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Project Title: Development of Methods to Evaluate Effectiveness of Restoring Aquatic Organism Passage
Principals: Jason Dunham, Michael Adams, Susan Haig, and Mark Miller, USGS Forest and Rangeland
Ecosystem Science Center, 3200 SW Jefferson Way, Corvallis, OR 97331; 541-750-7397, jdunham@usgs.gov ;
Bruce Hansen and Dede Olson USFS Pacific Northwest Research Station, 3200 SW Jefferson Way, Corvallis, OR
97331; 541-750-7311, bhansen@fs.fed.us; Steve Lanigan, Module Leader, Aquatic and Riparian Effectiveness
Monitoring Program, USDA Forest Service, Pacific NW Region, Resource Planning and Monitoring, POB 3623
333 SW First Ave., Portland, OR 97208; 503.808.2261; slanigan@fs.fed.us
Collaborators: Kim Clarkin, USFS San Dimas Technology and Development Center; Sandra Wilson-Musser,
USFS R6 Engineer; Jim Capurso, USFS R6 Fisheries Program Leader; Guillermo Giannico, Oregon State
University; Fisheries; Dan Shively, Fish Passage and Habitat Partnerships Coordinator, U.S. Fish and Wildlife
Service, Region 1 (OR, WA, ID, and Pacific Islands).
Background
Restoration of passage for fish and other aquatic organisms at stream-road crossings represents a major challenge,
involving a potential investment of hundreds of millions of dollars nationally, and even within individual states
(e.g., Oregon and Washington; GAO 2001). In recent years, passage at hundreds of stream-road crossings has been
restored, primarily by replacing barrier road culverts with bridges or stream simulation culverts designed to pass all
species and all life stages of aquatic life and simulate natural hydro-geomorphic processes (Stream Simulation
Group, 2008). Within Pacific Northwest US alone (Oregon and Washington) millions of dollars are spent annually
on projects to restore passage at stream-road crossings.
The case of the Pacific Northwest represents two questions of national significance: “Are current design standards
and construction methods for stream simulation culverts adequately re-establishing passage for aquatic biota?;”
and “How do we monitor and evaluate effectiveness of passage restoration?” Here we request support to contribute
to a major study of the effectiveness of aquatic organism passage impairment and restoration in the Pacific
Northwest region (PNW). This project has regional significance because the results will help managers in the
PNW evaluate the effectiveness of their investment in passage restoration. Outside of the region, results will have
national significance because results of this work can provide a model for application across the nation. The PNW
is uniquely poised for this effort, due to the existence of a strong infrastructure and working relationships among
diverse parties representing both government and university affiliated scientists and managers. In large part this
infrastructure has been supported by strong public interest in maintaining water quality and ecosystem processes
that support culturally and economically important salmon and trout in the region.
Most restoration projects in the PNW are motivated by concerns over fish passage, primarily for sensitive salmon
and trout species. The benefits of culvert restoration for salmon and trout have been assessed in a small number of
cases by direct observation of fish moving through replaced culverts or using them as habitat, or tracking marked
fish to determine if they can pass through restored road crossings. In some cases fish were shown to move through
replaced culverts, but in others, they did not move, for reasons that were not completely understood (Dave Heller,
U.S. Forest Service [Retired], personal communication). Success of passage restoration for other aquatic biota and
for juvenile salmonids is less well-known (Sagar et al. 2007). Furthermore, little is known about how passage
restoration might facilitate invasion by a variety of nonnative species (Fausch et al. 2009), a growing threat in
freshwaters of the region (Sanderson et al. 2008). Thus, while great progress toward restoring passage has been
made, we still understand little about the overall effectiveness of passage restoration with respect to achieving
agency goals such as maintaining viable populations of endemic species, and the diversity of aquatic life.
Our goal in this project is to improve our understanding of the effectiveness of programs for improving aquatic
organism passage, by addressing the following questions:
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1.
