Genome-wide analysis reveals demographic and life-history patterns associated with habitat modification in landlocked, deep-spawning sockeye salmon (Oncorhynchus nerka)

Genomics reveals repeated landlocking of diadromous fish on an isolated island

Landlocking of diadromous fish in freshwater systems can have significant genomic consequences. For instance, the loss of the migratory life stage can dramatically reduce gene flow across populations, leading to increased genetic structuring and stronger effects of local adaptation. These genomic consequences have been well-studied in some mainland systems, but the evolutionary impacts of landlocking in island ecosystems are largely unknown. In this study, we used a genotyping-by-sequencing (GBS) approach to examine the evolutionary history of landlocking in common smelt (Retropinna retropinna) on Chatham Island, a small isolated oceanic island 800 kilometres east of mainland New Zealand. We examined the relationship between Chatham Island and mainland smelt and used coalescent analyses to test the number and timing of landlocking events on Chatham Island. Our genomic analysis, based on 21,135 SNPs across 169 individuals, revealed that the Chatham Island smelt was genomically distinct from the mainland New Zealand fish, consistent with a single ancestral colonisation event of Chatham Island in the Pleistocene. Significant genetic structure was also evident within the Chatham Island smelt, with a diadromous Chatham Island smelt group, along with three geographically structured landlocked groups. Coalescent demographic analysis supported three independent landlocking events, with this loss of diadromy significantly pre-dating human colonisation. Our results illustrate how landlocking of diadromous fish can occur repeatedly across a narrow spatial scale, and highlight a unique system to study the genomic basis of repeated adaptation.

Genome-Wide Investigation of the Multiple Origins Hypothesis for Deep-Spawning Kokanee Salmon (Oncorhynchus nerka) across its Pan-Pacific Distribution

Salmonids have emerged as important study systems for investigating molecular processes underlying parallel evolution given their tremendous life history variation. Kokanee, the resident form of anadromous sockeye salmon (Oncorhynchus nerka), have evolved multiple times across the species' pan-Pacific distribution, exhibiting multiple reproductive ecotypes including those that spawn in streams, on lake-shores, and at lake depths >50 m. The latter has only been detected in 5 locations in Japan and British Columbia, Canada. Here, we investigated the multiple origins hypothesis for deep-spawning kokanee, using 9721 single nucleotide polymorphisms distributed across the genome analyzed for the vast majority of known populations in Japan (Saiko Lake) and Canada (Anderson, Seton, East Barrière Lakes) relative to stream-spawning populations in both regions. We detected 397 outlier loci, none of which were robustly identified in paired-ecotype comparisons in Japan and Canada independently. Bayesian clustering and principal components analyses based on neutral loci revealed 6 distinct clusters, largely associated with geography or translocation history, rather than ecotype. Moreover, a high level of divergence between Canadian and Japanese populations, and between deep- and stream-spawning populations regionally, suggests the deep-spawning ecotype independently evolved on the 2 continents. On a finer level, Japanese kokanee populations exhibited low estimates of heterozygosity, significant levels of inbreeding, and reduced effective population sizes relative to Canadian populations, likely associated with transplantation history. Along with preliminary evidence for hybridization between deep- and stream-spawning ecotypes in Saiko Lake, these findings should be considered within the context of on-going kokanee fisheries management in Japan.