LECTURE 1

Chapter 14
Professors Notes:
1) Trait variation is due to alternative version(alleles) of heritable factors(genes)
2) for each character an organism inherits 2 alleles, one from each parent
3) DOMINANT alleles mask recessive alleles
4) 2 alleles for a heritable character SEGREGATE during gamete formation & end up
in different gametes => LAW OF SEGREGATION
-PUNNETT SQURE => 3:1 RATIO
-Beginning of human genetics- hemophelia was recognized as hereditary ~500 A.D.
-1905: 1st published paper on a human genetic disorder
-Eugenics Movement: improve race by inducing young people to make a more
reasonable selection of marriage mates; to fall in love INTELLIGENTLY
A Section 1
Gregor Mendel and Genetics
-in the 1800s Gregor Mendel proposed that characteristics are passed to offspring
through discrete particles aka genes
-theory of BLENDING INHERITANCE, where parental characteristics are blended
together to generate the offspring characteristics, fails to explain mating results like
traits skipping generations
-in PARTICULATE INHERITANCE, parents give their offspring discrete heritable units
which can be expressed even if they do not appear in each generation
-a second problem w/ the theory of blending inheritance is that if the characteristics
of the offspring always exited qualitatively between those of the parents, eventually
all members of a species would become homogenous, displaying the SAME
characteristics
ex) particulate inheritance could explain how blue eyes and blond hair, for
example, often could disappear from a familys lineage for several
generations,only to have 2 brown haired, brown eyed parents give birth to a
blond, blue-eyed child
The basics of Mendels pea plant experiments
-Pea plants were good model b/c they have
1) multiple variable characters
2) short generation times
3) large numbers of offspring
4) controllable breeding
-Mendel first pollinated PURPLE flower with WHITE flower pollen; in the reciprocal
cross, WHITE plants with their stamens removed were pollinated with pollen from
PURPLE plants
-Mendel could breed plants that had different traits for the same character
-Before the cross-breeding experiments, Mendel first self-pollinated varieties for
multiple generations; this process gave rise to plants that only produced offspring
plants with the SAME trait => TRUE-BREEDING
-for the cross-breeding experiments, Mendel bred 2 true-breeding varieties that
differed at the character under investigation; Mendel bred TRUE BREEDING PURPLE
FLOWERED PLANTS with TRUE BREEDING WHITE FLOWERED PLANTS => PARENTAL
GENERATION(P GENERATION)
-the hybridization of the P generation results in hybrid offspring which constitute the
first filial generation, F1 generation. When 2 F1 hybrids mate, or when one F1 hybrid
self-pollinates, the offspring are part of the second filial generation, F2 generation.
Law of Segregation
- states that each individual has 2 factors that contribute to a phenotype and that
separate when gametes are formed
- individual organism has 2 alleles for every gene, one inherited from its mother and

one from its father; when this organism forms its own gametes, each gamete will
receive only one of these alleles, and this process is random
in the case of 2 different alleles at a particular locus, the organisms phenotype will
be determined by the dominant allele, which is able to mask the effects of the
recessive allele. In order for the recessive trait to be seen, both alleles carried by
the organism must be recessive
PUNNETT SQUAURE => diagram used to determine the ratio of diff. phenotypes and
genotypes in offspring, resulting from crossing parents with different combinations
of genotypes.
HOMOZYGOUS => 2 SAME ALLELES at a particular gene
HETEROZYGOUS => 2 DIFFERENT ALLELES at a particular gene
PHENOTYPE: organisms appearance, or observable characteristics
GENOTYPE: complete genetic make up
Law of Independent Assortment
-states that alleles of different genes assort independently of one another during
gamete formation
-MONOHYBRID CROSS=> mating btw. individuals who have diff. alleles at one genetic
locus of interest
-DIHYBRID CROSS=> cross btw. F1 offspring of 2 individuals that differ in 2 traits of
particular interest
Ex) Bb x Bb => B(brown), b(blue), BB(dark), Bb(Brown), bb(blue)
Section 2
Probability rules and simple Mendelian genetics
-P(X and Y) = P(X) x P(Y)
-P(X or Y) = P(X) + P(Y)
Section 3
Complex inheritance patterns from a single gene
-complete dominance occurs when the offspring always has the same phenotype as
one or both of its parents. one of the possible alleles is always dominant over the
other and always dictates the phenotypes
ex) BB(Brown) x bb(blue) = Bb(Brown)
-Incomplete dominance occurs when the heterozygous individuals display a different
phenotype than either the recessive or dominant homozygotes; neither of the alleles
are completely dominant, and the resulting intermediate phenotype is usually a blend
of the two possible traits.
ex) C^RC^R(Red) x C^BC^B(Blue) = C^RC^B(purple)
-Codominance: condition in which both alleles of a gene pair in a heterozygote are
fully expressed, with neither one being dominant or recessive to the other.
ex) I^AI^A(Type A) x I^BI^B(Type B) = I^AI^B(type AB)
PLEITROPY => occurs when single genes may affect multiple phenotypic characters,
such as multi-symptom diseases in humans, sickle-cell disease, or cystic fibrosis
Section 4
Tracing alleles through a family history
a pedigree is a diagram showing the ancestral relationships and transmission of
genetic traits over several generations in a family
in practical application, pedigrees can be used to predict the future occurrence of
heritable disorders
examining the pattern of the inheritance of a trait in a pedigree can help determine
whether it is being inherited as a dominant or recessive trait

