Recent physical connections may explain weak genetic structure in western Alaskan chum salmon (Oncorhynchus keta) populations

Population structure of chum salmon and selection on the markers collected for stock identification

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single-nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH-3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2-dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise F ST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.

Origin and Genetic Diversity of Lake Trout in the Togiak National Wildlife Refuge, Alaska

Lake trout Salvelinus namaycush is a slow-growing, late-maturing, cold-water-adapted species whose native distribution is described by the glaciated regions of North America. Southwestern Alaska, the western limit of the species range, has undergone repeated episodes of glacial advance and retreat. In this study, lake trout were sampled from 15 lakes in six drainages on or near Togiak National Wildlife Refuge (TNWR) in southwestern Alaska. Data from 14 microsatellite loci were used to test for genetic evidence that lake trout survived the most recent glacial advance in a local refugium, and to test the effect of habitat size, elevation, and drainage on within- and among-population variation. We could not infer that unglaciated lakes within the TNWR served as a refugium during the most recent glacial maximum. In a neighbor-joining tree, populations largely clustered by drainage, suggesting a single founding source for each drainage. An exception occurred in the Nushagak and Kuskokwim rivers, where evidence for stream capture was detected. Among-population variation, as measured by FST, was 0.35; pairwise FST within drainages ranged from 0.05 to 0.47, indicative of low gene flow, even within drainages, though individual-based analysis detected movement of lake trout among lakes within the Kanektok, Goodnews, and Nushagak rivers. Lake surface area was positively associated with allele richness, and negatively associated with FIS, indicating that smaller lakes in the TNWR harbor less genetic diversity and may have more limited adaptive potential.

Is isolation by adaptation driving genetic divergence among proximate Dolly Varden char populations?

Numerous studies of population genetics in salmonids and other anadromous fishes have revealed that population structure is generally organized into geographic hierarchies (isolation by distance), but significant structure can exist in proximate populations due to varying selective pressures (isolation by adaptation). In Chignik Lakes, Alaska, anadromous Dolly Varden char (Salvelinus malma) spawn in nearly all accessible streams throughout the watershed, including those draining directly to an estuary, Chignik Lagoon, into larger rivers, and into lakes. Collections of Dolly Varden fry from 13 streams throughout the system revealed low levels of population structure among streams emptying into freshwater. However, much stronger genetic differentiation was detected between streams emptying into freshwater and streams flowing directly into estuarine environments. This fine-scale reproductive isolation without any physical barriers to migration is likely driven by differences in selection pressures across freshwater and estuarine environments. Estuary tributaries had fewer larger, older juveniles, suggesting an alternative life history of smolting and migration to the marine environment at a much smaller size than occurs in the other populations. Therefore, genetic data were consistent with a scenario where isolation by adaptation occurs between populations of Dolly Varden in the study system, and ecological data suggest that this isolation may partially be a result of a novel Dolly Varden life history of seawater tolerance at a smaller size than previously recognized.

Genotyping by sequencing resolves shallow population structure to inform conservation of Chinook salmon (Oncorhynchus tshawytscha)

Recent advances in population genomics have made it possible to detect previously unidentified structure, obtain more accurate estimates of demographic parameters, and explore adaptive divergence, potentially revolutionizing the way genetic data are used to manage wild populations. Here, we identified 10 944 single-nucleotide polymorphisms using restriction-site-associated DNA (RAD) sequencing to explore population structure, demography, and adaptive divergence in five populations of Chinook salmon (Oncorhynchus tshawytscha) from western Alaska. Patterns of population structure were similar to those of past studies, but our ability to assign individuals back to their region of origin was greatly improved (>90% accuracy for all populations). We also calculated effective size with and without removing physically linked loci identified from a linkage map, a novel method for nonmodel organisms. Estimates of effective size were generally above 1000 and were biased downward when physically linked loci were not removed. Outlier tests based on genetic differentiation identified 733 loci and three genomic regions under putative selection. These markers and genomic regions are excellent candidates for future research and can be used to create high-resolution panels for genetic monitoring and population assignment. This work demonstrates the utility of genomic data to inform conservation in highly exploited species with shallow population structure.