Isolation and cross‐familial amplification of 41 microsatellites for the brook charr (Salvelinus fontinalis)

The brook charr (Salvelinus fontinalis; Osteichthyes: Salmonidae) is a phenotypically diverse fish species inhabiting much of North America. But relatively few genetic diagnostic resources are available for this fish species. We isolated 41 microsatellites from S. fontinalis polymorphic in one or more species of salmonid fish. Thirty‐seven were polymorphic in brook charr, 15 in the congener Arctic charr (Salvelinus alpinus) and 14 in the lake charr (Salvelinus namaycush). Polymorphism was also relatively high in Oncorhynchus, where 21 loci were polymorphic in rainbow trout (Oncorhynchus mykiss) and 16 in cutthroat trout (Oncorhynchus clarkii) but only seven and four microsatellite loci were polymorphic in the more distantly related lake whitefish (Coregonus clupeaformis) and Atlantic salmon (Salmo salar), respectively. One duplicated locus (Sfo228Lav) was polymorphic at both duplicates in S. fontinalis.     

Spatial patterns of hybridization between bull trout, <Emphasis Type="Italic">Salvelinus confluentus</Emphasis>, and brook trout, <Emphasis Type="Italic">Salvelinus fontinalis</Emphasis> in an Oregon stream network

Hybridization with introduced species represents a serious threat to the persistence of many native fish populations. Brook trout (Salvelinus fontinalis) have been introduced extensively throughout the native range of bull trout (S. confluentus) and hybridization has been documented in several systems where they co-exist and is seen as a significant threat to the persistence of bull trout populations. We identified a group of diagnostic microsatellite loci to differentiate bull trout and brook trout and then used these loci to examine the spatial distribution of hybrids in the Malheur River basin, Oregon USA. In random samples of approximately 100 fish from each of three creeks we identified 181 brook trout, 112 bull trout and 14 hybrids. Although bull trout, brook trout and hybrids were found in all three creeks, they were not evenly distributed; brook trout were primarily found in the lower sections of the creeks, bull trout further upstream, and hybrids in the areas of the greatest overlap. One creek with a population of brook trout in a headwater lake provided an exception to this pattern; brook trout were found distributed throughout the creek downstream of the lake. Several post-F1 hybrids were identified suggesting that hybrids are reproducing in the Malher River Basin. Mitochondrial DNA analysis indicated that both female bull trout and brook trout are involved in hybridization events. Analysis of population structure suggested that brook trout have established multiple spawning populations within the Malheur system. Data presented in this study suggest that relative abundance of brook trout and habitat quality are important factors to consider when evaluating the threat of hybridization to bull trout populations.     

Use of cover habitat by bull trout, <Emphasis Type="Italic">Salvelinus confluentus</Emphasis>, and lake trout, <Emphasis Type="Italic">Salvelinus namaycush</Emphasis>, in a laboratory environment

Lacustrine-adfluvial bull trout, Salvelinus confluentus, migrate from spawning and rearing streams to lacustrine environments as early as age 0. Within lacustrine environments, cover habitat provides refuge from potential predators and is a resource that is competed for if limiting. Competitive interactions between bull trout and other species could result in bull trout being displaced from cover habitat, and bull trout may lack evolutionary adaptations to compete with introduced species, such as lake trout, Salvelinus namaycush. A laboratory experiment was performed to examine habitat use and interactions for cover by juvenile (i.e., <80 mm total length) bull trout and lake trout. Differences were observed between bull trout and lake trout in the proportion of time using cover (F _1,22.6 = 20.08, P < 0.001) and bottom (F _1,23.7 = 37.01, P < 0.001) habitat, with bull trout using cover and bottom habitats more than lake trout. Habitat selection ratios indicated that bull trout avoided water column habitat in the presence of lake trout and that lake trout avoided bottom habitat. Intraspecific and interspecific agonistic interactions were infrequent, but approximately 10 times greater for intraspecific interactions between lake trout. Results from this study provide little evidence that juvenile bull trout and lake trout compete for cover, and that species-specific differences in habitat use and selection likely result in habitat partitioning between these species.     

