Evaluating the relative effectiveness and cost of contrasting techniques
for determining trout passage over culvert restoration sites
Principal Investigators:
Dr. Helen Neville (Trout Unlimited, Boise, ID, hneville@tu.org)
Dr. Douglas Peterson (US Fish & Wildlife Service, Helena, MT, doug_peterson@fws.gov).
September 15, 2010
Issue and Need:
Thousands of culverts across the western U.S. present passage barriers to inland trout
(e.g., Hendrickson et al. 2008), and as a result the U.S. Forest Service and other agencies
have dedicated a great deal of money towards removing or restoring culverts to allow
passage. Determining whether or not fish are actually passing through restoration sites,
however, is difficult, time-consuming and expensive and in general there is little direct
evidence of fish passage to confirm the effectiveness of these restoration efforts.
Clearly, there is a need to develop effective methods for determining successful passage
of aquatic organisms, not only to demonstrate “biological success” of restoration sites,
but to develop the scientific basis for future decision making and project planning.
Here, we outline a study plan to compare and contrast various techniques for measuring
inland trout movement, with the aim of providing a protocol useful to agency managers
for implementing effective and efficient techniques to determine fish passage on
restoration sites of interest. We capitalize on an on-going study of culvert impacts and
restoration effectiveness in cutthroat trout in Montana, which we describe first before
outlining our current study and plan for additional work.
Ongoing Lolo Creek Project: Background and Study Design
In 2008, the US Fish and Wildlife Service and Trout Unlimited, in collaboration with the
Lolo National Forest, began a research project to evaluate the demographic and genetic
1
response of cutthroat trout to barrier removal in the Lolo Creek watershed in western
Montana (Figure 1). The study uses a combination of presence/absence surveys,
estimates of relative abundance and age/size structure, and population-genetic
sampling to measure the demographic and genetic response of westslope cutthroat
trout to restored connectivity of the stream network. The objective is not simply to
measure if fish pass the improved road crossings, but also to generalize how quickly, and
by which mechanisms trout populations respond to restored connectivity.
The ongoing Lolo Creek study is modeled on a before-after-control-intervention (BACI)
design, where changes (detected as changes in genetic diversity, relative abundance,
size/age composition, occurrence, life history expression) are compared through time
for sites where barriers are removed (intervention or treatment) relative to where they
are not (controls). Control populations can either be populations that are expected to
remain isolated or that are already “connected” and will remain so. Demographic,
occupancy, and genetic sampling was carried out on all sites in 2008 (before culvert
replacement for ‘treatment’ sites) and is scheduled for 2010 (after culvert replacement
for ‘treatment’ sites) and 2012.
The Lolo Creek watershed was selected for this study based on Lolo National Forest
plans to remove or replace numerous culverts that were identified as partial or total
passage barriers. This provided an opportunity to concentrate multiple sample sites
within a single geographic area, and thus control for some confounding variables
(climate, hydrology, fish community) and reduce logistic and cost limitations associated
with having sample locations spread over large areas.
Ongoing Lolo Creek Project: Methods and Sampling 2008
The 2008 field season was dedicated to selecting the specific streams and road crossings
to include in the study, and conducting baseline (pre-barrier removal) demographic and
genetic sampling. Field crews conducted preliminary surveys to determine fish
2
occupancy in 12 tributaries in the upper Lolo Creek drainage, primarily in the East Fork
of Lolo Creek (and its tributaries) and Granite Creek (Figure 1). From this collection of
sites, we selected two “treatment streams” that are unnamed tributaries of East Fork
Lolo Creek and where culverts ranked as “partial barriers” by USFS Region 1 were
scheduled to be replaced with passage-friendly culverts in 2008 (Figure 2). These
streams were selected because the target species (westslope cutthroat trout) occurs
both upstream and downstream of the culvert location. We selected an “isolated
control” in Sally Basin Creek, also tributary to East Fork Lolo Creek, where fish barriers
exist but where no passage projects are planned (Figure 2).
