The Genetic Effects of Dams on Bull Trout (Salvelinus Confluentus)

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Molecular Ecology (2001) 10, 1153–1164

BlackwellFragmentation Science, Ltd 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 (Salvelinus confluentus) historically spawned in tributaries of the Clark 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 populations in upstream tributaries have been in decline. Each year adult bull trout return to the base of Cabinet Gorge Dam when most migratory bull trout begin their spawning migration. However, the origin of these fish is uncertain. We used eight microsatellite loci to compare bull trout collected at the base of Cabinet Gorge Dam to fish sampled from both above and further downstream from the dam. Our data indicate that Cabinet Gorge bull trout are most likely individuals that hatched in above-dam tributaries, reared in Lake Pend Oreille, and could not return to their natal tributaries to spawn. This suggests that the risk of outbreeding depression associated with passing adults over dams in the Clark Fork system is minimal compared to the potential genetic and demographic benefits to populations located 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

There are many examples of the extirpation of ana- Introduction dromous Pacific Salmon stocks that are unable to reach Habitat fragmentation may take dramatically different forms their spawning grounds after the construction of impas- in terrestrial and riverine habitats. Fragmentation of sable dams (National Resource Council 1996; Nehlsen terrestrial habitats is usually associated with alteration et al. 1991). However, relatively little work has explored in large tracts of land, precluding migration among the changes in the genetic population structure of fishes the remaining patches of suitable habitat. In riverine sys- caused by dams. The available data suggest that frag- tems, hydroelectric dams and irrigation diversions may mentation associated with dams has caused a loss of cause fragmentation at specific points along the stream genetic variation in anadromous steelhead isolated above corridor. impoundments (Nielsen et al. 1997). The effects that dams may have on fish species have been Hydroelectric dams may also impact nonanadromous documented throughout the world. The described popu- fishes. Some inland fish populations exhibit both resident lation declines are primarily due to the change from a and migratory life histories. Resident fish complete their riverine to a lacustrine environment and the isolation of lifecycle within small streams, while migratory individuals migratory fishes from their spawning and feeding grounds spawn in smaller streams but use larger bodies of water as (for example, Barthem et al. 1991; Wei et al. 1997; Ruban subadults and adults. Movement between habitats is crit- 1997). These disruptions may cause local extinction if crit- ical for the expression of all life histories within a popu- ical habitats are lost or no longer accessible. lation. If different life histories buffer a population against local extinction, the elimination of a life history type will Correspondence: Paul Spruell. Fax: (406) 243 4184; E-mail: increase the chance of extirpation. Additionally, habitat [email protected] fragmentation can preclude migration between populations

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1154 L. P. NERAAS and P. SPRUELL

Fig. 1 Approximate sample sites of bull trout from the lower Clark Fork River and Lake Pend Oreille. Numbers correspond to location descriptions in Table 1. White circles indicate locations below Cabinet Gorge Dam, black circles are locations above the dam, and the diamond is the sample collected at the base of the dam.

within a metapopulation, further increasing the chance of River (Fig. 1). The first, Thompson Falls Dam, was built in extirpation. 1913 near the town of Thompson Falls, Montana. In 1952, Bull trout (Salvelinus confluentus) are listed as threatened Cabinet Gorge Dam was constructed 10 km upstream from under the U.S. Endangered Species Act throughout the the mouth of the Clark Fork River. Six years later, in 1958, north-west United States (Federal Register 1999). One Noxon Rapids Dam was built 29 km upstream from factor leading to this decline is habitat fragmentation due Cabinet Gorge Dam. None of these hydroelectric to hydroelectric impoundments (Rieman & McIntyre 1993). developments have facilities for fish passage. Lake Pend Oreille, Idaho (Fig. 1) supports one of the One year after the closure of Cabinet Gorge Dam largest remaining bull trout metapopulations in the United Jeppson (1954) reported seeing ‘large numbers of bull States (Pratt & Huston 1993). However, bull trout were trout’ in the Clark Fork River below the dam, but no redds historically much more abundant in the system (Pratt & were observed. In 1961, the Idaho Department of Fish and Huston 1993). Bull trout from many different populations Game created a spawning channel just downstream of the continue to use the lake as rearing and over-wintering hab- dam in an attempt to mitigate the loss of upstream spawning itat. Prior to the construction of dams on the Clark Fork habitat. Biologists surveyed this site in the mid 1960s and river, large numbers of adfluvial bull trout that hatched in reported seeing 200–400 bull trout near the spawning tributaries of the Clark Fork River migrated freely to Lake channel (Pratt & Huston 1993). In subsequent surveys Pend Oreille as subadults and adults before returning to from 1984 to 1991, biologists saw bull trout but failed to their natal streams to spawn (Pratt & Huston 1993; Fig. 1). observe any redds below Cabinet Gorge Dam (Pratt & Within the last 90 years, a series of three hydroelectric Huston 1993). Overall it appears that the lower Clark Fork developments were constructed in the lower Clark Fork River dams have reduced the number of bull trout in