BISC 120 LECTURE NOTE 2

Chapter 15
-Mendels hereditary factors are located on chromosomes
-early studies of meiosis showed that the behavior of chromosomes parallels the
behavior of Mendels factors
-Both chromosomes and factors
-present in pairs in DIPLOID cells
-segregate during meiosis
-halve their copy numbers during meiosis and double their copy numbers at
fertilization
-THOMAS HUNT MORGANS FRUIT FLY experiments provided the first strong evidence
that genes are on chromosomes
- WHY FRUIT FLIES?
-easy to rear in lab
-short generation time(~10d)
-abundant offspring(100s per mating)
-only 4 pairs of chromosomes
-numerous mutation stocks now available
-WHAT HAPPENS WHEN GENES ARE LOCATED ON THE SAME CHROMOSOME?
-Morgan noticed that certain traits tended to be inherited together
-RECOMBINATION OF LINKED GENES: CROSSING OVER
-Morgan discovered that genes can be linked, but the linkage was incomplete,
as
evident from recombinant phenotypes
-Morgan proposed that some process must sometimes break the physical
connection between gens on the same chromosome
-that mechanism was the crossing over of homologous chromosomes
-SEX DETERMINATION
-in humans and many other animals, there is a chromosomal basis of sex
determination
-humans and other mammals have an X-Y sex determination system
-other animals have different methods of sex determination
-RECOMBINATION FREQUENCIES**** memorize the order
-INHERITANCE OF SEX-LINKED GENES
-the sex chromosomes have genes for many characters unrelated to sex
-a gene located on either sex chromosome is called a sex-linked gene
-sex linked genes follow specific patterns of inheritance
-SEX LINKED CONDITIONS INCLUDE

-Hemophilia
-Duchenne muscular dystrophy
-Color Blindness
Chapter 16
-WHAT IS THE GENETIC MATERIAL? (PROTEIN OR DNA?)
-GRIFFITH et al. showed that an unknown substance could TRANSFORM(CHANGE THE
GENOTYPE AND PHENOTYPE) BACTERIA
-HERSHEY AND CHASE used bacteriophage(a kind of virus) to determine what
substance the virus uses to reprogram bacterial cells
-FRANKLIN and WILKINS made X-ray diffraction images of DNA
-WATSON and CRICK used the X-ray images to deduce the double helix
-1953: WATSON AND CRICK RESOLVED 3D STRUCTURE OF DNA
-SYNTHESIZING A FUNCTIONAL GENOME: a team led by J.CRAIG VENTER has
succeeded in creating a synthetic bacterial genome and using it to control a cell
-DNA CONTAINS 3 COMPONENTS: NITROGEN-CONTAINING BASE, A PENTOSE
SUGAR(DEOXYRIBOSE), AND A PHOSPHATE GROUP

Lecture 3
DARWINIAN REVOLUTION
Top 5 myths about CHARLES DARWIN
MYTH 1)
Darwin was the first to propose that life on this planet evolved
-many people proposed evolutionary ideas before Darwin, and many others
paved the way for his theory, even if they did not believe in evolution
themselves
-Evolution ideas began w/ ancient Greeks
-Empedocles believed plants came first, then animal
-Developed a theory of struggle among animals that foreshadows natural selection
-ARISTOTLE believed life forms were fixed, but his Scala Naturae inspired
evolutionary theories
-LINNAEUS developed a classification system that played a role in Darwins
evolutionary arguments
-did not believe in evolution
-used classification system to reveal the divine order of life
-considered the father of taxonomy
-evolution was supported by the geologic theory of GRADUALISM, but NOT by
CATASTROPHISM
-CUVIER, a hard core Catastrophist
-Paleontologist
-found diff. fossils in diff. strata and inferred extinction
-believed boundaries btw. strata due to catastrophes
-HUTTON and LYELL advocated gradualism
-believed earths features explained by processes currently operating
-implied earth is >>6000 years old
-Darwins own grandfather(ERASMUS DARWIN) proposed evolutionary ideas
-a leading intellectual in 18th century England
-wrote prose and poetry discussing origins of life from a single ancestor,
transmutation of one species into another and effects of competition and sexual
selection on species change
-LAMARCKS theory was published the year Darwin was born(1809)
-developed comprehensive theory of evolution that included discredited thy of
inheritance of acquired characters
-ALFRED RUSSELL WALLACE independently described an evolutionary mechanism
almost identical to Darwins
A WHAT IS DARWINS THEORY?
-observation
1) Members of population often vary greatly in their traits, and some of these traits
are heritable.
2) All species are capable of producing more offspring than their environment can