The basic sampling design in each stream involved demographic and genetic sampling
along a longitudinal profile that encompassed identified fish passage barriers. Within
each stream, we selected 6-7 sample reaches above the culvert to be replaced
(‘treatment’ sites) or the lower-most culvert (isolated ‘control’ site). To determine
population structure of westslope cutthroat trout more generally in the connected East
Fork Lolo Creek drainage we conducted occupancy sampling (presence/absence) and
collected tissue from cutthroat trout at three additional locations (two in East Fork Lolo
Creek, one in Lost Park Creek, referred to below as “background populations”).
Collectively, the above samples were representative of the area in East Fork Lolo Creek
occupied by westslope cutthroat trout.
Single and multi-pass backpack electrofishing was used to collect trout species for tissue
samples (genetic analyses); determine occurrence, relative abundance, and size/age
structure; and tag fish (Passive Integrated Transponders or PIT) for subsequent markrecapture to estimate movement directly and measure individual growth between
years. Population genetic analysis of westslope cutthroat trout permits us to contrast
genetic diversity and population structure between connected vs. isolated sites, and
detect changes in the treatment streams that are associated with improved connectivity
For example, we would expect to observe increased genetic diversity within and
3
decreased genetic differentiation among sites after connectivity is restored. Sampling in
treatment streams was conducted in July 2008, prior to replacement of the most
downstream culverts in treatment streams 1 and 2 (see Figure 1).
Ongoing Lolo Creek Project: Brief summary of findings to date
Occupancy surveys conducted in 2008 indicated that native westslope cutthroat trout
and nonnative brook trout were the most common fish species detected at all sites. In
treatment streams, the relative abundance of westslope cutthroat trout generally
decreased with increasing elevation (i.e., as one moved upstream). Brook trout have
apparently not entirely invaded the isolated control stream (Sally Basin Creek; Figure 2).
Multiple fish passage barriers (culverts) are present in treatment and control streams
(Peterson, unpublished data). Thus trout in these streams may be subject to a serial
barrier effect, where migratory fish will encounter multiple partial (or total) barriers to
upstream movement. It has been proposed that the increased fecundity associated
with migratory life histories can contribute to greater population resilience (Rieman and
Dunham 2000; Neville et al. 2006) to environmental and biotic stressors, such as
competition with nonnative brook trout (e.g., Peterson et al. 2008). The decreased
relative abundance of westslope cutthroat trout in the two treatments streams with
increasing distance from the main stem (Figure 2, and and increasing number of
barriers, Peterson, unpublished data) is thus consistent with the hypothesis that
migratory cutthroat trout only infrequently spawn in upstream stream reaches. The
study is thus situated to test whether restoring passage for westslope cutthroat trout
will facilitate biotic resistance to effects of brook trout invasion. If the biotic resistance
hypothesis is correct, then we predict then that the relative abundance of westslope
cutthroat trout in the upstream reaches of treatment streams 1 and 2 will increase
through time as improved connectivity provides passage for the migratory life history.
Genetic analyses indicated significant genetic differentiation, lower genetic diversity,
and smaller effective population sizes in the westslope cutthroat trout populations in
4
the isolated control and two treatment streams relative to other sample locations
within the connected East Fork Lolo Creek drainage (Neville and Peterson, unpublished
data). These data are consistent with an “isolation effect” anticipated for trout
populations fragmented by passage barriers (e.g., Wofford et al. 2005, Neville et al.
2006b). These results illustrate two points relative to management. First, even partial
barriers can significantly limit gene flow in the westslope cutthroat trout populations.
Second, efforts to improve connectivity in the treatment streams is clearly warranted, as
very low effective populations sizes (Ne <50) indicate that westslope cutthroat trout
populations may be at high risk of inbreeding depression.