Freedom of movement. “How do individual organisms of selected species move through restored and unrestored stream-road crossings in relation to natural streams?” “How” as used here can refer to probability
of crossing through structures, rates of movement, timing of movements, or gene flow as inferred from
genetic analysis. These responses relate in short to “freedom of movement” of different organisms
and life stages through natural streams and different types of road crossings. Impairment of
movement is a key concern in restoring passage for aquatic biota.
2. Stream simulation. “How do un-restored crossings compare to restored crossings or natural
stream channels in terms of hydrological and geomorphic processes?” In other words, are current
procedures for restoration of road crossings producing structures that simulate natural physical
processes in streams? This question would be addressed by comparing natural channels to
restored and un-restored crossings with respect to simple geomorphic features (channel
morphology).
3. Population consequences. Species may be able to move across road crossings, but is it enough?
This question points to the population consequences for biota relative to the freedom of movement for
different species and life stages. “Do populations upstream of stream-road crossings have different
characteristics (species presence, demographic, and genetic characteristics) relative to those without
stream-road crossings?” “Does passage restoration also restore population processes as indicated by these
characteristics?”
4. Protocols. “Given results of this work in the PNW, what protocols, guidelines, and recommendations can
be developed for applications across the nation?” The results of this work will directly benefit managers in
the PNW by allowing them to evaluate the effectiveness of stream-road crossing restoration, but will also
serve a national interest in evaluating effectiveness for a much broader diversity of biota and stream
habitats.
Addressing these questions across Oregon and Washington will provide an important broad-scale evaluation that
can be used to quantify the success of passage restoration and evaluate trade-offs in terms of economic and
ecological costs and benefits of projects in different contexts (e.g., Peterson et al. 2008, Neville et al. 2009). This
project was initially conceived to evaluate crossings on Federal lands; however, a watershed approach is critical
when dealing with movement barriers, and the project would greatly benefit from additional funding from other
agencies so that State and private lands could also be included.
To recap, this project has direct relevance and inference to the Pacific Northwest, but more importantly represents a
model of collaborative effort between scientists and managers that can serve as a model nationwide. Results from
this and other similar projects are essential for adaptive management of local and national passage restoration
programs.
Methods
Task 1. Develop a database of culvert barriers, aquatic organism passage restoration projects, and related
geographic, biotic, road, and historical information on public and private lands in selected Oregon and
Washington watersheds.
We have initiated this effort in collaboration with Forest Service, Pacific Northwest Region (Region 6). Georeferenced culverts and passage restoration projects have been identified on six forests to date: the Siuslaw,
Umpqua, Wallowa-Whitman, Malheur, Umatilla and Fremont-Winema National Forests, with information
scheduled to arrive from other Forests in FY 2010 and 2011 (K. MacDonald and S. Wilson-Musser, U.S. Forest
Service, personal communication). We will work with the Region’s effort to geo-reference all projects throughout
Region 6 on forest lands in Fiscal Year 2011. We will also work with the Oregon-Washington BLM State Office
and USFWS to include their information in this database. Oregon Department of Fisheries and Wildlife, NOAA
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and USDI Bureau of Reclamation culvert data sets will provide data for other public and private crossings. Priority
basins for database development and field implementation will be on the Siuslaw National Forest (e.g., Nestucca,
Yaquina, Alsea, Siuslaw, and smaller coastal basins) and John Day River (Umatilla, Malheur, and WallowWhitman National Forests). These forests and watersheds represent a very large portion of the Pacific Northwest
Region, including vast tracts of BLM lands on the east and west sides of the Cascade Mountain crest. Sampling in
2011 will be conducted to provide representative information from remaining landtypes in the region.
Task 2. Apply database to develop a retrospective study design for evaluating effectiveness of aquatic organism
passage restoration in streams across the region.
