Blackwell Science, Ltd Fragmentation of riverine systems: the

Molecular Ecology (2001)

10

, 1153–1164

© 2001 Blackwell Science Ltd

Blackwell Science, Ltd

Fragmentation of riverine systems: the genetic effects of dams on bull trout (

Salvelinus confluentus

) in the Clark Fork River system

LUKAS P. NERAAS and PAUL SPRUELL

Wild Trout and Salmon Genetics Laboratory, Division of Biological Sciences, University of Montana, Missoula, MT 59812

Abstract

Migratory bull trout (


) historically spawned in tributaries of theClark Fork River, Montana and inhabited Lake Pend Oreille as subadult and adult fish.However, in 1952 Cabinet Gorge Dam was constructed without fish passage facilities dis-rupting the connectivity of this system. Since the construction of this dam, bull trout popu-lations in upstream tributaries have been in decline. Each year adult bull trout return tothe base of Cabinet Gorge Dam when most migratory bull trout begin their spawningmigration. However, the origin of these fish is uncertain. We used eight microsatellite locito compare bull trout collected at the base of Cabinet Gorge Dam to fish sampled from bothabove and further downstream from the dam. Our data indicate that Cabinet Gorge bulltrout are most likely individuals that hatched in above-dam tributaries, reared in Lake PendOreille, and could not return to their natal tributaries to spawn. This suggests that the riskof outbreeding depression associated with passing adults over dams in the Clark Fork sys-tem is minimal compared to the potential genetic and demographic benefits to populationslocated above the dams.

Keywords

: bull trout, fish passage, hydroelectric dams, migration, microsatellite,

Salvelinus

Received 18 August 2000; revision received 8 December 2000; accepted 8 December 2000

Introduction

Habitat fragmentation may take dramatically different formsin terrestrial and riverine habitats. Fragmentation ofterrestrial habitats is usually associated with alterationin large tracts of land, precluding migration amongthe remaining patches of suitable habitat. In riverine sys-tems, hydroelectric dams and irrigation diversions maycause fragmentation at specific points along the streamcorridor.

The effects that dams may have on fish species have beendocumented throughout the world. The described popu-lation declines are primarily due to the change from ariverine to a lacustrine environment and the isolation ofmigratory fishes from their spawning and feeding grounds(for example, Barthem

et al

. 1991; Wei

et al

. 1997; Ruban1997). These disruptions may cause local extinction if crit-ical habitats are lost or no longer accessible.

There are many examples of the extirpation of ana-dromous Pacific Salmon stocks that are unable to reachtheir spawning grounds after the construction of impas-sable dams (National Resource Council 1996; Nehlsen

et al

. 1991). However, relatively little work has exploredthe changes in the genetic population structure of fishescaused by dams. The available data suggest that frag-mentation associated with dams has caused a loss ofgenetic variation in anadromous steelhead isolated aboveimpoundments (Nielsen

et al

. 1997).Hydroelectric dams may also impact nonanadromous

fishes. Some inland fish populations exhibit both residentand migratory life histories. Resident fish complete theirlifecycle within small streams, while migratory individualsspawn in smaller streams but use larger bodies of water assubadults and adults. Movement between habitats is crit-ical for the expression of all life histories within a popu-lation. If different life histories buffer a population againstlocal extinction, the elimination of a life history type willincrease the chance of extirpation. Additionally, habitatfragmentation can preclude migration between populations

Correspondence: Paul Spruell. Fax: (406) 243 4184; E-mail:[email protected]

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, 10, 1153–1164

within a metapopulation, further increasing the chance ofextirpation.

Bull trout (


) are listed as threatenedunder the U.S. Endangered Species Act throughout thenorth-west United States (Federal Register 1999). Onefactor leading to this decline is habitat fragmentation dueto hydroelectric impoundments (Rieman & McIntyre 1993).

Lake Pend Oreille, Idaho (Fig. 1) supports one of thelargest remaining bull trout metapopulations in the UnitedStates (Pratt & Huston 1993). However, bull trout werehistorically much more abundant in the system (Pratt &Huston 1993). Bull trout from many different populationscontinue to use the lake as rearing and over-wintering hab-itat. Prior to the construction of dams on the Clark Forkriver, large numbers of adfluvial bull trout that hatched intributaries of the Clark Fork River migrated freely to LakePend Oreille as subadults and adults before returning totheir natal streams to spawn (Pratt & Huston 1993; Fig. 1).