Ongoing research – expanding the Lolo Creek project to include direct
assessment of movement through culverts
Now that the culverts have been removed in our Lolo creek treatment sites, we are also
evaluating whether resident fish are successfully passing through the replacement
culverts designed for passage by continuing the methods described above that focus on
population-level responses (i.e., characterization of population genetics, occupancy and
demographics). Additionally, we propose to use a capture-mark-recapture-detect
(CMRD) design using state-of-the-art PIT tag technology (Figure 3), and implement a
new genetic “sibship” method for direct evaluation of movement. Our objective is to
develop and implement a hierarchical monitoring design allowing us to partition the
data based on technique, cost, and effort, and determine the information gain relative
to cost and effort. Our primary target species is native westslope cutthroat trout, but
brook trout will be included in all field investigations (occupancy, CMRD, collection of
tissue samples).
A capture-mark-recapture-detect (CMRD) design to measure fish movement past
improved culverts
5
We plan to use a CMRD design to assess fish movement at improved road crossings.
The design involves capturing and marking trout (with PIT tags) above and below the
culvert or road crossing of interest, then using active capture (electrofishing), active
detection (mobile PIT antenna) and passive detection (stationary PIT antennas) to
measure movement of individuals past the road crossing. The proposed design
integrates many of the approaches used to estimate fish passage at road crossings in the
western US and elsewhere (e.g., Coffman 2005; Solcz 2007; Cahoon et al. 2007; Burford
et al. 2009). A strength of this design is that we will be able to compare and contrast
the relative effectiveness, and cost effectiveness, of techniques that collect data at
discrete times across space (electrofishing, mobile antenna) versus one that relies on
continuous data collection at a fixed location (stationary antenna). In practice the
stationary antennas will be operated continuously at each target culvert from spring
through fall, and active recapture and detection events will take place at multiple times
during that same time period. In addition, the active sampling techniques differ in
effort. Three people (one operator, two netters) are typical crew requirements for
electrofishing in small streams; and time allowances must be made to handle and
release capture fish. In contrast, a mobile back pack sized PIT tag antenna can be
operated by a crew of one or two people, and no fish handling is required as the tagged
fish will simply be detected (interrogated by the antenna) without physical capture.
Population-level vs. pedigree (sibship) genetic techniques to measure movement
Genetic data can be useful for monitoring a variety of biological questions, and in many
cases provide information that is difficult or impossible to attain with more traditional
methods (demographic, mark-recapture, telemetry), often at less expense (Neville et al.
2006a, Schwartz et al. 2006). However, while various genetic techniques are possible
for evaluating passage over restored culverts, their relative effectiveness and costs have
yet to be evaluated across differing field scenarios and species. Results from our above
work as well as work on two other western trout species (rainbow trout, Neville et al.
6
2009, as well as Lahontan cutthroat trout, Neville unpublished data), have
demonstrated genetic impacts of culverts using ‘traditional’ population-level genetic
metrics (i.e., heterozygosity, allelic richness, and estimates of effective population size).
By contrasting isolated with non-isolated sites, this collective work shows that
populations above culvert barriers generally have reduced genetic variability and
smaller effective sizes (Ne) than populations in connected habitats (see also Wofford et
al. 2005, Neville et al. 2006b). While the above population genetic metrics characterize
population responses over time, another technique may also be effective in actually
measuring movement directly. Hudy et al (2010) recently used genetic sibship analysis
and family reconstruction to characterize movement of young-of-year (yoy) brook charr,
and the authors of this study first realized the potential application of sibship analyses
for addressing culvert passage (Ben Letcher, personal communication). The idea behind
this approach is that finding siblings (as determined by genetic ‘fingerprinting’ and
pedigree analysis) on both sides of a restored culvert indicates movement of yoy across
the site; the direction of movement is inferred by ‘majority rule’, where it is assumed
the family originated on the side of the culvert where the most siblings were captured.
