2.r* σ2.r -0.138 0.500 -0.28 0.784
10 σ2.r* σ2.r -0.093 0.500 -0.19 0.853
20 σ2.r* σ2.r -0.031 0.501 -0.06 0.951
30 σ2.r* σ2.r 0.020 0.503 0.04 0.969
40 σ2.r* σ2.r 0.061 0.504 0.12 0.904
50 σ2.r* σ2.r 0.096 0.506 0.19 0.850

125
APPENDIX D: MATLAB SIMULATION PROGRAM CODE: CEILING MODEL

MATLAB code for stochastic demographic matrix model with ceiling density

dependent growth.
% MatSim.m Combines code from Morris & Doak (2002) Box 9.2 (LimitSens)
% and Box 7.5 (SimExt) to project a stochastic demographic population matrix
% with truncated normal vital rate distributions centered on "best" estimates.
clear all;
%*****************Simulation Parameters***********************
% Laysan finch data from McClung
meanvr = [0.6676 0.6357 0.6311 0.6311 0.6311 1.2955 0.9375 1.0714 0.6875];
% best estimates (MARK {Phi(g*t)p(t)})
SEvr = [0.0606 0.0783 0.08463 0.08463 0.08463 0.3368 0.2789 0.311665 0.3510334];
% std. err. vector
vrhi = [0.774 0.772 0.777 0.777 0.777 1.956 1.484 1.682 1.376];
% highest estimates
vrlo = [0.540 0.474 0.456 0.456 0.456 0.635 0.391 0.461 0]; % lowest estimates
syms Ss1 Ss2 Ss3 Ss4 Ss5 Sf1 Sf2 Sf3 Sf4 % symbolic variable definitions
Svr = [Ss1 Ss2 Ss3 Ss4 Ss5 Sf1 Sf2 Sf3 Sf4];% vector of symbolic variables
% symbolic definition of matrix:
mx = [0 Sf1*Ss1 Sf2*Ss1 Sf3*Ss1 Sf4*Ss1;
Ss1 0 0 0 0;
0 Ss2 0 0 0;
0 0 Ss3 0 0;
0 0 0 Ss4 Ss5];
tmax=100; % farthest future time horizon
reduction=0.9; % fractional loss of K by time tmax
maxruns=1; % number of times to simulate CDF
numreps=1000; % number of population growth realizations to simulate in each run
n0=[69;43;26;15;22];% initial pop. vector - 69-43-26-15-22 = SAD for n=350
Nx=20; % quasi-extinction threshold, relative to N
K0=321; % ceiling carrying capacity
%************************************************************
randn('state',sum(100*clock)); % seed random number generator
numvrs = length(meanvr); % get the number of vital rates
simnum = 0; % initialize sim counter(each sim = numreps replicate trajectories)
Results=[]; % initialize extinction probability CDF array
Nall=[]; % initialize plot for all trajectories
for i=1:maxruns % calculate ext. CDF "maxruns" times,
PrExt=zeros(1,tmax);% initialize counter to record extinctions
for j = 1:numreps % in each simulation, project pop tmax years numreps times
Nline=[]; % initialize population size plot
K=K0;
Kline=[K0];
n=n0; % starting at the initial pop vector,
sumweight=[1 1 1 1 1]; % weight population size by age classes
N=2*sum(sumweight'.*n); % initialize pop size before projecting
for t=1:tmax % for each future time,
% make normal random vital rates
sumweight=[1 1 1 1 1]; % if sumweight changed last "year",
$reset it
allvrs = -1*ones(1,numvrs);% bounded by high & low estimates
for k=1:numvrs % along vr vector, while outside bounds,
while allvrs(k) > vrhi(k)|allvrs(k) < vrlo(k)
allvrs(k) = meanvr(k) + SEvr(k)*randn; % keep trying
end;
end;
realmx = subs(mx,Svr,allvrs); % make random matrix from vr
n=round(realmx*n); % project the pop 1 year ahead
N=2*sum(sumweight'.*n); % get weighted sum of densities
if N>K % if N exceeds K, reduce sumweight so N drops to K
sumweight = sumweight*((1-((1/length(n))*((N-K)/K))));
n = round(sumweight'.*n);
% rescale pop vector so that mortality is equal across ages
end;
126
 if N<Nx % if quasi-extinct,
PrExt(t)=PrExt(t)+1; % update extinction counter
N=0; % zero out the population sum
Nline = [Nline zeros(1,(tmax-t+1))];
% fill the rest of the size vector
