Fragmentation of riverine systems: the genetic effects of

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1 Molecular Ecology (2001) 10, Fragmentation of riverine systems: the genetic effects of Blackwell Science, Ltd 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 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 disrupting 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 Introduction Habitat fragmentation may take dramatically different forms in terrestrial and riverine habitats. Fragmentation of terrestrial habitats is usually associated with alteration in large tracts of land, precluding migration among the remaining patches of suitable habitat. In riverine systems, hydroelectric dams and irrigation diversions may cause fragmentation at specific points along the stream corridor. The effects that dams may have on fish species have been documented throughout the world. The described population declines are primarily due to the change from a riverine to a lacustrine environment and the isolation of migratory fishes from their spawning and feeding grounds (for example, Barthem et al. 1991; Wei et al. 1997; Ruban 1997). These disruptions may cause local extinction if critical habitats are lost or no longer accessible. Correspondence: Paul Spruell. Fax: (406) ; spruell@selway.umt.edu There are many examples of the extirpation of anadromous Pacific Salmon stocks that are unable to reach their spawning grounds after the construction of impassable dams (National Resource Council 1996; Nehlsen et al. 1991). However, relatively little work has explored the changes in the genetic population structure of fishes caused by dams. The available data suggest that fragmentation associated with dams has caused a loss of genetic variation in anadromous steelhead isolated above impoundments (Nielsen et al. 1997). Hydroelectric dams may also impact nonanadromous fishes. Some inland fish populations exhibit both resident and migratory life histories. Resident fish complete their lifecycle within small streams, while migratory individuals spawn in smaller streams but use larger bodies of water as subadults and adults. Movement between habitats is critical for the expression of all life histories within a population. If different life histories buffer a population against local extinction, the elimination of a life history type will increase the chance of extirpation. Additionally, habitat fragmentation can preclude migration between populations 2001 Blackwell Science Ltd

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

3 ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1155 this system. Apparently, the construction of the spawning channel did not adequately compensate for the losses caused by the disruption of the migratory corridor. Large adult bull trout continue to congregate near the spillway of Cabinet Gorge Dam from the end of peak flow to early autumn when most migratory bull trout begin their spawning movements. The origin of those fish is uncertain but four hypotheses are likely. First, bull trout may have historically spawned in the mainstem of the Clark Fork River and have continued to persist there after the construction of the dam. Second, bull trout that hatched in tributaries to Lake Pend Oreille could have established a population below the dam after its construction. Third, the bull trout that return to Cabinet Gorge Dam may be remnants of individuals from upstream populations that became isolated in 1952 after the closure of the dam. Finally, bull trout that congregate at the base of Cabinet Gorge Dam may be migratory fish that hatched in tributaries above the dam and continue to pass downstream over the dam during annual outmigrations and are unable to return to their natal streams to spawn. Movements of tagged bull trout indicate that some individuals pass downstream over dams. Eight per cent of a radio tagged sample of migratory bull trout that originated in the Blackfoot River, MT, swam downstream over Milltown Dam (Swanberg 1997). Similarly, 18% of bull trout tagged in the Boise River system passed downstream over Arrowrock Dam ( Flatter 1998). The proportion of outmigrating juveniles that suffer a similar fate is currently unknown. However, these data suggest that hydroelectric impoundments can cause geographical and genetic isolation of migratory fish from their natal tributaries. The metapopulation dynamics and genetic population structure of bull trout in Lake Pend Oreille have been extensively explored and described by, Rieman & McIntyre (1993), Pratt & Huston (1993), Rieman & Dunham (2000), and Spruell et al. (1999). These descriptions suggest that metapopulation dynamics and alternate life history forms may buffer bull trout populations from local extinction events. This suggests that actions aiding movement within the system may begin to reverse the decline of these fragmented bull trout populations. Our objective was to determine the origin of adult bull trout that return to the base of Cabinet Gorge Dam. We used eight microsatellite loci to estimate the amount of connectivity, or gene flow, between populations within the basin. We also used these data to establish a baseline genetic data set representative of populations in the system. Using these data, we estimated the probable origin of the adult bull trout that return to the base of Cabinet Gorge Dam. Finally, we consider the genetic risks associated with the transport of fish over dams throughout the Lower Clark Fork River vs. risks associated with maintaining the existing migration barriers in the system. Methods Study location and individual collection Bull trout were collected from 10 tributaries of Lake Pend Oreille and eight tributaries to the Lower Clark Fork River ( Fig. 1, Table 1). Fish were captured using block nets, fish weirs, or electrofishing techniques while they were holding in tributaries prior to spawning. These individuals should be representative of the spawning aggregates in each tributary. Adult bull trout returning to the base of Cabinet Gorge Dam were collected in 1997, 1998, and 1999 either in a fish trap at the nearby Cabinet Gorge Hatchery or by boat-based electrofishing. A nonlethal fin clip was taken from each individual and stored in 95% ethanol. DNA was extracted from fin tissue with a Purgene kit (Gentra). Identification of hybrids Individuals from populations in which hybridization with non-native brook trout (Salvelinus fontinalis) was suspected were screened using PINE-PCR (Spruell et al., unpublished data). Three hybrids were eliminated from the original 17 individuals collected in Swamp Creek (15). Ten of the 33 Twin Creek (11) individuals were also removed from the sample due to hybridization. Of the hybrid individuals, a single individual from Twin Creek (11) was identified as a later generation hybrid. All remaining hybrids were first generation (F 1 ). It does not appear that there is continual introgression between species in these populations. Therefore, the remaining individuals from Swamp Creek (15) and Twin Creek (11) are probably not hybrids and were included in subsequent analyses. Microsatellite amplification and analysis We amplified eight microsatellite loci in an MJ Research PTC-100 thermocycler using profiles described by initial investigators of each locus (ONEµ7, 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 on a 7% denaturing polyacrylamide gel and visualized using a Hitachi FMBIO-100 fluorescent imager. Allele sizes were determined relative to a standard base pair size ladder (MapMarkerLow, Bioventures). Previously amplified products were included on each gel to ensure consistent scoring of 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