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ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1155

this system. Apparently, the construction of the spawning Methods channel did not adequately compensate for the losses caused by the disruption of the migratory corridor. Study location and individual collection Large adult bull trout continue to congregate near the spillway of Cabinet Gorge Dam from the end of peak flow Bull trout were collected from 10 tributaries of Lake Pend to early autumn when most migratory bull trout begin Oreille and eight tributaries to the Lower Clark Fork River their spawning movements. The origin of those fish is (Fig. 1, Table 1). Fish were captured using block nets, fish uncertain but four hypotheses are likely. First, bull trout weirs, or electrofishing techniques while they were holding may have historically spawned in the mainstem of the in tributaries prior to spawning. These individuals should Clark Fork River and have continued to persist there after be representative of the spawning aggregates in each the construction of the dam. Second, bull trout that hatched tributary. Adult bull trout returning to the base of Cabinet in tributaries to Lake Pend Oreille could have established Gorge Dam were collected in 1997, 1998, and 1999 either in a population below the dam after its construction. Third, a fish trap at the nearby Cabinet Gorge Hatchery or by the bull trout that return to Cabinet Gorge Dam may be boat-based electrofishing. A nonlethal fin clip was taken remnants of individuals from upstream populations that from each individual and stored in 95% ethanol. DNA was became isolated in 1952 after the closure of the dam. extracted from fin tissue with a Purgene kit (Gentra). Finally, bull trout that congregate at the base of Cabinet Gorge Dam may be migratory fish that hatched in tributar- Identification of hybrids ies above the dam and continue to pass downstream over the dam during annual outmigrations and are unable to Individuals from populations in which hybridization with return to their natal streams to spawn. non-native brook trout (Salvelinus fontinalis) was suspected Movements of tagged bull trout indicate that some indi- were screened using PINE-PCR (Spruell et al., unpublished viduals pass downstream over dams. Eight per cent of a data). Three hybrids were eliminated from the original 17 radio tagged sample of migratory bull trout that originated individuals collected in Swamp Creek (15). Ten of the 33 in the Blackfoot River, MT, swam downstream over Mill- Twin Creek (11) individuals were also removed from the town Dam (Swanberg 1997). Similarly, 18% of bull trout sample due to hybridization. Of the hybrid individuals, a tagged in the Boise River system passed downstream over single individual from Twin Creek (11) was identified as a Arrowrock Dam (Flatter 1998). The proportion of out- later generation hybrid. All remaining hybrids were first

migrating juveniles that suffer a similar fate is currently generation (F1). It does not appear that there is continual unknown. However, these data suggest that hydroelectric introgression between species in these populations. There- impoundments can cause geographical and genetic isola- fore, the remaining individuals from Swamp Creek (15) tion of migratory fish from their natal tributaries. and Twin Creek (11) are probably not hybrids and were The metapopulation dynamics and genetic population included in subsequent analyses. structure of bull trout in Lake Pend Oreille have been extensively explored and described by, Rieman & McIntyre Microsatellite amplification and analysis (1993), Pratt & Huston (1993), Rieman & Dunham (2000), and Spruell et al. (1999). These descriptions suggest that We amplified eight microsatellite loci in an MJ Research metapopulation dynamics and alternate life history forms PTC-100 thermocycler using profiles described by initial may buffer bull trout populations from local extinction investigators of each locus (ONEµ7, Scribner et al. 1996; events. This suggests that actions aiding movement within SFO18, Angers et al. 1995; FGT3, Sakamoto et al. 1994; the system may begin to reverse the decline of these frag- SCO19, E.B. Taylor, personal communication; OGO2, Olsen mented bull trout populations. et al. 1998; SSA311 and SSA456, Slettan et al. 1995; OTS101, Our objective was to determine the origin of adult bull Small et al. 1998). The amplified alleles were separated on trout that return to the base of Cabinet Gorge Dam. We a 7% denaturing polyacrylamide gel and visualized using used eight microsatellite loci to estimate the amount of a Hitachi FMBIO-100 fluorescent imager. Allele sizes were connectivity, or gene flow, between populations within the determined relative to a standard base pair size ladder basin. We also used these data to establish a baseline (MapMarkerLow, Bioventures). Previously amplified prod- genetic data set representative of populations in the sys- ucts were included on each gel to ensure consistent scoring tem. Using these data, we estimated the probable origin of of individuals across all gels (Spruell et al. 1999). the adult bull trout that return to the base of Cabinet Gorge Dam. Finally, we consider the genetic risks associated with Data analysis the transport of fish over dams throughout the Lower Clark Fork River vs. risks associated with maintaining the We used genepop to calculate heterozygosity values

existing migration barriers in the system. (HS), allele frequencies, FST, and deviations from Hardy–

