Science of the Total Environment 621 (2018) 1208–1223

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Science of the Total Environment

journal homepage: www.elsevier.com/locate/scitotenv

Identifying non-reference sites to guide stream restoration and

long-term monitoring☆
Ryan A. McManamay ⁎, John G. Smith, Robert T. Jett, Teresa J. Mathews, Mark J. Peterson
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States

H I G H L I G H T S G R A P H I C A L A B S T R A C T

• Reference sites have served as a stan-

dard to measure ecosystem restoration
success but do not elucidate impaired
processes
• Comparison of reference sites to bearing
sites, i.e. altered ecosystems, help iden-
tify constraints to effective restoration
• A spatial framework and case study are
used to identify bearing streams that
match biophysical conditions at re-
stored sites
• Out of N13,000 stream sites, a subset of
bearing sites were prioritized for use in
future long-term monitoring
• Bearing streams revealed disrupted pro-
cesses at play in restored sites and ex-
posed limitations of current reference sites

a r t i c l e i n f o a b s t r a c t

Article history: The reference condition paradigm has served as the standard for assessing the outcomes of restoration projects,
Received 15 June 2017 particularly their success in meeting project objectives. One limitation of relying solely on the reference condition
Received in revised form 11 October 2017 in designing and monitoring restoration projects is that reference conditions do not necessarily elucidate impair-
Accepted 12 October 2017
ments to effective restoration, especially diagnosing the causal mechanisms behind unsuccessful outcomes. We
Available online 1 November 2017
provide a spatial framework to select both reference and non-reference streams to guide restoration planning
Editor: Ouyang Wei and long-term monitoring through reliance on anthropogenically altered ecosystems to understand processes
that govern ecosystem biophysical properties and ecosystem responses to restoration practices. We then applied
Keywords: the spatial framework to East Fork Poplar Creek (EFPC), Tennessee (USA), a system receiving 30 years of reme-
Restoration diation and pollution abatement actions from industrialization, pollution, and urbanization. Out of N13,000
Anthropogenic disturbance stream reaches, we identified anywhere from 4 to 48 reaches, depending on the scenario, that could be used in
Contamination restoration planning and monitoring for specific sites. Preliminary comparison of fish species composition at
Stream these sites compared to EFPC sites were used to identify potential mechanisms limiting the ecological recovery
Fish communities
following remediation. We suggest that understanding the relative role of anthropogenic pressures in governing
Landscape alteration
ecosystem responses is required to successful, process-driven restoration.
© 2017 Elsevier B.V. All rights reserved.

☆ This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy.The United States Government retains and the
publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or
reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes.The Department of Energy will provide public access to these results
of federally sponsored research in accordance with the DOE Public Access Plan(http://energy.gov/downloads/doe-public-access-plan).
⁎ Corresponding author at: Environmental Sciences Division, Oak Ridge National Laboratory, Bldg 1504, MS-6351, Oak Ridge, TN 37831-6351, United States.
E-mail address: mcmanamayra@ornl.gov (R.A. McManamay).