Initial simulations demonstrate that sibship analyses may have greater power than
individual assignment-based methods (see below: Request for Further Funding) to
capture movement (Ben Letcher, personal communication), and similarly this method is
also likely to have greater power than the traditional population-based evaluations (e.g.,
using heterozygosity, Ne, differentiation) used in our previous work.
However, while the sibship approach offers great promise for evaluating immediate
movement over culverts in some areas and with some species, it may not be logistically
feasible or as powerful in certain scenarios we have faced in our study regions (USFS
Regions 1 and 4, see Figure 4). For instance, the sib-ship approach would be logistically
impossible in the an on-going study of Lahontan cutthroat trout (Neville, unpublished
data) , where culvert sites are at the confluence with the main stem river and the lower
reaches of tributaries are dry the majority of the year, making sampling for siblings at
7
the culvert sites physically impossible. In this system, movement through restored
culvert sites and among tributaries likely occurs through larger individuals migrating
when high flows seasonally connect the tributaries to the mainstem river. Similarly, in
the rainbow trout study area (Neville et al. 2009), sib-ship analyses would not be
possible because in the steep mountainous terrain of Idaho roads typically follow river
channels, and thus culverts are at the tributary confluence with large mainstem rivers.
In such instances, sampling yoy below the culvert would be impossible because suitable
spawning habitat is minimal and habitat is too large to sample effectively for yoy in the
mainstem river.
Furthermore, there may be important differences in the spawning and movement
behavior between trout species (and other fishes/organisms) that affect the power of
sibship analyses. For instance brook trout, the focus of the Hudy et al (2010) study,
spawn in the fall and it was feasible for the authors to sample them 4 months postemergence. In their study yoy were still ‘highly clumped’ at this time, yet the mean
dispersal distance was over 50 meters in the tributary and 100m in the ‘mainstem’ river
(assumedly a 2nd order stream). Cutthroat trout spawn in the early to late summer
depending on the local thermal and hydrologic regimes, and for logistical reasons we
can only sample cutthroat trout at low flows during the late summer and early fall,
when yoy have already emerged and are large enough to be safely captured by
electrofishing. As a result of the timing of sampling for yoy cutthroat trout, it is unlikely
that dispersal distances will be as large in our study, which may affect the power of
sibship analyses for addressing culvert passage. In some sense, assuming cutthroat
trout yoy disperse a minimum distance large enough to span a culvert site, the greater
family clumping expected at sampling in our system may actually increase the power to
detect movement by increasing the proportion of siblings per family we capture at the
culvert site. It may also reduce the spatial extent around the culvert we would need to
sample for reconstructing families and detecting movement. At the same time, we may
8
have decreased power to use this approach if siblings do not disperse far enough to
cross the culvert site by the time we sample.
Work plans for funded work 2010-2012
Fieldwork 2010:
Field work in 2010 will focus on three tasks (Table 2). First, we will conduct
demographic and population-level genetic sampling of trout populations in the primary
study streams (treatments and controls) and 5 “background sites” in the Lolo Creek
drainage (the original 3 mentioned above, plus 2 additional sites added in 2010, see
Figure 2). Genetic samples from the background sites will not be analyzed under the
current study, but will be collected to enable individual genetic assignment tests
pending further funding (see below: Request for Further Funding.) Second, we will
investigate the efficacy of different stationary antenna designs; estimate detection
efficiencies with stationary PIT antennas and mobile PIT antennas; and estimate capture
efficiency by electrofishing (see Figure 3). Preliminary investigations of the PIT tag
antennas will focus on one of the Lolo Creek treatment sites, and electrofishing capture
efficiency estimates will be made in five different streams in the Lolo Creek drainage.
