Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome

Molecular Ecology
By: , and 

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Abstract

A whole-genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalysed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD because gene duplicates (i.e., paralogs) are commonly filtered in genomic studies; such filtering may remove substantial portions of the genome in data sets from polyploid-origin species. We demonstrate a new method that enables genome-wide scans for signatures of selection at both nonduplicated and duplicated loci by taking locus-specific copy number into account. We apply this method to RAD sequence data from different ecotypes of a polyploid-origin salmonid (Oncorhynchus nerka) and reveal signatures of divergent selection that would have been missed if duplicated loci were filtered. We also find conserved signatures of elevated divergence at pairs of homeologous chromosomes with residual tetrasomic inheritance, suggesting that joint evolution of some nondiverged gene duplicates may affect the adaptive potential of these genes. These findings illustrate that including duplicated loci in genomic analyses enables novel insights into the evolutionary consequences of WGDs and local segmental gene duplications.

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Additional publication details

Publication type Article
Publication Subtype Journal Article
Title Screening of duplicated loci reveals hidden divergence patterns in a complex salmonid genome
Series title Molecular Ecology
DOI 10.1111/mec.14201
Volume 26
Issue 17
Year Published 2017
Language English
Publisher Wiley
Contributing office(s) Coop Res Unit Leetown
Description 14 p.
First page 4509
Last page 4522
Country Canada, United States