4.5 Article

Repurposing population genetics data to discern genomic architecture: A case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)

Journal

ECOLOGY AND EVOLUTION
Volume 9, Issue 3, Pages 1147-1159

Publisher

WILEY
DOI: 10.1002/ece3.4803

Keywords

genomic architecture; linkage disequilibrium; population genomics

Funding

  1. Alberta Agriculture and Forestry
  2. Natural Resources Canada - Canadian Forest Service
  3. Northwest Territories Environment and Natural Resources
  4. Manitoba Conservation and Water Stewardship
  5. Ministry of Natural Resources and Forestry
  6. Saskatchewan Ministry of Environment
  7. Natural Science and Engineering Research Council of Canada [NET GP 434810-12]
  8. Foothills Research Institute
  9. Weyerhaeuser Company
  10. West Fraser Timber Co. Ltd
  11. Laval University
  12. University of Alberta

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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.

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