Within the last 90 years, a series of three hydroelectricdevelopments were constructed in the lower Clark Fork

River (Fig. 1). The first, Thompson Falls Dam, was built in1913 near the town of Thompson Falls, Montana. In 1952,Cabinet Gorge Dam was constructed 10 km upstream fromthe mouth of the Clark Fork River. Six years later, in 1958,Noxon Rapids Dam was built 29 km upstream fromCabinet Gorge Dam. None of these hydroelectricdevelopments have facilities for fish passage.

One year after the closure of Cabinet Gorge DamJeppson (1954) reported seeing ‘large numbers of bulltrout’ in the Clark Fork River below the dam, but no reddswere observed. In 1961, the Idaho Department of Fish andGame created a spawning channel just downstream of thedam in an attempt to mitigate the loss of upstream spawninghabitat. Biologists surveyed this site in the mid 1960s andreported seeing 200–400 bull trout near the spawningchannel (Pratt & Huston 1993). In subsequent surveysfrom 1984 to 1991, biologists saw bull trout but failed toobserve any redds below Cabinet Gorge Dam (Pratt &Huston 1993). Overall it appears that the lower Clark ForkRiver dams have reduced the number of bull trout in

Fig. 1 Approximate sample sites of bulltrout from the lower Clark Fork River andLake Pend Oreille. Numbers correspond tolocation descriptions in Table 1. White circlesindicate locations below Cabinet Gorge Dam,black circles are locations above the dam,and the diamond is the sample collected atthe base of the dam.


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this system. Apparently, the construction of the spawningchannel did not adequately compensate for the lossescaused by the disruption of the migratory corridor.

Large adult bull trout continue to congregate near thespillway of Cabinet Gorge Dam from the end of peak flowto early autumn when most migratory bull trout begintheir spawning movements. The origin of those fish isuncertain but four hypotheses are likely. First, bull troutmay have historically spawned in the mainstem of theClark Fork River and have continued to persist there afterthe construction of the dam. Second, bull trout that hatchedin tributaries to Lake Pend Oreille could have establisheda population below the dam after its construction. Third,the bull trout that return to Cabinet Gorge Dam may beremnants of individuals from upstream populations thatbecame isolated in 1952 after the closure of the dam.Finally, bull trout that congregate at the base of CabinetGorge Dam may be migratory fish that hatched in tributar-ies above the dam and continue to pass downstream overthe dam during annual outmigrations and are unable toreturn to their natal streams to spawn.

Movements of tagged bull trout indicate that some indi-viduals pass downstream over dams. Eight per cent of aradio tagged sample of migratory bull trout that originatedin the Blackfoot River, MT, swam downstream over Mill-town Dam (Swanberg 1997). Similarly, 18% of bull trouttagged in the Boise River system passed downstream overArrowrock Dam (Flatter 1998). The proportion of out-migrating juveniles that suffer a similar fate is currentlyunknown. However, these data suggest that hydroelectricimpoundments can cause geographical and genetic isola-tion of migratory fish from their natal tributaries.

The metapopulation dynamics and genetic populationstructure of bull trout in Lake Pend Oreille have beenextensively explored and described by, Rieman & McIntyre(1993), Pratt & Huston (1993), Rieman & Dunham (2000),and Spruell

et al

. (1999). These descriptions suggest thatmetapopulation dynamics and alternate life history formsmay buffer bull trout populations from local extinctionevents. This suggests that actions aiding movement withinthe system may begin to reverse the decline of these frag-mented bull trout populations.

Our objective was to determine the origin of adult bulltrout that return to the base of Cabinet Gorge Dam. Weused eight microsatellite loci to estimate the amount ofconnectivity, or gene flow, between populations within thebasin. We also used these data to establish a baselinegenetic data set representative of populations in the sys-tem. Using these data, we estimated the probable origin ofthe adult bull trout that return to the base of Cabinet GorgeDam. Finally, we consider the genetic risks associated withthe transport of fish over dams throughout the LowerClark Fork River vs. risks associated with maintaining theexisting migration barriers in the system.

Methods

Study location and individual collection

Bull trout were collected from 10 tributaries of Lake PendOreille and eight tributaries to the Lower Clark Fork River(Fig. 1, Table 1). Fish were captured using block nets, fishweirs, or electrofishing techniques while they were holdingin tributaries prior to spawning. These individuals shouldbe representative of the spawning aggregates in eachtributary. Adult bull trout returning to the base of CabinetGorge Dam were collected in 1997, 1998, and 1999 either ina fish trap at the nearby Cabinet Gorge Hatchery or byboat-based electrofishing. A nonlethal fin clip was takenfrom each individual and stored in 95% ethanol. DNA wasextracted from fin tissue with a Purgene kit (Gentra).