https://doi.org/10.1016/j.scitotenv.2017.10.107
0048-9697/© 2017 Elsevier B.V. All rights reserved.
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
1. Introduction
The reference condition is considered by many as the standard or
benchmark for ecological assessments, including measuring the out-
comes of restoration projects (Stoddard et al., 2006; Hawkins et al.,
2010). Clearly defined goals are essential to objectively guiding and
measuring the success of restoration actions (Tear et al., 2005). Natural-
ly, conservation goals and the metrics by which they are evaluated are
typically based upon the selection of reference sites and the characteris-
tics they possess. Even so, there continues to be disagreement on how
best to evaluate a restoration project's success or failure (e.g., Palmer
et al., 2005; Bernhardt et al., 2007; Brewer and Menzel, 2009; Morandi
et al., 2014; Suding, 2011).
To aid in the process of reference selection, Stoddard et al. (2006)
recommended some standard terminology for use in defining reference
conditions. Stoddard et al. (2006) urge that the term “reference” be pre-
served for systems absent of human disturbance and then suggest terms
for several alternative conditions, i.e. “minimally disturbed condition”,
“historical condition”, “least disturbed condition”, and “best attainable
condition”. While their terminology has been adapted by some, what
constitutes an appropriate reference site remains an important yet un-
settled issue, as evidenced by the focus of several recent major reviews
(e.g., Dallas, 2013; Hawkins et al., 2010; Morandi et al., 2014) and re-
search efforts (e.g., Feio et al., 2013; Kosnicki et al., 2014; Ode et al.,
2016). The debate over defining “reference condition” stems, in part,
from many regions across the globe having little or no populations of
undisturbed sites for adequate representation in biological integrity
analyses (Brewer and Menzel, 2009; Dallas, 2013; Feio et al., 2013;
Kosnicki et al., 2014).
Regardless of how reference streams are defined, the main precept
of the reference stream paradigm suggests that context is necessary to
assess biophysical conditions at non-reference sites and interpret
what those values mean relative to a given standard (Hawkins et al.,
2010). Reference conditions, however, are not the only benchmark
that provides context in interpreting the outcomes of ecological assess-
ments (Brewer and Menzel, 2009). Streams of varying disturbance re-
gimes, and the ecological communities they support, also provide
additional dimensions in assessing the ecological status of a restoration
project and understanding the nature of disrupted mechanisms (or pro-
cesses) influencing ecological patterns. We term these systems “bearing
streams”, as they provide a point of orientation that bears witness to the
desired endpoint. “Bearing trees”, as defined by the US Department of
Agriculture Forest Service, do not mark the true property corner, but
bears witness to that location (USFS, 2013).In other words, they serve
as a bearing and distance to the true property corner.
Bearing streams provide a point-of-reference rather than serve as
the reference condition, as defined by Stoddard et al. (2006). Identifying
both reference and disturbed streams in post-restoration monitoring
(e.g., Violin et al., 2011) help to elucidate the impaired processes, and
by doing so, they assist in appropriately setting goals and guiding restora-
tion practices to achieve a given endpoint (Roni et al., 2008). In many
cases, restoration occurs in areas of intense cumulative disturbance aris-
ing from multiple independent and interacting agents, all of which act
upon the physiochemical and biological processes that shape the ecolog-
ical community. Teasing apart the relative roles of each disturbance agent
is a difficult, but necessary, step in guiding restoration practice; however,
elucidating roles of disturbance is unlikely via direct comparison with ref-
erence sites lacking any disturbance. In situations where some distur-
bances can be ameliorated via restoration while others will remain
active agents, selecting bearing streams impacted by individual distur-
bances may be advantageous in understanding disturbance-mediated
processes, which only become evident after long-term monitoring.
A great deal of effort has been expended in identifying regional pools
of reference streams to provide standards or benchmarks for biological
assessments (Hughes et al., 1986; Whittier et al., 2007; Dallas, 2013:
Lunde et al., 2013; Ode et al., 2016).Many of these studies utilize
1209
geospatial approaches to characterize landscape conditions and biolog-
ical survey information to identify best representatives of reference con-
ditions within a region. Developing reference standard criteria is
completely appropriate for regional biological assessments, i.e. Indica-
tors of Biological Integrity (Ode et al., 2016); however, these criteria
are typically represented by hundreds of reference sites where biologi-
cal information is available (e.g., Lunde et al., 2013) and not necessarily
selected based on the specific physiochemical properties or anthropo-
genic disturbance regimes that approximate conditions at individual
restoration sites. Indeed, restoration practices require very specific
guidance to set realistic expectations and appropriate actions (Suding,
2011). Additionally, we suggest that non-reference sites help provide
some of this guidance. Programs that monitor the effectiveness of resto-
ration may arbitrarily select reference sites that either match pre-con-
ceived preferences or are convenient (e.g., easily sampled, accessible,
part of existing sampling regimes, etc). For example, the justification
for selecting restoration comparison sites (reference or non-reference)
is typically based on access or priority from social emphasis (e.g.,
Violin et al., 2011; Kondolf et al., 2008). To avoid human-generated
biases, a comprehensive geographic approach to selecting reference
and non-reference sites (i.e., bearing streams) is recommended, espe-
cially not limiting the selection to only sites biologically sampled.
Herein, we present a spatial framework as a 1st-step screening
criteria to identify bearing streams (both reference and non-reference
condition) to guide stream restoration. The framework is structured as
a step-wise procedure that requires managers clearly define and revisit
goals and objectives of restoration while also evaluating all potential
streams that could approximate those goals. First, we provide a brief
overview of the spatial framework and its elements. Then we apply
the framework to a case study of East Fork Poplar Creek, the focus of a
30-year pollution remediation and biological monitoring program.
Multi-dimensional impacts from large-scale chemical contamination
and urbanization and the sheer complexity of the ecosystem present
an ideal situation requiring the additional context of non-reference
streams to isolate impaired physical and ecological mechanisms still at
play in the stream.
2. Spatial framework
The proposed framework includes six main elements, which can be
used to incrementally screen and reduce the potential number of bear-
ing streams (Fig. 1). The elements are collectively drawn from our re-
view of the literature related to: developing candidate reference sites
(e.g., Hughes et al., 1986), lack of suitable reference sites (e.g., Dallas,
2013), understanding watershed disturbances to prioritize restoration
efforts (e.g., Beechie et al., 2008), using typologies to infer reference
conditions (Hawkins et al., 2010), evaluating local and landscape con-
straints to assess ecosystem recovery following restoration (e.g.,
Suding, 2011), principles of successful restoration outcomes (Palmer
et al., 2005), and adaptive management (Murcia and Aronson, 2014).
Spatial extent, disturbance regime, physical template, and ecological
community (all described below) are more essential elements in identi-
fying potential reference sites, whereas, the remaining elements (previ-
ous sampling and accessibility) are more a matter of preference (Fig. 1).
An important point to illuminate, however, is that the order of steps or
elements may not necessarily reflect the priority of restoration goals.
For instance, goals for restoration commonly have an ecological focus
and include increasing species richness and population recruitment, re-
instating ecosystem services, or establishing unrepresented functional
groups, all of which are pertinent. While these goals most closely align
with the ecological community element (step 3, Fig. 1), ecological con-
ditions are contingent upon the previous three steps. In particular, the
anthropogenic disturbance regime and physical characteristics can
serve as surrogates for ecosystem state and structure, respectively,
with each exerting progressively less control on subsequent elements.
While the selection of bearing streams should be aligned with clearly-
1210 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
Fig. 1. Six elements of the proposed spatial framework to incrementally screen potential
reference or bearing streams to meet desired conditions. The first four elements are
essential whereas the last two are a matter of preference.
defined conservation objectives to guide and measure the success of
restoration actions (Tear et al., 2005), the current state, structure, and
ecological composition of an ecosystem reflects past and present pertur-
bations (Beisner et al., 2003). In this case, the disturbance regime is the
most import determinant of ecosystem state.
2.1. Spatial extent
The spatial extent determines the population of streams from which
potential bearing streams are selected. Ecoregions provide an appropri-
ate and convenient geographic context to organize streams because wa-
tersheds within these areas have similar landforms, soil, vegetation,
land use, and ecological communities (Omernik, 1987; Hughes et al.,
1986).Even still, watersheds within ecoregions tend to have their own
chemical, physical, and biological signatures (Hughes et al., 1986) and
may provide an additional template to determine a region of potential
stream candidates.
2.2. Anthropogenic disturbance regime
Placing the immediate focus of reference site identification on the
anthropogenic disturbance regime rather than desired future condition
shifts attention away from static endpoints to a mechanistic restoration
of processes that control those endpoints.Because restoration is aimed
at improving biophysical conditions, typical reference sites are those
that have little to no anthropogenic influence, as this is representative
of the end-goal. This gives the term “reference” a connotation of
“good” or “better”, as opposed to serving its true definition as a “base-
line” or “point of orientation”. This does not insinuate that reference
site selection should avoid pristine areas, but that the selection of refer-
ence sites need not always be confined to low-disturbance conditions.
Identifying streams of varying individual disturbance levels can be
achieved at a high-level by screening sites based on landscape-level an-
thropogenic disturbance regimes or potential chemical disturbances
(Supplementary material 1).
2.3. Physical template
The physical template determines the process by which disturbance
regimes influence ecological communities. Ideally, bearing streams will
be selected based on possessing similar (or desired) physical attributes
to that of the restoration project.Determining the physical properties of
streams, however, is no small task, typically requiring intensive field in-
vestigation. While this is especially true in cases of gathering detailed
measurements to properly design stream channels, this amount of
work is unrealistic for screening many potential candidates.Large-scale
stream classification systems provide an inventory of different physical
types of streams for a given region.For example, Olivero Sheldon et al.
(2015) developed a 6-layer stream classification for NHD stream
reaches for the Mid-Appalachian Region of the United States, which in-
cludes the Tennessee River Basin (Fig. 2). The six layers included stream
size, gradient, temperature (mean summer), hydrology, buffering ca-
pacity, and confinement (Fig. 2, for a description see Supplementary
material). The advantage of layered approaches is that investigators
can select any number of physical properties that have relevance to
the restoration objectives of interest. Additionally, each of the stream
layers represent reference conditions as they were developed based
on natural stream reach attributes (e.g., size, gradient) or were modeled
from empirical observations collected from streams with minimal an-
thropogenic disturbances (Olivero Sheldon et al., 2015). Thus, stream
classifications provide a template to establish the reference condition
for streams undergoing restoration (Hawkins et al., 2010) while also
providing a framework to select surrounding streams with similar phys-
ical and chemical properties.
2.4. Ecological condition
As mentioned previously, objectives for restoration are commonly
ecologically related. Ecological objectives may include increasing popu-
lation size or habitat for a species, increasing the species richness of
entire communities, and/or establishing functional groups, functional
processes, and ecosystem services (Bernhardt et al., 2005). Past ap-
proaches to identifying pools of reference sites excluded streams not
previously sampled for ecological communities (e.g., Feio et al., 2013;
Lunde et al., 2013; Ode et al., 2016). Given that b5% of the nation's
area has been systematically surveyed for aquatic taxa (Troia and
McManamay, 2016), this screening criteria would exclude the majority
of streams from further consideration. To consider all potential streams
as candidates, modeling estimated ecological conditions using species
distribution models (Huang and Frimpong, 2015) or estimating ecolog-
ical processes within unsampled stream reaches may be required
(Kosnicki et al., 2014).This modeling process should not be done in iso-
lation from the physical template. One mechanism for ensuring ecolog-
ical conditions are ‘physically relevant’ is to use the physical template as
predictors for ecological models.Based on pre-determined objectives,
streams that meet the ecological criteria can be selected as candidates;
however, this is a challenging exercise and requires expert input. For in-
stance, investigators must identify specific species, functional groups,
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223 1211

Fig. 2. Stream classification layers used to characterize the natural physical template of streams in the Tennessee River Basin, USA.The six-layer stream classification was produced by
Olivero Sheldon et al. (2015). Buffering capacity is not shown. Descriptions of stream classes are provided in the Supplementary material.

