Janet L. Loxterman

Temporal and Spatial Genetic Structure among Some Pacific Herring Populations in Puget Sound and the Southern Strait of Georgia

Abstract We investigated temporal and spatial genetic variation in Pacific herring Clupea pallasii collections from six sites in Puget Sound (PS) and the southern Strait of Georgia (SOG), using 12 microsatellite loci. Loci were highly variable with up to 70 alleles per locus (mean = 30.67 alleles), and observed heterozygosity was high (mean = 0.823). Analysis of molecular variance (AMOVA) indicated significant structure, with over twice as much variance among sites as among collection years, although among-site variance was mainly due to Cherry Point and Squaxin Pass collections. In an AMOVA excluding Cherry Point and Squaxin Pass, only temporal variance was significant. With the exception of the Cherry Point and Squaxin Pass collections, pairwise genotypic and F ST tests show some differences among collection years within a site and some genetic overlap among most PS and SOG collections. The Cherry Point and Squaxin Pass collections had no differences in genotypic distributions among collection years, an...

Fine scale population genetic structure of pumas in the Intermountain West

In this study, I examined the population genetic structure of subpopulations of pumas (Pumaconcolor) in Idaho and surrounding states. Patterns of genetic diversity, population structure, levels of inbreeding, and the relationship between genetic differentiation and dispersal distance within and between 15 subpopulations of pumas were compared. Spatial analyses revealed that the Snake River plain was an important barrier to movement between northern and southern regions of Idaho. In addition, subpopulations south of the Snake River plain exhibited lower levels of genetic diversity, higher levels of inbreeding, and a stronger pattern of isolation by distance relative to subpopulations north of the Snake River plain. Lower levels of diversity and restricted gene flow are likely the result of historically lower population sizes in conjunction with more recent changes in habitat use and available dispersal corridors for movement. The subdivision of puma populations north and south of the Snake River plain, along with the patterns of genetic diversity within regions, indicate that landscape features are affecting the population genetic structure of pumas in Idaho. These results indicate that information about the effects of landscape features on the distribution of genetic diversity should be considered when designing plans for the management and conservation of pumas.

Fine-Scale Population Structure of Rainbow Trout in the Spokane River Drainage in Relation to Hatchery Stocking and Barriers

Abstract We used 13 microsatellite loci to examine population structure in rainbow trout Oncorhynchus mykiss collected from 20 tributaries and 3 main stems in the greater Spokane River drainage. Populations displayed some excess homozygosity and linkage disequilibrium, which was more pronounced in upper tributary collections and probably the result of small effective population sizes or structuring within tributaries. In general, population structure followed geographic structure; collections from creeks within sub-drainages were the most closely related, and collections from different tributaries were genetically distinct. Comparisons with cutthroat trout O. clarkii indicated little to no introgression. Comparisons with steelhead (anadromous rainbow trout), coastal rainbow trout O. mykiss irideus, and inland rainbow trout from hatcheries suggested introgression by hatchery fish into some wild populations. Introgression was suspected in populations from stocked tributaries and tributaries that lacked barr...

Watershed boundaries and geographic isolation: patterns of diversification in cutthroat trout from western North America

BackgroundFor wide-ranging species, intraspecific variation can occur as a result of reproductive isolation from local adaptive differences or from physical barriers to movement. Cutthroat trout (Oncorhynchus clarkii), a widely distributed fish species from North America, has been divided into numerous putative subspecies largely based on its isolation in different watersheds. In this study, we examined mtDNA sequence variation of cutthroat trout to determine the major phylogenetic lineages of this polytypic species. We use these data as a means of testing whether geographic isolation by watershed boundaries can be a primary factor organizing intraspecific diversification.ResultsWe collected cutthroat trout from locations spanning almost the entire geographic range of this species and included samples from all major subspecies of cutthroat trout. Based on our analyses, we reveal eight major lineages of cutthroat trout, six of which correspond to subspecific taxonomy commonly used to describe intraspecific variation in this species. The Bonneville cutthroat trout (O. c. utah) and Yellowstone cutthroat trout (O. c. bouvieri) did not form separate monophyletic lineages, but instead formed an intermixed clade. We also document the geographic distribution of a Great Basin lineage of cutthroat trout; a group typically defined as Bonneville cutthroat trout, but it appears more closely related to the Colorado River lineage of cutthroat trout.ConclusionOur study indicates that watershed boundaries can be an organizing factor isolating genetic diversity in fishes; however, historical connections between watersheds can also influence the template of isolation. Widely distributed species, like cutthroat trout, offer an opportunity to assess where historic watershed connections may have existed, and help explain the current distribution of biological diversity across a landscape.

Insular arctic ground squirrels (Spermophilus parryii) of the North Pacific: indigenous or exotic?

Abstract We lack critical information for oceanic archipelagos worldwide related to the origin and status of insular faunas. In southwestern Alaska, in particular, a need exists to tease apart whether specific insular populations are naturally occurring or are the result of exotic introductions by humans. We analyzed variation in mitochondrial sequences of the cytochrome-b gene and 8 nuclear microsatellite loci across 215 individuals representing 17 populations (12 insular) to refine our understanding of the history of the previously identified Southwest clade of arctic ground squirrels (Spermophilus parryii). We found significant geographic structure that suggests long-term isolation and diversification (Ushugat Island and Cold Bay), but we also documented closely related populations that are likely the result of human-mediated introductions. The latter instances (Kavalga and Unalaska islands) corroborate reports from early Alaska explorers.