Identification of hybrids

Individuals from populations in which hybridization withnon-native brook trout (

Salvelinus fontinalis

) was suspectedwere screened using PINE-PCR (Spruell

et al

., unpublisheddata). Three hybrids were eliminated from the original 17individuals collected in Swamp Creek (15). Ten of the 33Twin Creek (11) individuals were also removed from thesample due to hybridization. Of the hybrid individuals, asingle individual from Twin Creek (11) was identified as alater generation hybrid. All remaining hybrids were firstgeneration (F

1

). It does not appear that there is continualintrogression between species in these populations. There-fore, the remaining individuals from Swamp Creek (15)and Twin Creek (11) are probably not hybrids and wereincluded in subsequent analyses.

Microsatellite amplification and analysis

We amplified eight microsatellite loci in an MJ ResearchPTC-100 thermocycler using profiles described by initialinvestigators of each locus (

ONE

µ

7

, Scribner

et al

. 1996;

SFO18

, Angers

et al

. 1995;

FGT3

, Sakamoto

et al

. 1994;

SCO19

, E.B. Taylor, personal communication;

OGO2

, Olsen

et al

. 1998;

SSA311

and

SSA456

, Slettan

et al

. 1995;

OTS101

,Small

et al

. 1998). The amplified alleles were separated ona 7% denaturing polyacrylamide gel and visualized usinga Hitachi FMBIO-100 fluorescent imager. Allele sizes weredetermined relative to a standard base pair size ladder(MapMarkerLow, Bioventures). Previously amplified prod-ucts were included on each gel to ensure consistent scoringof individuals across all gels (Spruell

et al

. 1999).

Data analysis

We used

genepop

to calculate heterozygosity values(

H

S

), allele frequencies,

F

ST

, and deviations from Hardy–


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Molecular Ecology

, 10, 1153–1164

Weinberg expectations (Raymond & Rousset 1995). Weused a Cavalli-Sforza and Edwards chord distance (CSE) toestimate the genetic similarity among populations (Cavalli-Sforza & Edwards 1967). A

upgma

dendrogram was gener-ated using

phylip

(Felsenstein 1993). This dendrogramallowed us to visualize the genetic similarity among sampleswithin the system.

To estimate the probable origins of Cabinet Gorge bulltrout we used Paetkau’s online calculator to conduct an‘assignment test’. This test determines the most probableorigin of each individual based on the expected genotypicfrequencies of each sample (Paetkau

et al

. 1997).

Results

Variation within sample sites

The amount of variation detected in these samples wassimilar to earlier microsatellite studies in this system(Spruell

et al

. 1999). All eight of the loci analysed werepolymorphic in at least one sample site (Appendix I). Aftercorrecting for multiple tests (Rice 1989), we found nodeviations from Hardy–Weinberg proportions in any of thesamples analysed. Expected heterozygosity averaged 0.362and ranged from 0.269 to 0.473 (Table 1). The number ofalleles per sample ranged from 16 to 24 and averaged 20.5(Table 1).

In four sites (2, 13, 18, and 19), individuals were collectedin two consecutive years. After combining probabilities

across all loci (Sokal & Rohlf 1995), we found no statistic-ally significant differences in genotypic frequencies betweentemporal samples within any of the four sites. Therefore,we pooled the temporal samples from each site in all sub-sequent analyses. The samples collected at the base ofCabinet Gorge dam in 1997 (12a), 1998 (12b), and 1999 (12c)were not pooled since we cannot assume they represent asingle spawning population.

Differentiation among samples

Differences in allele frequencies suggest that there is sub-stantial genetic differentiation among populations (

F

ST

= 0.137).A

upgma

dendrogram based on CSE chord distance wasused to visualize the relative genetic similarity amongsamples (Fig. 2).