guilds, or ecological processes as targets for restoration. Bearing candi-
dates are then selected that best approximate those targets.
2.5. Previous sampling and accessibility
When planning a monitoring regime, the logistics of including addi-
tional monitoring efforts will likely be a factor included in prioritizing
sites, especially if resources are limited. Preferences are usually shown
for sites that are easily accessible, which considers proximity to a
home base and ease of access. Driving times can be estimated from
road network analysis to determine the feasibility of sampling various
locations based on their distance. The potential to access the stream
by foot has to also be taken into consideration, such as determining
road crossings or land ownership.
Additionally, many ecological processes require several years to de-
cades to fully capture; hence, determining the success of restoration ef-
forts requires long-term monitoring and consideration of the extent and
nature of previous sampling. However, as noted above, selecting only
sites previously sampled for ecological communities, especially under
rigorous sampling procedures, will limit the pool of candidate streams.
Thus, we re-emphasize that such criteria should be optional. Studies
evaluating the effectiveness of restoration have shown the importance
of proper control designs in detecting changes (Gowan and Fausch,
1996) as well as the effect of study duration on findings (White et al.,
1212 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
2011). Of the many experimental designs, the control-treatment pairing
(CTP) design (Eberhardt, 1976) and subsequent Before-After-Control-
Impact (BACI) and paired BACI (BACIP) designs (Stewart-Oaten et al.,
1986) have been considered among the most robust sampling strategies
to evaluate restoration effectiveness, especially if multiple controls are
used (Underwood, 1994). However, anticipating the implementation
of restoration practices years in advance and adequately preparing an
appropriate experimental design is typically an exception, not generally
a reality. Presumably, this may be a result of limited resources. Prioritiz-
ing bearing streams based on pre-existing sampling would make full
use of existing resources and assist in preparing an analysis. Obviously,
the type of sampling regimen should be considered as more information
will be available as discrete singular sampling events as opposed to sys-
tematic sampling with repeated surveys.
3. Case study
We applied the spatial framework to identify potential bearing
streams for East Fork Poplar Creek (EFPC) Tennessee, a system impacted
by substantial chemical contamination, channel alteration, and urbani-
zation followed by intense remediation and pollution abatement efforts.
For over 30 years, EFPC has been the focus of large-scale remediation ef-
forts and a long-term biological monitoring program (Peterson, 2011;
Loar et al., 2011), a sampling regimen that included reference streams
as comparisons to impacted sites. Given that reference sites were select-
ed three decades ago based on expert judgement, we questioned
whether a spatial approach might yield comparable or different results.
3.1. Study site and background
East Fork Poplar Creek originates within the U.S. Department of
Energy's Y-12 National Security Complex in eastern Tennessee, USA
(Fig. 3). EFPC drains a 55 km2 watershed before joining Bear Creek
and eventually flowing to Poplar Creek, an arm of Watt's Bar Reservoir
on the Clinch River System (Fig. 3). After exiting the Y-12 Complex
boundary ~2 km downstream of its origin, EFPC flows ~15 km through
the city of Oak Ridge before reentering the Department of Energy's Oak
Ridge Reservation where it flows an additional 8 km before its conflu-
ence with Poplar Creek. The EFPC watershed is highly urbanized, with
developments exceeding 80% developed land cover in the upper
reaches and 45% in lower reaches.
As part of the Manhattan Project, the Y-12 Complex was constructed
in 1943 to produce uranium and help fabricate nuclear weapons (Loar
et al., 2011). Because the Y-12 Complex is situated in the headwaters
of EFPC, operations have released significant contaminant loads to the
stream.In 1985, at least 250 different effluent and storm water outfalls
discharged into the headwaters of EFPC. Effluent discharges such as
cooling tower blowdown and process wastewaters contributed signifi-
cant loads of chlorine to the stream, while other contaminants entered
EFPC through erosion and surface runoff (Kasten, 1986; Loar et al.,
2011). Byproducts of operations in wastewaters included substantial
quantities of heavy metals, organic solvents, polychlorinated biphenyls
(PCBs), and mercury. It has been estimated that N 100,000 kg of mercury
was released into the stream causing extensive contamination of the
surface water, sediments, and floodplain soils (Loar et al., 2011).
Over a two-decade period beginning in 1985, several major remedial
actions, pollution abatement projects, and operational changes were
completed at the Y-12 Complex under several federal regulations in-
cluding a renewed National Pollutant Discharge and Elimination System
permit (Clean Water Act), the Resource Conservation and Recovery Act,
and the Superfund program established by the Comprehensive Environ-
mental Response, Compensation, and Liability Act (CERCLA). Some of
the major remedial actions included construction of a Central Pollution
Control Facility, relining drains from sanitary and storm sewers, dechlo-
rination of cooling water discharges, implementation of flow manage-
ment program, construction of a mercury treatment system, mercury
remediation of the floodplain in lower EPFC, and a bank stabilization
project to reduce erosion of mercury-contaminated soils (Loar et al.,
2011).For a more comprehensive review of the impacts and remedia-
tion to the system, please see Loar et al. (2011) and Brooks and
Southworth (2011).
As a condition of the NPDES permit, the Biological Monitoring and
Abatement Program (BMAP) was initiated in 1985 to evaluate and doc-
ument the ecological effects of implementing a Water Pollution Control
Program and remediation actions (Peterson, 2011). One of the tasks in-
cluded in the BMAP to help fulfill the requirements of the program was
monitoring the fish community in the stream. Five fish community sam-
pling sites were established at locations immediately below the Y-12
Complex and extending 19 km downstream (Ryon, 2011) (Fig. 3).
Drainage areas for sampling sites ranged from 1.6 to 49 km2. Two near-
by reference streams, Brushy Fork (40 km2) and Hinds Creek (45 km2),
were selected as representative of conditions in EFPC in the absence of
the Y-12 Complex and industrial effluents (Ryon, 2011). Topographic
maps were scanned to identify a pool of potential sites, and then a re-
connaissance survey of each prospective site was completed to deter-
mine each site's suitability. These reference streams did not represent
pristine conditions, but most closely approximated the “historical con-
dition” (Stoddard et al., 2006). The sites are indicative of rural-agricul-
ture influenced systems typical of the Ridge and Valley Ecoregion and
provide an estimate of likely conditions had the Y-12 Complex not
been built.
3.2. Applying the spatial framework
We used three scenarios to identify potential bearing stream candi-
dates for each of the five EFPC fish community sites. The first scenario
(S1) selected candidate streams impacted by agricultural land use sim-
ilar to the criteria used for the current set of “reference sites”. This pro-
vides a comparison of the degree to which existing reference sites
match their intended purpose. In contrast to S1, the second scenario
(S2) selected sites experiencing urbanization, as to provide a baseline
comparison that isolates the conflicting effects of contaminant amelio-
ration from the remaining urban impacts. Additionally, S1 and S2
sought sites having a fish species assemblage very similar to the desired
EFPC ecological community and that were located within a 45 min drive
(~55 km radius) from home base (Oak Ridge National Laboratory). Fi-
nally, the third scenario (S3) selected “least disturbed” streams having
little anthropogenic disturbance and/or falling within protected areas
and, to some extent, relaxed the criteria for similarity in desired species
composition. S3 also increased the acceptable driving time to include
potential candidate streams within a 90 min drive (~ 110 km radius)
from home base. We then compared bearing streams identified through
the S1–3 scenarios to the existing reference streams.
3.2.1. Spatial extent
EFPC is located on the edge of the Ridge and Valley (RV) Ecosystem
(in proximity to the Central Appalachian (CA) and Southwestern Appa-
lachian (SWA) Ecoregions (Fig. 4A). Fish assemblages within EFPC are
influenced by neighboring ecoregions as evidenced by occasional detec-
tion of species that are hypothesized to immigrate from the CA and SWA
(closest known source populations for those species occur in CA and
SWA). We considered the spatial extent to be an area bounding the in-
tersection of the RV, CA, and SWA Ecoregions within the middle water-
sheds of the greater Tennessee River Basin (Fig. 4A). Potential reference
streams were spatially represented as stream reach segments within
the NHDplus V2 dataset (HSC, 2017). This area provided 13,519
NHDplus stream reaches that serve as the population of potential refer-
ence stream candidates.
3.2.2. Anthropogenic disturbance regime
Disturbance variables were summarized for local stream reach
catchments and for the entire upstream network contributing to each
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223 1213