support, and many offspring fail to survive or reproduce

**MALTHUS BASIC THEORY: unless at or below subsistence level, a population's
fertility will tend to move.
MYTH 2)
Darwin went to the Galapagos, studied the beaks of finches, and thus discovered
evolution
-Darwin didnt know many of his samples were finches until an ornithologist
figured it out
-THE ORIGIN OF SPECIES(1859)
-513 pg
- ~5 pages devoted to the Galapagos
- Finches are never mentioned
-evidence for adaptive radiation in finches came much later
-instead, Darwin based his theory on a wide diversity of geological and biological
observations
MYTH 3)
Darwins On the Origin of Species document numerous examples of natural
selection in action
-Darwin observed extensive ARTIFICAL SELECTION
-however, documentation of NATURAL SELECTION in action is more recent
MYTH 4)
Evolution is a theory about the origin of life
-Darwin did believe that all organisms on Earth trace their origin to a single ancestor
-however, he was not at all clear on how life itself originated
MYTH 5)
Darwin was an atheist bent on bringing down the Church
-Darwins religious views were complicated and changed throughout his life
-raised as a Christian and studied to become a clergyman
-very uncomfortable w/ conflict btw. his theory and biblical teachings, and this
likely delayed publication of THE ORIGIN
-experienced a loss of faith after the death of his 9-year old daughter Annie
-in later life he described himself as an Agnostic, but never an Atheist

Lecture 4
Ch.22 Section 3 - Case For and Against Evolution
Argument 1: Evolution cannot be observed and therefore cannot be proven
Rebuttal: evolution is observed all the time!

-we cant observe the ENTIRETY of evolution and therefore rely on diverse lines
of evidence, just as we do in other fields

Argument 2: There are no transitional fossils

Rebuttal: The fossil record is spotty, but there ARE transitional forms
i.e. transition between fish and tetrapods; transition between reptile and birds;
transition between horse species; transition from land mammals to whales;
transitional fossil flatfish with partially migrated eyes

Argument 3: Chance cannot create complexity

Rebuttal:Mutations are random; but selection is NOT

Argument 4: the first step toward complex adaptations could not have been
favored(=irreducible complexity)
Rebuttal:Initial steps will be favored if they offer even a slight advantage, even
for an entirely different purpose

Argument 5: Natural selection violates the second law of thermodynamics(entropy

will increase in an isolated system)
Rebuttal: The earth is not an isolated system
Argument 6: Evolution is only a theory
Rebuttal: evolution is both a fact and an enormously well-supported
theory(THEORY=WELL-SUBSTANTIATED EXPLANATION OF A SET OF
NATURAL PHENOMENA IN SCIENCE)
Fact - species change over time
Theory - species change over time due to the combined forces of mutation,
migration, genetic drift and natural selection

Evidence for Evolution:

Direct observations of evolutionary change:
-Changes in beak size in Galapagos finches
-Predation-induced changes in guppy coloration
-Industrial melanism in moths
-Evolution of resistance to antibacterial and antiviral drugs
-Evolution of pesticide resistance
-Changes in soapberry bug beak length

Homologous characters
-Similarities due to common ancestry
-Anatomical homologies/ Molecular homologies
i.e. Mammalian forelimbs: homologous structures with very different functions
-Vestigial traits: historical remnants of traits for ancestors
-MOLECULAR HOMOLOGY: GENETIC CODE
Fossil record
-Why does it matter if evolution is true or not?
-Evolutionary thinking is crucial to agriculture
-One way to slow the evolution of pesticide resistance is to provide REFUGIA

Evolution thinking is crucial to medicine

-Tremendous increase in antibiotic resistance had led to:
1) longer hospital stays
2) higher treatment costs
1) 2~3 fold higher mortality in hospitalized patients

-Biomedical field tends to avoid the term evolution when describing evolutionary
processes

-Fixing the antibiotic problem will require greater evolutionary awareness from
doctors, patients, and farmers.