The dendrogram (Fig. 2) suggests that there is substan-tial differentiation between samples collected in tributariesto Lake Pend Oreille and those collected in lower ClarkFork River tributaries. Swamp Creek (15) exists as an out-lier (Fig. 2) due to its high frequency of a normally rareallele at the

SFO18

locus, and a low frequency of a normallycommon allele at the

FGT3

locus (Appendix I).In all samples from Lake Pend Oreille tributaries, pro-

portionally more individuals were assigned to their popu-lation of origin than to any other site (Table 2). This is alsotrue for seven of the eight lower Clark Fork River samples.However, two samples with high heterozygosities (Table 1),the East Fork Bull River (13) and Gold Creek (4) are exceptions

Population number

Sample location Number

Expected heterozygoisty

Number of alleles

Below Dam1 Grouse Creek 40 0.335 192 Trestle Creek* 105 0.340 233 Granite Creek 35 0.355 204 Gold Creek 47 0.394 215 Morris Creek 22 0.288 166 Savage Creek 41 0.364 197 East Fork Lightning Creek 81 0.386 238 Porcupine Creek 40 0.297 209 Rattle Creek 19 0.285 2010 upper Lightning Creek 24 0.342 2011 Twin Creek 23 0.386 19

Dam12a Cabinet Gorge Dam 1997 15 0.472 2212b Cabinet Gorge Dam 1998 28 0.431 2312c Cabinet Gorge Dam 1999 25 0.388 21

Above Dam13 East Fork Bull River* 60 0.397 2414 Rock Creek 30 0.383 2315 Swamp Creek 14 0.316 1916 Graves Creek 30 0.399 1817 Prospect Creek 30 0.413 2018 Thompson River* 43 0.269 1819 Fishtrap Creek* 57 0.366 23

Table 1 Sample sites, number, expected heter-ozygosity and average number of alleles perlocus for bull trout collected from tributariesto the lower Clark Fork River and Lake PendOreille. Population numbers correspond tosample sites indicated in Fig. 1. The asterisk (*)indicates sites at which samples were collectedin multiple years


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to this observation. Individuals from these two samplesare not preferentially assigned to any site. Rather, they aredistributed throughout the system.

Individuals that did not get assigned back to their ori-ginal collection were not assigned at random. Individualsfrom below-dam sites that were not assigned back to theiroriginal sample site are most frequently assigned toanother below-dam site. Similarly, individuals from above-dam sites that were not assigned back to their originalsample site are most frequently assigned to another above-dam site. Table 2 separates above-dam and below-damsites into quadrants, where this observation is mostapparent (Table 2).

Cabinet Gorge Dam samples

The samples collected at Cabinet Gorge Dam in 1997 (12a),1998 (12b), and 1999 (12c) do not cluster together on thedendrogram. These results are unexpected for temporalsamples collected from a single isolated bull trout popu-lation (Spruell

et al

. 1999). The Cabinet Gorge samples aredispersed with the lower Clark Fork River samples (Fig. 2).This suggests that bull trout sampled from the base ofCabinet Gorge Dam (12a, 12b, 12c) are more geneticallysimilar to samples collected from tributaries located abovethe dam.

The results of the assignment test also support the gen-etic similarity of Cabinet Gorge samples with those fromabove-dam tributaries. The Cabinet Gorge Dam samples(12a, 12b, 12c) did not proportionally have more individualsassigned back to their sample origin (Table 2). The 1998(12b) and 1999 (12c) Cabinet Gorge Dam samples had moreindividuals assigned to the above dam sites (Table 2). The1997 (12a) Cabinet Gorge Dam sample had 56% of thesample assigned to below dam sites (Table 2). However,these results may be due to a small sample size (Table 1).

Discussion

Relationships among sample sites

The microsatellite data suggest substantial genetic differen-tiation among samples collected from spawning aggregatesabove and below Cabinet Gorge Dam. This differentiationis based primarily on differences in allele frequencies. Allof the alleles observed were found throughout the system.However, one allele (

SCO19

*

202

) is represented in LakePend Oreille by a single allele copy in a heterozygousindividual from Trestle Creek (2). This allele is present insix of the seven populations from the lower Clark ForkRiver. This difference in allelic distribution further supportsthe genetic differentiation among samples above and belowCabinet Gorge Dam.

Swamp Creek (15), an exception to this pattern, is highlydifferentiated from all remaining samples. This deviationis probably being driven by a high frequency of a rare allele(

SFO

*

156

)

,

and a low frequency of a normally commonallele (

FGT3

*

165

; Appendix I). Accurate estimates of thebull trout population size in Swamp Creek (15) are notavailable. However, only four redds were found in a 1993survey (Pratt & Huston 1993) suggesting that the popula-tion exists at low numbers and is prone to the effects ofgenetic drift. Hybridization with brook trout may also beacting to reduce the effective populations size in SwampCreek.