4 1156 L. P. NERAAS and P. SPRUELL Population number location Number Expected heterozygoisty Below Dam 1 Grouse Creek Trestle Creek* Granite Creek Gold Creek Morris Creek Savage Creek East Fork Lightning Creek Porcupine Creek Rattle Creek upper Lightning Creek Twin Creek Dam 12a Cabinet Gorge Dam b Cabinet Gorge Dam c Cabinet Gorge Dam Above Dam 13 East Fork Bull River* Rock Creek Swamp Creek Graves Creek Prospect Creek Thompson River* Fishtrap Creek* Number of alleles Table 1 sites, number, expected heterozygosity and average number of alleles per locus for bull trout collected from tributaries to the lower Clark Fork River and Lake Pend Oreille. Population numbers correspond to sample sites indicated in Fig. 1. The asterisk (*) indicates sites at which samples were collected in multiple years Weinberg expectations ( Raymond & Rousset 1995). We used a Cavalli-Sforza and Edwards chord distance (CSE) to estimate the genetic similarity among populations (Cavalli- Sforza & Edwards 1967). A upgma dendrogram was generated using phylip (Felsenstein 1993). This dendrogram allowed us to visualize the genetic similarity among samples within the system. To estimate the probable origins of Cabinet Gorge bull trout we used Paetkau s online calculator to conduct an assignment test. This test determines the most probable origin of each individual based on the expected genotypic frequencies of each sample (Paetkau et al. 1997). Results Variation within sample sites The amount of variation detected in these samples was similar to earlier microsatellite studies in this system (Spruell et al. 1999). All eight of the loci analysed were polymorphic in at least one sample site (Appendix I). After correcting for multiple tests ( Rice 1989), we found no deviations from Hardy Weinberg proportions in any of the samples analysed. Expected heterozygosity averaged and ranged from to (Table 1). The number of alleles per sample ranged from 16 to 24 and averaged 20.5 (Table 1). In four sites (2, 13, 18, and 19), individuals were collected in two consecutive years. After combining probabilities across all loci (Sokal & Rohlf 1995), we found no statistically significant differences in genotypic frequencies between temporal samples within any of the four sites. Therefore, we pooled the temporal samples from each site in all subsequent analyses. The samples collected at the base of Cabinet Gorge dam in 1997 (12a), 1998 (12b), and 1999 (12c) were not pooled since we cannot assume they represent a single spawning population. Differentiation among samples Differences in allele frequencies suggest that there is substantial genetic differentiation among populations (F ST = 0.137). A upgma dendrogram based on CSE chord distance was used to visualize the relative genetic similarity among samples (Fig. 2). The dendrogram ( Fig. 2) suggests that there is substantial differentiation between samples collected in tributaries to Lake Pend Oreille and those collected in lower Clark Fork River tributaries. Swamp Creek (15) exists as an outlier (Fig. 2) due to its high frequency of a normally rare allele at the SFO18 locus, and a low frequency of a normally common allele at the FGT3 locus (Appendix I). In all samples from Lake Pend Oreille tributaries, proportionally more individuals were assigned to their population of origin than to any other site (Table 2). This is also true 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