These data will be used to estimate statistical power to detect passage based on
numbers of marked fish. Third, we will implement a new field protocol in the two
treatment streams to sample yoy to allow for sibship analyses of movement across the
restoration sites (Figure 5). For population-level evaluation of genetic characteristics, it
is typically advised to avoid sampling yoy which may represent spatial clusters of siblings
and thus over-represent families and bias estimates of genetic parameters in the
‘population’ (Hansen et al. 1997). For sibship analyses, in contrast, we obviously want
to sample yoy and our sampling needs to straddle the culvert directly (Figure 5).
Furthermore, an important consideration in developing sampling protocols for sibship
analysis is the spatial extent of sampling and the number of fish in a collection required
above and below the culvert. To evaluate the minimum sampling intensity required, we
9
propose to target sampling 300 m upstream and downstream of the replaced culverts
and stratify collections by distance from the culvert (e.g., 100m vs. 200m vs. 300m; see
Figure 5) to facilitate statistical power analyses based on samples collected within each
stratum vs all strata.
Analyses 2010:
In the fall and winter of 2010, preliminary data will be used to estimate statistical power
to detect passage based on numbers of marked fish (Tables 1 and 2). We will also
conduct preliminary power and sample size estimation for the sibship analysis using the
existing (2008) population- and individual-level genetic data for westslope cutthroat
trout in the Lolo Creek sites (Tables 1 and 2). Sampling design considerations and the
statistical power of the sibship method to estimate passage also depend on the life
history of target species and its influence on the spatial distribution of related
individuals, as well as general levels of genetic diversity within and among individuals at
a given location. While these considerations have been more thoroughly addressed for
brook trout by a collaborating group (J. Coombs, M. Hudy, B. Letcher, K. Nislow) that
work primary in USFS Region 9 (Figure 4), they have not yet been considered for
cutthroat trout.
We will also produce an interim project report for the Lolo Creek study that summarizes
the demographic and population-level genetic data collected during 2008-2010.
Fieldwork 2011:
In the current study, we plan to use the lessons learned in 2010 to design and
implement the hierarchical monitoring design beginning in spring 2011 (Table 2). First,
our current funding allows for implementing the CMRD at total of four sites where
culverts have been removed or replaced. Two of these sites will be our two treatment
streams in the Lolo Creek drainage (Figure 2) plus two additional sites to be determined,
10
either in the Lolo NF or elsewhere in USFS Region 1 (Figure 4). The treatments in Lolo
Creek involve replacement by a full culvert. The additional sites can either serve as a
replicate for cutthroat trout (target species) within the same road crossing type (full
culvert) placed in the Lolo Creek drainage or elsewhere, or could also replicate a
different crossing improvement type (bottomless arch, rock weir). We will coordinate
with Lolo NF and USFS Region 1 on the disposition and location of the two additional
RMRD sites.
Second, we will collect additional sib-ship genetic samples of yoy trout in our two Lolo
Creek treatment streams for a temporal analysis of movement based on sibship (Table
1), pending additional funding.
Analyses 2011-12:
Activities during fall 2011-spring 2012 include data collection associated with genetic
assays (sibship genotyping); data compilation, synthesis, and analyses (CMRD, sibship,
population genetic); and preparation of the final project report (Table 2).
Application of findings from the ongoing study
The ongoing study will evaluates whether restoring connectivity (by replacing barriers at
road crossings) actually leads to expression of desirable population attributes (e.g., life
history and genetic diversity, balanced population structure) expected to facilitate
persistence of westslope cutthroat trout, a native fish of conservation concern in
western North America. Our study is also designed to compare and contrast the cost
and effectiveness of various demographic, mark-recapture, and genetic techniques to
assess the individual and population-level metrics of trout passage at improved road
crossings. Based on this information, we will develop a sampling protocol that biologists
can use to evaluate passage at road crossings of interest.
11
By synthesizing these two datasets (direct movement vs. population responses), we can
also make inference as to whether detection of movement of individuals always
correlates to the population-level response.