Fig. 3. Study site map of East Fork Poplar Creek (EFPC) within the Tennessee River Basin, USA (upper left panel). The EFPC watershed (grey region) is shown in relation to Department of
Energy sites, including the Y-12 National Security Complex (Y12), Oak Ridge National Laboratory (ORNL), and the East Tennessee Technology Park (ETTP) (top left panel). The five EFPC
study sites occur within four different natural stream class typologies (combination of stream size, gradient, hydrology, buffering capacity, and valley confinement).

local stream reach based on the National Fish Habitat Partnership
(NFHP) (Esselman et al., 2013; NFHP, 2017). Examples of variables
within the NFHP included urban and agricultural land cover (e.g., Sup-
plementary material), dams, road crossings, and National Pollution Dis-
charge Elimination System permits, among several other attributes
(Esselman et al., 2013). These variables were used to create a cumula-
tive disturbance index, which provides a surrogate of landscape alter-
ation risk to fish habitats (e.g., Supplementary material, Esselman et
al., 2013; NFHP, 2017). To determine the protected status of each stream
reach, we summarized the percentage of riparian floodplain area classi-
fied as protected land (Fig. 4D). Floodplain areas were delineated using
the Valley Confinement Algorithm (Nagel et al., 2014), which identifies
floodplains as areas inundated at 5 × bankfull width height (Fig. 4D).
Protected land coverages were available through the Protected Area
Database (USGS, 2016).
Identifying potential candidate bearing streams that isolate effects of
individual disturbances is challenging, as this requires establishing suit-
able thresholds. Thresholds for agriculture land cover have been docu-
mented far less than those for urbanization. Burcher and Benfield
(2006) found that agriculturally impaired streams with an average of
35% agricultural land cover in their upstream watersheds had signifi-
cantly less fish species richness than comparison sites. However, Utz
et al. (2009) found that invertebrate communities showed significant
shifts beyond 25% upstream agriculture within the Southeastern Coastal
plain whereas Midway et al. (2015) found no negative relationships be-
tween fish richness and agriculture within the same region. In concur-
rence with Utz et al. (2009), we used 25% upstream agriculture as a
threshold for S1 (% agriculture in streams depicted in Fig. 4E). As men-
tioned previously, EFPC's watershed ranges from 45 to 80% developed
land cover. Based on several studies, ecological degradation has been
observed with as little as 10% upstream urbanization (King et al.,
2005), but consistently observed beyond 25% upstream urbanization
(Paul and Meyer, 2001; Walsh et al., 2005; Utz et al., 2009). For S2, we
conservatively selected all streams having at least 25% developed land
cover in their upstream watersheds (% urbanization in streams depicted
in Fig. 4C). For S3, streams deemed “least disturbed condition” were se-
lected that had “very low” or “low” NFHP cumulative disturbance indi-
ces and/or had at least 50% of their riparian floodplain overlapping
protected conservation lands (see Fig. 4D).
3.2.3. Physical template
To characterize physical stream types, we used the 6-layer stream
classification developed by Olivero Sheldon et al. (2015). Among the
13,519 stream reaches within the defined spatial extent, all six physical
1214 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223

Fig. 4. Examples of geospatial data layers representing different elements of the spatial framework applied to screening candidate bearing streams for East Fork Poplar Creek. A) The spatial
extent used to determine the population of candidate bearing streams included three Ecoregions within watersheds of the middle Tennessee River Basin. B) The diversity of simplified
stream class typologies (47 unique types) among 13,519 stream reaches were used to screen potential bearing stream candidates. C) The percentage of developed lands within the
cumulative upstream area of each stream reach was used in the urban-impact scenario, S2. D) The percentage of protected lands within each stream reach's floodplain was used to
screen candidate sites in the least disturbed condition scenario, S3. E) The percentage of agricultural lands within the cumulative upstream area of each stream reach was used in the
agriculture-impact scenario, S1. F) The distribution and type of survey of locations of previous fish sampling. An inset shows the EFPC sites relative to current reference sites (Hinds
Creek, HCK20.6, and Brushy Fork, BFK7.6).

layers collectively yielded 767 unique stream type combinations.
Because the number of physical typologies was overtly complex to
inform meaningful decision making, Olivero Sheldon et al. (2015)
simplified stream types by consolidating the size, gradient, hydrology,
and temperature classes and excluding confinement and buffering
layers. This yielded 47 unique stream types, which provide a more
manageable number of typologies to identify potential reference
candidates (Fig. 4B). Interestingly, both the complex and simplified
stream classification schemes yield four different types of streams for
the EFPC sites (Fig. 3). For each EFPC site, we selected streams that
matched their respective simplified stream types under all three
scenarios.
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223 1215