The database will provide us with a “population of pipes” or culverts from which a sample can be taken to draw
inference about culvert and passage conditions across the larger region. These locations will be populated with data
relating to landscape conditions (stream size, elevation, valley slopes, stream gradient, drainage size, latitude,
longitude, type of disturbance, time since disturbance, distance upstream of mainstem river), biotic conditions
(species suspected or known to be present), and characteristics of the crossings themselves (e.g., degree of passage
impairment as determined by ground measurements; e.g., streambed and particle size within culverts, K. Clarkin,
personal communication; Harris 2005). This initial “filtering” of sites is meant to provide the foundation for a
robust study design. More detailed on-the-ground measurements will supplement this information in locations
selected for field sampling.
We will employ a retrospective study design, rather than a “before-after” comparison so we can conduct work
quickly in a broad geographic area, and cover a wide range of conditions that represent diverse landscape and biotic
conditions in the region. Our work will focus on comparisons of biological and selected physical responses (see
Appendix 2). Measurements of these responses would be recorded above and below existing (un-restored) culvert
barriers, sites with restored passage, and reference sites lacking a culvert or other structure that could impede
passage (reference sites). This will require us to select sites with adequate lengths of accessible upstream and
downstream reaches to sample.
Our goal would be to sample a minimum of 30 areas with specific locations representing each of three categories of
stream crossings (un-restored culvert, restored, and reference section without culvert). This totals to 90 specific
locations. We understand these categories of stream crossings may not be clear. For example, in reality, culverts as
well as natural locations represent gradients of “passability” for different species and life stages. To account for
this issue, we will measure physical characteristics of culverts and natural stream reaches during our field surveys
(Appendix 2) so we can statistically adjust for these effects (e.g., physical habitat covariates).
It is also possible that we may adapt our approach to compare “above-below” locations for stream-road crossings to
“above only.” In many cases culverts cross tributary streams that directly flow into a larger mainstem stream – thus
a downstream reach is very limited in size or practically absent. In this case it is only possible to compare upstream
locations. We have successfully employed this approach before (Neville et al. 2009). One consequence of this
situation is that mark-recapture of individuals to evaluate movement is constrained by lack of adequate habitat
below a culvert (e.g., a small number of individuals to mark in a stream below a culvert).
A final potential situation is the possibility that few culvert barriers remain for some stream types (e.g., larger fishbearing channels). Thus there are very few “un-restored culvert” locations. If this is the case, we will compare two
basic categories of stream reaches: natural streams and restored stream crossings. This approach also allows us to
account for the influences of key factors such as stream size, time since restoration, design characteristics, and local
habitat potential to support key species. In studies of passage impairment in other systems, time of isolation (since
a barrier was installed) was a key variable (Morita et al. 2009), thus we expect time since restoration to be
important.
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Our database will allow us to troubleshoot these issues and adapt our study approach to clearly address the
questions posed herein. The main constraint determining our design will be locations of stream crossings that have
been restored and have followed AOP prescriptions.
Task 3. Implement effectiveness monitoring at selected sites to evaluate alternative measures of organism
responses within the study design – based on forthcoming summary of methods for evaluating the effectiveness of
aquatic organism passage (FS-WO contract with USGS; Dunham PI).
Our initial focus will be to determine culvert passage responses based on four classes of methods: 1) mark and
recapture of individuals to assess movement through stream-road crossings or reference sites; 2) demography as
indicated by the presence of different life stages for selected species; 3) occupancy modeling to estimate
probabilities of detection and presence for selected species and/or life stages; and 4) genetic analyses of
connectivity across the road crossing (e.g., Neville et al. 2009). Each of these methods provides unique
perspectives on the responses of biota to passage impairment or restoration.
Mark and recapture and demography are the two methods implemented most commonly in field applications.
These approaches can indicate effectiveness, but also come with some critical assumptions. For example, if mark
and recapture fails to detect movement at stream crossings, lack of movement could be due to a variety of factors
unrelated to “passability” such as insufficient numbers of marked individuals (low relocation or recapture
probability) or insufficient frequency, duration or timing of monitoring to detect movement.