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1156 L. P. NERAAS and P. SPRUELL

Table 1 Sample sites, number, expected heter- Population Sample Expected Number ozygosity and average number of alleles per number location Number heterozygoisty of alleles locus for bull trout collected from tributaries to the lower Clark Fork River and Lake Pend Below Dam Oreille. Population numbers correspond to 1 Grouse Creek 40 0.335 19 sample sites indicated in Fig. 1. The asterisk (*) 2 Trestle Creek* 105 0.340 23 indicates sites at which samples were collected 3 Granite Creek 35 0.355 20 in multiple years 4 Gold Creek 47 0.394 21 5 Morris Creek 22 0.288 16 6 Savage Creek 41 0.364 19 7 East Fork Lightning Creek 81 0.386 23 8 Porcupine Creek 40 0.297 20 9 Rattle Creek 19 0.285 20 10 upper Lightning Creek 24 0.342 20 11 Twin Creek 23 0.386 19 Dam 12a Cabinet Gorge Dam 1997 15 0.472 22 12b Cabinet Gorge Dam 1998 28 0.431 23 12c Cabinet Gorge Dam 1999 25 0.388 21 Above Dam 13 East Fork Bull River* 60 0.397 24 14 Rock Creek 30 0.383 23 15 Swamp Creek 14 0.316 19 16 Graves Creek 30 0.399 18 17 Prospect Creek 30 0.413 20 18 Thompson River* 43 0.269 18 19 Fishtrap Creek* 57 0.366 23

Weinberg expectations (Raymond & Rousset 1995). We across all loci (Sokal & Rohlf 1995), we found no statistic- used a Cavalli-Sforza and Edwards chord distance (CSE) to ally signiﬁcant differences in genotypic frequencies between estimate the genetic similarity among populations (Cavalli- temporal samples within any of the four sites. Therefore, Sforza & Edwards 1967). A upgma dendrogram was gener- we pooled the temporal samples from each site in all sub- ated using phylip (Felsenstein 1993). This dendrogram sequent analyses. The samples collected at the base of allowed us to visualize the genetic similarity among samples Cabinet Gorge dam in 1997 (12a), 1998 (12b), and 1999 (12c) within the system. were not pooled since we cannot assume they represent a To estimate the probable origins of Cabinet Gorge bull single spawning population. trout we used Paetkau’s online calculator to conduct an ‘assignment test’. This test determines the most probable Differentiation among samples origin of each individual based on the expected genotypic frequencies of each sample (Paetkau et al. 1997). Differences in allele frequencies suggest that there is sub-

stantial genetic differentiation among populations (FST = 0.137). A upgma dendrogram based on CSE chord distance was Results used to visualize the relative genetic similarity among samples (Fig. 2). Variation within sample sites The dendrogram (Fig. 2) suggests that there is substan- The amount of variation detected in these samples was tial differentiation between samples collected in tributaries similar to earlier microsatellite studies in this system to Lake Pend Oreille and those collected in lower Clark (Spruell et al. 1999). All eight of the loci analysed were Fork River tributaries. Swamp Creek (15) exists as an out- polymorphic in at least one sample site (Appendix I). After lier (Fig. 2) due to its high frequency of a normally rare correcting for multiple tests (Rice 1989), we found no allele at the SFO18 locus, and a low frequency of a normally deviations from Hardy–Weinberg proportions in any of the common allele at the FGT3 locus (Appendix I). samples analysed. Expected heterozygosity averaged 0.362 In all samples from Lake Pend Oreille tributaries, pro- and ranged from 0.269 to 0.473 (Table 1). The number of portionally more individuals were assigned to their popu- alleles per sample ranged from 16 to 24 and averaged 20.5 lation of origin than to any other site (Table 2). This is also (Table 1). true for seven of the eight lower Clark Fork River samples. In four sites (2, 13, 18, and 19), individuals were collected However, two samples with high heterozygosities (Table 1), in two consecutive years. After combining probabilities the East Fork Bull River (13) and Gold Creek (4) are exceptions

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ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1157

The results of the assignment test also support the gen- 12a 12b 12c etic similarity of Cabinet Gorge samples with those from 19 14 11 above-dam tributaries. The Cabinet Gorge Dam samples 16 13 15 (12a, 12b, 12c) did not proportionally have more individuals assigned back to their sample origin (Table 2). The 1998 18 (12b) and 1999 (12c) Cabinet Gorge Dam samples had more individuals assigned to the above dam sites (Table 2). The 1997 (12a) Cabinet Gorge Dam sample had 56% of the sample assigned to below dam sites (Table 2). However, 17 these results may be due to a small sample size (Table 1).