3.2.4. Ecological condition

For each EFPC site, we generated lists of resident and infrequent fish
species, along with fish hypothesized to historically occur at that site but
are currently absent (Supplementary material 1). All fish species detect-
ed during the last 2 years (2 sampling periods per year) were consid-
ered resident whereas all other species detected over the course of all
sampling events were considered infrequent. List of hypothesized his-
toric residents were generated according to current and historic occur-
rence records from the greater Oak Ridge Reservation (Ryon and Loar,
1988; Krumholz, 1954) and occurrence records in the proximate region
and species habitat descriptions (Etnier and Starnes, 1993). The resul-
tant list of all resident, intermittent, and historic resident species across
all EFPC sites totaled 50 fish (Supplementary material 1).
The objective was to select bearing sites that best approximate the
full list of potential fish species for each site; however, only a subsample
of streams have been sampled. Furthermore, sampling records vary
considerably from discrete single-species occurrences to routinely sur-
veyed community records. For all stream reaches to be considered as
potential bearing site candidates, the probability of a species presence
must be estimated using species distribution models (SDMs) (Fig. 5).
Occurrence records were compiled from multiple open-access reposito-
ries for the region of interest (Troia and McManamay, 2016). All records
were summarized by NHDplus stream reaches. Because of widely vary-
ing sampling methods, detection probabilities based on survey methods
were estimated for each species occurrence within a stream reach. Oc-
currence records within each stream reach were classified as single-spe-
cies occurrence (SS), community survey (CS), or a combination of both
(SCS). All stream reach occurrences were then summarized into 12-
digit hydrologic unit (HUC12) watersheds, which typically contain mul-
tiple NHDplus reaches. Species detection probabilities were estimated
for SS, CS, and SCS survey types based on occurrence in HUC12 water-
sheds using survey-specific patch occupancy modeling in PRESENCE
2.0 (USGS, 2017). Patch occupancy models included survey type and
the number of occurrences according to each survey type (survey covar-
iate). PRESENCE software is flexible in that not all surveys have to have
been conducted within all HUC12 watersheds in order for the models to
estimate patch occupancy and detection probabilities. Survey-specific
detection probabilities, once estimated, were then back applied to the
stream reach scale based on the type of survey that was conducted
within that reach. Detection probabilities were then included as vari- Fig. 5. An example of mapping desired ecological conditions in stream reaches. Species
ables in SDMs to control for imperfect detections. SDMs were construct- distribution models, such as that for snubnose darter (Etheostoma simotreum), were
ed for each of the 50 fish species using their detection probabilities and developed for 50 species. Lists of potential and desired species were compiled for each
105 landscape-scale variables within boosted regression trees (Elith et of the five East Fork Poplar Creek (EFPC) sites and transformed into binary matrices of
species presence-absences.Bray-Curtis dissimilarity values were calculated from the
al., 2008) to model species probability of occurrence within NHDplus comparison of EFPC species-presence-absence matrices and the matrix of species-
stream reaches (Fig. 5) as binomial distributions in the Generalized occurrence probabilities from SDMs. Streams with low dissimilarity values suggest
Boosted Regression Model (gbm) package in the R programming envi- predicted fish communities most closely approximate desired ecological conditions.
ronment (Ridgeway, 2017). Variables used within SDMs are provided
in the Supplementary material. as such. In all scenarios, we provided binary indications of whether
Species occurrence probabilities for all stream reaches and lists of stream reaches have been previously sampled, had access from a road,
presence/absences of all potential species within EFPC sites were orga- or were located within a given driving time from home base. Previous
nized in a stream reach-by-species matrix. Non-metric multi-dimen- sampling was summarized by reach as either single-species occurrences
sional scaling (NMDS) based on Bray-Curtis dissimilarities was used to or community surveys (Fig. 4F). Road access was determined if a road
ordinate stream reaches in multivariate space based on community crossed a given stream reach.
composition. Pairwise dissimilarity values from each EFPC site to all To determine driving distances (and estimated driving time), we
stream reaches were extracted from the dissimilarity matrix (Fig. 5). compiled all primary and secondary roads for counties intersecting
Dissimilarity vectors for each EFPC site were partitioned into five cate- the spatial extent (Fig. 6). All roads were then used to build a geometric
gories of incrementally increasing values based on the Jenks natural network of edges (road lines) and their ends or intersections with other
breaks classification method (Jenks, 1967) (Fig. 5). For the S1 and S2 roads (nodes). Our location at Oak Ridge National Laboratory was used
scenarios, reaches with dissimilarities falling within the lowest Jenks as the starting point, each stream reach's centroid was used as the des-
category were selected. For the S3 scenario, we relaxed the selection tination. Using the Origin-Destination Cost Matrix tool in Arc GIS (10.2),
of community similarity to include reaches falling within the 1st and we calculated pairwise road network distances between the starting
2nd categories (lowest and second-to-lowest values). point and all stream reach destinations (Fig. 6). Assuming an average
speed of 45 mile h−1, we then calculated travel times to all stream
3.2.5. Previous sampling and accessibility reaches. For S1–S2, we identified stream reaches falling within a
Both previous sampling and accessibility are considered preferential 45-min driving radius (55 km) whereas for S3, we expanded the accept-
attributes of potential bearing stream candidates and thus, were treated able range to a 90-min driving radius (110 km).
1216 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
3.2.6. Bearing stream candidates
Locations of bearing stream candidates and their characteristics are
provided in an interactive map (Supplementary material, Interactive
Map). Depending on the EFPC site, the S1 scenario identified anywhere
from 9 to 48 potential bearing stream candidates that met the criteria
for disturbance regime, physical template, and ecological condition
(Appendix 1). In contrast, S2 identified fewer candidates (2 to 16) as
did S3 (10 to 28 reaches), depending on EFPC site (Appendix 1). This
makes sense as agriculture is wide-spread through the region. Candi-
date bearing streams were more proximate to EFPC and displayed
more spatial clustering (less spatial variation) in the S2 scenario com-
pared to the S1 and S3 scenarios (Appendix 1) (note that driving dis-
tance was not included in screening sites, but as an optional variable).
In all three scenarios, bearing stream candidates varied according to
whether they were previously sampled, had road access, or occurred
within the desired driving-time window (Appendix 1). Had we also
used these attributes to screen potential sites, the selection of candidate
reaches would have been more restrictive and would have resulted in
far less, if any, reaches for some sites.
None of the bearing stream candidates were identical to the individ-
ual stream reaches currently used as reference streams (Brushy Fork
and Hinds Creek); however, bearing stream candidates were identified
within stream reaches located within those same river systems, at times
directly upstream and downstream of the reference reaches. For exam-
ple, of the bearing stream candidates identified in the agriculture
scenario (S1) for EFK24.4, EFK23.4, and EFK6.3 sites, 48%, 100%, and
4% of those sites were located on the Hinds Creek or Brushy Fork
river systems. Additionally, one site on Brushy Fork was found as a
bearing stream candidate for EFK24.4 for the least disturbance (S3)
scenario.None of the bearing stream candidates for the urban-impacted
scenario (S2) overlapped with existing reference stream reaches.
3.3. Hypothesized mechanisms of disturbance
Further consideration of potential bearing sites may benefit from a
comparison of ecological conditions at restoration sites to that of poten-
tial stream candidates. Additionally, evaluating ecological conditions
through a trait lens can elucidate potential underlying mechanisms,
Fig. 6. Distances were calculated from the start position (home base) to all possible stream reach destinations using a road network. Examples of distances for two random stream reaches
(Site A and B) are provided.
such as environmental filters or anthropogenic constraints, influencing
the composition of fish communities. We organized species by fish life
histories, which represent a continuum of tradeoffs among parental
care, fecundity, spawning periodicity, body size, and longevity
(Winemiller and Rose, 1992). Fish life-history groups represent three
divergent strategies: equilibrium, opportunistic, and periodic species.
Equilibrium species are small-bodied, have small clutches of eggs, and
have high parental care (e.g., Banded sculpin, Cottus carolinae). Oppor-
tunistic fishes are also typically small-bodied fish that mature early
and have little parental investment, moderate fecundity, and multiple
spawning bouts (e.g., Spotfin shiner, Cyprinella spiloptera). Periodic
species are large fish with late maturation, large clutch sizes, and
low parental investment (e.g., Black redhorse, Moxostoma duquesnei).
All fish species under consideration were assigned to one of the three
life history groups (McManamay and Frimpong, 2015, Supplementary
material 1).
We evaluated trends (1985–2015) in fish species richness according
to life history strategies at all EFPC sites. We then compared these values
to patterns in fish richness at current reference sites and potential bear-
ing sites under the three scenarios. At candidate sites, fish richness
within each life history group was estimated using the sum of species
occupancy probabilities from SDMs. This method reduces the need to
define thresholds for species presence while accounting for uncertainty
in species occurrence, but also avoids overpredicting richness (Dubuis
et al., 2011; Calabrese et al., 2014).
Fish richness increased in an upstream-to-downstream direction
and increased with time at all EFPC sites, except EFK 24.4 (Fig. 7). Typi-
cally, bearing stream candidates had higher total fish richness than re-
spective EFPC sites, specifically opportunistic and equilibrium life
histories at EFK 6.3 and 13.8 and all life history strategies at remaining
EFPC sites. No periodic species have been detected at EFK 24.4 and op-
portunistic species have not been collected since 1988 at this site.
There were cases in which richness was lower at some candidate sites
than EFPC sites within a given scenario; however, this primarily oc-
curred at EFK 6.3 and EFK 13.8. Interestingly, candidate sites within
the S3 scenario (least disturbed condition) had relatively low values
for richness. Existing reference streams had similar richness values to
that of bearing stream candidates.
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223 1217

4. Discussion streams to guide restoration actions at a given location via long-term

Our spatial framework identified both low-disturbance and non-ref-
erence sites to be used as comparisons to restoration sites in order to
guide restoration actions or long-term monitoring. Rather than develop
a substantive pool of reference sites within a region (e.g., Ode et al.,
2016), our framework narrowed the selection of potential bearing
streams down to a handful of sites that mirrored well-defined end-
points of disturbance regimes, physiochemical properties, and ecologi-
cal conditions. For example, out of 13,519 potential stream candidates,
we identified anywhere from 2 to 48 reaches that could serve as bearing
monitoring (Supplementary material, Interactive Map). These reaches
could further be refined based on other criteria, such as previous sam-
pling, accessibility, and proximity. This level of specificity is needed to
appropriately guide restoration, adaptive management, and long-term
monitoring efforts.
There are two general approaches for selecting reference or non-ref-
erence sites that are important to distinguish from our framework. As
mentioned previously, the first approach develops a pool of reference
sites to provide regional standards, primarily water quality criteria
(e.g., Hughes et al., 1986; Ode et al., 2016). In recent years, the vast

