The influence of hydrographic structure and seasonal run timing on genetic diversity and isolation-by-distance in chum salmon (Oncorhynchus keta)

Abstract

We used 20 microsatellite loci to compare genetic diversity and patterns of isolation-by-distance among three groups of chum salmon ( Oncorhynchus keta ) from two physically distinct watersheds in western Alaska, USA. The results were consistent with the hypothesis that gene flow decreases as the complexity of the hydrographic system increases. Specifically, higher gene flow was inferred among 11 populations from a nonhierarchical collection of short coastal rivers in Norton Sound compared with 29 populations from a complex hierarchical network of inland tributaries of the Yukon River. Within the Yukon River, inferred gene flow was highest among 15 summer-run populations that spawn in the lower drainage, compared with 14 fall-run populations that spawn in the upper drainage. The results suggest that the complexity of the hydrographic system may influence population connectivity and hence the level of genetic diversity of western Alaska chum salmon. Finally, evidence of isolation-by-time, when controlling for geographic distance, supported the hypothesis that genetic divergence in Yukon River chum salmon is influenced by seasonal run timing. However, evidence of isolation-by-distance, when controlling for season run timing, indicated the populations are not sufficiently isolated, spatially or temporally, to prevent gene flow. Dispersal among summer- and fall-run populations may play a role in maintaining genetic diversity.

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

“…Previous work demonstrated an IBD pattern among Yukon populations (Olsen et al. ), but we did not. Our results are consistent with the idea that as the mouth of the Yukon River shifted to the north, it may have disrupted population structure in that habitat and erased IBD patterns that had been previously established.…”

Comparative landscape genetic analysis of three Pacific salmon species from subarctic North America

“…In addition to the habitat features discussed below, these differences between the coastal and inland collections may reflect differences in the complexity of freshwater migration. For example, studies of chum and Atlantic salmon (Salmo salar) suggest gene flow is greater among populations closer to the coast because the migration is shorter and less navigationally complex than for populations further inland (Primmer et al 2006;Olsen et al 2008). The results from this study suggest populations high in the Yukon River drainage are the most likely to be genetically isolated.…”

“…The genetic data consisted of microsatellite genotypes drawn mostly from genetic baselines developed for mixedstock analysis and to describe population structure (e.g., Flannery et al 2006;Crane et al 2007;Olsen et al 2008). For the present study, we added genotypes for coho and Chinook from Norton Sound following the protocol of Crane et al (2007) and Seeb et al (2007).…”

“…All samples were collected from mature adults except for juvenile coho salmon from Clear Creek and the Fishing Branch River in the Yukon River watershed. Although some Chinook and chum samples were collected as much as 19 years apart, previous studies using many of these samples (e.g., Beacham et al 2006;Olsen et al 2008) show that differences at this temporal scale contribute little to the overall estimates of population divergence.…”

Landscape heterogeneity and local adaptation define the spatial genetic structure of Pacific salmon in a pristine environment

“…Decreases in gene flow owing to isolation by distance can result from two factors: (1) individuals are more likely to stray into the most geographically proximate populations (Olsen et al 2008), and (2) barriers may limit gene flow in particular locations (Dupanloup et al 2002;Guillot et al 2009). In Pacific salmon, approximately 95-99 % of individuals home to their natal spawning habitat as adults; the remainder are termed 'strays' and may reproduce with non-natal populations (Quinn 2005).…”