Request for Further Funding for Genetics Component:
We propose additional genetic analyses to extend the application of our findings more
broadly for WCT and other species. Funding to collect additional genetic data will allow
1) a spatially broader assessment (including 4 additional sites) of the effectiveness of
sibship analyses for capturing movement, 2) a temporal evaluation of the sibship
method (i.e., characterization of differences in movement across years 2010 and 2011 in
our treatment sites), and 3) a comparative evaluation of the effectiveness of population
genetic approaches, sib-ship analyses, and individual assignment tests (see below) for
demonstrating movement after culvert restoration.
Further funding would allow us to perform sibship analyses at the 2 additional
westslope cutthroat trout streams mentioned above (i.e., the two additional CMRD
sites), as well as 2 other streams in Region 4 housing another species of trout
(Bonneville or Yellowstone cutthroat trout, or redband trout, to be determined) (Table
1; Figure 4). For both sets of streams (= 4 additional tributaries) we will execute both
population-level and sib-ship analyses as described above. Evaluating and contrasting
genetic methods over 6 total sites will enable more confidence in our findings in general
and a more thorough evaluation, in particular, of the sampling scheme necessary to
successfully implement sibship analyses in different environments and in 2 different
species. Further-more, we request funding to analyze the samples collected in 2010
(under our current funding, see Table 1, part A) from the 5 “background” Lolo Creek
samples (Figure 2), to enable evaluation of a third genetic technique in our two
treatment streams. Individual-based genetic ‘assignment tests’ may be used to follow
direct movement of individuals (Manel et al. 2003), and are proving promising for
evaluating movement of Lahontan cutthroat trout across 3 culvert restoration sites
12
(Neville, unpublished data, to be used as a third sub-species comparison in this study,
see Table 1). In this method, individual fish are probabilistically assigned to the most
likely population of origin from a set of sampled populations, and movement is evident
if an individual is assigned to a population different from where it was captured.
Implementation of the approach requires sampling of all or most of the potential source
populations for the individuals being evaluated (Manel et al. 2005), and thus having
genetic data from these adjacent background sites would improve the accuracy of these
analyses.
Benefit and application of additional proposed work
Implementing the full study design proposed above would provide significant insight on
the comparative utility and cost effectiveness of various genetic techniques for
determining fish passage over restored culvert sites. Genetic data can be useful for
addressing various questions of ecological, evolutionary and conservation interest, and
in some cases can offer greater power and cost-effectiveness than traditional field
methods (e.g., census or mark-recapture) (Schwartz et al. 2006). Yet to our knowledge,
there has been no study contrasting the effectiveness of different genetic techniques for
tracking movement over restored culverts (although collaborators are proposing
concurrent studies under this body of funding in different regions of the country). Our
study design is particularly powerful because we evaluate these techniques across
multiple culverts (and potentially 2 types of restoration sites), across species, and in the
context of comprehensive CMRD analyses that will provide documentation of direct
movement via an independent technique. Collectively, this information will be used to
guide managers faced with documenting the success of culvert replacements across
expansive landscapes as to the most effective and cost-efficient techniques for
determining fish passage.
13
References
Burford, D.D, T.E. McMahon, J.E. Cahoon, and M. Blank. 2009. Assessment of trout
passage through culverts in a large Montana drainage during summer low flow.
North American Journal of Fisheries Management 29:739-752.
Cahoon, J.E., T. McMahon, A. Solcz, M. Blank, and O. Stein,. 2007. Fish passage in
Montana culverts: phase II – passage goals. FHWA/MT-07-010/8181. Montana
State University, Bozeman. 64 pp.
Coffman, J.S. 2005. Evaluation of a predictive model for upstream fish passage through
culverts. MS thesis, James Madison University, Harrisonburg, VA. 111 pp.
Hansen, M. M., E. E. Nielsen, and K.-L. D. Mensberg. 1997. The problem of sampling
families rather than populations: relatedness among individuals in samples of
juvenile brown trout Salmo trutta L. Molecular Ecology 6:469-474.