01 Discussion 07 03 06 Relationships among sample sites 08 05 The microsatellite data suggest substantial genetic differen- 10 02 04 09 tiation among samples collected from spawning aggregates

0.1 above and below Cabinet Gorge Dam. This differentiation is based primarily on differences in allele frequencies. All Fig. 2 upgma dendrogram based on Cavalli-Sforza & Edwards’ of the alleles observed were found throughout the system. (1967) chord distance for bull trout sampled from tributaries to However, one allele (SCO19*202) is represented in Lake Lake Pend Oreille and the lower Clark Fork River. Numbers Pend Oreille by a single allele copy in a heterozygous denote sample locations from Table 1 and Fig. 1. White circles indicate locations below Cabinet Gorge Dam, black circles are individual from Trestle Creek (2). This allele is present in locations above the dam, and diamonds are samples collected at six of the seven populations from the lower Clark Fork the base of the dam in three consecutive years (12a = 1997, River. This difference in allelic distribution further supports 12b = 1998, 12c = 1999). Lines under the location number indicate the genetic differentiation among samples above and below geographical location relative to the dam. Cabinet Gorge Dam. Swamp Creek (15), an exception to this pattern, is highly to this observation. Individuals from these two samples differentiated from all remaining samples. This deviation are not preferentially assigned to any site. Rather, they are is probably being driven by a high frequency of a rare allele distributed throughout the system. (SFO*156), and a low frequency of a normally common Individuals that did not get assigned back to their ori- allele (FGT3*165; Appendix I). Accurate estimates of the ginal collection were not assigned at random. Individuals bull trout population size in Swamp Creek (15) are not from below-dam sites that were not assigned back to their available. However, only four redds were found in a 1993 original sample site are most frequently assigned to survey (Pratt & Huston 1993) suggesting that the popula- another below-dam site. Similarly, individuals from above- tion exists at low numbers and is prone to the effects of dam sites that were not assigned back to their original genetic drift. Hybridization with brook trout may also be sample site are most frequently assigned to another above- acting to reduce the effective populations size in Swamp dam site. Table 2 separates above-dam and below-dam Creek. sites into quadrants, where this observation is most Twin Creek (11) is also an exception to the clustering of apparent (Table 2). populations above or below Cabinet Gorge Dam. Twin Creek (11) enters the Clark Fork River approximately 5 km downstream of Cabinet Gorge Dam but is genetically more Cabinet Gorge Dam samples similar to above-dam sites. Spawning habitat in Twin The samples collected at Cabinet Gorge Dam in 1997 (12a), Creek (11) is marginal (Pratt & Huston 1993) and may have 1998 (12b), and 1999 (12c) do not cluster together on the resulted in a small population subject to the effects of dendrogram. These results are unexpected for temporal genetic drift. Twin Creek (11) is similar to Swamp Creek samples collected from a single isolated bull trout popu- (15) in that it also contains bull trout × brook trout hybrids. lation (Spruell et al. 1999). The Cabinet Gorge samples are Another explanation for Twin Creek’s (11) genetic simil- dispersed with the lower Clark Fork River samples (Fig. 2). arity to upriver populations (Fig. 2) is straying by adults This suggests that bull trout sampled from the base of originating in lower Clark Fork River tributaries. They Cabinet Gorge Dam (12a, 12b, 12c) are more genetically may enter and spawn in Twin Creek (11), the nearest avail- similar to samples collected from tributaries located above able tributary since their migratory corridor is blocked by the dam. Cabinet Gorge Dam. The poor habitat conditions in Twin

