Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
| Main Authors: | Trevoy, Stephen A.L., Janes, Jasmine K., Muirhead, Kevin, Sperling, Felix A.H. |
|---|---|
| Format: | info dataset Journal |
| Terbitan: |
, 2019
|
| Subjects: | |
| Online Access: |
https://zenodo.org/record/4976609 |
Daftar Isi:
- 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 re-sampling of specimens. Filtering only for missing data and minor allele frequency, we used a combination of principle 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.
- 187_MPB_FemGenome175 Wild-caught and 13 lab-bred mountain pine beetle (Dendroctonus ponderosae) specimens from western Canada. Double-Digest RAD sequencing, aligned to the female D. ponderosae draft genome [Keeling et al. Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest. Genome Biology. 2013;14(3):1. doi:10.1186/gb-2013-14-3-r27], and compiled in STACKSF1_in_F.vcf