Lecture 5
Chapter 23 Section 1-2
-Populations evolve, individuals do not
-Hardy-Weinberg Principle can be used to test whether population is evolving
Population: localized group of individuals of the same species that can
interbreed and produce fertile offspring
Evolution: change in the genetic composition of a population from generation to
generation
-given a series of assumptions, allele frequencies and genotype frequencies will not
change between generations
Assumptions: NO SELECTION
NO MUTATION
NO MIGRATION
INFINITELY LARGE POPULATION
RANDOM MATING
-if these assumptions are met, allele and genotype frequencies will not change
between generations

TERMINOLOGY:
imagine a population made of 100 diploid individuals: 40 AA, 40 Aa, and 20 aa
GENOTYPE FREQUENCIES: 40/100 AA, 40/100 Aa, 20/100 aa
ALLELE FREQUENCIES: (80+40)/200A, (40+40)/200 a
GENOTYPE NUMBERS: 40 AA, 40 Aa, 20 aa

Multiplication rule: combined probability of independent events occurring together is

the product of their individual probabilities
Addition rule: combined probability of 2 mutually exclusive events is the sum of their
individual probabilities

p+q =1; p^2+2pq+q^2 = 1

How to test HW:

test whether observed genotype numbers match expected genotype
numbers(calculated from allele frequencies)

HW forms the basis of microevolutionary studies

-it serves as a null model - if a population does not conform to HWE we can look at
which assumptions are violated(i.e. which evolutionary forces are acting)
-practical applications in medicine, agriculture, forensics

Evolutionary processes
-Mutation and sexual recombination produce new variation
-Selection, drift, and gene flow alter allele frequencies in a population

Mutation
-The raw material of evolution
-a two edged sword - most mutations are deleterious but a few are beneficial and
these provide the basis for evolutionary change

Kinds of mutations
1) Point mutation:
-single-base substitutions caused by DNA polymerase errors in either DNA

synthesis or DNA repair

-sickle cell anemia results from a single point mutation
1) Insertions/Deletion(Indels):
-Indels can cause addition or loss of amino acids, frameshifts, or truncated
proteins
1) Gene duplications
-Duplication of a short stretch of DNA
-Caused by unequal crossovers during meiosis, or strand slippage during DNA
replication
-Duplicates may either maintain function, gain a new function, or lose
function(pseudogenes)

Gene duplication has given rise to variety of gene families

-gene families are sets of genes that have similar DNA sequence but vary in
composition and functions
-i.e. organisms from bacteria to humans harbor a diverse family of heat shock
proteins involved in folding and unfolding proteins, transporting proteins across
membranes and general stress response
1) Chromosome inversions (results in new gene order: ABCDEF -> ABEDCF
2) Polyploidization
-polyploid organisms have more than 2 sets of chromosomes
-polyploidy usually occurs b/c of a failure in reduction division at meiosis which
results in a 2n gamete.
Polyploidy can cause instant speciation
-when a mutant 2n gamete fuses with a normal 1n gamete, the resultant 3n
offspring is

typically sterile due to problems at meiosis

-if the mutant 2n gamete is lucky enough to fuse with another mutant 2n
gamete

the resultant 4n offspring is instantly reproductively isolated

Single mutations rarely produce significant adaptive change. Most mutations are
neutral or deleterious

Sex reshuffles the gene pool

1) random assortment of chromosomes
-with 23 pairs of chromosomes humans can produce >8 million combinations of
intact chromosomes
1) Crossing over within chromosomes
-With crossing over, a single human couple is theoretically capable of producing
more a number of combinations greater than the total number of people that
have ever lived
1) Fertilization

Lecture 6
Chapter 23 Sec. 3-4
Natural Selection
-differential survival and/or reproduction results in certain alleles being passed to the
next generation in greater proportions
Random Genetic Drift
-changes in allele frequencies within populations which result from chance variation
in individual survival and reproduction
-most important in small population
-can result in maladaptive evolution

Sampling Error alters allele frequencies in finite population

-from 50% black marbles and 50% red marbles, if you remove 4 marbles, you might
not be surprised to get 3 black and 1 red or even all red

Bottleneck effect: occurs when size of the population is suddenly reduced

Founder effect: new colony starts by few members of the original population

Gene flow
-consists of genetic additions or subtractions from a population, resulting from
movement of fertile individuals or gametes
-causes a population to gain or lose alleles
-tends to reduce differences between populations over time