Demography is usually considered in terms of total abundance of individuals or life stages. Changes in
demography associated with changes in passage should be expected, as abundance is a product of movement
(emigration and immigration) as well as other processes (births and deaths). The expected direction of change in
abundance can be difficult to predict, however, because 1) these four processes (birth, death, immigration,
emigration) are operating simultaneously and can be impossible to isolate, and 2) influences of migratory life
history variability. The latter is important because restoration of passage may lead to increased rates of emigration
and lower abundance, or alternatively increases in immigration and increases in density. These effects depend on
the tendency of fish to migrate, which can vary dramatically for many species.
Occupancy modeling is useful for species that show variability in occupancy in relation to passage conditions.
Unlike movement, occupancy can be determined in a single visit. Unlike demography, sampling for occupancy is
much less intensive and expensive. Occupancy does not provide detailed information, but can be an extremely
powerful and cost-effective method for analyzing multiple species and population impacts of passage restoration
and impairment.
Genetic analyses, like occupancy, require only a single site visit for sample collections. Indirect inferences about
individual movement and effective population sizes from genetic markers are widely applied and can provide
insights that are impossible to reveal through studies of individual movement, demography, or occupancy (e.g.,
Neville et al. 2006). Genetic analyses can also detect influences such as cryptic hybridization (Neville et al. 2009)
that other methods cannot detect. Costs of genetic analyses are comparable to other methods, but applications are
limited to species with enough individuals to provide sufficient sample sizes (e.g., 30-50 individuals).
In conclusion, these very brief examples illustrate the complementary nature of each approach to evaluating biotic
responses to passage or connectivity. Each method offers potentially unique insights into understanding biotic
responses, and newer approaches (occupancy and genetics) offer some distinct advantages that can be evaluated in
the study proposed herein. In addition to biotic responses, selected physical variables will also be measured at sites
to be used in evaluation of physical effects of stream crossings as well as for covariates in analyses of species’
responses (Appendix 2).
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Because mark-recapture and genetic analyses are more intensive than other methods (occupancy, demography,
physical habitat) described herein, we will evaluate these responses for a selected subset of species and sites. We
will conduct an evaluation of occupancy, demography, and physical responses at all locations. The species we
chose to study in more detail for mark-recapture and genetics will be determined by management priority, species
prevalence, and expected species abundance – the latter to be determined in part by the database we are assembling.
In general, we would like to more intensively study at least one salmon or trout species that is widespread and
commonly impacted by stream-road crossings. On forests where we have geo-referenced culvert information, for
example, this would be represented by coastal cutthroat trout Oncorhynchus clarkii (e.g., Siuslaw National Forest in
2011) or redband O. mykiss and bull trout Salvelinus confluentus (e.g., John Day River in 2011). We would also
like to select a non-salmonid species, potentially a stream-living amphibian, such as the coastal giant salamander,
Dicamptodon tenebrosus or coastal tailed frog Ascaphus truei, and potentially others (e.g., sculpin or crayfish).
The non-salmonid species will be selected based on their different modes of movement and expected dispersal
abilities. For example, sculpins (Cottus, sp.) are small-bodied species that lack a swim bladder. We would expect
these species to be less likely to pass through culverts than stronger swimmers, such as salmon and trout (LeMoine
2007).
Task 4. Evaluate alternative methods for monitoring effectiveness of aquatic organism passage based on study
results. See appendix 2 for more detailed discussion of alternative methods.
Based on results of our work, we will be able to evaluate the efficacy of the four classes of approaches for
evaluating the responses of biota to passage impairment or restoration. Our evaluation will focus on the questions
posed in the beginning of this proposal relating to individual and population responses of native species, as well as
invasion by nonnative species (Neville et al. 2009; Fausch et al. 2009). Which of these methods provides the best
indication of the degree of passage impairment or restoration and its effects? How are the answers complementary,
or perhaps even contradictory? Which are most useful in terms of practical applications for land management and
regulatory agencies?