Fig. 7. Comparison of fish richness within life history groups at East Fork Poplar Creek (EFPC) sites, candidate bearing streams under the three scenarios, and at existing reference sites.
Richness values for EFPC sites and existing reference sites represent maximum species detected for each year (1986–2015).Richness values for candidate bearing streams represent
values for multiple independent streams. A richness value for each stream was calculated as the sum of species occupancy probabilities for that stream reach.
1218 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
majority of these studies have used Geographic Information Systems
(GIS) to characterize the natural and anthropogenic characteristics of
sites with existing biological monitoring data (e.g., Whittier et al.,
2007; Feio et al. 2013; Ode et al., 2016). While the reference-pool ap-
proach can identify a large number of sites representative of the natural
environmental gradients present within a region (Ode et al., 2016), this
approach only yields a temporal snapshot of biophysical conditions.
Furthermore, the biological criteria developed from reference pools
may be influenced by various sampling regimes with variable levels of
sampling effort and quality control (Ode et al., 2016). Moreover, refer-
ence pools may not provide the level of biophysical specificity or tempo-
ral extent needed for monitoring an individual restoration project.
In contrast to developing regional reference pools, the second ap-
proach entails handpicking one to several reference or non-reference
sites as comparisons in field studies monitoring the outcomes of resto-
ration. We use the term “approach” loosely here as there is very little lit-
erature formalizing a procedure for identifying reference sites for
monitoring restoration outcomes (Whittier et al., 2007). Ideally, sites
used as comparisons are identified prior to restoration taken place and
are monitored jointly with restored sites in BACI or BACIP-like designs
(Stewart-Oaten et al., 1986; Underwood, 1994). In many cases,
however, the temporal extent of monitoring is truncated because resto-
ration actions have already ensued or resource limitations preclude
more robust sampling; thus, space is replaced for time and restored
sites are compared to unrestored (i.e., non-reference) and reference
(i.e., pristine) sites (e.g., Violin et al., 2011). In these studies, selection
of comparison sites tends to be somewhat haphazard as very little
justification is provided beyond generic similarities in basin attributes
(e.g., size), description of disturbance (or lack thereof), or spatial prox-
imity. Potentially, this leads to selecting sites that are biased by personal
preferences and not reflective of standard criteria. For instance, Whittier
et al. (2007) found that reference sites handpicked by state and federal
resource agencies were more representative of regional disturbed con-
ditions than least-disturbed conditions.
Our framework is similar but divergent from past efforts in a few
ways. First, we focus considerable attention on identifying non-
reference sites, whereas most efforts have arguably focused on defining
reference conditions (we discuss the benefits of non-reference sites
more thoroughly in subsequent sections). Akin to the intent of the sec-
ond approach mentioned above, our principle objective is to provide an
approach to identify a few sites with desired biophysical specificity to
guide restoration actions through long-term monitoring. Like the refer-
ence-pool approach, however, we use very rich geospatial analyses to
consider thousands of potential sites thereby avoiding human-biases
in the selection of comparison sites. Another distinction is that our
framework isolates sites for future monitoring, rather than selecting
sites for their static pre-assessed conditions; however, SDMs and
existing biological monitoring information, where available, can pro-
vide a snapshot of biological conditions at potential comparison sites
to identify potential impaired processes. We used synthesized biological
information to depict ecological conditions at bearing streams rather
than rely on empirical biological survey information. The benefit of
using SDMs to predict likely fish assemblage composition is that our as-
sessment considered all streams, not just those with previous commu-
nity sampling. However, the obvious limitation is that ecological
conditions are estimated and hence, prone to uncertainty. Ideally, the
selection of sites should be conducted prior to restoration taking place
to appropriately inform monitoring designs. We reiterate the impor-
tance of long-term monitoring in detecting and understanding impaired
biophysical dynamics to appropriately guide restoration (Muotka et al.,
2002).
A noteworthy similarity of our framework and that of other ap-
proaches is the use of ecosystem classifications to stratify site selection.
Stream typologies have commonly been used to stratify site selection
for environmental monitoring efforts (e.g., Wollock et al., 2004). For ex-
ample, Feio et al. (2014) used stream typologies including size, geology,
and hydrologic regimes ensure pools of lead disturbed sites had repre-
sentation across river types. Likewise, Harris (1999) used cluster analy-
sis to group riparian vegetation within different floodplain landforms as
a strategy to identify context-specific reference riparian communities.
Hawkins et al. (2010) suggests that classifications or typologies based
on natural patterns provide an estimation of reference conditions as a
benchmark for ecological assessments. The advantage of developing
classifications based on natural patterns is that these can be easily ex-
tended to infer reference conditions while providing a guide to select
comparison sites sharing a similar geophysical context. In accordance
with this approach, we use stream classifications to identify bearing
streams, but we also suggest that natural classes should be considered
in conjunction with anthropogenic disturbance regimes to appropriate-
ly understand biophysical conditions. As an example, the Ecological
Limits of Hydrologic Alteration framework (ELOHA) uses natural hydro-
logic classes to understand ecological responses to human-induced al-
terations in streamflow regimes (Poff et al., 2010). The assumption is
that streams of similar hydrologic character would respond similarly
to hydrologic alteration (Arthington et al., 2006).
4.1. Utility of including non-reference streams
Non-reference systems have been an under-utilized resource in res-
toration planning and long-term monitoring, despite the growing
awareness that the ‘reference condition’, as defined by Stoddard et al.
(2006), is becoming quite rare. A very common limitation in forming
appropriate standards or benchmarks for evaluating restoration out-
comes is the absence of suitable reference sites (Brewer and Menzel,
2009; Dallas, 2013; Feio et al., 2013; Kosnicki et al., 2014). Within the
US, at least 39% of stream habitats for fish are jeopardized by landscape
alterations (Esselman et al., 2013) and as much as 80% of streams show
some sign of hydrologic alteration (McManamay et al., 2017).
In some cases, non-reference systems may better characterize the
biophysical properties that managers desire to restore. For example,
within the upper Tennessee River System (USA), the largest river sys-
tems are regulated by dams, but yet contain the richest and most di-
verse fish faunas (McManamay et al., 2015). In other situations,
systems of reference quality are not desired or warranted. For example,
studies examining the biological impacts of a fly ash spill into Watts Bar
Reservoir, TN due to a dike failure at Tennessee Valley Authority's Kings-
ton Fossil plant used a non-impacted arm of the reservoir as the “refer-
ence” site as comparison to downstream “impacted” sites (Mathews et
al., 2014; Smith et al., 2016). In this case, the reference condition was
represented by a completely unnatural and man-made system, a reser-
voir, which was far more appropriate than a free-flowing stream in eval-
uating potential background contaminant levels.
The inclusion of bearing streams in our analysis provided a temporal
snapshot of potential mechanisms limiting restoration; however, the
full utility of bearing streams become realized when they are included
in long-term monitoring efforts. Long-term patterns promote the devel-
opment of sophisticated models to tease apart constraints to effective
restoration and promote adaptive management. We suggest that the in-
clusion of carefully selected, non-reference sites can improve restora-
tion planning, prioritization, and monitoring in three main ways. First,
non-reference streams serve as a control to explain potential variation
of disturbances still at play in unrestored sites (e.g., Violin et al., 2011).
These comparisons deepen the understanding of biophysical processes
impaired by watershed disturbances (e.g., Violin et al., 2011)
(Appendix 1), which is unlikely via direct comparison with undisturbed
reference sites. In situations where some biophysical properties are
ameliorated via restoration while others remain actively disrupted, iso-
lating the role of individual disturbances requires careful selection of
bearing systems. For instance, EFPC sites experience compounded dis-
turbances primarily from intense urbanization, channelization, and ri-
parian modification while the main focus of restoration has been
reducing chemical contamination (e.g., mercury) (Loar et al., 2011).
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
Comparing physical and ecological patterns in EFPC to sites impacted by
urbanization could help isolate impacts of chemical contamination on
ecological recovery (Appendix 1). Additionally, comparing species and
functional community composition of EFPC to surrounding agricultural-
ly-impaired sites (majority of streams in region) yields information on
common species and traits that would be expected in EFPC had industri-
alization not taken place (Appendix 2).
Bearing streams also assist in identifying thresholds and constraints
of ecosystem responses to disturbance and restoration, respectively. As
is often the case, local conditions are an artifact of larger-scale distur-
bances at play within entire watersheds or surrounding landscapes
(Booth, 2005); hence, the scope of restoration projects should align
with the scales at which disturbances operate (Bernhardt and Palmer,
2011). Systems severely impacted by acute or chronic disturbances or
altered by unprecedented human influences may have reached a new
state of equilibrium (Beisner et al., 2003), undergone regime shifts
(e.g., Hilt et al., 2011), exceeded thresholds in which ecosystems are
likely responsive to restoration (Miller and Bestelmeyer, 2016), or
completely emerged as self-organized novel ecosystems (Hobbs et al.,
2009). Furthermore, these new states of self-organization may be irre-
versible (Clewell et al., 2005), due in large part to surpassed threshold
exceedances (Miller and Bestelmeyer, 2016). Comparisons to non-ref-
erence sites experiencing individual, rather than compounded, distur-
bances help to identify thresholds and their exceedances. These
“gradients of alteration” (Miller and Bestelmeyer, 2016) isolate poten-
tial disturbance thresholds, while simultaneously identifying con-
straints to effective restoration (e.g., limits to colonization, Bond and
Lake, 2003; Miller and Hobbs, 2007). The nature of cause-effect, stress-
or-ecosystem-response relationships (Davies and Jackson, 2006),
specifically the linearity or non-linearity (Walsh et al., 2005), are impor-
tant in understanding the stages at which ecosystem transition to alter-
nate states or in identifying thresholds, beyond which new ecosystems
emerge.
Lastly, bearing systems provide a means to promote adaptive man-
agement by generating hypotheses on how disturbances and restora-
tion organize ecosystem function (Appendix 1), thereby reducing
uncertainty and risk in making restoration decisions (Walters, 1997).
Bearing systems help to reveal causal mechanisms governing ecosystem
processes under various disturbance regimes, and thus, identify alterna-
tive hypotheses. When viewed within the context of adaptive manage-
ment, alternative hypotheses translate into different restoration actions,
which are analogous to ecosystem-level experimental manipulations to
inform subsequent decision-making (Palmer and Bernhardt, 2006;
Konrad et al., 2011).
4.2. Applying the spatial framework to EFPC: a case study
We applied the spatial framework to identify bearing streams as ad-
ditional monitoring sites for comparison to restoration efforts in EFPC.
This afforded an opportunity to examine the degree to which our frame-
work identified bearing streams similar to existing reference sites,
based on following the same objectives for their selection. To provide
a reference scenario comparable to the criteria used to identify the cur-
rent set of reference sites, we identified bearing stream candidates im-
pacted by agriculture (e.g., S1 scenario) that mirrored the physical
template and desired ecological conditions of EFPC sites. Given that
36% of streams in the region have at least 25% upstream agricultural
land cover, it was not surprising that the S1 scenario yielded the most
candidate bearing streams compared to other scenarios. Indeed, agricul-
tural impairment would be the expected norm for EFPC had industrial-
ization of the Y12 Complex not taken place. While S1 bearing stream
candidates were not identical to the stream reaches currently used as
reference sites, our framework identified several candidate stream
reaches immediately up and downstream from existing reference sites
and many more were identified within the same river systems. These
results suggest that the framework performs well at finding sites that
1219
mirror the objectives of investigators, assuming the original selection
of the two reference sites was objective and unbiased by personal pref-
erences. This also suggests the framework offers significant time savings
given that the original reference site candidates were preliminarily
identified on topographic maps and followed up by site visits with man-
ual field measurements (Loar et al., 1992).
As would be expected, bearing stream candidates within the urban-
impacted scenario (S2) and the least disturbance scenario (S3) were not
found on the same river systems as current reference sites (an exception
is that one bearing site for EFK24.4 was located on upper Brushy Fork for
the S3 scenario). While not a surprising outcome, the number of bearing
stream candidates identified under these scenarios implies that a diver-
sity of non-reference systems could, in theory, be selected to inform the
monitoring of restoration outcomes. Furthermore, the objectives used
to select these bearing streams will yield highly divergent results.
Bearing stream candidates also allowed to us to examine the ade-
quacy of existing reference streams in representing desired ecological
conditions. Based on species distribution models, we compared
30 years of ecological recovery in fish communities (or lack thereof) at
EFPC sites to observed and predicted fish species assemblages at
existing reference sites and bearing streams, respectively. Values for
total richness of fish species were similar between existing reference
streams and bearing streams for the EFK6.3, 13.8, and 18.6 sites
(Fig. 7); however, for EFK24.4 and EFK23.4 sites, fish species richness
predicted by SDMs for bearing stream candidates was noticeably
lower than observed richness values in HCK20.6. Relying on HCK20.6
as reference stream for the two upper EFPC sites may be misleading
and overestimate the potential species richness that could be attained
at these sites.Indeed, most of the bearing stream candidates identified
for EFK24.4 and EFK23.4 had smaller drainage areas than HCK20.6.
Beyond assessing the adequacy of existing reference sites, compari-
sons of ecological conditions at bearing stream candidates and EFPC
sites provided additional dimensionality in teasing apart the relative in-
fluence of many compounded disturbances in constraining the ecologi-
cal effectiveness of restoration (Appendix 2). A general observation was
that fish species richness remained lower in three of the EFPC sites com-
pared to reference streams and bearing streams (Fig. 7). Ecological re-
covery was more pronounced at downstream sites, which were closer
to sources of colonists (e.g., McManamay et al., 2016) and removed
from sources of physiochemical disturbances that ameliorated with
distance downstream. EFPC consistently has lower numbers of opportu-
nistic fish species than surrounding urban, agriculture, and low-distur-
bance streams. We surmise this is the result of artificially-induced
ecosystem stability arising from intense and chronic disturbances
(Beisner et al., 2003; Hilt et al., 2011), whereas opportunistic fish prefer
naturally variant environments (Olden and Kennard, 2010). Additional-
ly, many opportunistic fish are lithophilic, broad-cast spawners
(Winemiller, 2005), which require clean and porous sand and gravel
(Balon, 1975). Intense urbanization and dramatic flood pulses in up-
stream portions of EFPC have likely removed some of these finer mate-
rials or induced embeddedness of bed sediments in other areas.
Using species richness values from disturbed systems when setting
objectives for restoration creates some challenges. For example, ecolog-
ical endpoints for restoration in EFPC are likely to be an artifact of spe-
cies pools present in the surrounding impaired landscape, which
surprisingly may be artificially high. For example, fish richness was typ-
ically higher for bearing streams in the agriculture and urbanization sce-
narios than in the least disturbance scenario – a somewhat
counterintuitive result. We conjecture this pattern is not an artifact of
our SDMs. While agriculture and urbanization land use practices have
contributed to degradation of many streams in the ecoregion (Zheng
et al., 2008; Brown et al., 2005), we attribute higher richness to in-
creased numbers of generalists (Midway et al., 2015; Meador and
Goldstein, 2003), native-invasive species (Scott and Helfman, 2001),
but also endemic fluvial specialists, such as lamprey species
(Ichthyomyzonspp.) or River chubs (Nocomis micropogon), whose
1220 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223