Natural selection is the primary mechanism of adaptive evolution

-natural selection accumulates and maintains favorable genotypes in a population
-depends on existence of heritable, genetic variation

Modes of Selection:
Stabilizing
Directional
Disruptive
Sexual:
-natural selection for mating success
-can result in sexual dimorphism
-sexually selected traits may be bad for survival

Preservation of Genetic Variation

-various mechanisms help to preserve genetic variation in a population
1) diploidy: maintains genetic variation in the form of hidden recessive alleles
2) balancing selection: occurs when natural selection maintains 2 or more forms in
pop.
-leads to a state called balanced polymorphism
-heterozygote advantage is one form of balancing selection
-negative frequency-dependent selection is another form of balancing selection

Natural selection doesnt produce perfect organisms

i.e.) humans have fondness for fats, sugar, alcohol, tobacco, sloth; poorly
designed knees; back problems; fragile eyes; helpless infants; useless appendix

Lecture 7
Chapter 24 Sec.1-2
Are species real?
-species are the fundamental unit of organization in nature
-Ornithologist Ernst Mayr identified 137 birds in Papua New Guinea
-Native Papuans already had names for 136 species. There are about 8.7 +/- 1.3
million SE

No single species concept can be applied in all situation

1) morphological: defines a species by structural features
2) ecological: views a species in terms of its ecological niche
3) phylogenetic: defines a species as the smallest group of individuals that share a
common ancestor
4) biological: actually or potentially capable of interbreeding

Biological species concept is most popular, but does not work in all situations
-asexual taxa
-fossils
-taxa not amenable to breeding studies

No species concept works in all situations

-many species have few distinguishing morphological characters
-often have too little information to apply ecological or phylogenetic concepts
-fossils rarely distinguish taxa down to the species level
Two types of reproductive barriers
1) Prezygotic barriers impede mating or hinder fertilization if mating does occur:
A. habitat isolation(wrong place)
-2 species encounter each other rarely, or not at all, b/c they occupy different
habitats
-i.e. marine iguanas vs. land iguana
A. temporal isolation(wrong time)
-species that breed at different times of the day, different seasons, or different years
cannot mix their gametes
-i.e. 13 vs 17 year cicadas
A. behavioral isolation(no attraction)
-courtship rituals and other behaviors unique to a species are effective barriers
-i.e. Laysan albatross courtship
A. mechanical isolation(cant copulate/pollinate)
-morphological differences can prevent successful mating
-i.e. anthers not positioned to put pollen on a bee, but will put pollen on a bird
A. gametic isolation(cant fertilize)
-sperm of one species may not be able to fertilize eggs of another species
-i.e. many broadcast spawning marine invertebrates

1) Postzygotic barriers prevent hybrid zygote from developing into a viable, fertile
adult
A. Reduced hybrid viability
-Genes of the different parent species may interact and impair the hybrids

development
-i.e. Rana pipiens x Rana sylvatica hybrids do not survive more than a day
A. Reduced hybrid fertility
-even if hybrids are vigorous, they may be sterile due to problems at meiosis
-i.e. Ligers(males sterile)
A. Hybrid breakdown
-some first-generation(F1) hybrids are fertile, but when they mate with another F1
hybrid or with either parent species, offspring of the next generation are feeble or
sterile(i.e. the tidepool copepod Tigriopus californicus)

Modes of Speciation
1. Allopatric(allos=other, patra=homeland)
-gene flow impeded by physical or geographic barrier
-selection and drift lead to reproductive isolation
1. Sympatric(sym=same, patra=homeland)
-takes place in geographically overlapping population
-can occur through chromosome changes or through non-random mating

Instant speciation through polyploidization

-polyploidy: extra sets of chromosomes due to accidents during cell division
-an autopolyploid has more than 2 chromosome sets, all derived from one species
-an allopolyploid has chromosomes derived from 2 different species
i.e. coffee, sugar cane, bread wheat, potatoes, bananas, peanuts, apples

Sympatric speciation via mechanisms other than polyploidy is more controversial

-could occur by switches in habitat, food preference or mate choice
-debate continues over whether this is common, and whether isolation can persist in
the face of gene flow

Sympatric speciation in maggot flies?