Decline of the Migratory Form in Bull Charr, Salvelinus Confluentus, and Implications for Conservation

Large-bodied, migratory life history forms of bull charr, Salvelinus confluentus, were historically abundant in northwestern North America, but many remaining populations of this now-threatened species presently persist as small-bodied residents isolated in headwater streams. We examined whether the migratory form has been lost from headwater populations of bull charr and their potential for re-establishment. Upstream and downstream movement of bull charr and other salmonids from three tributary populations in the Bitterroot River drainage, Montana, was measured with weirs over a 17-month period. The migratory life history was rare or absent in two tributaries but still present at a low level in a third. In contrast, substantial numbers (n = 1745) of juvenile and adults of other salmonids (brown trout, Salmo trutta, cutthroat trout, Oncorhynchus clarki, and mountain whitefish, Prosopium williamsoni) were captured near tributary mouths, indicating a migratory life history was common in other species. Apparent decline of the migratory life history in bull charr was not directly related to damming suggesting other downstream mortality factors (predation, temperature) also are involved. Isolated, nonmigratory forms have increased risk of extinction, and restoration of the population connectivity via the re-establishment of migratory stocks is an important conservation goal for bull charr recovery. However, the factors governing migratory tendency remain unclear.     

Genetic variation,inheritance, and quaternary structure of malic enzyme in brook trout (Salvelinus fontinalis)

Electrophoretic variation is described for malic enzyme (ME) for the first time in brook trout (Salvelinus fontinalis). Since the quaternary structure of ME was not clear from examination of banding patterns in brook trout alone, ME phenotypes in rainbow trout (Salmo gairdneri) × brook trout hybrids as well as in esocid species demonstrated that ME is tetrameric. A model of two duplicated loci is proposed to account for the observed variation. One locus (ME-2) is fixed and one locus (ME-1) is variable with three electrophoretically distinct alleles; the protein products of ME-1 are reduced in activity relative to the protein products of ME-2. Joint segregation was examined between ME-1 and ten other biochemical loci in brook trout, and between ME-1, ME-2, and nine other biochemical loci in a splake—lake trout (Salvelinus namaycush) × brook trout hybrid—backcross. All pairwise examinations showed random assortment except ME-2 with an isocitrate dehydrogenase locus (IDH-3), which showed complete linkage in the splake backcross. This may be due to a chromosomal aberration.Authorized for publication as Paper No. 5599 in the Journal Series of The Pennsylvania Agricultural Experiment Station, University Park, Pennsylvania, in cooperation with the Benner Spring Fish Research Station, The Pennsylvania Fish Commission, Bellefonte, Pennsylvania. M.S. was supported by an NSF Graduate Fellowship.     

Spawning and emergence phenology of bull trout Salvelinus confluentus under differing thermal regimes

Median bull trout Salvelinus confluentus breeding was 2 weeks earlier in a cool stream than in a proximate warmer stream, aligning with expectations for salmonids, followed by emergence timing calculated to be 6 weeks later in the cool stream than the warm stream. This pattern is consistent with both site-specific adaptation and thermal spawning threshold hypotheses for life-history event timing in this threatened species.     

Effectiveness of lake trout (Salvelinus namaycush) suppression in Lake Pend Oreille,Idaho: 2006–2016

The nonnative lake trout (Salvelinus namaycush Walbaum, 1792) population in Lake Pend Oreille, Idaho increased exponentially during 1999–2006. This led to an unsustainable level of predation mortality on kokanee (Oncorhynchus nerka Walbaum, 1792), increased the conservation threat to native bull trout (Salvelinus confluentus Suckley, 1859), and jeopardized the popular recreational fishery for kokanee and rainbow trout (Oncorhynchus mykiss Walbaum, 1792). In response, lake trout were suppressed since 2006 using incentivized angling, gill netting, and trap netting. From 2006 through 2016, 193,982 lake trout were removed (50% by gill netting; 44% by angling; 6% by trap netting). During this period, age-8 + (adult) lake trout abundance declined by 64%, age-3 (recruit) abundance declined by 56%, and mean total annual mortality (A) was 31.1%. Lake trout did not show evidence of a density-dependent response. Kokanee did not collapse and rebounded to abundances not observed since before lake trout expansion. Bull trout abundance declined during suppression, but the population was sustained. Lake trout suppression allowed a harvest fishery for kokanee and trophy fishery for rainbow trout to be restored. We conclude that suppression can be an effective management action for mitigating effects of nonnative lake trout in a large, deep lake.