5 ORIGINS OF BULL TROUT AT CABINET GORGE DAM a 19 12b 14 12c The results of the assignment test also support the genetic similarity of Cabinet Gorge samples with those from above-dam tributaries. The Cabinet Gorge Dam samples (12a, 12b, 12c) did not proportionally have more individuals assigned back to their sample origin ( Table 2). The 1998 (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, these results may be due to a small sample size (Table 1) Fig. 2 upgma dendrogram based on Cavalli-Sforza & Edwards (1967) chord distance for bull trout sampled from tributaries to Lake Pend Oreille and the lower Clark Fork River. Numbers denote sample locations from Table 1 and Fig. 1. White circles indicate locations below Cabinet Gorge Dam, black circles are locations above the dam, and diamonds are samples collected at the base of the dam in three consecutive years (12a = 1997, 12b = 1998, 12c = 1999). Lines under the location number indicate geographical location relative to the dam. to this observation. Individuals from these two samples are not preferentially assigned to any site. Rather, they are distributed throughout the system. Individuals that did not get assigned back to their original collection were not assigned at random. Individuals from below-dam sites that were not assigned back to their original sample site are most frequently assigned to another below-dam site. Similarly, individuals from abovedam sites that were not assigned back to their original sample site are most frequently assigned to another abovedam site. Table 2 separates above-dam and below-dam sites into quadrants, where this observation is most apparent (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 the dendrogram. These results are unexpected for temporal samples collected from a single isolated bull trout population (Spruell et al. 1999). The Cabinet Gorge samples are dispersed with the lower Clark Fork River samples ( Fig. 2). This suggests that bull trout sampled from the base of Cabinet Gorge Dam (12a, 12b, 12c) are more genetically similar to samples collected from tributaries located above the dam Discussion Relationships among sample sites The microsatellite data suggest substantial genetic differentiation among samples collected from spawning aggregates above and below Cabinet Gorge Dam. This differentiation is based primarily on differences in allele frequencies. All of the alleles observed were found throughout the system. However, one allele (SCO19*202) is represented in Lake Pend Oreille by a single allele copy in a heterozygous individual from Trestle Creek (2). This allele is present in six of the seven populations from the lower Clark Fork River. This difference in allelic distribution further supports the genetic differentiation among samples above and below Cabinet Gorge Dam. Swamp Creek (15), an exception to this pattern, is highly differentiated from all remaining samples. This deviation is probably being driven by a high frequency of a rare allele (SFO*156), and a low frequency of a normally common allele (FGT3*165; Appendix I). Accurate estimates of the bull trout population size in Swamp Creek (15) are not available. However, only four redds were found in a 1993 survey ( Pratt & Huston 1993) suggesting that the population exists at low numbers and is prone to the effects of genetic drift. Hybridization with brook trout may also be acting to reduce the effective populations size in Swamp Creek. Twin Creek (11) is also an exception to the clustering of 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 similar to above-dam sites. Spawning habitat in Twin Creek (11) is marginal (Pratt & Huston 1993) and may have resulted in a small population subject to the effects of genetic 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 similarity to upriver populations ( Fig. 2) is straying by adults originating in lower Clark Fork River tributaries. They may enter and spawn in Twin Creek (11), the nearest available tributary since their migratory corridor is blocked by Cabinet Gorge Dam. The poor habitat conditions in Twin

