Matthew R. Campbell

Status of Yellowstone Cutthroat Trout in Idaho

Abstract In this study, we electrofished 961 study sites to estimate the abundance of trout (in streams only) throughout the upper Snake River basin in Idaho (and portions of adjacent states) to determine the current status of Yellowstone cutthroat trout Oncorhynchus clarkii bouvierii and other nonnative salmonids and to assess introgressive hybridization between Yellowstone cutthroat trout and rainbow trout O. mykiss. Yellowstone cutthroat trout were the most widely distributed species of trout, followed by brook trout Salvelinus fontinalis, rainbow trout and rainbow trout × Yellowstone cutthroat trout hybrids, and brown trout Salmo trutta. Of the 457 sites that contained Yellowstone cutthroat trout, less than half also contained nonnative salmonids and only 88 contained rainbow trout and hybrids. In the 11 geographic management units (GMUs) for which sample size permitted abundance estimates, the number of 100-mm and larger trout was estimated to be about 2.2 ± 1.2 million (mean ± confidence interval); ...

Hybridization and Introgression in a Managed, Native Population of Yellowstone Cutthroat Trout: Genetic Detection and Management Implications

Abstract Since the mid-1920s, the Idaho Department of Fish and Game has cultured Yellowstone cutthroat trout Oncorhynchus clarki bouvieri at Henrys Lake to offset declines in natural production and for use in stocking programs throughout Idaho. Since the mid-1970s, they have also produced F1 hybrids: female Yellowstone cutthroat trout × male rainbow trout O. mykiss. The ability of fishery managers, when selecting broodstock, to visually distinguish returning cutthroat trout from F1 hybrids is, therefore, crucial to avoid accidental introduction of rainbow trout genes into the hatchery-supplemented cutthroat trout population. To evaluate this ability, fish identified by staff as putative cutthroat trout or hybrids (an array of phenotypic characters are used), were sampled during two spawning seasons. Phenotypically identified fish were genetically tested using species-specific restriction fragment length polymorphisms (RFLPs) of nuclear and mitochondrial DNA gene loci and diagnostic allozyme loci. Current ...

A genetic evaluation of relatedness for broodstock management of captive, endangered Snake River sockeye salmon, Oncorhynchus nerka

The use of captive broodstocks is becoming more frequently employed as the number of species facing endangerment or extinction throughout the world increases. Efforts to rebuild the endangered Snake River sockeye salmon, Oncorhynchus nerka, population have been ongoing for over a decade, but the use of microsatellite data to develop inbreeding avoidance matrices is a more recent component to the program. This study used known genealogical relationships among sockeye salmon offspring to test four different pairwise relatedness estimators and a maximum-likelihood (M-L) relatedness estimator. The goal of this study was to develop a breeding strategy with these estimators that would minimize the loss of genetic diversity, minimize inbreeding, and determine how returning anadromous adults are incorporated into the broodstock along with full-term hatchery adults. Results of this study indicated that both the Mxy and RQG estimators had the lowest Type II error rates and the M-L and RR estimators had the lowest Type I error rates. An approach that utilizes a combination of estimators may provide the most valuable information for managers. We recommend that the M-L and RR methods be used to rank the genetic importance of returning adults and the Mxy or RQG estimators be used to determine which fish to pair for spawning. This approach provides for the best genetic management of this captive, endangered population and should be generally applicable to the genetic management of other endangered stocks with no pedigree.

