A species' genetic structure often varies in response to ecological and landscape processes that differ throughout the species' geographic range, yet landscape genetics studies are rarely spatially replicated. The Cope's giant salamander (Dicamptodon copei) is a neotenic, dispersal-limited amphibian with a restricted geographic range in the Pacific northwestern USA. We investigated which landscape factors affect D. copei gene flow in three regions spanning the species' range, which vary in climate, landcover and degree of anthropogenic disturbance. Least cost paths and Circuitscape resistance analyses revealed that gene flow patterns vary across the species' range, with unique combinations of landscape variables affecting gene flow in different regions. Populations in the northern coastal portions of the range had relatively high gene flow, largely facilitated by stream and river networks. Near the southeastern edge of the species' range, gene flow was more restricted overall, with relatively less facilitation by streams and more limitation by heat load index and fragmented forest cover. These results suggested that the landscape is more difficult for individuals to disperse through at the southeastern edge of the species' range, with terrestrial habitat desiccation factors becoming more limiting to gene flow. We suggest that caution be used when attempting to extrapolate landscape genetic models and conservation measures from one portion of a species' range to another.

Life-history characteristics are an important determinant of a species' dispersal abilities. We predict that variation in life history can influence population-level genetic patterns. To test this prediction, we estimate population-level genetic structure for two sympatric species of stream-breeding salamander. The Cope's giant salamander (Dicamptodon copei) rarely metamorphoses into a terrestrial adult, thereby limiting overland dispersal and potentially gene flow. In contrast, the Pacific giant salamander (D. tenebrosus) commonly metamorphoses, which is expected to facilitate overland dispersal and gene flow. Three sets of analyses based on microsatellite data support these hypotheses, showing that D. tenebrosus displays minimal population-level genetic structuring and no pattern of isolation by distance, whereas D. copei displays a high degree of population-level genetic structure and significant isolation by distance. Specifically, nearly all pairwise F(ST )values were significantly different from 0 between populations of D. copei, with fewer than half the pairwise F(ST )values significant from 0 in D. tenebrosus. Additionally, Structure analyses indicated eight genetic clusters for D. copei but only one genetic cluster for D. tenebrosus. Finally, Mantel tests showed significant correlations between stream and overland distance with genetic distance for D. copei but no significant correlations of either landscape feature for D. tenebrosus at the scale of the study. These results provide a case study of the link between life-history variation and population genetic patterns while controlling for phylogeny and environmental variation.

Efforts to taxonomically delineate species are often confounded with conflicting information and subjective interpretation. Advances in genomic methods have resulted in a new approach to taxonomic identification that stands to greatly reduce much of this conflict. This approach is ideal for species complexes, where divergence times are recent (evolutionarily) and lineages less well defined. The California Roach/Hitch fish species complex is an excellent example, experiencing a convoluted geologic history, diverse habitats, conflicting species designations and potential admixture between species. Here we use this fish complex to illustrate how genomics can be used to better clarify and assign taxonomic categories. We performed restriction-site associated DNA (RAD) sequencing on 255 Roach and Hitch samples collected throughout California to discover and genotype thousands of single nucleotide polymorphism (SNPs). Data were then used in hierarchical principal component, admixture, and FST analyses to provide results that consistently resolved a number of ambiguities and provided novel insights across a range of taxonomic levels. At the highest level, our results show that the CA Roach/Hitch complex should be considered five species split into two genera (4 + 1) as opposed to two species from distinct genera (1 +1). Subsequent levels revealed multiple subspecies and distinct population segments within identified species. At the lowest level, our results indicate Roach from a large coastal river are not native but instead introduced from a nearby river. Overall, this study provides a clear demonstration of the power of genomic methods for informing taxonomy and serves as a model for future studies wishing to decipher difficult species questions. By allowing for systematic identification across multiple scales, taxonomic structure can then be tied to historical and contemporary ecological, geographic or anthropogenic factors.

Because of their similar appearance and frequent hybridization, juvenile steelhead Oncorhynchus mykiss and coastal cutthroat trout O. clarkii clarkii are difficult to distinguish visually. Nevertheless, field biologists often use visual methods to classify juvenile individuals. This study investigated hybridization between these species and determined the accuracy of field identification where hybridization occurred. Using a five-point classification system, two evaluators identified 500 fish collected from three watersheds in Humboldt County, California. Individuals were then genotyped at seven single-copy nuclear DNA genes and one mitochondrial gene, all assumed to be diagnostic for each species. Single-locus Hardy-Weinberg equilibrium, pairwise genotypic disequilibrium, and cytonuclear disequilibrium calculations revealed that subpopulations of these species were mating assortatively. Presumptive F 1 hybrid individuals were rare, whereas introgressed individuals were more common. These presumptive later-generation backcross hybrids were produced with both parental species but were more frequently produced with coastal cutthroat trout. Interspecific matings appeared to be bidirectional. Conditional classification probabilities between evaluator identifications and genotypes showed that both evaluators had moderate to substantial success identifying individuals less than 85 mm total length, whereas individuals 85 mm and larger were identified less successfully. Evaluators successfully identified coastal cutthroat trout but had moderate difficulty identifying steelhead (sometimes misidentified as hybrids) and always misidentified hybrids as coastal cutthroat trout. Although visual identifications are not without error, approximately unbiased estimates of the percentage of hybrids may be generated from a combination of visual assignments and supplementary genetic analyses.