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1158 L. P. NERAAS and P. SPRUELL 0.08 0.05 0.05 0.22 0.35 0.02 0.05 —— —— — 0.02 0.05 — 0.12 0.03 —— 0.74 0.05 0.03 0.07— 0.020.03 0.03 — 0.070.70 0.02— 0.08 0.03———— 0.07 0.03 0.03 — 0.03 0.10 ———— 0.70 0.10 ————— ————— ————— — ———— 0.07 —— — —— — 0.86 — —— — ——— is based on genotypic frequences at eight is based on genotypic frequences 0.03 ———— —————— —————— — 0.03 0.13 — —————— — 0.03 0.050.13 0.030.02 0.03 0.07 0.05 0.050.12 0.10 0.07 0.12 0.02 rs correspond to sample sites in Table 1 and Fig. rs correspond to sample sites in Table 0.040.04 0.02 0.03 — — — — 0.08 0.07 0.08 0.020.04 0.00 0.03 ————— — ——— 0.13 0.040.07 0.08— 0.07 0.10 0.07 0.18 0.04 Dam Above Dam ——— ——— 0.04———— 0.13 0.040.00 0.12 0.02 —— 0.39 0.04 0.04 0.09 0.070.00 0.140.09 0.070.09 0.08 0.07 0.070.13 0.07 0.02 0.07 0.20 0.07 0.11 0.04 0.12 0.14 0.08 0.02 0.13 0.12 0.08 0.13 0.07 0.07 0.07 — 0.17— 0.00 0.130.33 0.04 0.20 0.04 0.050.16 0.08 0.04 —————— 0.05 0.110.42 0.08 0.04 0.07—— 0.07 —— —— — — 0.08 0.05 —— — 0.47 0.03 ———— ——— ——— 0.05 0.060.09 0.110.33 0.13 0.01 0.060.02 0.00 0.03 0.04 0.01 0.01 0.020.05 0.04 0.12 0.050.46 0.11 0.06 0.17 0.04 0.14 0.05 0.020.02 0.01 0.00 0.03 — — ——— —— 0.73 — —— —— ——— ————————— — —————————— —— —— 0.09 0.13 0.04 0.05 0.02 0.02 0.04 0.04 ——————— ——————— 0.030.34 0.09 — — 0.03 0.06 ——— 0.03 0.03 0.040.41 0.09 0.04 0.040.15 0.03 0.03 0.11 0.04 0.09 0.020.01 0.00 0.110.01 0.05 0.04 0.06 0.02 0.01 0.030.01 0.06 0.09 0.02 0.65 — — — — — ——— —— ——— — — ——— — —— —— Location of sample collection Below Dam 123456789101112a12b12c13141516171819 The proportional assignment of all individuals represented in the Lake Pend Oreille/lower Clark Fork River data set. Assignment Clark Fork River data set. in the Lake Pend Oreille/lower assignment of all individuals represented The proportional 4 12b 12c 14 15 17 19 Table 2 Table Below Dam 1 235 678 0.08 9 0.0510 0.03 11 Dam 0.0512a 0.05 0.04 0.02 0.08 0.05 0.03Above Dam 0.1413 0.04 0.04 0.06 0.00 0.09 0.09 0.04 16 0.10 0.1418 0.05 0.09 0.06 microsatellite loci. The bolded diagonal is the proportion of individuals that were assigned back to their sample origin. Numbe loci. The bolded diagonal is the proportion of individuals that were microsatellite of Proportion individuals assigned to each location

ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1159

Creek (11) may limit juvenile survival, producing a (12a) sample are not accurate due to a low sample size. population ‘sink’ that is only maintained by the annual This interpretation is further supported by the CSE upgma spawning of these blocked fish. dendrogram that clusters the 1997 (12a) sample with above dam samples. We cannot dismiss the possibility that a founding event Genotypic assignment test could have taken place immediately after the closure of the We used Paetkau’s assignment test to estimate the origins Cabinet Gorge impoundment in 1952. Our data, however, of bull trout returning to Cabinet Gorge Dam. Our power do not support the hypothesis of a single founding event. to assign individuals to a specific population is limited by We expect founders to contribute only a subset of alleles to the low number of individuals collected from some sites. their progeny. Genetic drift should also eliminate alleles However, the overall pattern of assignment either above or and would most likely produce a reduction in the popu- below the dam should not be altered by this limitation. lation’s heterozygosity. We would expect similar results The results of the genotypic assignment test support if a small population of historic mainstem spawners were the differentiation among sites above and below Cabinet responsible for the adult bull trout that return to Cabinet Gorge Dam. Individuals collected from Lake Pend Oreille Gorge Dam each year. tributaries are much more likely to be assigned to other The data are more consistent with the results expected lake tributaries than to upriver sites. Similarly, individuals from a sample representing multiple populations. Samples from tributaries to the lower Clark Fork River are more collected independently from the same spawning aggreg- likely to be assigned to other sites above Cabinet Gorge ate should cluster together on allele frequency-based den- Dam. drograms. The samples from Cabinet Gorge Dam (12a, 12b, Most individuals are assigned back to the site from 12c) do not conform with this observation (Fig. 2). Sim- which they were captured. Only samples collected in the ilarly, individuals from a population are usually assigned East Fork Bull River (13) and at the base of Cabinet Gorge back to the population from which they were collected. Dam (12a, 12b, 12c) were assigned to another site more Two Cabinet Gorge Dam samples (12b and 12c) are prefer- frequently than to their site of capture. Individuals from entially assigned to samples from tributaries above the Gold Creek (4) were also assigned back to their origin with dam rather than back to their initial sampling location. low frequency. However, individuals from populations These data support the hypothesis that Cabinet Gorge with high levels of variation may be assigned to various Dam adults are a mixture composed primarily of migrat- populations by chance. ory individuals from tributaries to the Clark Fork River Samples from Cabinet Gorge Dam (12a, 12b, 12c) also that pass downstream over the dam to rear in Lake Pend have high levels of variation (Table 1). Two of the Cabinet Oreille. Gorge Dam samples, 12b and 12c, are assigned preferentially to above dam populations (Table 2). However, Genetic risks associated with passage the 12a samples have 56% of their sample assigned to below dam sites. This observation may be due to a low Genetic data alone cannot determine the source of the fish sample size (n = 15). We expect these results if the Cabinet returning to Cabinet Gorge Dam and the four hypotheses Gorge samples are composed of individuals from multiple we proposed are not mutually exclusive. However, we can populations. use these data to better assess the genetic risks associated with passing adult bull trout that return to the base of Cabinet Gorge Dam. Probable origins of Cabinet Gorge Dam bull trout There are two major genetic concerns that must be These data allow us to examine the hypotheses that we addressed prior to the initiation of fish passage. First, if the proposed to explain the presence of adult bull trout at the bull trout below Cabinet Gorge Dam are not of upstream base of Cabinet Gorge Dam. It is highly unlikely that bull origin, passage may cause outbreeding depression by intro- trout collected at the base of Cabinet Gorge Dam originated ducing genes from individuals that are not locally adapted from bull trout native to Lake Pend Oreille tributaries. ( Phillip 1991; Waples 1992). Alternatively, if some fish are Allele frequency differences indicate substantial genetic uniquely adapted to reproduce and survive in the main- differentiation between Cabinet Gorge samples and bull stem Clark Fork River below Cabinet Gorge Dam, passage trout collected from tributaries to Lake Pend Oreille. In could eliminate a large proportion of those individuals, addition, the SCO19*202 allele is extremely rare in Lake increasing the chance of extirpation for that population. Pend Oreille tributaries but is common in lower Clark Fork It is clear that fish collected at Cabinet Gorge Dam are tributaries (Appendix I). This allele is found in two of the genetically more similar to populations located above the three samples collected at the dam. We suspect that the dam. This relationship suggests that passing fish above the assignment test results for the 1997 Cabinet Gorge Dam dam is unlikely to produce severe outbreeding depression.