Hudy, M., J. A. Coombs, K. H. Nislow, and B. H. Letcher. 2010. Dispersal and withinstream spatial population structure of brook trout revealed by pedigree
reconstruction analysis. Transactions of the American Fisheries Society.
Manel, S., O. E. Gaggiotti, and R. S. Waples. 2005. Assignment methods: matching
biological questions with appropriate techniques. Trends in Ecology and
Evolution 20:136-142.
Manel, S., M. K. Schwartz, G. Luikart, and P. Taberlet. 2003. Landscape genetics:
combining landscape ecology and population genetics. Trends in Ecology &
Evolution 18:189-197.
Neville, H., J. Dunham, and M. Peacock. 2006a. Assessing connectivity in salmonid
fishes with DNA microsatellite markers. Pages 318-342 in K. Crooks and M. A.
Sanjayan, editors. Connectivity Conservation. Cambridge University Press,
Cambridge.
Neville, H., J. Dunham, A. Rosenberger, J. Umek, and B. Nelson. 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.
Neville, H. M., J. B. Dunham, and M. M. Peacock. 2006b. Landscape attributes and life
history variability shape genetic structure of trout populations in a stream
network. Landscape Ecology 21:901-916.
Schwartz, M. K., G. Luikart, and R. S. Waples. 2006. Genetic monitoring as a promising
tool for conservation and management. Trends in Ecology & Evolution 22:25-33.
Solcz, A. 2007. Assessment of culvert passage of Yellowstone cutthroat trout in a
Yellowstone River spawning tributary using a passive integrated transponder
system. Master’s thesis. Montana State University, Bozeman.
Wofford, J. E. B., R. E. Gresswell, and M. A. Banks. 2005. Influence of barriers to
movement on within-watershed genetic variation of coastal cutthroat trout.
Ecological Applications 15:628-637.
14
Table 1. Summary of research questions addressed by ongoing and proposed study.
Category
Research question addressed
General population
response
Long-term population response of trout to restored connectivity
(before-after design) in westslope cutthroat trout and Lahontan
cutthroat trout
Relative effectiveness of different demographic (occupancy, population
size, age distribution) and capture-mark-recapture-detection (CMRD)
methods
(a) Relative effectiveness of different genetic assessment methods
(population vs. individual assignment vs. sibship) to detect fish passage
(at a site)
Non-genetic
methods
Genetic methods
Temporal sensitivity
of genetic methods
Genetic vs. nongenetic methods
Sites (sample size, # streams or
crossings)
Lolo Creek (3)
Maggie Creek (Lahontan) (3)a
Lolo Creek (2), Region 1 (2)
(a) Lolo Creek (2), Region 1 (2),
Region 4 (2)
(b) Lolo Creek (2), Region 1 (2),
Region 4 (2), Maggie Creek
(Lahontan) (3) a
(a) Lolo Creek (2)
(b) Relative effectiveness of different genetic assessment methods
among species (westslope vs. lahontan vs. to bd determined)
(a) Consistency of sibship analysis to detect passage in consecutive
years (post treatment)
(b) Consistency of individual-based assignment tests to detect passage
(b) Maggie Creek (Lahontan) (3)a
in alternate years (post treatment)
Cost-effectiveness of genetic methods (sibship) vs. capture-markLolo Creek (2), Region 1 (2)
recapture-detect (CMRD) methods to directly assess movement through
improved crossings b
a
Maggie Creek Lahontan cutthroat trout project funded through a separate (non-FS) grant to Trout Unlimited. Only population
genetics and individual assignment tests being analyzed in this study.
b
There is the option to contrast by location, species, or crossing type depending on choice of Region 1 site. We will confer with the
Region 1 fish program manager and the Lolo NF about the selection of these sites.
15
Table 2. Timeline and lead coordinator for (A) currently funded tasks and (B) additional tasks proposed in this funding request.