Sex-Specific Dispersal Patterns of Wolverines: Insights from Microsatellite Markers

Abstract Dispersal of individuals can be defined as movement and settling outside the natal home range. Such dispersal is often sex-biased among vertebrates, and is generally expected to be male-biased in polygynous mammals. We used microsatellite markers scored on harvested wolverines (Gulo gulo) to test the prediction of male-biased dispersal in a population in the western Brooks Range, Alaska. Our analyses suggested a high rate of dispersal within the population, but provided no support for sex differences in dispersal tendencies across the sampled spatial scale. Previous studies have implied male-biased dispersal among wolverine populations on an interpopulation scale. We suggest 3, not exclusive, explanations to reconcile these differences: low power to detect sex biases in dispersal tendencies in this panmictic population; a scale-dependent component in dispersal tendencies, where males are overrepresented among interpopulation migrants; and lower reproductive success for dispersing females compared to more philopatric ones.

Range-wide comparisons of northern leatherside chub populations reveal historical and contemporary patterns of genetic variation

Patchily distributed species are those taxa whose populations occupy geographically insular habitats and their conservation often depends on an understanding of the relationship among disjunct populations. The objective of our study was to use molecular data and analytical techniques to separate the effects of historical and contemporary processes influencing the distribution of a high-desert minnow, the northern leatherside chub (Lepidomeda copei). Individuals from 23 populations were sequenced for 1,140 base pairs of the cytochrome B gene of the mitochondrial genome and genotyped at seven nuclear microsatellite loci. We estimated gene flow and examined population structure using both microsatellite and mtDNA data. Low sequence divergence and the distribution of shared haplotypes in multiple watersheds suggest historical connectivity between populations over a large geographic area. In contrast, patterns of microsatellite diversity indicate that populations of leatherside chub are isolated from one another with low levels of contemporary gene flow between populations. Our results suggest that populations of leatherside chub were historically more widely inter-connected and have recently been isolated, likely through a combination of natural and anthropogenic habitat fragmentation. As populations become increasingly isolated, they are more vulnerable to extirpation as a result of stochastic events. For northern leatherside chub, recent isolation and lack of gene flow among populations may affect their long-term survival in the arid landscapes of the Great Basin and surrounding watersheds because of widespread and increasing habitat alteration and fragmentation.

Connections and containers: Using genetic data to understand how watershed evolution and human activities influence cutthroat trout biogeography

Species with large geographic distributions often exhibit complex patterns of diversity that can be further complicated by human activities. Cutthroat trout (Oncorhynchus clarkii) are one of the most widely distributed freshwater fish species in western North America exhibiting substantial phenotypic and genetic variability; however, fish stocking practices have translocated populations outside of their native range and may have obscured intraspecific boundaries. This study focuses on cutthroat trout populations representing three distinct evolutionary clades that are found intermixed within a contact zone between the Bonneville and upper Snake River watersheds in the western United States. We used mitochondrial and microsatellite genetic data, as well as historical stocking records, to evaluate whether populations of cutthroat trout in the contact zone are native or are introduced. We found significant genetic differentiation and fine-scale genetic population structure that was organized primarily by watershed boundaries. While we detected increased genetic diversity in some areas in close proximity to the greatest number of stocking events, the highly organized population structure both within and between areas of the contact zone indicates that the populations are native to the watersheds. Intermixing of distinct evolutionary lineages of cutthroat trout appears to be the result of historical connections between paleodrainages. Our analyses provide a context for understanding how genetic data can be used to assess the status of populations as native or introduced.

The phylogeography of westslope cutthroat trout

Identifying units of conservation of aquatic species is fundamental to informed natural resources science and management. We used a combination of mitochondrial and nuclear molecular methods to identify potential units of conservation of westslope cutthroat trout, a taxon native to montane river basins of the northwestern U.S. and southwestern Canada. Mitogenomic sequencing identified two major lineages composed of nine monophyletic clades, and a well-supported subclade within one of these, largely delineated by river basins. Analyses of microsatellites and single nucleotide polymorphisms corroborated most of these groupings, sometimes with less resolution but demonstrating more complex connections among clades. The mitochondrial and nuclear analyses revealed that Pleistocene glacial cycles profoundly influenced the distribution and divergence of westslope cutthroat trout, that this taxon crossed the Continental Divide in two separate events, and that genetically pure but nonindigenous fish were widely distributed. Herein, we recognize nine geographically discrete, cytonuclear lineages largely circumscribed by major river basins as potential units of conservation: 1) John Day; 2) Coeur d’Alene; 3) St. Joe; 4) North Fork Clearwater; 5) Salmon; 6) Clearwater headwaters; 7) Clearwater-eastern Cascades; 8) neoboreal, consisting of most of the Columbia upstream from central Washington, the Fraser in British Columbia, and the South Saskatchewan in Alberta; and 9) Missouri.