Twin Creek (11) is also an exception to the clustering ofpopulations above or below Cabinet Gorge Dam. TwinCreek (11) enters the Clark Fork River approximately 5 kmdownstream of Cabinet Gorge Dam but is genetically moresimilar to above-dam sites. Spawning habitat in TwinCreek (11) is marginal (Pratt & Huston 1993) and may haveresulted in a small population subject to the effects ofgenetic drift. Twin Creek (11) is similar to Swamp Creek(15) in that it also contains bull trout

×

brook trout hybrids.Another explanation for Twin Creek’s (11) genetic simil-

arity to upriver populations (Fig. 2) is straying by adultsoriginating in lower Clark Fork River tributaries. Theymay enter and spawn in Twin Creek (11), the nearest avail-able tributary since their migratory corridor is blocked byCabinet Gorge Dam. The poor habitat conditions in Twin

15

01

13

12c14

12b

16

18

17

07

06

05 1004 09

02

03

08

11

12a

19

0.1

Fig. 2 upgma dendrogram based on Cavalli-Sforza & Edwards’(1967) chord distance for bull trout sampled from tributaries toLake Pend Oreille and the lower Clark Fork River. Numbersdenote sample locations from Table 1 and Fig. 1. White circlesindicate locations below Cabinet Gorge Dam, black circles arelocations above the dam, and diamonds are samples collected atthe base of the dam in three consecutive years (12a = 1997,12b = 1998, 12c = 1999). Lines under the location number indicategeographical location relative to the dam.


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Table 2

The proportional assignment of all individuals represented in the Lake Pend Oreille/lower Clark Fork River data set. Assignment is based on genotypic frequences at eightmicrosatellite loci. The bolded diagonal is the proportion of individuals that were assigned back to their sample origin. Numbers correspond to sample sites in Table 1 and Fig. 1

Proportion of individuals assigned to each location

Location of sample collection

Below Dam Dam Above Dam

1 2 3 4 5 6 7 8 9 10 11 12a 12b 12c 13 14 15 16 17 18 19

Below Dam

1

0.65

0.04 0.09 0.04

—

0.02 0.04

—

0.05 0.08

— — —

0.04 0.02 0.03

— — — — —

2 0.08

0.41

0.03 0.09

—

0.05 0.12

—

0.16 0.04

— — —

0.04

—

0.03

— — — — —

3 0.05 0.03

0.34

0.09

— — —

0.08 0.05

—

0.04 0.13 0.04 0.12 0.02

— — — —

0.02 0.054

—

0.04 0.03

0.13

— —

0.05 0.06 0.11 0.13

— — — — — — — — — —

5

—

0.15 0.03 0.11

0.73

0.05 0.11 0.06

— — — — — —

0.03

— — — — — —

6 0.05 0.04

—

0.04 0.05

0.46

0.09

— —

0.17 0.00

— — — — — —

0.03 0.07

— —

7 0.05 0.02 0.03 0.04 0.09 0.10

0.33

—

0.05

—

0.00

— — —

0.05 0.03 0.07

— — — —

8

—

0.04 0.09 0.02 0.00 0.05 0.06

0.47

0.11 0.08 0.04 0.07 0.07

—

0.13 0.03

— — — — —

9 0.08 0.14 0.06 0.09 0.14 0.05 0.09 0.06

0.42

0.13 0.04 0.20 0.04

—

0.02

— — — — — —

10 0.05 0.04 0.00 0.04

—

0.17 0.04 0.14 0.05

0.33

— —

0.07 0.08 0.02 0.03

—

0.03 0.03

— —

11

—

0.01 0.11 0.04

— —

0.01 0.06 0.00 0.04

0.39

0.13 0.04 0.08 0.07 0.10

— — — —

0.08

Dam

12a

—

0.01

—

0.02

— —

0.02 0.03

— —

0.04

0.07

0.04

—

0.05

—

0.07

—

0.03

—

0.0512b

— — —

0.02

— — —

0.03

— —

0.04

—

0.00

—

0.05 0.10

— —

0.07 0.02 0.0312c

— —

0.03 0.06

— — — — — — — — —

0.08

0.12 0.07

—

0.03

—

0.02 0.05

Above Dam

13

— — —

0.04

—

0.02 0.01

— — — —

0.07 0.18 0.04

0.12

0.03

— —

0.03

—

0.0514

—

0.02

— — —

0.02 0.00 0.03

— —

0.09 0.07 0.14 0.08 0.02

0.13

—

0.10

—

0.12 0.0315

—

0.01 0.03 0.06

— — — — — — — — — —

0.02

—

0.86

— — — —

16

— — —

0.04

— —

0.01 — — — 0.00 0.07 0.07 0.20 0.12 0.13 — 0.70 0.07 0.02 0.0817 — 0.01 0.09 0.02 — — 0.01 — — — 0.09 0.07 0.07 0.04 0.02 0.13 — — 0.70 — —18 — — 0.03 — — — — — — — 0.09 0.07 0.11 0.08 0.08 0.07 — 0.10 — 0.74 0.2219 — — 0.03 — — — — — — — 0.13 0.07 0.14 0.12 0.07 0.07 — — — 0.05 0.35