Existing or proposed sample sites are located in the Lolo Creek drainage in western Montana (Lolo), USFS Northern Region 1 (R1), or
USFS Intermountain Region (R4). The Lolo Creek sites are in R1.
16
Figure 1. Location of Lolo Creek drainage (272.4 mi2 drainage area), tributary to the Bitterroot
River (2,855 mi2) in western Montana. The Bitterroot River flows from south to north, and Lolo
Creek flows generally from west to east. Culverts scheduled for replacement in 2008-09 by
USFS contractors are also noted. The primary study area is in the East Fork Lolo Creek.
17
Figure 2. Schematic of East Fork Lolo Creek drainage (31.9 mi2) showing the location of
replaced culverts and fish sampling sites included in the Lolo Creek fish passage monitoring and
evaluation study. The primary study streams two unnamed tributaries (Treatment 1 and
Treatment 2) where the most downstream culverts were replaced in 2008 with the intent of
providing aquatic organism passage; and Sally Basin Creek which is considered a ‘control’
stream because the culvert near its mouth has not been replaced. These three primary study
streams have multiple sample locations (yellow circles) to characterize the demography and
genetics of those populations (see yellow symbols). Sample locations directly above existing
and replaced culverts in the three primary study streams are obscured by the culvert symbols in
this schematic. Five additional sample sites (filled black circles) in East Fork Lolo Creek and Lost
Park Creek are locations where at large or ‘background’ samples of westslope cutthroat trout
were taken to determine population structure in the drainage and characterize the putative
sources of colonists to the reconnected tributaries, and permit individual-level genetic analysis
of post-treatment dispersal.
18
Non-genetic methods for detecting passage at
individual culverts
Culvert
“false”
culvert
12
Mark & “recapture”
Zone A
Mark
“Recapture” methods:
1. ACTIVE: Recapture by electrofishing
2. ACTIVE: Detection by mobile antenna
3. PASSIVE: Detection by stationary antennas
1. e-fish
2. Mobile antenna
34
Stationary
PIT antennas
flow
Mark & “recapture”
Zone B
Cost
1. Equipment & supplies
2. Labor and travel
3. Stationary antennas
12
34
Marking methods
1. Batch: finclip or elastomer
2. Individual: 13-mm PIT tags
Figure 3. Schematic of hierarchical capture-mark-recapture-detect (CMRD) design to
measure movement past individual culverts using both active capture and active and
passive detection. The objective will be to determine the most efficient technique for
measuring passage, in terms of information gain relative to cost/effort. For example,
the approach will be to assess whether simple mark-recapture of marked fish vs.
multiple stationary antennas on either side of the culvert vs. a single antenna placed
above the culvert is the most efficient technique.
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Figure 4. US Forest Service (USFS) regional administrative boundaries. The ongoing and
proposed work focuses on sites in R1 and R4. (map from:
www.fs.fed.us/contactus/regions.shtml)
20
Sibship sampling by strata
Culvert
B3
B2
B1
A3
A1
A2
flow
300m
BELOW CULVERT
300m
ABOVE CULVERT
Figure 5. Schematic of initial sampling design for applying sibship analyses to detect
movement of cutthroat trout past improved culverts in small streams. We plan to
sample up to 100 young of the year (yoy) both above and below the target culvert
during late summer-early fall at two streams in the Lolo Creek drainage. Spawning and
movement behavior and subsequent dispersal of yoy trout will affect the power of
sibship analysis to assess passage, thus we need to determine the spatial extent of
sampling relative to culvert location (how far above and below the culvert) needed to
apply sibship analysis given the genetic diversity in the target populations.
Consequently, we propose to divide sampling into three 100m reaches within strata
above (A1-A3) and below (B1-B3) the culvert. Additional samples will be collected for
traditional population-level analyses upstream from the sibship sampling strata.
21