Relative contributions of neutral and non-neutral genetic differentiation to inform conservation of steelhead trout across highly variable landscapes

Mounting evidence of climatic effects on riverine environments and adaptive responses of fishes have elicited growing conservation concerns. Measures to rectify population declines include assessment of local extinction risk, population ecology, viability, and genetic differentiation. While conservation planning has been largely informed by neutral genetic structure, there has been a dearth of critical information regarding the role of non‐neutral or functional genetic variation. We evaluated genetic variation among steelhead trout of the Columbia River Basin, which supports diverse populations distributed among dynamic landscapes. We categorized 188 SNP loci as either putatively neutral or candidates for divergent selection (non‐neutral) using a multitest association approach. Neutral variation distinguished lineages and defined broad‐scale population structure consistent with previous studies, but fine‐scale resolution was also detected at levels not previously observed. Within distinct coastal and inland lineages, we identified nine and 22 candidate loci commonly associated with precipitation or temperature variables and putatively under divergent selection. Observed patterns of non‐neutral variation suggest overall climate is likely to shape local adaptation (e.g., potential rapid evolution) of steelhead trout in the Columbia River region. Broad geographic patterns of neutral and non‐neutral variation demonstrated here can be used to accommodate priorities for regional management and inform long‐term conservation of this species.

Genetic Variation and Structure of Chinook Salmon Life History Types in the Snake River

We evaluated 25 inland populations of Chinook salmon Oncorhynchus tshawytscha in the Snake River with 13 microsatellite loci to test for contemporary genetic differentiation at three scales: between life history types, among regions within life history types, and among populations within regions. The genetic distance and diversity of natural Chinook salmon populations were also contrasted with those of Chinook salmon from several hatcheries. The results provide strong evidence for reproductive isolation among ocean- and stream-type life histories (F ST range, 0.080-0.120). Regional structuring of stream-type Chinook salmon within subbasins was also significant, as all populations were differentiated (F ST range, 0.017-0.045), but populations generally clustered together by region in a neighbor-joining dendrogram. This evidence suggests high levels of philopatry to natal areas in stream-type Chinook salmon, but ocean-type collections were not significantly different from one another (F ST range, 0.001-0.002). Higher levels of genetic diversity in ocean- type (306 total alleles; allelic richness, 16.5) than in stream-type collections (206 total alleles; allelic richness, 12.2) may also reflect variable levels of gene flow within each life history type and colonization history. The genetic similarity of populations within regions suggests gene flow not only from transplanted stocks but also from natural dispersal that provides metapopulation structure. None of the 25 populations in this study offered significant evidence for a genetic bottleneck (M ratio , 0.68) despite apparent demographic bottlenecks in several populations throughout the Snake River drainage in the last century. The combination of dispersal through metapopulation dynamics and transfers of hatchery stocks may be responsible for reducing the genetic bottleneck signal.

Incidence of Hybridization between Naturally Sympatric Westslope Cutthroat Trout and Rainbow Trout in the Middle Fork Salmon River Drainage, Idaho

Abstract Introgressive hybridization has been widely reported for westslope cutthroat trout (WCT) Oncorhynchus clarkii lewisi and rainbow trout (RBT) O. mykiss and is often a result of introductions of nonnative RBT into previously allopatric populations of westslope cutthroat trout. The WCT evolved in sympatry with RBT in a portion of its native range. Few studies have evaluated natural hybrid zone structure in sympatric populations or the effects of nonnative introductions within sympatric populations. We used one mitochondrial DNA marker and three co-dominant nuclear DNA markers to examine 17 populations of WCT that were sympatric with native RBT-steelhead (anadromous RBT). As 5 of the 11 sample locations were situated downstream of stocked headwater mountain lakes, we wanted to determine the effects of headwater lake introductions on naturally sympatric populations of WCT and RBT-steelhead below the lakes. Hybrids were found in streams below stocked and unstocked headwater lakes. Our results indicated...