Working with the SDTDC physical effectiveness working group and local program managers, we will seek to
correlate physical culvert variables with biotic measures of passage effectiveness. One objective is to determine
what degree of physical similarity to the natural channel is required to reliably create conditions passable by a
broad array of species and life stages. For example, must a streambed with nature-like structure be constructed
inside a culvert? Can simple placement of rock and gravel in culverts pass biota? Another objective is to identify
common characteristics that appear to impede ‘free’ passage. Examples might be uniform, flat channel beds, and
rock weirs without a dip to concentrate low flows into a swimmable notch.
Task 5. Provide annual reports of progress to all collaborators, lead annual working group progress report and
information-sharing meetings, and provide a series of recommendations in a peer-reviewed final report.
Research is an incremental process and we will strive in this work to provide regular, annual updates of progress
that can be used immediately by supporting management agencies. We will work directly with agencies to both
collect and share information on a short timeframe, and to integrate our results with those of other groups working
on monitoring methods development. Most importantly, we will produce interim reports that will be distributed as
different components of the research are completed. Ultimately, we will seek to publish key results in peerreviewed scientific journals to provide agencies with credible supporting scientific information.
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Appendix 1: References
Clarkin, K., A. Connor, M.J. Furniss, B. Gubernick, M. Love, K. Moynan, and S.
Wilson-Musser. 2005. National inventory and assessment procedure – for identifying barriers to aquatic
organism passage at stream-road crossings. USDA Forest Service National Technology and Development
Program, San Dimas, CA.
Condrey M.J. and P. Bentzen. 1998. Characterization of coastal cutthroat trout (Oncorhynchus clarki
clarki) microsatellites and their conservation in other salmonids. Molecular Ecology 7:787-789.
Fausch, K.D., Rieman, B.E., Dunham, J.B., Young, M.K. and Peterson, D.P. 2009. The invasion versus
isolation dilemma: tradeoffs in managing native salmonids with barriers to upstream movement.
Conservation Biology 23:859-870.
GAO (U.S. General Accounting Office). 2001. Restoring fish passage through culverts on Forest
Service and BLM lands in Oregon and Washington could take decades. GAO-02-136: Washington, DC:
U.S. Government Accounting Office. 29 p.
Harris, R.R. 2005. Monitoring the effectiveness of culvert fish passage restoration. Report to California
Department of Fish and Game, Salmon and Steelhead Trout Restoration Account Agreement No.
P0210566. Available online:
http://forestry.berkeley.edu/comp_proj/DFG/Monitoring%20the%20Effectiveness%20of%20Culvert%20
Fish%20Passage%20Restora.pdf
Hedrick P. 2005. A standardized genetic differentiation measure. Evolution 59:1633-1638.
Jones O. and J. Wang. 2009. COLONY: a program for parentage and sibship inferences from multilocus
genotype data. Molecular Ecology Resources 10:551-555.
Jost L. 2008. GST and its relatives do not measure differentiation. Molecular Ecology 17:4015-4026.
Le Moine, M. 2007. Barriers to upstream migration of prickly sculpin Cottus asper and coastrange
sculpin Cottus aleuticus. M.S. Thesis, Western Washington University.
MacKenzie D.I., J. D. Nichols, J. A. Royle, K. H. Pollock, L. L. Bailey, and J. E. Hines. 2006. Occupancy
estimation and modeling. Academic Press, Boston, MA, USA.
Miller M.P., D.W. Blinn, and P. Keim. 2002. Correlations between observed dispersal capabilities and
patterns of genetic differentiation in populations of four aquatic insect species from the Arizona White
Mountains, U.S.A. Freshwater Biology 47:1660-1673.
Morita, K., S. H. Morita, and S. Yamamoto. 2009. Effects of habitat fragmentation by damming on
salmonid fishes: lessons from white-spotted charr in Japan. Ecological Research 24: 711-722.
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Neville, H.N., J.B. Dunham, and M.M. Peacock. 2006. Assessing connectivity in salmonid fishes with
DNA microsatellite markers. Pages 318-342 in K. Crooks and M.A. Sanjayan, editors. Connectivity
conservation: maintaining connections in nature, Cambridge University Press.