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Creek (11) may limit juvenile survival, producing apopulation ‘sink’ that is only maintained by the annualspawning of these blocked fish.

Genotypic assignment test

We used Paetkau’s assignment test to estimate the originsof bull trout returning to Cabinet Gorge Dam. Our powerto assign individuals to a specific population is limited bythe low number of individuals collected from some sites.However, the overall pattern of assignment either above orbelow the dam should not be altered by this limitation.

The results of the genotypic assignment test supportthe differentiation among sites above and below CabinetGorge Dam. Individuals collected from Lake Pend Oreilletributaries are much more likely to be assigned to otherlake tributaries than to upriver sites. Similarly, individualsfrom tributaries to the lower Clark Fork River are morelikely to be assigned to other sites above Cabinet GorgeDam.

Most individuals are assigned back to the site fromwhich they were captured. Only samples collected in theEast Fork Bull River (13) and at the base of Cabinet GorgeDam (12a, 12b, 12c) were assigned to another site morefrequently than to their site of capture. Individuals fromGold Creek (4) were also assigned back to their origin withlow frequency. However, individuals from populationswith high levels of variation may be assigned to variouspopulations by chance.

Samples from Cabinet Gorge Dam (12a, 12b, 12c) alsohave high levels of variation (Table 1). Two of the CabinetGorge Dam samples, 12b and 12c, are assigned prefer-entially to above dam populations (Table 2). However,the 12a samples have 56% of their sample assigned tobelow dam sites. This observation may be due to a lowsample size (n = 15). We expect these results if the CabinetGorge samples are composed of individuals from multiplepopulations.

Probable origins of Cabinet Gorge Dam bull trout

These data allow us to examine the hypotheses that weproposed to explain the presence of adult bull trout at thebase of Cabinet Gorge Dam. It is highly unlikely that bulltrout collected at the base of Cabinet Gorge Dam originatedfrom bull trout native to Lake Pend Oreille tributaries.Allele frequency differences indicate substantial geneticdifferentiation between Cabinet Gorge samples and bulltrout collected from tributaries to Lake Pend Oreille. Inaddition, the SCO19*202 allele is extremely rare in LakePend Oreille tributaries but is common in lower Clark Forktributaries (Appendix I). This allele is found in two of thethree samples collected at the dam. We suspect that theassignment test results for the 1997 Cabinet Gorge Dam

(12a) sample are not accurate due to a low sample size.This interpretation is further supported by the CSE upgmadendrogram that clusters the 1997 (12a) sample with abovedam samples.

We cannot dismiss the possibility that a founding eventcould have taken place immediately after the closure of theCabinet Gorge impoundment in 1952. Our data, however,do not support the hypothesis of a single founding event.We expect founders to contribute only a subset of alleles totheir progeny. Genetic drift should also eliminate allelesand would most likely produce a reduction in the popu-lation’s heterozygosity. We would expect similar resultsif a small population of historic mainstem spawners wereresponsible for the adult bull trout that return to CabinetGorge Dam each year.

The data are more consistent with the results expectedfrom a sample representing multiple populations. Samplescollected independently from the same spawning aggreg-ate should cluster together on allele frequency-based den-drograms. The samples from Cabinet Gorge Dam (12a, 12b,12c) do not conform with this observation (Fig. 2). Sim-ilarly, individuals from a population are usually assignedback to the population from which they were collected.Two Cabinet Gorge Dam samples (12b and 12c) are prefer-entially assigned to samples from tributaries above thedam rather than back to their initial sampling location.These data support the hypothesis that Cabinet GorgeDam adults are a mixture composed primarily of migrat-ory individuals from tributaries to the Clark Fork Riverthat pass downstream over the dam to rear in Lake PendOreille.