break;
end;
K=K0; % apply CONSTANT K
Kline=[Kline K];
Nline = [Nline N]; % add current pop size to the pop vector
end; % for t
Kmat=[Kline;Kline];
K=K0;
Nall = [Nall; Nline]; % add completed trajectory to the N-array
disp(simnum)
simnum = simnum + 1; % increment simulation counter
end; % for j
end; % for i
Kmax=max(Kmat);
PrExt=cumsum(PrExt/numreps);% sum extinctions at each time to get CDF
Results=[Results PrExt]; % store the result
x=0:(tmax-1); % set the x-axis to the correct length for the time horizon
plot(x,Nall) % plot all the population size trajectories
xlabel('Years into the future'),ylabel('Population size'),title('All Population
Size Trajectories')
axis([0 tmax 0 (1.1*max(max(Nall)))])
figure
plot(x,min(Nall),'b:',x,median(Nall),'r-',x,max(Nall),'b:') % plot the median of
the population sizes
xlabel('Years into the future'),ylabel('Population size'),title('Median
Population Size')
axis([0 tmax 0 (1.1*max(max(Nall)))])
figure
plot(x,(Results),'b-') % plot the extinction CDF
xlabel('Years into the future'),ylabel('Cumulative probability of quasi-
extinction'),title('Extinction CDF')
axis([0 tmax 0 1])
figure
x=0:(length(Kmax)-1);
plot(x,(Kmax),'b-') % plot the trend in K
xlabel('Years into the future'),ylabel('Carrying capacity (K)')
axis([0 tmax 0 (1.1*K0)])

127
Shown below are the changes to the ceiling model code shown above that were used to

implement density dependence in matrix elements.

for i=1:maxruns % calculate ext. CDF "maxruns" times,

PrExt=zeros(tmax,1);% initialize counter to record extinctions
for j = 1:numreps % in each sim, project pop tmax years numreps times
repnum = repnum + 1;
disp(repnum)
Nline=[]; % initialize population size plot
n=n0; % starting at the initial population vector,
N=2*(sumweight*n); % compute weighted sum of starting densities
for t=1:tmax% for each future time, make normal random vital
$ rates bounded by high & low estimates
allvrs = -1*ones(numvrs,1);
for k=1:numvrs, % along vr vector, while out of CI bounds,
while allvrs(k) > vrhi(k)|allvrs(k) < vrlo(k)
allvrs(k) = meanvr(k) + SEvr(k)*randn; % keep trying
end;
end;
allvrs = (1 - ((N-K)/K))*allvrs;% scale vital rates to density
realmx = subs(mx,Svr,allvrs); % make a random matrix from the vr vector
n=realmx*n; % project the population 1 year ahead
N=2*(sumweight*n); % compute weighted sum of current densities
if N<Nx % if quasi-extinct,
PrExt(t)=PrExt(t)+1;% update extinction counter
N=0; % zero out the population sum
Nline = [Nline zeros(1,(tmax-t+1))]; % fill rest of size vector
break;
end;
Nline = [Nline N]; % add current pop size to the popn. size vector
end; % for t
Nall = [Nall; Nline]; % add completed trajectory to the N-vector array
end; % for j
end; % for i

128
 APPENDIX E:

MATLAB code to generate a factorial combination of risk estimates across a range of

four supplementation intensities and six supplementation frequencies for the three extant
Laysan finch populations, plus an additional population identical to that at PHR-
Southeast Island. Iterations in which the supplement number and the initial size of the
extra population are set to zero generate risk volumes for the scenario of no management
action. Removing code associated with biotic invasion effects and storm effects would
give the SLR-only scenario, and eliminating temporal adjustments to the carrying
capacity variable K, in turn, would give the baseline scenario of constant carrying
capacity.