habitat needs are met in other impaired systems, but apparently not in
EFPC. Appropriate restoration will require understanding whether
members of ecological communities in impacted systems are the result
of artificial inflation in species richness or remnants of species-rich eco-
systems of the past.
We emphasize that our 1st order comparisons between EFPC sites
and bearing sites should be further evaluated through long-term moni-
toring and analyses (Peterson, 2011). The hypothesized causal mecha-
nisms generated from these preliminary comparisons provide grounds
for fostering adaptive management by suggesting new restoration ac-
tions. Specifically, the absence of river chub and lamprey species suggest
multiple factors including limited recolonization potential and habitat
limitations, possibly a lack of suitable habitat. Continued evaluation of
bearing streams could help elucidate the likelihood of alternative man-
agement approaches, such as reintroduction efforts or habitat restora-
tion efforts.
5. Conclusions
We provided a framework to identify specific low-disturbance and
non-reference sites as comparisons to restoration sites. Substantial liter-
ature exists on defining reference conditions (Hawkins et al., 2010;
Dallas, 2013; Ode et al., 2016), prioritizing restoration actions (Bohn
and Kershner, 2002; Beechie et al., 2008), or developing appropriate
restoration endpoints (Palmer et al., 2005; Tear et al., 2005; Miller and
Hobbs, 2007). In contrast, the scientific literature is deficient of exam-
ples where reference or altered ecosystems are identified, prioritized,
and specifically tailored to guide restoration actions.
Isolating, understanding, and repairing impaired processes are keys
to successful restoration (Roni et al., 2008), yet successful restoration
outcomes are rarely documented (Palmer et al., 2010). Ultimately, this
suggests that current restoration practice is failing to address the most
important processes governing ecosystem impairments, or in the
least, the nature of those processes and the scale at which they operate.
We suggest that more studies evaluate gradients of ecosystem
alteration (Miller and Bestelmeyer, 2016) or incorporate systems
representing a diversity of disturbances in restoration monitoring and
assessments to identify the causal mechanisms behind ecosystem im-
pairment, appropriately design restoration projects, or learn from and
iteratively adapt to restoration actions that fail to meet project objec-
tives. However, we suggest that these disturbed systems be selected
under rigorous approaches to meet the site specifications needed to ad-
equately guide restoration. By using comprehensive and rich geospatial
coverage of all streams for consideration, the process minimizes
human-generated biases in the arbitrary selection of potential streams
that do not align with prioritized objectives. Hence, the structure of
the framework is meant to provide a reality-check as to ensure the de-
sired ecological outcomes match the constraints imposed by the condi-
tion of the landscape and physical properties of streams.
Acknowledgements
The study was authored by employees of UT-Battelleunder contract
DE-AC05-00OR22725 with the US Department of Energy. This research
was sponsored by the Environmental Compliance Department of the
Y-12 National Security Complex and by the Oak Ridge National
Laboratory's Environmental Protection Services Division's Water
Quality Programs. We thank Allison Fortner and two anonymous re-
viewers for providing valuable comments on earlier versions of this
manuscript.