Genetic risks associated with passage

Genetic data alone cannot determine the source of the fishreturning to Cabinet Gorge Dam and the four hypotheseswe proposed are not mutually exclusive. However, we canuse these data to better assess the genetic risks associatedwith passing adult bull trout that return to the base ofCabinet Gorge Dam.

There are two major genetic concerns that must beaddressed prior to the initiation of fish passage. First, if thebull trout below Cabinet Gorge Dam are not of upstreamorigin, passage may cause outbreeding depression by intro-ducing genes from individuals that are not locally adapted(Phillip 1991; Waples 1992). Alternatively, if some fish areuniquely adapted to reproduce and survive in the main-stem Clark Fork River below Cabinet Gorge Dam, passagecould eliminate a large proportion of those individuals,increasing the chance of extirpation for that population.

It is clear that fish collected at Cabinet Gorge Dam aregenetically more similar to populations located above thedam. This relationship suggests that passing fish above thedam is unlikely to produce severe outbreeding depression.


1160 L . P. N E R A A S and P. S P R U E L L


Additionally, these data do not support the existence ofa unique population at the base of Cabinet Gorge Dam.Therefore, it is unlikely that passing individuals from thisgroup of fish will negatively impact a small mainstem-spawning population. The risks associated with passingradio tagged adults are minimal compared to the potentialgenetic and demographic benefits to populations locatedabove the dam.

Conclusion

Our data suggest that re-establishing connectivity be-tween Lake Pend Oreille and tributaries of the lowerClark Fork River may be beneficial for the persistence ofbull trout populations. In addition to Cabinet Gorge Dam,Noxon Rapids and Thompson Falls Dams limit migrationof aquatic fauna. Labour-intensive projects focused onsingle species and individual hydroelectric projects areprobably inefficient and are not long-term solutions to theproblem. Construction of facilities that allow species tomigrate freely throughout the system are currently beingconsidered. Restoring the connectivity that historicallyexisted will increase the evolutionary potential of aquaticfauna in the system and is a more desirable approach tosystem-wide management.

Acknowledgements

This project was funded by a grant from Avista Corporation andby a grant to LPN from the Davidson Honors College at theUniversity of Montana. We thank Chip Corsi, Chris Downs, KarenPratt, Pat Saffel, and Ginger Gillin-Thomas for helpful discussionson the Lake Pend Oreille/lower Clark Fork River system. We alsothank Andrew Whiteley, Aaron Maxwell, Zach Wilson, and KathyKnudsen for their valuable suggestions regarding this system.Zach Wilson also collected the genetic data from tributaries toLake Pend Oreille. Fred W. Allendorf, Damian M. Cremins, Ellie K.Steinburg, and Kristina Ramstad offered helpful comments onearlier versions of this paper. Finally, we thank Bruce Rieman forhis assistance with the PBR and his other immeasurable contribu-tions to this work.

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Appendix I

Sample size (n) and allele frequencies at eight polymorphic loci for bull trout collected in the Lake Oend Oreille/lower Clark Fork system.Sample locations correspond to Figure1 and Table 1

Sample site n

1 402* 1053 354 475 226 417 818 409 1910 2411 2312b 1512b 2812c 2613* 6014 3015 1416 3017 3018* 4319* 37

Sample site

ONEµ7 SFO18 OTS101

*218 *244 *150 *156 *100 *112

1 0.676 0.324 1.000 — 0.538 0.4622 0.971 0.029 0.867 0.133 0.762 0.2383 0.700 0.300 0.900 0.100 0.986 0.0144 0.777 0.223 0.798 0.202 0.909 0.0915 1.000 — 0.659 0.341 1.000 —6 1.000 — 0.659 0.341 0.825 0.1757 0.994 0.006 0.762 0.238 0.809 0.1918 0.900 0.100 0.931 0.069 1.000 —9 0.947 0.053 0.974 0.026 0.917 0.08310 0.792 0.208 0.917 0.083 0.938 0.06211 0.841 0.159 0.957 0.043 1.000 —12b 0.800 0.200 0.692 0.308 0.967 0.03312b 0.852 0.148 0.839 0.161 1.000 —12c 0.896 0.104 0.940 0.060 0.854 0.14613 0.813 0.187 0.847 0.153 0.939 0.06114 0.931 0.069 0.914 0.086 0.983 0.01715 0.643 0.357 0.107 0.893 0.833 0.16716 1.000 — 0.717 0.283 1.000 0.00017 0.630 0.370 0.714 0.286 0.983 0.01718 0.895 0.105 0.962 0.038 1.000 —19 0.892 0.108 0.924 0.076 0.941 0.059