% PROGRAM RiskVols.m
% Calculates by simulation the probability that a population
% following the RICKER logistic model and starting at Nc will fall
% below the quasi-extinction threshold Nx at or before time tmax
% REQUIRES THE FILES chi2rv.m, gammarv.m, and betarv.m
clear all;
rand('state',sum(100*clock)); % seed uniform random number generator
RiskVolMat=[];
for Ksize=80:80:320
for IPS=0:30:30
for SupNum=0:10:30 % number of finches added to each PHR population per
supplementation event
for SupInt=5:5:30 % time interval for supplementing PHR populations from Laysan
for z=1:10 % loop to create replicate risk volumes across pops for each
factor combo
%****************** PARAMETERS FOR ALL SIMULATIONS *************************
NxMax=30; % upper bound for quasi-extinction threshold
tmax=100; % time horizon
NumReps=100; % number of replicate population trajectories
%**************************************************************************
% GRASS POPULATION
%****************** POPULATION-SPECIFIC PARAMETERS *************************
Gr=0.6367; % intrinsic rate of increase
GSEr=0.3413; % standard deviation for rate of increase
GCI_r=[-0.1703,1.4437]; % confidence interval for r
GK0=32.429; % carrying capacity
GSEK=6.0983; % standard deviation of carrying capacity
GCI_K=[18.009,46.85]; % confidence interval for K
Gsigma2=0.0411713; % environmental variance
GCI_sig2=[0.018784,0.1511064]; % confidence interval for sigma^2
Gq=9; % the number of transitions in the data set
GNc=30; % starting population size
Greduction=0.5; % proportional reduction in Grass K over time horizon
Gplantprob=0.03; % probability that an alien plant will invade
Gplanteffect=0.75; % fraction of K remaining due to plant invasion
Gpredprob=0.01; % probability that shipwreck or other vector will introduce
rats or other predators
Gpredeffect= -4.6; % ln(proportion of finches surviving predation for 1
year)
Gpathprob=0.01; % probability that shipwreck or other vector will introduce
malarial mosquitos
Gpatheffect= -0.5; % ln(proportion of finches surviving malaria for 1 year)
Gstormprob=0.05; % annual probability of survival-reducing storms
Gstormeffect= -0.22+(0.2*randn); % ln(proportion of finches surviving a
severe storm)
%**************************************************************************
129
 % GRASS POPULATION, QUADRATIC K-TREND
%**************************************************************************
GResults=[]; % initialize array of CDFs, 1 each at all Nx's
for GNx=0:NxMax % iterate simulations across range of quasi-extinction
thresholds
GExtMat=[]; % initialize array of extinct populations across Sims
for j=1:NumReps
GN=GNc; % population starts at Nc, future is zeroed
GExtinct=zeros(1,tmax); % initialize counter to record extinctions
% generate a random r within its confidence interval
Grrnd=inf;
while Grrnd<GCI_r(1)|Grrnd>GCI_r(2)
Grrnd=Gr+GSEr*randn;
end;
% generate a random K within its confidence interval
GKrnd0=inf;
while GKrnd0<GCI_K(1)|GKrnd0>GCI_K(2)
GKrnd0=GK0+GSEK*randn;
end;
% generate a random sigma^2 within its confidence interval
Gsig2rnd=inf;
while Gsig2rnd<GCI_sig2(1)|Gsig2rnd>GCI_sig2(2)
Gsig2rnd=Gsigma2*chi2rv(Gq-1)/(Gq-1);
end;
Gsigma=sqrt(Gsig2rnd);
GKrnd=GKrnd0;
for t=1:tmax, % For each future time,
if rand < Gpredprob % If there are catastrophes,
GN=[GN round(GN(t).*exp(Gpredeffect))]; % apply them...
elseif rand < Gpathprob
GN=[GN round(GN(t).*exp(Gpatheffect))];
elseif rand < Gstormprob
GN=[GN round(GN(t).*exp(Gstormeffect))];
elseif rem(t,SupInt)==0
% get new N from the RICKER logistic with random environmental effects
AND add supplement
GN=[GN round(GN(t).*exp(Grrnd*(1-
(GN(t)./GKrnd))+Gsigma*randn))+SupNum];
else
% otherwise, get new N from the RICKER logistic with random environmental
effects.