Appendix 1
Bearing stream candidates identified under the (A) agriculture impacts scenario, (B) urban impacted scenario, and (C) low-disturbance scenario.
Bearing candidates (pies) are color-coded to indicate whether they provide road access, are located within 45-m drive, have been previously sam-
pled, or none of the above. Existing reference sites (stars) are also provided as a comparison to bearing candidates within the agriculture impacts
scenario.

Appendix 2. Hypotheses regarding observed response to restoration generated from comparisons with predicted fish species compositions at
bearing sites

Scenario General observation Hypothesized mechanisms behind ecological responses to restoration

All Total fish species richness was generally lower at EFPC sites than bearing streams, Multivariate and cumulative disturbances are at play in EFPC as opposed to
especially EFK18.7, EFK23.4, and EFK24.4 sites. Opportunistic species richness
was more noticeably lower in EFPC sites than bearing streams.
All Fish communities at downstream EFPC sites display stronger recoveries than
upstream sites. Differences in species richness between EFPC and bearing streams to Y12-Complex). Urban landcover exceeds 80% of watershed area in upper
are more pronounced at upstream sites.
All Species richness was extremely low at EFK24.4 (only 4 species) and the
community was comprised of only equilibrium species.
S1 Agriculturally-impaired streams represented the most numerous candidate
singular disturbance agents acting on bearing stream communities. Several
cyprinid species, primarily opportunists, are missing from EFPC. Opportunistic
species favor naturally variable environments that promote competition over
niche space (e.g., larger river systems or alternatively, systems with flashy flows
followed by periodic intermittency) (Olden and Kennard, 2010); however,
maintained high levels of anthropogenic disturbance create an artificially stabile
system (Beisner et al., 2003), which is favored by equilibrium species
(Winemiller, 2005). Additionally, members of Nocomis, a genus of
mound-building chubs, are absent from EFPC sites but found in surrounding
streams. Nocomis chubs are considered keystone species are their mounds are for
utilized for spawning by many cyprinid opportunists (Peoples and Frimpong,
2015).
Disturbance agents, such as sources of contaminants, are higher upstream (closer
sections of EFPC. Channelization and entrenchment is extensive in the upper
reaches. Downstream EFPC sites are closer to sources of colonists from adjacent
watersheds with lower disturbances. Connectivity has dramatic influence on
ecological recovery of restored ecosystems (McManamay et al., 2016)
The entirety of upper EFPC's flow emerges as industrial effluent from the Y-12
Complex b1 km upstream of EFK24.4.Additionally, an impoundment is located no
N1 km downstream of EFK24.4, which prevents colonists from migrating to the
site. EFK24.4 is characterized as having high impervious surface, highly controlled
flows from industrial operations, channelized stream banks, and lack of finer
substrates. Such extreme cases of anthropogenic disturbances transition into
alternative ecosystem states of artificial stability (Beisner et al., 2003). Stable and
resource limiting environments are highly conducive to dominance by
equilibrium strategists (Winemiller, 2005; Olden and Kennard, 2010).
Within the Ridge and Valley Ecoregion (RVE), most low-gradient river systems
 R.A. McManamay et al. / Science of the Total Environment 621 (2018) 1208–1223
(continued)
Scenario General observation
bearing streams and generally, had higher species richness than multiple EFPC
sites and other bearing streams.
S2 Streams impacted by urbanization represented the smallest number of bearing
streams compared to other scenarios. Similar to agriculture, urbanized bearing
streams had higher species richness than many EFPC sites, had the highest
number of total species at 2 EFPC sites, and the highest number of opportunistic have commonly been observed with increased urbanization under various
species among all scenarios at 3 EFPC sites.
S3 Low-disturbance streams consistently had less species than other bearing stream Low disturbance systems may not represent the most species-rich systems
scenarios, but still had higher species richness than 3 of the respective EFPC sites. (Midway et al., 2015) for numerous reasons. First, streams falling under
Appendix 3. Supplementary data
Supplementary data associated with this article can be found in the online version, at https://doi.org/10.1016/j.scitotenv.2017.10.107. These data
include the Google map of the bearing stream candidates identified in the case study for each of the EFPC sites and each of the scenarios.
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Further reading
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community monitoring to assess pollution abatement effectiveness. Environ.
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