Neville H, Dunham J, Rosenberger A, Umek J, Nelson B. 2009. Influences of wildfire, habitat size, and
connectivity on trout in headwater streams revealed by patterns of genetic diversity. Transactions of the
American Fisheries Society 138:1314-1327.
Peterson, D.P., Rieman, B.E., Dunham, J.B., Fausch, K.D., Young, M.K., 2008, Analysis of trade-offs
between threats of invasion by nonnative brook trout (Salvelinus fontinalis) and intentional isolation for
native westslope cutthroat trout (Oncorhynchus clarkii lewisi): Canadian Journal of Fisheries and Aquatic
Sciences 65: 557-573.
Sagar, J.P., Olson, D.H. Schmitz, R.A. 2007. Survival and growth of larval coastal giant salamanders
(Dicamptodon tenebrosus) in streams in the Oregon Coast Range. Copeia. 1: 123-130.
Sanderson, BL, KA Barnas, M Rub. 2009. Non-indigenous species of the Pacific Northwest: an
overlooked risk to endangered salmon? BioScience 59: 245-256.
Spear S.F., J. Baumsteiger, and A. Storfer. 2008. Newly developed polymorphic microsatellite markers
for the frogs of the genus Ascaphus. Molecular Ecology Resources 8:936-938.
Stream-Simulation Group, Forest Service. 2008. Stream Simulation: An Ecological Approach to
Providing Passage for Aquatic Organisms at Road-Stream Crossings. 0877 1801P. San Dimas, CA: U.S.
Department of Agriculture, Forest Service, San Dimas Technology and Development Center.
Wenburg J.K., P. Bentzen, and C.J. Foote. 1998. Microsatellite analysis of genetic population structure in
an endangered salmonid: the coastal cutthroat trout (Oncorhynchus clarki clarki). Molecular Ecology
7:733-749.
Wofford J.E.B., R.E. Gresswell, and M.E. Banks. 2005. Influence of barriers to movement on withinwatershed genetic variation of coastal cutthroat trout. Ecological Applications 15:628-637.
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Appendix 2: Detail on measured responses
Individual movement - Individual movement will be monitored using a mark and recapture approach.
This will be applied to a subset of the most abundant species we encounter. We anticipate these will
include tailed frogs, trout, and sculpins (Cottus, sp.), and signal crayfish (Pacifasticus lenisculus). The
primary motivation behind selection of focal species will be management importance and representation
of species with different dispersal abilities. Individuals captured upstream and downstream of culverts
and reference reaches will be marked with a fin clip (fish), uncured elastomer (a colored non-toxic resin
injected subcutaneously) or tail clip (amphibians and crayfish). When possible we will also use doublemarks to evaluate tag loss in selected sites. Marked individuals will be released to their capture locations.
At a later date, the site will be revisited and marked individuals will be recaptured. Movement will be
indicated by individuals moving from downstream to upstream of culverts or reference sites, or vice-versa.
This protocol is essentially what is being used now on the ground by field personnel for evaluating
aquatic organism passage. We will evaluate this protocol in relation to other methods described herein.
Occupancy – This study is fundamentally concerned with the occurrence of various aquatic organisms in
various patches. The patches are above barrier, below barrier, above restored passage, below restored
passage, and reference patches. We can survey all of these patches and collect data on where the
organisms of interest are detected. The problem is that even exhaustive surveys are not perfect and
organisms will be missed in some patches where they are present. Occupancy models provide a solution
for this problem (MacKenzie et al. 2006). The design of occupancy studies incorporates methods to
estimate the probability of detecting an organism that is present. Occupancy models estimate this
probability of detection and use it to achieve an unbiased estimate of the probability that a patch is
occupied. Moreover, occupancy models allow us to determine the effect of other parameters (like habitat
variables) on the probability of occupancy or on the probability of the change in occupancy (like
colonization of a patch after restoration of the channel). Occupancy studies are relatively un-intensive
and therefore easy to implement at a large number of sites. In the current study, we will, among other
things, use occupancy models to test the hypothesis that the occupancy rate of patches that are upstream
of restored passages are comparable to patches that are downstream of restored passages and barriers.
