Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae). Issue 3 (26th December 2018)

• Record Type: Journal Article
• Authors: Trevoy, Stephen A. L.; Janes, Jasmine K.; Muirhead, Kevin; Sperling, Felix A. H.
• Is Part Of: Ecology and evolution. Volume 9:Issue 3(2019)
• Page Start: 1147
• Page End: 1159
• Publication Date: 2018-12-26
• Subjects: genomic architecture -- linkage disequilibrium -- population genomics; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.4803
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: Genetic surveys of the population structure of species can be used as resources for exploring their genomic architecture. By adjusting filtering assumptions, genome‐wide single‐nucleotide polymorphism (SNP) datasets can be reused to give new insights into the genetic basis of divergence and speciation without targeted resampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principal components analysis and linkage disequilibrium network analysis to distinguish three cohorts of variable SNPs in the mountain pine beetle in western Canada, including one that was sex‐linked and one that was geographically associated. These marker cohorts indicate genomically localized differentiation, and their detection demonstrates an accessible and intuitive method for discovering potential islands of genomic divergence without a priori knowledge of a species' genomic architecture. Thus, this method has utility for directly addressing the genomic architecture of species and generating new hypotheses for functional research. Abstract : The mountain pine beetle (MPB, Dendroctonus ponderosae ) is a nonmodel organism of great economic interest to the forestry and tourism industries of western Canada. With the combined use of linkage network and principal components analysis (PCA), we describe a novel method for determining sex using SNP markers, and a putative island of genomic divergence between Canadian populations of MPB.