Spawning Habitat and Geography Influence Population Structure and Juvenile Migration Timing of Sockeye Salmon in the Wood River Lakes, Alaska

Abstract

The strict homing of sockeye salmon Oncorhynchus nerka results in reproductively isolated populations that often spawn in close proximity and share rearing habitat. High spawning fidelity enables these populations to adapt to local conditions, resulting in a wide range of life history characteristics and genetic variation within individual watersheds. The Wood River system in southwestern Alaska provides a pristine, well‐studied system in which to examine fine‐scale population structure and its influences on juvenile life histories. Adult sockeye salmon spawn in lake beaches, rivers, and small tributaries throughout this watershed, and juveniles rear in five nursery lakes. We genotyped 30 spawning populations and 6,066 migrating smolts at 45 single nucleotide polymorphism loci, two of which are candidates for positive selection in the study system. We show that there is significant genetic structure (FST = 0.032) in the Wood River lakes and that divergence is generally related to spawning rather than nursery habitat (hierarchical analysis of molecular variance; P < 0.05). Four groups of populations were identified based on genetic structure and used to determine the composition of unknown mixtures of migrating smolts using a Bayesian modeling framework. We demonstrate that smolt migration timing is related to genetic structure; stream and river populations dominate catches in early June, while beach spawners and the populations in Lake Kulik are more prevalent from mid‐June to early September. Age‐2 smolts are primarily produced by the Lake Kulik and beach spawning populations, showing that genetic differences may reflect divergent freshwater and migration life history strategies. These results indicate that local adaptation to spawning habitat influences genetic divergence in the Wood River lakes, affecting both adult and juvenile life stages of sockeye salmon.

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

“…The two sockeye salmon MHC SNPs are found in one exon (One_MHC2_190) and one intron (One_MHC2_251) within a Major Histocompatibility Complex (MHC) class II gene (Miller and Withler 1996;Miller et al 2001;Limborg et al 2011). Several studies support the adaptive nature of MHC polymorphisms related to pathogen-mediated selection (Dionne et al 2009;Evans and Neff 2009;McGlauflin et al 2011;Gomez-Uchida et al 2011). Differences in the spawning and rearing habitats (i.e.…”

“…The lake ecotype is the typical form of sockeye salmon that spends about half its life in a nursery lake before emigrating to the marine environment to mature, whereas the sea/river ecotype is a rarer form that rears in the freshwater environment for a much shorter and more variable period of time. Large differences in MHC allele frequencies between geographically proximate populations of the two ecotypes have been observed elsewhere throughout the range of sockeye salmon (Creelman et al 2011;Gomez-Uchida et al 2011;McGlauflin et al 2011). The two sockeye salmon MHC SNPs are found in one exon (One_MHC2_190) and one intron (One_MHC2_251) within a Major Histocompatibility Complex (MHC) class II gene (Miller and Withler 1996;Miller et al 2001;Limborg et al 2011).…”

An assessment of parasite infestation rates of juvenile sockeye salmon after 50 years of climate warming in southwest Alaska

“…Because 90-95% of the sockeye salmon juveniles collected in the Wood River system were age-1 fish, and because age-2 fish typically have 2-6X higher infestation rates compared to age-1 smolts, only age-1 smolts were used in this comparison between the historic and recent sampling periods. There have been no long-term changes in the proportion of age-1 and age-2 smolts in the system (Crawford 2001;McGlauflin 2010).…”

Marine trophic diversity in an anadromous fish is linked to its life-history variation in fresh water

“…Stocks (i.e. aggregates of populations) of sockeye salmon are often characterized by considerable genetic structure among component populations, including those in this study [6]. Geomorphic conditions in spawning habitats impose constraints on body size and shape.…”

“…The Wood River system of Bristol Bay, Alaska (59816 0 N, 158838 0 W) supports sockeye salmon displaying a wide variety of lifehistory characteristics associated with geomorphic conditions [5], distributed across a genetically structured population complex [6]. Sockeye typically spend 1-2 years rearing in fresh water, then 1-3 years at sea prior to returning to natal sites to spawn.…”