Sample site

FGT3

*165 *167 *169 *171 *173 *175 *179

1 0.658 0.237 0.053 — 0.053 — —2 0.362 0.048 0.100 — 0.490 — —3 0.657 0.071 0.100 — 0.171 — —4 0.596 0.128 0.032 — 0.245 — —




5 0.357 0.048 0.048 — 0.548 — —6 0.671 0.195 0.024 — 0.110 — —7 0.450 0.244 0.094 0.006 0.206 — —8 0.571 0.057 0.057 — 0.314 — —9 0.556 0.111 — — 0.333 — —10 0.646 0.146 0.083 — 0.125 — —11 0.550 0.125 — — 0.325 — —12b 0.500 0.115 0.038 — 0.346 — —12b 0.679 0.161 0.054 — 0.107 — —12c 0.708 0.167 0.021 — 0.104 — —13 0.692 0.175 — — 0.125 — 0.00814 0.500 0.224 0.086 — 0.155 0.034 —15 0.192 0.346 0.346 — 0.115 — —16 0.567 0.317 — — 0.117 — —17 0.534 0.086 — — 0.379 — —18 0.698 0.093 0.093 — — 0.116 —19 0.778 0.056 0.056 — 0.069 0.042 —

Sample site

SCO19

*174 *178 *188 *200 *202 *212 *216

1 0.932 — 0.014 — — — 0.0542 0.851 0.067 — 0.014 0.005 — 0.0633 0.500 — — 0.186 — — 0.3144 0.745 — — 0.064 — — 0.1915 0.950 — 0.050 — — — —6 0.902 — 0.098 — — — —7 0.772 — 0.198 0.006 — — 0.0248 0.814 — — 0.114 — — 0.0729 0.816 — — 0.026 — — 0.15810 0.979 — — — — — 0.02111 0.294 — — 0.500 — — 0.20612b 0.300 — — 0.367 0.100 — 0.23312b 0.393 — 0.018 0.321 0.018 — 0.25012c 0.444 — — 0.444 — — 0.11213 0.380 — 0.065 0.472 0.009 0.009 0.06514 0.467 — — 0.333 0.017 — 0.18315 0.900 — — 0.050 — — 0.05016 0.315 — — 0.407 0.130 — 0.14817 0.283 — — 0.022 0.196 — 0.49918 0.157 — — 0.800 0.043 — —19 0.236 — — 0.569 0.014 — 0.181

Sample site

OGO2 SSA311 SSA456

*150 *154 *156 *162 *112 *120 *157 *159

1 0.050 — 0.325 0.625 0.128 0.872 0.775 0.2252 0.150 0.063 0.466 0.321 0.010 0.990 0.486 0.5143 0.029 0.176 0.529 0.266 — 1.000 0.714 0.2864 0.213 0.160 0.298 0.329 0.053 0.947 0.611 0.3895 0.386 — 0.409 0.205 — 1.000 0.528 0.4726 0.220 0.037 0.293 0.450 0.188 0.812 0.462 0.5387 0.185 0.074 0.432 0.309 0.099 0.901 0.605 0.3958 0.375 0.347 0.167 0.111 0.056 0.944 0.778 0.2229 0.083 0.028 0.417 0.472 0.026 0.974 0.737 0.263

Sample site

FGT3

*165 *167 *169 *171 *173 *175 *179

Appendix I Continued




10 0.292 0.063 0.313 0.332 0.188 0.812 0.458 0.54211 0.023 0.432 0.318 0.227 0.205 0.795 0.525 0.47512b 0.067 0.267 0.333 0.333 0.200 0.800 0.433 0.56712b 0.161 0.375 0.411 0.053 0.232 0.768 0.357 0.64312c 0.125 0.458 0.354 0.063 0.180 0.820 0.480 0.52013 0.173 0.564 0.200 0.063 0.176 0.824 0.372 0.62814 0.071 0.304 0.571 0.054 0.232 0.768 0.315 0.68515 0.100 0.700 0.200 — — 1.000 0.923 0.07716 0.250 0.393 0.357 — 0.217 0.783 0.383 0.61717 — 0.107 0.839 0.054 0.300 0.700 0.328 0.67218 — 0.553 0.447 — 0.107 0.893 0.238 0.76219 0.069 0.583 0.278 0.070 0.351 0.649 0.338 0.662

Sample site

OGO2 SSA311 SSA456

*150 *154 *156 *162 *112 *120 *157 *159

Appendix I Continued


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