-subset of US populations switched hosts from hawthorn to apple < 200 years ago
-partially isolated by ecology, not mate choice
-also, some evidence that genetic differences arose in allopatry before flies came
together
Sympatric speciation in cichlid fish?
-Lake Victoria only 12000 years old and has >500 cichlid spp
-could be driven by subtle mate choices in sympatry
-could also be micro-allopatric
Anthropogenic effects may cause species to merge back together

Lecture 8
Ch.24 Section 3, Ch.25 Sec.1-2
Macroevolution
Critique of macroevolutions:
1) irreducible complexity
-rebuttal: pieces of complex systems often have functions of their own
-i.e. bacterial flagellum made of parts that could serve other function
-i.e. eyes with a range of complexity still function
1) No one has observed the evolution of new species
-rebuttal 1: there has been little time to observe the origin of new species, since
human history spans < 0.006% of biological history
-rebuttal 2: we have observed the origin of new species?
-many cases of speciation via laboratory selection experiments
-many cases of new species originating by spontaneous polyploidy and/or
hybridization
-many cases of new species arising naturally w/o polyploidy or hybridization

1) PUNCTUATED EQUILIBRIUM not explained by Darwinian theory

-rebuttal: punctuations that appear abrupt in the fossil record may take tens of
thousands of years
-periods of apparent stasis may belie extensive biochemical changes not detectable
in the fossil record
-slight genetic changes may result in major phenotypic changes

The evolution of genes controlling development(evo-devo) is responsible for

particular large phenotypic changes

Changes in Rate and Timing(Heterochrony)

-Includes:
-changes in the relative growth rates of different body parts(allometry)
-changes in the timing of reproductive vs. somatic development
relatively rapid reproductive growth results in paedomorphosis - sexually
mature adults with juvenile morphology

Allomatric growth: differential growth rates in different body parts

-changes in allometric growth lead to differences in human vs. chimp adults
Paedomorphic pets
-relative to ancestral wolves domesticated dogs have
-softer fur, larger head&eyes, droopier ears, submissive behavior, shorter
muzzle

Changes in Spatial Pattern

-alteration in genes controlling the placement and organization of body parts cause
major evolutionary change
-homeotic genes control body plans by controlling the developmental fate of groups

of cells
-the products of one class of homeotic genes, called Hox genes, provide positional
information in animal embryos
-changes in Hox genes controlled evolution from fish fins to tetrapod limbs
-duplication of Hox genes affected the evolution of vertebrates from invertebrates
-Hox genes drove evolution of insect body plans

Hallmarks of Macroevolution
1) Evolution is not goal oriented
-fossil record often shows apparent trends
-important to consider not just the surviving branch, but the entire evolutionary bush
-the appearance of an evolutionary trend does not imply that there is some intrinsic
drive toward a particular phenotype
1) Evolution DOESNT equal progress from simple to complex
-b/c all organisms evolved from a common ancestor, we all have as many years of
evolution behind us. Some lineages become more complex, others become simplified
-Chimps are more highly evolved than we are!
1) Novel features often arise through intermediate stages, each of which serve a
function(partial wings can be adaptive)
2) Evolution recycles features and puts them to new uses
-many characters evolved for purposes other than those for which they are currently
used( =exaptation)
-feathers evolved for insulation, co-opted for flight
-protein used for cell adhesion in multicellular organisms first evolved in single
celled choanocytes
1) Evolution leaves baggage behind
-appendix(human evolutionary baggage)
-trachea and esophagus share opening(leads to choking)

-blind spot

Lecture 9
Chapter 26 Sec 1-3 : Phylogenetic Systematics
Phylogeny: evolutionary history of a species or group of related species
Taxonomy: science of naming and classifying organisms
Systematics: scientific system for classifying organisms
Phylogenetic systematics: classification of organisms by their order of branching on
an evolutionary tree

Old-school taxonomy
-developed by Carolus Linnaus in 18th century
-includes 2 part format for scientific names(binomial nomenclature) and hierarchical
classification system(e.g. Kingdon, Phylum, Class, Order, Family, Genus, Species
-still in use today(although Domain has been added as the most inclusive hierarchical
category)

Taxonomic tips
-species is both the singular and the plural form
-genus is singular, genera is plural
-in a binomial name, the first letter of the genus(but not the species) is capitalized,
i.e. Homo sapiens
-the entire binomial is italicized or less commonly, underlined

Old-school Linnaean categories have been criticized because they dont always form
monophyletic groups
A. monophyletic
B. paraphyletic
C. polyphyletic

PhyloCode
-proposed classification system
-only monophyletic groups would be recognized
-most species names would remain unchanged
-traditional taxonomic ranks(family,order,class...) would no longer exist

How to read phylogenetic tree

-node: branch point where lineages diverge
-sister taxa
-basal taxon
-polytomy: an unresolved pattern of divergence

Phylogenies are inferred from homologous characters not analogous characters

Analogous structures or molecular sequences that evolved independently are also

called homoplasies

How are phylogenetic trees constructed?