     

Conservation genetics of bull trout: Geographic distribution of variation at microsatellite loci

We describe the genetic population structure of65 bull trout (Salvelinus confluentus)populations from the northwestern United Statesusing four microsatellite loci. Thedistribution of genetic variation as measuredby microsatellites is consistent with previousallozyme and mitochondrial DNA analysis. Thereis relatively little genetic variation withinpopulations (H ^S = 0.000 – 0.404,average H ^S = 0.186, but substantialdivergence between populations (F ^ST = 0.659). In addition, those populations that had low genetic variation forallozymes also tended to have low geneticvariation at microsatellite loci. Microsatellite analysis supports the existenceof at least three major geneticallydifferentiated groups of bull trout: (1)``Coastal' bull trout populations, (2) ``SnakeRiver' populations, which also include the JohnDay, Umatilla, and Walla Walla Rivers and, (3)populations from the upper Columbia River,primarily from the Clark Fork basin. Withinthe major assemblages, populations are furthersubdivided, primarily at the river basin level. Most of the genetic similarities we havedetected probably reflect patterns of historicisolation and gene flow. However, in somecases, genetic drift and low levels ofvariation appear to have influenced therelationships inferred from these data. Finally, we suggest using a hierarchicalapproach to direct management actions inspecies such as bull trout for which most ofthe genetic variation exists among populationsand local populations in close proximitytypically are genetically distinct.     

Fragmentation of riverine systems: the genetic effects of dams on bull trout (Salvelinus confluentus) in the Clark Fork River system

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.     

Sampling large geographic areas for rare species using environmental DNA: a study of bull trout Salvelinus confluentus occupancy in western Montana

This study tested the efficacy of environmental DNA (eDNA) sampling to delineate the distribution of bull trout Salvelinus confluentus in headwater streams in western Montana, U.S.A. Surveys proved fast, reliable and sensitive: 124 samples were collected across five basins by a single crew in c. 8 days. Results were largely consistent with past electrofishing, but, in a basin where S. confluentus were known to be scarce, eDNA samples indicated that S. confluentus were more broadly distributed than previously thought.     

Summer and fall microhabitat utilization of juvenile bull trout and cutthroat trout in a wilderness stream, Idaho

Microhabitat use and availability were evaluated and compared between different size classes of juvenile resident bull trout (Salvelinus confluentus) and cutthroat trout (Oncorhynchus clarki) in a small wilderness stream within the South Fork Clearwater River basin, Idaho. The objective was to determine if utilization of measured habitat characteristics changed from summer to late fall. Sampling of fish was conducted with night snorkeling. During the summer, smaller juvenile bull trout (<66 mm) total length (TL) were associated with shallow stream margins over coarse substrates. In the fall, they moved to significantly deeper, lower velocity water, and closer to cover (p<0.05), but maintained their association with coarse substrates. During the summer, larger juvenile bull trout and larger juvenile cutthroat trout (66–130 mm TL) occupied significantly deeper water than smaller juvenile bull trout (p<0.05). Generally, larger juvenile bull trout were found closer to the bottom and in lower velocity water than larger juvenile cutthroat trout (p<0.05). In the fall, larger juvenile bull trout and larger juvenile cutthroat trout were associated with significantly deeper, lower velocity water located closer to cover than in summer (p<0.05). However, cutthroat trout occupied slightly deeper water over finer substrates than bull trout. Deep water with low velocities evidently provide important rearing areas for large bull trout and large cutthroat trout in the fall. Land management practices that maintain such environments will benefit these species.     

Daily temperature experience and selection by adfluvial bull trout (<Emphasis Type="Italic">Salvelinus confluentus</Emphasis>)

Bull trout (Salvelinus confluentus) are a thermally sensitive cold-water species with a threatened conservation status across much of North America. To improve our understanding of bull trout thermal ecology, we tagged more than 150 adults with temperature-sensing acoustic biotelemetry transmitters and monitored the animals in a British Columbia reservoir for two years. Thermal resource selection was estimated in open water from the summer to autumn as the system transitioned to isothermal conditions. On average, bull trout thermal history tracked seasonal changes and remained close to the optimum temperatures for growth and metabolism. As summer progressed, bull trout increasingly selected temperatures of 11–15 °C as they became less available within the water column. Selection indicated the movement to shallower waters where 11–15 °C temperatures existed. The results show that bull trout mainly occupy a narrow range of temperatures which suggests the importance of cold-water refuge for the species.     