6 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 eight microsatellite 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 a 12b 12c Below Dam Dam 12a b c Above Dam L. P. NERAAS and P. SPRUELL

7 ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1159 Creek (11) may limit juvenile survival, producing a population sink that is only maintained by the annual spawning of these blocked fish. Genotypic assignment test We used Paetkau s assignment test to estimate the origins of bull trout returning to Cabinet Gorge Dam. Our power to assign individuals to a specific population is limited by the low number of individuals collected from some sites. However, the overall pattern of assignment either above or below the dam should not be altered by this limitation. The results of the genotypic assignment test support the differentiation among sites above and below Cabinet Gorge Dam. Individuals collected from Lake Pend Oreille tributaries are much more likely to be assigned to other lake tributaries than to upriver sites. Similarly, individuals from tributaries to the lower Clark Fork River are more likely to be assigned to other sites above Cabinet Gorge Dam. Most individuals are assigned back to the site from which they were captured. Only samples collected in the East Fork Bull River (13) and at the base of Cabinet Gorge Dam (12a, 12b, 12c) were assigned to another site more frequently than to their site of capture. Individuals from Gold Creek (4) were also assigned back to their origin with low frequency. However, individuals from populations with high levels of variation may be assigned to various populations by chance. s from Cabinet Gorge Dam (12a, 12b, 12c) also have high levels of variation (Table 1). Two of the Cabinet Gorge Dam samples, 12b and 12c, are assigned preferentially to above dam populations (Table 2). However, the 12a samples have 56% of their sample assigned to below dam sites. This observation may be due to a low sample size (n = 15). We expect these results if the Cabinet Gorge samples are composed of individuals from multiple populations. Probable origins of Cabinet Gorge Dam bull trout These data allow us to examine the hypotheses that we proposed to explain the presence of adult bull trout at the base of Cabinet Gorge Dam. It is highly unlikely that bull trout collected at the base of Cabinet Gorge Dam originated from bull trout native to Lake Pend Oreille tributaries. Allele frequency differences indicate substantial genetic differentiation between Cabinet Gorge samples and bull trout collected from tributaries to Lake Pend Oreille. In addition, the SCO19*202 allele is extremely rare in Lake Pend Oreille tributaries but is common in lower Clark Fork tributaries (Appendix I). This allele is found in two of the three samples collected at the dam. We suspect that the assignment 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 upgma dendrogram that clusters the 1997 (12a) sample with above dam samples. We cannot dismiss the possibility that a founding event could have taken place immediately after the closure of the Cabinet Gorge impoundment in Our data, however, do not support the hypothesis of a single founding event. We expect founders to contribute only a subset of alleles to their progeny. Genetic drift should also eliminate alleles and would most likely produce a reduction in the population s heterozygosity. We would expect similar results if a small population of historic mainstem spawners were responsible for the adult bull trout that return to Cabinet Gorge Dam each year. The data are more consistent with the results expected from a sample representing multiple populations. s collected independently from the same spawning aggregate should cluster together on allele frequency-based dendrograms. The samples from Cabinet Gorge Dam (12a, 12b, 12c) do not conform with this observation ( Fig. 2). Similarly, individuals from a population are usually assigned back to the population from which they were collected. Two Cabinet Gorge Dam samples (12b and 12c) are preferentially assigned to samples from tributaries above the dam rather than back to their initial sampling location. These data support the hypothesis that Cabinet Gorge Dam adults are a mixture composed primarily of migratory individuals from tributaries to the Clark Fork River that pass downstream over the dam to rear in Lake Pend Oreille. Genetic risks associated with passage Genetic data alone cannot determine the source of the fish returning to Cabinet Gorge Dam and the four hypotheses we proposed are not mutually exclusive. However, we can use these data to better assess the genetic risks associated with passing adult bull trout that return to the base of Cabinet Gorge Dam. There are two major genetic concerns that must be addressed prior to the initiation of fish passage. First, if the bull trout below Cabinet Gorge Dam are not of upstream origin, passage may cause outbreeding depression by introducing genes from individuals that are not locally adapted ( Phillip 1991; Waples 1992). Alternatively, if some fish are uniquely adapted to reproduce and survive in the mainstem Clark Fork River below Cabinet Gorge Dam, passage could 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 are genetically more similar to populations located above the dam. This relationship suggests that passing fish above the dam is unlikely to produce severe outbreeding depression.

