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

Morten T. Limborg, Wesley A. Larson, Lisa W. Seeb, James E. Seeb

A whole genome duplication (WGD) doubles the entire genomic content of a species and is thought to have catalyzed adaptive radiation in some polyploid-origin lineages. However, little is known about general consequences of a WGD since 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 non-duplicated 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 non-diverged 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. This article is protected by copyright. All rights reserved.