Nuclear DNA identification of migrating bull trout captured at the Puget Sound Energy diversion dam on the White River,Washington State

Bull trout (Salvelinus confluentus) is a char listed as threatened under the United States Endangered Species Act throughout its range in the coterminous United States. Substantial morphological similarities between bull trout and Dolly Varden (S. malma) make field identification difficult. This has resulted in an incomplete understanding of their distribution and abundance in Washington State where these two species occur sympatrically. We used three diagnostic nuclear loci to determine the species of char collected at a trap on the White River in southern Puget Sound (Washington State, USA). Each of the 104 samples revealed the expected bull trout genotype at all three loci. This work presents three principle results: (i) the presence of a migratory bull trout population in southern Puget Sound; (ii) no evidence of migratory Dolly Varden over 3 years; and (iii) no evidence of hybridization was detected. These results also demonstrate how molecular markers can provide information essential to the conservation and management of these species.     

Salmonid predator–prey dynamics in Lake Pend Oreille,Idaho, USA

Our objective was to evaluate the long-term sustainability of lake trout Salvelinus namaycush and rainbow trout Oncorhynchus mykiss populations subjected to a range of fishing mortality (F) in Lake Pend Oreille, Idaho, USA, while providing for bull trout Salvelinus confluentus and kokanee Oncorhynchus nerka recovery. In order to achieve our objective, we developed a density-dependent stochastic predator–prey simulation model for the three major predators (lake trout, rainbow trout, and bull trout) on kokanee in Lake Pend Oreille. As F increased from 0.0 to 1.0, lake trout numbers in 2015 declined 90% for gillnetting, 76% for angling, and 48% for trap netting. At fishing mortality rates observed in Lake Pend Oreille during 2006, all methods combined and angling alone suppressed the lake trout population, but not gillnetting or trap netting alone. As F increased from 0.0 to 0.3, rainbow trout numbers in 2015 declined by 38%. Abundance of adult bull trout increased by 5.8% per year during 1996–2006, after implementation of no-kill regulations, which met the Federal Recovery Plan criterion of a stable or increasing trend in abundance. By 2010, total consumption of kokanee by lake trout, rainbow trout, and bull trout would increase by 20% if fishing mortality on lake trout and rainbow trout declined by 30% from 1996 levels, and would decrease by 14% if fishing mortality on lake trout and rainbow trout increased by 30% from 1996 levels. At rates of fishing mortality exerted on lake trout and rainbow trout in 2006, the likelihood of kokanee collapse was 65% within the next decade. Therefore, fishing mortality would need to be at least 6% higher on both lake trout and rainbow trout to reduce the likelihood of kokanee collapse to 50%. We conclude that kokanee biomass is presently out of balance with predation in Lake Pend Oreille, because kokanee production cannot compensate for all predation loss. Our findings suggest that a combination of unusually high kokanee production and unusually low predation are likely needed for kokanee to survive the next decade in Lake Pend Oreille.     

Repeatability of movement behaviour in a wild salmonid revealed by telemetry

Movement estimates derived from sub‐daily tracking of radio‐tagged bull trout Salvelinus confluentus on the Columbia River, British Columbia, Canada, were used to test whether interindividual variation in behaviour was repeatable among contexts, both short‐ and long‐term. Interindividual variation in S. confluentus behaviour was consistent across contexts. These findings emphasize the potential for telemetry as a tool in animal personality and temperament research.     

Comparing competitive ability and associated metabolic traits between a resident and migratory population of bull trout against a non-native species

Juvenile bull trout Salvelinus confluentus from two geographically and ecologically distinct populations were compared with regard to their ability to compete with non-native brook trout Salvelinus fontinalis in an artificial stream, and with respect to their rates of oxygen consumption. Bull trout collected from a migratory population foraged more successfully against brook trout competitors than those from a resident population, capturing more of a limited amount of food items presented. The migratory population was also more aggressive (measured by the number of nips, chases and lateral threat displays) against brook trout competitors than the resident population. Bull trout from the migratory population had a higher oxygen consumption rate (203 mg O₂ kg · hr^-1) in the field than similar sized fish from the resident population (183 mg O₂ kg · hr^-1). These results suggest native bull trout have population-level variation in competitive ability against a non-native species and such competitive ability is positively associated with metabolism and migratory life history.     