Demography – Obtaining estimates of a full suite of demographic parameters is outside of the scope of
work for this proposal. As an alternative, we will summarize information representing demographic
variability that can be collected in a single site visit. Depending on the species encountered, this will be
quantified in terms of number of life stages present and relative proportions, or size frequency
distributions. These measures will be compared above and below culverts or reference sites to identify
differences (e.g., paired t-tests, Kolmogorov-Smirnov test for size frequency distributions).
Genetics − Despite perceptions of high mobility, genetic analyses may discern genetic structure patterns
in aquatic organisms, even at small spatial scales (Miller et al. 2002). Culverts and passages within stream
pose the potential for exacerbating these patterns. In this component of the project, microsatellite markers
will be used to identify genetic structure patterns and quantify effects of culverts at each study site. For
each species at each of 50 sites, we will genotype ~50 individuals (split evenly between “upstream” and
“downstream” locations) at 10 microsatellite loci. This project therefore nominally will strive to analyze
2,500 specimens from each focal species. Well-characterized microsatellite markers exist for some of our
potential focal species (i.e., Oncorhynchus clarkii clarkii: Condrey and Bentzen 1998, Wenburg et al.
1998, Wofford et al. 2005; Ascaphus truei: Spear et al. 2008), however, de novo development of an
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appropriate panel of markers may be required for other species examined. In our analyses, differentiation
of “upstream” and “downstream” locations at each site will be quantified using Jost’s D (Jost 2008), a
metric that provides a standardized measure of genetic structure that is not influenced by underlying
genetic diversity levels (Hedrick 2005, Jost 2008). Consequently, we will be able to more rigorously
compare differentiation levels both within and among species when performing statistical analyses.
Furthermore, we will also apply an approach designed to exploit inferences of sibship and parentage using
genetic data. In this case, we will identify putative full sibling groups or parent/offspring relationships at
each site using program COLONY (Jones and Wang 2009). If full siblings or parent-offspring pairs are
found on different sides of a culvert, then evidence will exist suggesting that the structure does not serve
as a barrier to movement for the species in question.
Physical habitat – We will work with hydrologists and geomorphologists currently working with the San
Dimas Technology and Development Center to identify a key set of variables that will quantify physical
responses upstream and downstream of culverts or reference sites (e.g., Harris 2005). We anticipate this
will involve measures to quantify substrate size distributions and basic channel morphologies.
Method
Individual movement
Advantage
Direct assessment of movement of
individuals at stream-road
crossings
Occupancy
Allows estimation of detection and
presence probabilities, and
potentially qualitative estimates of
abundance. Can be applied to a
wide range of species and requires
only a single site visit.
Provides an absolute estimate of
abundance and distribution of size
or age classes at the time of
sampling. Other parameters (e.g.,
survival, recruitment) may be
estimated with additional efforts.
Provides an estimate of individual
movement-related parameters and
population parameters based on a
single collection of tissues for
DNA samples and only a single
site visit.
Demography
Genetics
Limitations
May be difficult to detect due to loss of
marks, timing of recaptures, number of
marked individuals. This leads to a higher
number of “false” negatives. Also requires
a species is abundant enough to provide a
sufficient number of marked individuals.
Therefore applies to a limited number of
species – those that are most abundant.
Movement is not directly observed.
Modeling can be complex.
Abundance is a common response in field
measurements but difficult to interpret
biologically. Estimation of demographic
parameters beyond abundance (e.g.,
survival) can be labor and computationally
intensive.
Applies only to species that occur in great
enough abundance to provide sufficient
sample sizes. Genetic analysis cannot be
conducted by most field personnel.
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