8 1160 L. P. NERAAS and P. SPRUELL Additionally, these data do not support the existence of a unique population at the base of Cabinet Gorge Dam. Therefore, it is unlikely that passing individuals from this group of fish will negatively impact a small mainstemspawning population. The risks associated with passing radio tagged adults are minimal compared to the potential genetic and demographic benefits to populations located above the dam. Conclusion Our data suggest that re-establishing connectivity between Lake Pend Oreille and tributaries of the lower Clark Fork River may be beneficial for the persistence of bull trout populations. In addition to Cabinet Gorge Dam, Noxon Rapids and Thompson Falls Dams limit migration of aquatic fauna. Labour-intensive projects focused on single species and individual hydroelectric projects are probably inefficient and are not long-term solutions to the problem. Construction of facilities that allow species to migrate freely throughout the system are currently being considered. Restoring the connectivity that historically existed will increase the evolutionary potential of aquatic fauna in the system and is a more desirable approach to system-wide management. Acknowledgements This project was funded by a grant from Avista Corporation and by a grant to LPN from the Davidson Honors College at the University of Montana. We thank Chip Corsi, Chris Downs, Karen Pratt, Pat Saffel, and Ginger Gillin-Thomas for helpful discussions on the Lake Pend Oreille/lower Clark Fork River system. We also thank Andrew Whiteley, Aaron Maxwell, Zach Wilson, and Kathy Knudsen for their valuable suggestions regarding this system. Zach Wilson also collected the genetic data from tributaries to Lake Pend Oreille. Fred W. Allendorf, Damian M. Cremins, Ellie K. Steinburg, and Kristina Ramstad offered helpful comments on earlier versions of this paper. Finally, we thank Bruce Rieman for his assistance with the PBR and his other immeasurable contributions to this work. References Angers B, Bernatchez L, Angers A, Desgroseillers (1995) Specific microsatellite loci for brook charr (Salvelinus fontinalis, Mitchill) reveal strong population subdivision on a microgeographic scale. Journal of Fish Biology, 47, Barthem RB, Ribeiro MB, Petrere M (1991) Life strategies of some long-distance migratory catfish in relation to hydroelectric dams in the Amazon Basin. Biological Conservation, 55, Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Evolution, 21, Federal Register (1999) Endangered and threatened wildlife and plants; determination of threatened status for bull trout in the coterminous United States. Federal Register, 64, Felsenstein J (1993) PHYLIP (Phylogeny Inference Package), Version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle. Flatter B (1998) Life History and population status of migratory bull trout (Salvelinus confluentus) in Arrowrock Reservoir, Idaho. Final report to the United States Department of the Interior, Bureau of Reclamation, Pacific Northwest Region. Boise, Idaho. Jeppson P (1954) Location and evaluation of spawning areas in Lake Pend Oreille and tributaries upstream from Albeni Falls Dam in Idaho with special reference to kokanee, April 1, 1953 March 31, Job completion report. Federal Aid to Fish and Wildlife Restoration. Idaho Department of Fish and Game, Boise, Idaho. National Resource Council (1996) Upstream: salmon and society in the Pacific Northwest. Committee on Protection and Management of Pacific Northwest Anadromous Salmonids, Portland, OR & Seattle, WA. Nehlsen W, Williams JE, Lichatowich JA (1991) Pacific salmon at the crossroads: stocks risk from California, Oregon, Idaho and Washington. Fisheries, 16, Nielsen JL, Carpanzano C, Fountain MC, Gan CA (1997) Mitochondrial DNA and nuclear microsatellite diversity in hatchery and wild Oncorhynchus mykiss from freshwater habitats in southern California. Transactions of the American Fisheries Society, 12, Olsen JB, Bentzen P, Seeb JE (1998) Characterization of seven microsatellite loci derived from pink salmon. Molecular Ecology, 7, Paetkau D, Waits LP, Clarkson PL, Craighead L, Strobek C (1997) An empirical evaluation of genetic distance statistics using microsatellite data from bear (Ursidae) populations. Genetics, 147, Phillip DP (1991) Genetic implications of stocking Florida largemouth bass, Micropterus salmoides floridanus. Canadian Journal of Fisheries and Aquatic Sciences, 48 (Suppl. 1), Pratt KL, Huston JE (1993) Status of bull trout (Salvelinus confluentus) in Lake Pend Oreille and the lower Clark Fork River. Draft Report prepared for the Washington Water Power Company, Spokane, Washington. Raymond M, Rousset F (1995) genepop (version 1.2): population genetics software for exact tests and ecumenicism. Journal of Heredity, 83, Rice WR (1989) Analyzing tables of statistical tests. Evolution, 43, Rieman BE, Dunham JB (2000) Metapopulation and Salmonids: a synthesis of life history patterns and empirical observations. Ecology of Freshwater Fish, 9, Rieman BE, McIntyre JD (1993) Demographic and habitat requirements for conservation of bull trout. General Technical Report INT-302. U.S. Forest Service, Intermountain Research Station, Ogden Utah. Ruban GI (1997) Species structure, contemporary distribution and status of the Siberian sturgeon, Acipenser baerii. Enivironmental Biology of Fishes, 48, Sakamoto T, Okamoto N, Ikeda Y (1994) Dinucleotide repeat polymorphism of rainbow trout, FGT3. Journal of Animal Science, 72, Scribner KT, Gust J, Fields RL (1996) Isolation and characterization of novel microsatellite loci: cross-species amplification and population genetic applications. Canadian Journal of Fisheries and Aquatic Sciences, 53, Slettan A, Olsaker I, Lie O (1995) Atlantic salmon, Salmo salar, microsatellites at the SSOSL25, SSOSL311, SSOSL417 loci. Animal Genetics, 27,