Objective: Speckled Dace Rhinichthys osculus is small cyprinoid fish that is widespread in western North America. In California and elsewhere it is currently treated as a single species with multiple subspecies, many undescribed. However, these subspecies may represent evolutionary lineages that are cryptic species because they cannot be distinguished using standard morphometric techniques. In this study, we attempt to determine evolutionary lineages within California populations of Speckled Dace using the population genetic and genomic information. Methods: We used restriction site-associated DNA sequencing to extract thousands of single-nucleotide polymorphisms across the genome to identify genetic differences among all the samples from 38 locations in the western USA, with a focus on California. We performed principal component analysis, admixture analysis, estimated pairwise values of the genetic differentiation index F ST , and constructed molecular phylogenies to characterize population genetic and phylogenetic relationships among sampled Speckled Dace populations. Result: Our analyses detected three major lineages of Speckled Dace in California that align with geography: (1) Sacramento River, central California coast, Klamath River, and Warner Basin; (2) Death Valley and Lahontan Basin; and (3) Santa Ana River basin, in southern California. These lineages fit well with the geologic history of California, which has promoted long isolation of populations of Speckled Dace and other fishes. Conclusion: The presence of distinct evolutionary lineages indicates that SpeckledDace in California should be managed with distinct population segments to preserve within-species diversity. This study highlights the importance of genetic analyses for conservation and management of freshwater fishes.

The Devils Hole pupfish (Cyprinodon diabolis; DHP) is an icon of conservation biology. Isolated in a 50 m(2) pool (Devils Hole), DHP is one of the rarest vertebrate species known and an evolutionary anomaly, having survived in complete isolation for thousands of years. However, recent findings suggest DHP might be younger than commonly thought, potentially introduced to Devils Hole by humans in the past thousand years. As a result, the significance of DHP from an evolutionary and conservation perspective has been questioned. Here we present a high-resolution genomic analysis of DHP and two closely related species, with the goal of thoroughly examining the temporal divergence of DHP. To this end, we inferred the evolutionary history of DHP from multiple random genomic subsets and evaluated four historical scenarios using the multispecies coalescent. Our results provide substantial information regarding the evolutionary history of DHP. Genomic patterns of secondary contact present strong evidence that DHP were isolated in Devils Hole prior to 20-10 ka and the model best supported by geological history and known mutation rates predicts DHP diverged around 60 ka, approximately the same time Devils Hole opened to the surface. We make the novel prediction that DHP colonized and have survived in Devils Hole since the cavern opened, and the two events (colonization and collapse of the cavern's roof) were caused by a common geologic event. Our results emphasize the power of evolutionary theory as a predictive framework and reaffirm DHP as an important evolutionary novelty, worthy of continued conservation and exploration.

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Most coho salmon Oncorhynchus kisutch in Washington state spawn at 3 y of age, creating the potential for three temporal populations or “broodlines” at each spawning site. This is generally prevented by a portion of males in each site that mature and reproduce at 2 y of age, resulting in population structure in which the geographic component is stronger than the temporal component. The Quilcene National Fish Hatchery, located on Big Quilcene River in the Hood Canal region of Washington state, selected against late returning coho salmon by excluding all but the earliest returning fish from its broodstock for an unknown number of generations, and restricted gene flow among broodlines by excluding 2-y-old males for 27 generations. The resulting hatchery population exhibited three distinct broodlines that returned in alternating years: an “early” broodline that arrived 1 mo before the wild fish, a “late” broodline that arrived at the same time as the wild fish, and a “middle” broodline that arrived in between these two broodlines. We evaluated temporal and geographic components of population genetic structure in coho salmon from the Quilcene National Fish Hatchery and nine other sites from Puget Sound and the Strait of Juan de Fuca using 10 microsatellite loci. Genetic diversity at the Quilcene National Fish Hatchery was lowest in the early broodline and highest in the late broodline. Divergence among broodlines at the Quilcene National Fish Hatchery was greater than that observed at any other site, and was also greater than that observed between any of the sites. This apparent reversal of the relative magnitudes of temporal and geographic components for this species emphasizes the importance of variable age-at-maturity in shaping population genetic structure.