Genomic islands of divergence linked to ecotypic variation in sockeye salmon

Abstract

Regions of the genome displaying elevated differentiation (genomic islands of divergence) are thought to play an important role in local adaptation, especially in populations experiencing high gene flow. However, the characteristics of these islands as well as the functional significance of genes located within them remain largely unknown. Here, we used data from thousands of SNPs aligned to a linkage map to investigate genomic islands of divergence in three ecotypes of sockeye salmon (Oncorhynchus nerka) from a single drainage in southwestern Alaska. We found ten islands displaying high differentiation among ecotypes. Conversely, neutral structure observed throughout the rest of the genome was low and not partitioned by ecotype. One island on linkage group So13 was particularly large and contained six SNPs with F > 0.14 (average F of neutral SNPs = 0.01). Functional annotation revealed that the peak of this island contained a nonsynonymous mutation in a gene involved in growth in other species (TULP4). The islands that we discovered were relatively small (80-402 Kb), loci found in islands did not show reduced levels of diversity, and loci in islands displayed slightly elevated linkage disequilibrium. These attributes suggest that the islands discovered here were likely generated by divergence hitchhiking; however, we cannot rule out the possibility that other mechanisms may have produced them. Our results suggest that islands of divergence serve an important role in local adaptation with gene flow and represent a significant advance towards understanding the genetic basis of ecotypic differentiation.

Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence‐related genes

“…(), and Larson et al. () RAD‐tags compared to our SNPs, the same causal locus may be implicated in both cases. Supporting this, SNPs on the 7K array found to be associated with age at maturity in Teno salmon by Johnston et al.…”

“…(, RAD‐tag 64477), and Larson et al. (, RAD‐tag 41305) did not align with the S. salar genome, but mapped unambiguously on the O. mykiss genome ≈36 kb from 68810 between the genes lrr9 and dhrs7 (Figure ). No other (ecotype associated or neutral) RAD‐tag from Veale and Russello () mapped within this haploblock or adjacent candidate haploblocks on Ssa09.…”

An ancient selective sweep linked to reproductive life history evolution in sockeye salmon

“…39 between shore-spawning sockeye salmon and stream-spawning kokanee in Redfish Lake, Idaho, USA within the Snake River catchment, a tributary of the Columbia River. No other SNP was identified as being as significantly divergent between any pair of shore- or stream-spawning ecotypes in either of these studies, or in a recently published study comparing beach- and river-spawning sockeye salmon from Alaska (which did not include this locus) 40 . Furthermore, no other SNP has been recorded across multiple comparisons of shore- and stream-spawning ecotypes across these studies 39, 40 .…”

Ancient chromosomal rearrangement associated with local adaptation of a postglacially colonized population of Atlantic Cod in the northwest Atlantic

“…Genetic diversity, particularly when associated with fitness‐related traits, is expected to promote sustainability and persistence (Hilborn, Quinn, Schindler, & Rogers, ; Schindler et al., ). The increasing availability of genomic tools for nonmodel organisms creates the opportunity to study population structure and genetic variation with unprecedented resolution (Allendorf, Hohenlohe, & Luikart, ; Benestan et al., ; Bradbury et al., ; Hemmer‐Hansen, Therkildsen, Meldrup, & Nielsen, ; Van Wyngaarden et al., ), and improves our ability to characterize the evolutionary processes that influence intraspecific diversity (Bourret et al., ; Bradbury et al., ; Funk, McKay, Hohenlohe, & Allendorf, ; Larson et al., ; Moore et al., ). As genomic data on the basis of intraspecific diversity accumulate, there is increasing evidence that structural rearrangements, such as chromosomal inversions, may be important to the evolution of diversity by facilitating adaptive differences among populations and ultimately speciation (Hoffmann & Rieseberg, ; Jones et al., ; Joron et al., ; Lamichhaney et al., ; Lowry & Willis, ).…”