A. Cladistics is one approach to reconstructing phylogeny
-groups species into clades(ancestor and all its descendants)
-focuses on shared, derived characters
-uses principles of maximum parsimony or maximum likelihood
A. Outgroup
-a species or group of species that is closely related to the group of species being
studied, but clearly not as related as any study group members are to each other
I.

Maximum parsimony: the best tree requires the fewest changes

-evolution may not be parsimonious for any given character

I.

Maximum likelihood is an alternative approach to reconstructing phylogeny

-the best tree is the tree w/ the highest likelihood given certain rules about how
DNA changes over time
-more computationally intensive than maximum parsimony appraches

Lecture 10
Chapter 26 Sec.4-6 Insights from Molecular Systematics
-Molecular trees span both short and long periods of time b/c molecules evolve at
different rates
-Conserved sequences like ribosomal RNA(rRNA) resolve deep divergences
-Rapidly evolving sequences like mitochondrial DNA(mtDNA) resolve more recent
divergence

Molecular phylogenies rely on 2 types of homologous genes: orthologous and

paralogous

-orthologs: genes diverging due to species lineages separating

-paralogs: genes evolving in parallel within species after a duplication

Molecular phylogenies track evolutionary time if we assume a molecular clock

Molecular clocks: yardstick for measuring absolute time of evolutionary change based
on the observation that some genes and other regions of genomes appear to evolve
at constant rates
Neutral Theory:
-states that much evolutionary change in genes and proteins has no effect n fitness
and therefore is not influenced by Darwinian selection
-states that the rate of molecular change in these genes and proteins should be
regular like a clock
-originally developed by Motoo Kimura

Difficulties with Molecular Clocks

-molecular clocks are imprecise
-clock rates vary among genes and among species
-clock rates need to be calibrated with independent data

Practical applications of phylogenetics

1. Dating the origin of HIV
-phylogeny provides clues about where HIV came from, and approximately when it
colonized humans
1. HIV infections in Libyan hospital
-six foreign medics accused of deliberately infecting the children
-medics sentenced to death but eventually released under deal brokers
-evidence suggesting medics are innocent
many children co-infected w/ hepatitis(dirty needles)

at least one child infected w/ HIV after medics were arrested

Strong evidence of innocence comes from phylogeny

The Aftermath
-Libyan National Experts Committee said the Western reports lacked epidemiological
evidence and scientific proof
-114 Nobel laureates signed petition urging that the scientific evidence be permitted
in court
-Libyan court upheld death sentence
-Death sentence commuted and prisoners eventually freed after complex
negotiations involving aid, trade, debt write-offs and payments sent to the infected
childrens families
1. Source of SARS
-Phylogeny supports hypothesis that virus originated in bats
-bats appear to be a reservoir for a number of human viruses(ebola,hendra,nipah)

Why are so many viruses jumping to humans from other animals in recent times?
-human populations expanding into animals territory
-different species increasingly brought together in markets, farms, ranches
-increased travel and trade between regions
1. Source of 2009 H1N1 outbreak
-virus derived from avian, swine, and human strains, all circulating in pigs
-molecular clock analysis suggests that ancstors of the 2009 outbreak had been
circulating undetected for btw. 9-17 years
1. Plagues in the 6th, 14th, and 19th centuries
-samples from modern victims and skeletal remains show that all 3 plagues caused
by the bacterium Yersinia pestis

Lecture 11
51.1- 51.5
Behavioral Evolution
What Is Behavior?

Behavior
A

What an animal does and how it does it

A Includes muscular and nonmuscular activity

Proximate vs. Ultimate Questions

Proximate, or how, questions about behavior

A

Focus on the environmental stimuli that trigger a behavior

Focus on the genetic, physiological, and anatomical mechanisms underlying a

behavioral act

Ultimate, or why, questions about behavior

A Address the evolutionary significance of a behavior

Schooling in fish
A

How? Sense movement of other fish by sight

line

(eyes on sides of head) and lateral

A Why? Minimize predation, reduce friction

Ethology
A

The study of behavior, especially under natural conditions

Discipline developed in mid-1900s (Tinbergen, von Frisch, Lorenz)

Fixed Action Patterns

A

Sequence of unlearned behaviors that are largely unchangeable

Usually carried to completion once initiated

Triggered by external stimuli

Fixed action pattern in sticklebacks: The red belly of an intruding male stimulates
attack from resident male