Discriminating between a Neurotropic Myxobolus sp. and M. cerebralis, the Causative Agent of Salmonid Whirling Disease

Abstract While screening salmonids for Myxobolus cerebralis, the causative agent of whirling disease, we detected a neurotropic Myxobolus sp. that is morphologically similar to the M. cerebralis spore in brain and other nervous tissue. We developed a polymerase chain reaction (PCR)–based diagnostic technique to differentiate the two species of Myxobolus. Primers were designed for a 277-base-pair (bp) sequence within the 18S ribosomal DNA (rDNA) gene, and the restriction enzyme Mse-I was chosen to cut the amplified product into diagnostic fragments. When electrophoresed in an acrylamide gel, M. cerebralis yielded a two-band pattern while the neurotropic Myxobolus sp. yielded a three-band pattern. This diagnostic method has resolved cases in which the pepsin–trypsin digest screening test indicated Myxobolus spores but histological examination or PCR was negative for M. cerebralis. We were also able to eliminate M. kisutchi as the neurotropic Myxobolus sp. using spores from infected coho salmon Oncorhynchus ...

Influences of Habitat and Hybridization on the Genetic Structure of Redband Trout in the Upper Snake River Basin, Idaho

Abstract The genetic structure of redband trout Oncorhynchus mykiss gairdnerii in the upper Snake River basin was investigated at various scales using 13 microsatellite loci. The majority of the genetic variation was partitioned between streams, although differentiation among watersheds was significant. This diversity was probably historically partitioned at the watershed scale when steelhead O. mykiss (anadromous rainbow trout) were present, with the exception of small, isolated, headwater streams where there may have been only resident trout. Genetic structure appears to have been altered by a combination of factors, including habitat fragmentation and hybridization with hatchery trout. Redband trout populations in the desert and montane environments both experienced reduced gene flow, but the desert populations displayed higher degrees of genetic differentiation. There was also a significant inverse relationship between the degree of genetic differentiation and the level of allelic diversity. Interspec...

Estimating Abundance and Life History Characteristics of Threatened Wild Snake River Steelhead Stocks by Using Genetic Stock Identification

Abstract Assessments of threatened wild Snake River steelhead Oncorhynchus mykiss have historically been limited due to a lack of stock-specific information and difficulties in field sampling efforts. We used genetic stock identification (GSI) to estimate the composition of wild adult steelhead migrating past Lower Granite Dam on the Snake River between August 24 and November 25, 2008. Further, we combined genetic data with information on sex, length, age, and run timing to examine for differences in life history or demography among stocks. In total, 1,087 samples collected at the dam were genotyped with 13 standardized steelhead microsatellite loci and a new modified Y-chromosome-specific assay that differentiates sex. A genetic baseline of 66 populations was used to complete GSI of unknown-origin samples from Lower Granite Dam. Large differences in reporting group (stock) contributions were observed for the run as a whole; the Snake River–lower Clearwater River reporting group had the largest single con...

Multiscale Genetic Structure of Yellowstone Cutthroat Trout in the Upper Snake River Basin

Populations of Yellowstone cutthroat trout Oncorhynchus clarkii bouvierii have declined throughout their native range as a result of habitat fragmentation, overharvest, and introductions of nonnative trout that have hybridized with or displaced native populations. The degree to which these factors have impacted the current genetic population structure of Yellowstone cutthroat trout populations is of primary interest for their conservation. In this study, we examined the genetic diversity and genetic population structure of Yellowstone cutthroat trout in Idaho and Nevada with data from six polymorphic microsatellite loci. A total of 1,392 samples were analyzed from 45 sample locations throughout 11 major river drainages. We found that levels of genetic diversity and genetic differentiation varied extensively. The Salt River drainage, which is representative of the least impacted migration corridors in Idaho, had the highest levels of genetic diversity and low levels of genetic differentiation. High levels of genetic differentiation were observed at similar or smaller geographic scales in the Portneuf River, Raft River, and Teton River drainages, which are more altered by anthropogenic disturbances. Results suggested that Yellowstone cutthroat trout are naturally structured at the major river drainage level but that habitat fragmentation has altered this structuring. Connectivity should be restored via habitat restoration whenever possible to minimize losses in genetic diversity and to preserve historical processes of gene flow, life history variation, and metapopulation dynamics. However, alternative strategies for management and conservation should also be considered in areas where there is a strong likelihood of nonnative invasions or extensive habitat fragmentation that cannot be easily ameliorated.