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

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.

Continent‐wide population genomic structure and phylogeography of North America’s most destructive conifer defoliator, the spruce budworm (Choristoneura fumiferana)

“…As the continental glacier melted and retreated, glacial Lake Spruce budworm populations can undergo massive outbreaks and have the ability to disperse hundreds of kilometers (Dobesberger, Lim, & Raske, 1983;Greenbank, Schaefer, & Rainey, 1980), and it is thereby unlikely that current subpopulation structure is upheld solely by physical isolation and genetic drift that occurred during the LGM. This region of the chromosome may be a genomic outlier region, also coined "island of genomic differentiation" or "speciation island," containing a barrier locus (or loci) that contributes to reproductive isolation (Trevoy et al, 2019;Turner, Hahn, & Nuzhdin, 2005;Wolf & Ellegren, 2017). With no physical barriers, movement of individuals between geographic regions is possible, but the success rate of colonization by hybrids or dispersing individuals may be low either due to reproductive incompatibility (unlikely in this case) or the lack of necessary adaptations to the new environment (Hendry, 2017 Eastern subpopulations were on linkage group 4, and were located on the chromosome between 37.33 and 40.68 cM.…”

“…Overall, nine of the top ten contributing SNPs that differentiated the Central and Eastern subpopulations were on linkage group 4, and were located on the chromosome between 37.33 and 40.68 cM. This region of the chromosome may be a genomic outlier region, also coined "island of genomic differentiation" or "speciation island," containing a barrier locus (or loci) that contributes to reproductive isolation (Trevoy et al, 2019;Turner, Hahn, & Nuzhdin, 2005;Wolf & Ellegren, 2017). It is also possible that this region has arisen through linked selection via genetic drift or background selection, and the associated loci are not necessarily relevant to population divergence (Wolf & Ellegren, 2017).…”

“…The subclustering pattern of individuals within the central and eastern geographic regions along the PCA axes 1 and 2 was indicative of the data containing SNPs within a linkage block (see also Trevoy, Janes, Muirhead, & Sperling, 2019…”

“…To investigate this further, we reran PC analysis with specimens from the western geographic region (Alaska, Yukon) removed, to obtain SNP loading values associated with the three subclusters along axis 1. We then sorted the SNP loading values from highest to lowest to view the top contributing SNPs, graphed the loading values, and determined whether there was a set of high contributing SNPs both similar to each other in loading values and comparatively higher than the next consecutive contributing SNP, as documented inTrevoy et al (2019). We then searched for these SNPs in the published C. fumiferana linkage map Linkage map details."…”

Rapid Adaptation to Temperature via a Potential Genomic Island of Divergence in the Invasive Green Crab, Carcinus maenas

“…This approach uses network analysis to identify SNP clusters with unusually high within-group LD relative to the larger data set, without requiring information on their relative position in the genome. Such clustering may indicate the action of specific evolutionary processes on the genome, and the patterns by which clustered SNPs are distributed across genes and populations may further inform the nature of these processes (Kemppainen et al, 2015;Trevoy et al, 2019). For example, inversion polymorphisms and other extended genomic regions of decreased recombination are characterized by SNP clusters that separate individuals into three groups representing the two homozygous states (minor and major allele) and heterozygotes.…”