When presented with unrealistic models

A As long as some red is present, the attack behavior occurs

Another fixed action pattern: Goose egg retrieval behavior
Imprinting
A

Includes both learned and innate components

Generally irreversible

Develops only during critical period

Evolution of Social Behavior

Sexual Selection

Altruism & Kin Selection

A Human Sociobiology
Sexual Selection
A

Selection for mating success

May oppose natural selection

May lead to sexual dimorphism

A Involves intra-sexual competition and inter-sexual choice

Asymmetries in sexual reproduction
A

Females typically have larger parental investment or PI (sperm is cheap)

A
A

Female reproductive success low and stable- limited by number of pregnancies she
can carry

A
A Male reproductive success highly variable - limited by number of successful matings
In some species, sex roles reverse
A In seahorses and pipefish, males carry young in pouch and provide all parental care
Consequences of reproductive asymmetry
A

Sex with low PI should be competitive

A Sex with high PI should be choosy

Evolution of Social Behavior

Sexual Selection

Altruism & Kin Selection

Human Sociobiology

Darwin (1859) thought that atruism presented a special difficulty, which at first seemed to
me inscrutable, and actually fatal to my whole theory
Individuals do not act for the good of the species because cheater alleles will win
Instead, individuals may maximize their inclusive fitness (the total effect an individual has
on proliferating its genes) by enhancing the reproductive success of relatives (e.g. kin
selection)
Evolution of Social Behavior

Sexual Selection

Altruism & Kin Selection

Human Sociobiology

Do women prefer mates who differ at loci involved in immunity (MHC)?

Contraceptive use alters preference for masculine vs. feminine faces

Lecture 12
Conservation Biology and Conservation Genetics (56.1,56.2)

Conservation biology is a young field that integrates:

A

Ecology

Behavioral ecology

Physiology

Molecular biology

Genetics

A Evolution
The field of Conservation Biology has grown in response to concerns over loss of
biodiversity
A

Official reports show that were losing diversity at all levels (ecosystem diversity,
species diversity, genetic diversity)

Why preserve biodiversity?

Why preserve biodiversity?
We cant afford to lose biodiversity!
In total, ecosystem services are estimated to be worth ~$33 trillion per year!
How is genetics used to aid conservation?
1. Diagnose populations or species at genetic risk
Small populations may be at genetic risk due to:
A

Inbreeding depression

A Low genetic variation

Inbreeding depression
A

Breeding with close relatives increases the chance the parents will share the same
deleterious recessive alleles

Deleterious recessives are then exposed as homozygotes in the offspring

Low genetic variation

A

Can result in reduced ability to adapt to environmental changes, such as alterations in

climate or the introduction of new pathogens
Species often harbor genetic variation to deal with challenges theyve never experienced

Examples:
A

Melanic moths

Heavy metal tolerance in plants

Pesticide tolerance

Tolerance of climatic change

Species with low genetic variation are particularly vulnerable to environmental challenges
Species with low genetic variation are particularly vulnerable to environmental challenges
Low genetic variation and small population size can interact to cause an extinction vortex
Extinction vortex in prairie chickens

Populations of the greater prairie chicken were fragmented by agriculture and later
found to exhibit decreased fertility

To test the extinction vortex hypothesis, scientists imported genetic variation by

transplanting birds from larger populations

The declining population rebounded, confirming it had been on its way down an
extinction vortex

How large does a population need to be to maintain evolutionary potential?

A Maintenance of neutral diversity requires an effective population size of ~500 - 5000
Effective population size (Ne) is generally lower than actual population size (N)

Factors reducing N include:

e

Fluctuations in population size over time

Inbreeding

Overlapping generations

Unequal family sizes

A Unequal sex ratios

How is genetics used to aid conservation?
Do polar bears deserve high priority for conservation?
Does the tuatara deserve high priority for conservation?
Do Catalina Bison deserve high priority for conservation?
Genetic data shows 45% of Catalina bison have cattle mtDNA! (Vogel, Tenggardjaja,
Edmands, Halbert, Derr & Hedgecock, 2007)
Does the San Clemente Loggerhead Shrike deserve high priority for conservation?
Shrike was listed as Endangered in 1977

Arguments for listing

A

Occurs only on San Clemente Island

Rare (down to 17 wild individuals at one point)

Arguments against listing

A

Not clear that the subspecies is morphologically distinct from other subspecies

A Genetic data suggests hybridization among subpecies

Does the San Clemente island fox deserve priority for conservation?
Four of the six subspecies currently listed as federally endangered
Southern subspecies introduced
by humans?????
San Clemente fox not listed as Endangered

Arguments for listing

A

Occurs only on San Clemente Island

Rare (numbers dropped by >50% in 10 years)

Morphologically and genetically distinct

Arguments against listing

A

Could be considered an introduced subspecies

Foxes eat endangered shrikes