GN=[GN round(GN(t).*exp(Grrnd*(1-(GN(t)./GKrnd))+Gsigma*randn))];
end;
if GN(t+1)<=GNx % if quasi-extinct,
GN(t+1)=0; % zero out the population
GExtinct(t)=GExtinct(t)+1; % update extinction counter
end;
% apply NONLINEAR (QUADRATIC) decrease to K
GKlin=GKrnd0*(1-(Greduction*(t/tmax)));
GKquad=GKrnd0*(1-(Greduction*((t/tmax)^2)));
GKrnd=GKlin-(GKquad-GKlin); % apple sea level rise K trend
if rand < Gplantprob % if a plant invades
GKrnd=Gplanteffect*GKrnd; % decrease K to the "planteffect" fraction
end;
end; % at the end of each replicate population run
GExtMat=[GExtMat; GExtinct];
end; % "NumReps" loop - completes one batch of replicate trajectories
GPE=sum(GExtMat)/NumReps;
GResults=[GResults; GPE];
end; % "Nx" loop - completes replicate batches to get CDF change vs. Nx
GKquadRisk=sum(sum(GResults));
disp(GKquadRisk)
130
 %**************************************************************************
% SOUTHEAST POPULATION
%****************** POPULATION-SPECIFIC PARAMETERS *************************
Sr=0.4215; % intrinsic rate of increase
SSEr=0.2441; % standard deviation for rate of increase
SCI_r=[-0.106,0.9489]; % confidence interval for r
SK0=321.2; % carrying capacity
SSEK=97.3; % standard deviation of carrying capacity
SCI_K=[111,531.5]; % confidence interval for K
Ssigma2=0.083746; % environmental variance
SCI_sig2=[0.044889,0.208297]; % confidence interval for sigma^2
Sq=15; % the number of transitions in the data set
SNc=350; % starting population size
Sreduction=0.9; % proportional reduction in Southeast K over time horizon
Splantprob=0.03; % probability that an alien plant will invade
Splanteffect=0.75; % fraction of K remaining due to plant invasion
Spredprob=0.01; % probability that shipwreck or other vector will introduce
rats or other predators
Spredeffect= -4.6; % ln(proportion of finches surviving predation for 1
year)
Spathprob=0.01; % probability that shipwreck or other vector will introduce
malarial mosquitos
Spatheffect= -0.5; % ln(proportion of finches surviving malaria for 1 year)
Sstormprob=0.05; % annual probability of survival-reducing storms
Sstormeffect= -0.22+(0.2*randn); % ln(proportion of finches surviving a
severe storm)
%**************************************************************************
% SOUTHEAST POPULATION, QUADRATIC K-TREND
%**************************************************************************
SResults=[]; % initialize array of CDFs, 1 each at all Nx's
for SNx=0:NxMax % iterate simulations across range of quasi-extinction
thresholds
SExtMat=[]; % initialize array of extinct populations across Sims
for j=1:NumReps
SN=SNc; % population starts at Nc, future is zeroed
SExtinct=zeros(1,tmax); % initialize counter to record extinctions
% generate a random r within its confidence interval
Srrnd=inf;
while Srrnd<SCI_r(1)|Srrnd>SCI_r(2)
Srrnd=Sr+SSEr*randn;
end;
% generate a random K within its confidence interval
SKrnd0=inf;
while SKrnd0<SCI_K(1)|SKrnd0>SCI_K(2)
SKrnd0=SK0+SSEK*randn;
end;
% generate a random sigma^2 within its confidence interval
Ssig2rnd=inf;
while Ssig2rnd<SCI_sig2(1)|Ssig2rnd>SCI_sig2(2)
Ssig2rnd=Ssigma2*chi2rv(Sq-1)/(Sq-1);
end;
Ssigma=sqrt(Ssig2rnd);
SKrnd=SKrnd0;
for t=1:tmax, % For each future time,
if rand < Spredprob % If there are catastrophes,
SN=[SN round(SN(t).*exp(Spredeffect))]; % apply them...