9 ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1161 Small MP, Beacham TD, Withler RE, Nelson RJ (1998) Discriminating coho salmon (Oncorhynchus kisutch) populations within the Fraser River, British Columbia, using microsatellite DNA markers. Molecular Ecology, 7, Sokal RR, Rohlf FJ (1995) Biometry: the Principles and Practice of 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: microsatellite analysis of bull trout populations. Ecology of Freshwater Fish, 8, Swanberg TR (1997) Movements of and habitat use by fluvial bull trout in the Blackfoot River, Montana. Transaction of the American Fisheries Society, 126, Waples RS (1992) Genetic effects of stock transfers of fish. In: Protection of Aquatic Biodiversity. Proceedings of the world fisheries Congress (eds Philipp DP, Epifanio JM, Marsden JE, Claussen), pp American Fisheries Society. Wei Q, Ke F, Zhang J et al. (1997) Biology, fisheries, and conservation of sturgeons and paddlefish in China. Environmental Biology Fishes, 48, Lukas P. Neraas is a Research Specialist and Paul Spruell is a Research Assistant Professor in the Wild Trout and Salmon Genetics Laboratory at the University of Montana. Our laboratory uses molecular techniques to address questions of conservation biology in native salmonids. This work is part of an ongoing study of bull trout population dynamics in the Lake Pend Oreille/Clark Fork River system.

10 1162 L. P. NERAAS and P. SPRUELL Appendix I size (n) and allele frequencies at eight polymorphic loci for bull trout collected in the Lake Oend Oreille/lower Clark Fork system. locations correspond to Figure1 and Table 1 site n * b 15 12b 28 12c 26 13* * 43 19* 37 site ONEµ7 SFO18 OTS101 *218 *244 *150 *156 *100 * b b c site FGT3 *165 *167 *169 *171 *173 *175 *

11 ORIGINS OF BULL TROUT AT CABINET GORGE DAM 1163 Appendix I Continued site FGT3 *165 *167 *169 *171 *173 *175 * b b c site SCO19 *174 *178 *188 *200 *202 *212 * b b c site OGO2 SSA311 SSA456 *150 *154 *156 *162 *112 *120 *157 *

12 1164 L. P. NERAAS and P. SPRUELL Appendix I Continued site OGO2 SSA311 SSA456 *150 *154 *156 *162 *112 *120 *157 * b b c