Network Analysis of Linkage Disequilibrium Reveals Genome Architecture in Chum Salmon

We examined patterns of LD using network analysis to identify an overlapping chromosome inversion and sex-determining region in chum salmon. The signal of the inversion was strong enough to show up as false population substructure when the entire dataset was analyzed, while the effect of the sex-determining region on population structure was only obvious after restricting analysis to the sex chromosome. Understanding the extent and geographic distribution of inversions is now a critically important part of genetic analyses of natural populations. Our results highlight the importance of analyzing and understanding patterns of LD in genomic dataset and the perils of excluding or ignoring loci exhibiting LD. Blindly excluding loci in LD would have prevented detection of the sex-determining region and chromosome inversion while failing to understand the genomic features leading to high-LD could have resulted in false interpretations of population structure.

Source: G3: Genes Genomes Genetics - May 3, 2020 Category: Genetics & Stem Cells Authors: McKinney, G., McPhee, M. V., Pascal, C., Seeb, J. E., Seeb, L. W. Tags: Investigations Source Type: research