elseif rand < Spathprob
SN=[SN round(SN(t).*exp(Spatheffect))];
elseif rand < Sstormprob
SN=[SN round(SN(t).*exp(Sstormeffect))];
elseif rem(t,SupInt)==0

131
 % get new N from the RICKER logistic with random environmental effects
AND add supplement
SN=[SN round(SN(t).*exp(Srrnd*(1-
(SN(t)./SKrnd))+Ssigma*randn))+SupNum];
else
% get new N from the RICKER logistic with random environmental effects.
SN=[SN round(SN(t).*exp(Srrnd*(1-(SN(t)./SKrnd))+Ssigma*randn))];
end;
if SN(t+1)<=SNx % if quasi-extinct,
SN(t+1)=0; % zero out the population
SExtinct(t)=SExtinct(t)+1; % update extinction counter
end;
% apply NONLINEAR (QUADRATIC) decrease to K
SKlin=SKrnd0*(1-(Sreduction*(t/tmax)));
SKquad=SKrnd0*(1-(Sreduction*((t/tmax)^2)));
SKrnd=SKlin-(SKquad-SKlin);
if rand < Splantprob % if a plant invades
SKrnd=Splanteffect*SKrnd; % decrease K to the "planteffect" fraction
end;
end; % at the end of each replicate population run
SExtMat=[SExtMat; SExtinct];
end; % "NumReps" loop - completes one batch of replicate trajectories
SPE=sum(SExtMat)/NumReps;
SResults=[SResults; SPE];
end; % "Nx" loop - completes replicate batches to get CDF change vs. Nx
SEKquadRisk=sum(sum(SResults));
disp(SEKquadRisk)
%***********************************************************************
% LAYSAN POPULATION
%****************** POPULATION-SPECIFIC PARAMETERS *********************
Lr=0.75464; % intrinsic rate of increase
LSEr=0.23224; % standard deviation for rate of increase
LCI_r=[0.275324,1.23395]; % confidence interval for r
LK0=11636; % carrying capacity
LSEK=1029.6; % standard deviation of carrying capacity
LCI_K=[9511.3,13761]; % confidence interval for K
Lsigma2=0.09594; % environmental variance
LCI_sig2=[0.059009,0.182816]; % confidence interval for sigma^2
Lq=26; % the number of transitions in the data set
LNc=9911; % starting population size
Lreduction=0.3; % proportional reduction in Laysan K over time horizon
Lintrinsicat=0.037037; % annual probability of an outlying growth rate
crashes=[-0.9706]; % vector of observed extreme growth rate
Lplantprob=0.03; % probability that an alien plant will invade
Lplanteffect=0.75; % fraction of K remaining due to plant invasion
Lpredprob=0.01; % probability that shipwreck or other vector will introduce
rats or other predators
Lpredeffect= -2.3; % ln(proportion of finches surviving predation for 1
year)
Lpathprob=0.01; % probability that shipwreck or other vector will introduce
malarial mosquitos
Lpatheffect= -0.5; % ln(proportion of finches surviving malaria for 1 year)
Lstormprob=0.05; % annual probability of survival-reducing storms
Lstormeffect= -0.22+(0.2*randn); % ln(proportion of finches surviving a
severe storm)
%**************************************************************************
% LAYSAN POPULATION, QUADRATIC K-TREND
%**************************************************************************
LResults=[]; % initialize array of CDFs, 1 each at all Nx's
for LNx=0:NxMax % iterate simulations across range of quasi-extinction
thresholds
LExtMat=[]; % initialize array of extinct populations across Sims
132
 for j=1:NumReps
LN=LNc; % population starts at Nc, future is zeroed
LExtinct=zeros(1,tmax); % initialize counter to record extinctions
% generate a random r within its confidence interval
Lrrnd=inf;
while Lrrnd<LCI_r(1)|Lrrnd>LCI_r(2)
Lrrnd=Lr+LSEr*randn;
end;
% generate a random K within its confidence interval
LKrnd0=inf;
while LKrnd0<LCI_K(1)|LKrnd0>LCI_K(2)
LKrnd0=LK0+LSEK*randn;
end;
% generate a random sigma^2 within its confidence interval
Lsig2rnd=inf;
while Lsig2rnd<LCI_sig2(1)|Lsig2rnd>LCI_sig2(2)
Lsig2rnd=Lsigma2*chi2rv(Lq-1)/(Lq-1);
end;
Lsigma=sqrt(Lsig2rnd);
LKrnd=LKrnd0;
for t=1:tmax, % For each future time,
if rand < Lintrinsicat % If there is an intrinsic catastrophe...