1160 L. P. NERAAS and P. SPRUELL

Additionally, these data do not support the existence of 3.5c. Distributed by the author. Department of Genetics, Univer- a unique population at the base of Cabinet Gorge Dam. sity of Washington, Seattle. Therefore, it is unlikely that passing individuals from this Flatter B (1998) Life History and population status of migratory bull trout (Salvelinus confluentus) in Arrowrock Reservoir, Idaho. Final group of fish will negatively impact a small mainstem- report to the United States Department of the Interior, Bureau of spawning population. The risks associated with passing Reclamation, Pacific Northwest Region. Boise, Idaho. radio tagged adults are minimal compared to the potential Jeppson P (1954) Location and evaluation of spawning areas in Lake genetic and demographic benefits to populations located Pend Oreille and tributaries upstream from Albeni Falls Dam in Idaho above the dam. with special reference to kokanee, April 1, 1953 — March 31, 1954. Job completion report. Federal Aid to Fish and Wildlife Restoration. Idaho Department of Fish and Game, Boise, Idaho. Conclusion National Resource Council (1996) Upstream: salmon and society in the Pacific Northwest. Committee on Protection and Management Our data suggest that re-establishing connectivity be- of Pacific Northwest Anadromous Salmonids, Portland, OR & tween Lake Pend Oreille and tributaries of the lower Seattle, WA. Clark Fork River may be beneficial for the persistence of Nehlsen W, Williams JE, Lichatowich JA (1991) Pacific salmon at bull trout populations. In addition to Cabinet Gorge Dam, the crossroads: stocks risk from California, Oregon, Idaho and Noxon Rapids and Thompson Falls Dams limit migration Washington. Fisheries, 16, 4–21. of aquatic fauna. Labour-intensive projects focused on Nielsen JL, Carpanzano C, Fountain MC, Gan CA (1997) Mito- chondrial DNA and nuclear microsatellite diversity in hatchery single species and individual hydroelectric projects are and wild Oncorhynchus mykiss from freshwater habitats in probably inefficient and are not long-term solutions to the southern California. Transactions of the American Fisheries Society, problem. Construction of facilities that allow species to 12, 397–417. migrate freely throughout the system are currently being Olsen JB, Bentzen P, Seeb JE (1998) Characterization of seven considered. Restoring the connectivity that historically microsatellite loci derived from pink salmon. Molecular Ecology, existed will increase the evolutionary potential of aquatic 7, 1087–1089. fauna in the system and is a more desirable approach to Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobek C (1997) An empirical evaluation of genetic distance statistics using system-wide management. microsatellite data from bear (Ursidae) populations. Genetics, 147, 1943–1957. Acknowledgements Phillip DP (1991) Genetic implications of stocking Florida large- mouth bass, Micropterus salmoides floridanus. Canadian Journal This project was funded by a grant from Avista Corporation and of Fisheries and Aquatic Sciences, 48 (Suppl. 1), 58–65. by a grant to LPN from the Davidson Honors College at the Pratt KL, Huston JE (1993) Status of bull trout (Salvelinus confluentus) University of Montana. We thank Chip Corsi, Chris Downs, Karen in Lake Pend Oreille and the lower Clark Fork River. Draft Report Pratt, Pat Saffel, and Ginger Gillin-Thomas for helpful discussions prepared for the Washington Water Power Company, Spokane, on the Lake Pend Oreille/lower Clark Fork River system. We also Washington. thank Andrew Whiteley, Aaron Maxwell, Zach Wilson, and Kathy Raymond M, Rousset F (1995) genepop (version 1.2): population Knudsen for their valuable suggestions regarding this system. genetics software for exact tests and ecumenicism. Journal of Zach Wilson also collected the genetic data from tributaries to Heredity, 83, 248–249. Lake Pend Oreille. Fred W. Allendorf, Damian M. Cremins, Ellie K. Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, Steinburg, and Kristina Ramstad offered helpful comments on 223–225. earlier versions of this paper. Finally, we thank Bruce Rieman for Rieman BE, Dunham JB (2000) Metapopulation and Salmonids: a his assistance with the PBR and his other immeasurable contribu- synthesis of life history patterns and empirical observations. tions to this work. Ecology of Freshwater Fish, 9, 51–64. Rieman BE, McIntyre JD (1993) Demographic and habitat requirements References for conservation of bull trout. General Technical Report INT-302. U.S. Forest Service, Intermountain Research Station, Ogden Utah. Angers B, Bernatchez L, Angers A, Desgroseillers (1995) Specific Ruban GI (1997) Species structure, contemporary distribution and microsatellite loci for brook charr (Salvelinus fontinalis, Mitchill) status of the Siberian sturgeon, Acipenser baerii. Enivironmental reveal strong population subdivision on a microgeographic Biology of Fishes, 48, 221–230. scale. Journal of Fish Biology, 47, 117–185. Sakamoto T, Okamoto N, Ikeda Y (1994) Dinucleotide repeat poly- Barthem RB, Ribeiro MB, Petrere M (1991) Life strategies of some morphism of rainbow trout, FGT3. Journal of Animal Science, 72, long-distance migratory catfish in relation to hydroelectric 2766. dams in the Amazon Basin. Biological Conservation, 55, 339–345. Scribner KT, Gust J, Fields RL (1996) Isolation and characterization Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: of novel microsatellite loci: cross-species amplification and models and estimation procedures. Evolution, 21, 550–570. population genetic applications. Canadian Journal of Fisheries and Federal Register (1999) Endangered and threatened wildlife and Aquatic Sciences, 53, 883–841. plants; determination of threatened status for bull trout in the Slettan A, Olsaker I, Lie O (1995) Atlantic salmon, Salmo salar, coterminous United States. Federal Register, 64, 58910–58933. microsatellites at the SSOSL25, SSOSL311, SSOSL417 loci. Animal Felsenstein J (1993) PHYLIP (Phylogeny Inference Package), Version Genetics, 27, 57–64.

ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1161

Small MP, Beacham TD, Withler RE, Nelson RJ (1998) Discriminat- Congress (eds Philipp DP, Epifanio JM, Marsden JE, Claussen), ing coho salmon (Oncorhynchus kisutch) populations within pp. 51–69. American Fisheries Society. the Fraser River, British Columbia, using microsatellite DNA Wei Q, Ke F, Zhang J et al. (1997) Biology, fisheries, and conserva- markers. Molecular Ecology, 7, 141–155. tion of sturgeons and paddlefish in China. Environmental Biology Sokal RR, Rohlf FJ (1995) Biometry: the Principles and Practice of Fishes, 48, 241–255. Statistics in Biological Research. W. H. Freeman, New York 887pp. Spruell P, Rieman BE, Knudsen KL, Utter FM, Allendorf FW (1999) Genetic population structure within streams: microsatel- Lukas P. Neraas is a Research Specialist and Paul Spruell is lite analysis of bull trout populations. Ecology of Freshwater Fish, a Research Assistant Professor in the Wild Trout and Salmon 8, 114–121. Genetics Laboratory at the University of Montana. Our laboratory Swanberg TR (1997) Movements of and habitat use by fluvial bull uses molecular techniques to address questions of conservation trout in the Blackfoot River, Montana. Transaction of the American biology in native salmonids. This work is part of an ongoing study Fisheries Society, 126, 735–746. of bull trout population dynamics in the Lake Pend Oreille/Clark Waples RS (1992) Genetic effects of stock transfers of fish. In: Fork River system. Protection of Aquatic Biodiversity. Proceedings of the world fisheries

1162 L. P. NERAAS and P. SPRUELL

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

140 2* 105 335 447 522 641 781 840 919 10 24 11 23 12b 15 12b 28 12c 26 13* 60 14 30 15 14 16 30 17 30 18* 43 19* 37

