Genomic Islands of Divergence Reveal Signature of Selection on the Alternate Homeolog in Upper Fraser River Sockeye Run-Timing Groups.

Authors

Ben J G Sutherland, Cory Williamson, Brian Toth, Gordon Sterritt

Published in

Molecular ecology. Volume 35. Issue 20. Pages e70594.

Abstract

Effective wildlife conservation and management depends on a thorough understanding of both neutral and adaptive intraspecific genomic variation. Population structure is often well understood in many ecologically or economically important species, but the extensive population genomic resources required to characterize putatively adaptive variation and punctuated genomic regions is typically only recently available for some species, if available at all. Here, we explore recently published whole-genome resequencing data in the upper Fraser River and identify a large island of divergence separating Nechako Watershed populations with different return migration timings (i.e., run timing). The island of divergence at 56.3-58.0 Mbp of Chr18 has extended homozygosity and reduced Tajima's D in sockeye salmon Oncorhynchus nerka from the Nadina River, Stellako River and the Stuart-Summer run timing group, but not the geographically proximal Early Stuart sockeye. In the populations without the Stuart-Summer haploblock, genetic variation is similar to elsewhere in the chromosome. Gene content in the haploblock includes leucine rich-repeat containing 9-like (lrrc9-like) and the surrounding homeologous region to the lrrc9 region of Chr12. lrrc9 is within a conserved and selected island of divergence associated with life history traits and run timing throughout the species range and lrrc9-like has recently been associated with run timing in other salmonids. By also inspecting the samples in the present work at the Chr12 haploblock, three genotypic states were observed throughout the region, with the Stuart River run timing groups mainly comprised of the reference haplotype. No other regions of major differentiation were observed in the analysed samples in the Chilcotin or Quesnel River systems. These results provide additional evidence for the importance of both homeologous regions holding lrrc9 and lrrc9-like in different geographic regions and underscore the uniqueness of upper Fraser River sockeye in this potentially adaptive island of divergence.

PMID:
42888892
Bibliographic data and abstract were imported from PubMed on 17 Oct 2026.

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