LN=[LN round(LN(t).*exp(crashes))]; % apply it, otherwise...
elseif rand < Lpredprob % If there are extrinsic catastrophes,
LN=[LN round(LN(t).*exp(Lpredeffect))]; % apply them...
elseif rand < Lpathprob
LN=[LN round(LN(t).*exp(Lpatheffect))];
elseif rand < Lstormprob
LN=[LN round(LN(t).*exp(Lstormeffect))];
else
% get new N from the RICKER logistic with random environmental effects
LN=[LN round(LN(t).*exp(Lrrnd*(1-(LN(t)./LKrnd))+Lsigma*randn))];
end;
if LN(t+1)<=LNx % if quasi-extinct,
LN(t+1)=0; % zero out the population
LExtinct(t)=LExtinct(t)+1; % update extinction counter
end;
% apply NONLINEAR (QUADRATIC) decrease to K
LKlin=LKrnd0*(1-(Lreduction*(t/tmax)));
LKquad=LKrnd0*(1-(Lreduction*((t/tmax)^2)));
LKrnd=LKlin-(LKquad-LKlin);
if rand < Lplantprob % if a plant invades
LKrnd=Lplanteffect*LKrnd; % decrease K to the "planteffect" fraction
end;
end; % at the end of each replicate population run
LExtMat=[LExtMat; LExtinct];
end; % "NumReps" loop - completes one batch of replicate trajectories
LPE=sum(LExtMat)/NumReps;
LResults=[LResults; LPE];
end; % "Nx" loop - completes replicate batches to get CDF change vs. Nx
LayKquadRisk=sum(sum(LResults));
disp(LayKquadRisk)
%**************************************************************************
% SUPPLEMENTAL POPULATION "A"
%****************** POPULATION-SPECIFIC PARAMETERS *************************
Ar=0.4215; % intrinsic rate of increase
ASEr=0.2441; % standard deviation for rate of increase
ACI_r=[-0.106,0.9489]; % confidence interval for r
AK0=Ksize; % carrying capacity
ASEK=0.3*Ksize; % standard deviation of carrying capacity
ACI_K=[0.3456*Ksize,1.655*Ksize]; % confidence interval for K
Asigma2=0.083746; % environmental variance
133
 ACI_sig2=[0.044889,0.208297]; % confidence interval for sigma^2
Aq=15; % the number of transitions in the data set
ANc=IPS; % starting population size
Areduction=0.9; % proportional reduction in Southeast K over time horizon
Aplantprob=0.03; % probability that an alien plant will invade
Aplanteffect=0.75; % fraction of K remaining due to plant invasion
Apredprob=0.01; % probability that shipwreck or other vector will introduce
rats or other predators
Apredeffect= -4.6; % ln(proportion of finches surviving predation for 1
year)
Apathprob=0.01; % probability that shipwreck or other vector will introduce
malarial mosquitos
Apatheffect= -0.5; % ln(proportion of finches surviving malaria for 1 year)
Astormprob=0.05; % annual probability of survival-reducing storms
Astormeffect= -0.22+(0.2*randn); % ln(proportion of finches surviving a
severe storm)
%**************************************************************************
% SUPPLEMENTAL POPULATION "A", QUADRATIC K-TREND
%**************************************************************************