ONEµ7 SFO18 OTS101 Sample site *218 *244 *150 *156 *100 *112

1 0.676 0.324 1.000 — 0.538 0.462 2 0.971 0.029 0.867 0.133 0.762 0.238 3 0.700 0.300 0.900 0.100 0.986 0.014 4 0.777 0.223 0.798 0.202 0.909 0.091 5 1.000 — 0.659 0.341 1.000 — 6 1.000 — 0.659 0.341 0.825 0.175 7 0.994 0.006 0.762 0.238 0.809 0.191 8 0.900 0.100 0.931 0.069 1.000 — 9 0.947 0.053 0.974 0.026 0.917 0.083 10 0.792 0.208 0.917 0.083 0.938 0.062 11 0.841 0.159 0.957 0.043 1.000 — 12b 0.800 0.200 0.692 0.308 0.967 0.033 12b 0.852 0.148 0.839 0.161 1.000 — 12c 0.896 0.104 0.940 0.060 0.854 0.146 13 0.813 0.187 0.847 0.153 0.939 0.061 14 0.931 0.069 0.914 0.086 0.983 0.017 15 0.643 0.357 0.107 0.893 0.833 0.167 16 1.000 — 0.717 0.283 1.000 0.000 17 0.630 0.370 0.714 0.286 0.983 0.017 18 0.895 0.105 0.962 0.038 1.000 — 19 0.892 0.108 0.924 0.076 0.941 0.059

FGT3 Sample site *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 — —

ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1163

Appendix I Continued

FGT3 Sample site *165 *167 *169 *171 *173 *175 *179

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 — 0.008 14 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 —

SCO19 Sample site *174 *178 *188 *200 *202 *212 *216

1 0.932 — 0.014 — — — 0.054 2 0.851 0.067 — 0.014 0.005 — 0.063 3 0.500 — — 0.186 — — 0.314 4 0.745 — — 0.064 — — 0.191 5 0.950 — 0.050 — — — — 6 0.902 — 0.098 — — — — 7 0.772 — 0.198 0.006 — — 0.024 8 0.814 — — 0.114 — — 0.072 9 0.816 — — 0.026 — — 0.158 10 0.979 — — — — — 0.021 11 0.294 — — 0.500 — — 0.206 12b 0.300 — — 0.367 0.100 — 0.233 12b 0.393 — 0.018 0.321 0.018 — 0.250 12c 0.444 — — 0.444 — — 0.112 13 0.380 — 0.065 0.472 0.009 0.009 0.065 14 0.467 — — 0.333 0.017 — 0.183 15 0.900 — — 0.050 — — 0.050 16 0.315 — — 0.407 0.130 — 0.148 17 0.283 — — 0.022 0.196 — 0.499 18 0.157 — — 0.800 0.043 — — 19 0.236 — — 0.569 0.014 — 0.181

OGO2 SSA311 SSA456 Sample site *150 *154 *156 *162 *112 *120 *157 *159

1 0.050 — 0.325 0.625 0.128 0.872 0.775 0.225 2 0.150 0.063 0.466 0.321 0.010 0.990 0.486 0.514 3 0.029 0.176 0.529 0.266 — 1.000 0.714 0.286 4 0.213 0.160 0.298 0.329 0.053 0.947 0.611 0.389 5 0.386 — 0.409 0.205 — 1.000 0.528 0.472 6 0.220 0.037 0.293 0.450 0.188 0.812 0.462 0.538 7 0.185 0.074 0.432 0.309 0.099 0.901 0.605 0.395 8 0.375 0.347 0.167 0.111 0.056 0.944 0.778 0.222 9 0.083 0.028 0.417 0.472 0.026 0.974 0.737 0.263

1164 L. P. NERAAS and P. SPRUELL

Appendix I Continued

OGO2 SSA311 SSA456 Sample site *150 *154 *156 *162 *112 *120 *157 *159

10 0.292 0.063 0.313 0.332 0.188 0.812 0.458 0.542 11 0.023 0.432 0.318 0.227 0.205 0.795 0.525 0.475 12b 0.067 0.267 0.333 0.333 0.200 0.800 0.433 0.567 12b 0.161 0.375 0.411 0.053 0.232 0.768 0.357 0.643 12c 0.125 0.458 0.354 0.063 0.180 0.820 0.480 0.520 13 0.173 0.564 0.200 0.063 0.176 0.824 0.372 0.628 14 0.071 0.304 0.571 0.054 0.232 0.768 0.315 0.685 15 0.100 0.700 0.200 — — 1.000 0.923 0.077 16 0.250 0.393 0.357 — 0.217 0.783 0.383 0.617 17 — 0.107 0.839 0.054 0.300 0.700 0.328 0.672 18 — 0.553 0.447 — 0.107 0.893 0.238 0.762 19 0.069 0.583 0.278 0.070 0.351 0.649 0.338 0.662