Extensive feeding on sockeye salmon Oncorhynchus nerka smolts by bull trout Salvelinus confluentus during initial outmigration into a small,unregulated and inland British Columbia river

Stomach contents were collected and analysed from 22 bull trout Salvelinus confluentus at the edge of the Chilko Lake and Chilko River in British Columbia, Canada, during spring outmigration of sockeye salmon Oncorhynchus nerka smolts. Twenty of the 22 (>90%) stomachs contained prey items, virtually all identifiable prey items were outmigrant O. nerka smolts and stomach contents represented a large portion (0·0–12·6%) of estimated S. confluentus mass. The results demonstrate nearly exclusive and intense feeding by S. confluentus on outmigrant smolts, and support recent telemetry observations of high disappearance rates of O. nerka smolts leaving large natural lake systems prior to entering high‐order unregulated river systems.     

Cytogenetic identification of genomic elements of brook trout (Salvelinus fontinalis) in the karyotype of Arctic char (Salvelinus alpinus) from the aquaculture broodstock

Growing interest of Arctic char (Salvelinus alpinus) aquaculture in Europe, and the fact that it can easily hybridize with brook trout (Salvelinus fontinalis) resulting in fertile progeny, led us to investigate fish from the farmed stocks. Chromosomes of sampled Arctic char were examined using conventional and molecular cytogenetic (FISH) techniques in order to determine possible contamination of genomic elements of brook trout. Investigated fish possessed karyotypes composed of 80–82 chromosomes and up to three chromosome fragments. Using staining methods and FISH approach enabled identification of the brook trout chromosomes in the eight out of twenty‐two examined Arctic char. Specific location of AT‐, GC‐ positive and NOR sites observed on chromosomes as well as chromosome fragments in the karyotypes of several individuals points on past chromosomal rearrangements in fish from examined broodstock. Based on our results, it may be assumed that individuals with the brook trout genomic elements, although phenotypically identified as Arctic chars, were hybrids. Our results highlights that special care should be taken to protect gene pools of brook trout and Arctic char in farms where both species are cultured.     

Genetic diversity is related to climatic variation and vulnerability in threatened bull trout

Understanding how climatic variation influences ecological and evolutionary processes is crucial for informed conservation decision‐making. Nevertheless, few studies have measured how climatic variation influences genetic diversity within populations or how genetic diversity is distributed across space relative to future climatic stress. Here, we tested whether patterns of genetic diversity (allelic richness) were related to climatic variation and habitat features in 130 bull trout (Salvelinus confluentus) populations from 24 watersheds (i.e., ~4–7th order river subbasins) across the Columbia River Basin, USA. We then determined whether bull trout genetic diversity was related to climate vulnerability at the watershed scale, which we quantified on the basis of exposure to future climatic conditions (projected scenarios for the 2040s) and existing habitat complexity. We found a strong gradient in genetic diversity in bull trout populations across the Columbia River Basin, where populations located in the most upstream headwater areas had the greatest genetic diversity. After accounting for spatial patterns with linear mixed models, allelic richness in bull trout populations was positively related to habitat patch size and complexity, and negatively related to maximum summer temperature and the frequency of winter flooding. These relationships strongly suggest that climatic variation influences evolutionary processes in this threatened species and that genetic diversity will likely decrease due to future climate change. Vulnerability at a watershed scale was negatively correlated with average genetic diversity (r = ?0.77; P < 0.001); watersheds containing populations with lower average genetic diversity generally had the lowest habitat complexity, warmest stream temperatures, and greatest frequency of winter flooding. Together, these findings have important conservation implications for bull trout and other imperiled species. Genetic diversity is already depressed where climatic vulnerability is highest; it will likely erode further in the very places where diversity may be most needed for future persistence.     

Twelve microsatellite loci for lake trout (Salvelinus namaycush)

We describe 12 microsatellite loci isolated from lake trout (Salvelinus namaycush). The number of alleles at these loci ranged from two to 11 with an average of 5.3 alleles per locus. The expected heterozygosity ranged from 0.29 to 0.76, with an average of 0.68. Accidental (or illegal) introductions of lake trout into watersheds are decimating native trout populations in the northern Rocky Mountains, and these loci will be useful for identifying the source of these introductions and for estimating the number of founding individuals.