AResults=[]; % initialize array of CDFs, 1 each at all Nx's
for ANx=0:NxMax % iterate simulations across range of quasi-extinction
thresholds
if IPS==0
break
else
AExtMat=[]; % initialize array of extinct populations across Sims
for j=1:NumReps
AN=ANc; % population starts at Nc, future is zeroed
AExtinct=zeros(1,tmax); % initialize counter to record extinctions
% generate a random r within its confidence interval
Arrnd=inf;
while Arrnd<ACI_r(1)|Arrnd>ACI_r(2)
Arrnd=Ar+ASEr*randn;
end;
% generate a random K within its confidence interval
AKrnd0=inf;
while AKrnd0<ACI_K(1)|AKrnd0>ACI_K(2)
AKrnd0=AK0+ASEK*randn;
end;
% generate a random sigma^2 within its confidence interval
Asig2rnd=inf;
while Asig2rnd<ACI_sig2(1)|Asig2rnd>ACI_sig2(2)
Asig2rnd=Asigma2*chi2rv(Aq-1)/(Aq-1);
end;
Asigma=sqrt(Asig2rnd);
AKrnd=AKrnd0;
for t=1:tmax, % For each future time,
if rand < Apredprob % If there are catastrophes,
AN=[AN round(AN(t).*exp(Apredeffect))]; % apply them...
elseif rand < Spathprob
AN=[AN round(AN(t).*exp(Apatheffect))];
elseif rand < Sstormprob
AN=[AN round(AN(t).*exp(Astormeffect))];
elseif rem(t,SupInt)==0
% get new N from the RICKER logistic with random environmental effects
AND add supplement
AN=[AN round(AN(t).*exp(Arrnd*(1-
(AN(t)./AKrnd))+Asigma*randn))+SupNum];
else
% get new N from the RICKER logistic with random environmental effects.
AN=[AN round(AN(t).*exp(Arrnd*(1-(AN(t)./AKrnd))+Asigma*randn))];
end;
134
 if AN(t+1)<=ANx % if quasi-extinct,
AN(t+1)=0; % zero out the population
AExtinct(t)=AExtinct(t)+1; % update extinction counter
end;
% apply NONLINEAR (QUADRATIC) decrease to K
AKlin=AKrnd0*(1-(Areduction*(t/tmax)));
AKquad=AKrnd0*(1-(Areduction*((t/tmax)^2)));
AKrnd=AKlin-(AKquad-AKlin);
if rand < Aplantprob % if a plant invades
AKrnd=Aplanteffect*AKrnd; % decrease K to the "planteffect" fraction
end;
end; % at the end of each replicate population run
AExtMat=[AExtMat; AExtinct];
end; % "NumReps" loop - completes one batch of replicate trajectories
APE=sum(AExtMat)/NumReps;
AResults=[AResults; APE];
end; % "Nx" loop - completes replicate batches to get CDF change vs. Nx
end; % "if-else" loop to set translocation population off or on (IPS=0 or 30)
if IPS~=0
AEKquadRisk=sum(sum(AResults));
disp(AEKquadRisk)
RiskVolMat=[RiskVolMat;GKquadRisk;SEKquadRisk;LayKquadRisk;AEKquadRisk];
else
RiskVolMat=[RiskVolMat;GKquadRisk;SEKquadRisk;LayKquadRisk];
end; % "if" loop to give 4-pop risks if IPS not 0 (translocation), 3 pops
otherwise
end; % z-loop to get replicate risk volumes
end; % SupInt loop to get runs across interval lengths for each SupNum
end; % SupNum loop
end; % IPS loop
end; % Ksize loop

135
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