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Data from: Distinct sources of gene flow produce contrasting population genetic dynamics at different range boundaries of a Choristoneura budworm
Blackburn, Gwylim S.; Brunet, Bryan M. T.; Muirhead, Kevin; Cusson, Michel; Béliveau, Catherine; Levesque, Roger C.; Lumley, Lisa M.; Sperling, Felix A. H. — 2017-10-27 Populations are often exposed to multiple sources of gene flow, but accounts are lacking of the population genetic dynamics that result from these interactions or their effects on local evolution. Using a genomic clines framework applied to 1195 SNPs, we documented genome-wide, locus-specific patterns of introgression between Choristoneura occidentalis biennis spruce budworms and two ecologically divergent relatives, C. o. occidentalis and C. fumiferana, that it interacts with at alternate boundaries of its range. We observe contrasting hybrid indexes between these hybrid zones, no overlap in ‘gene flow outliers’ (clines showing relatively extreme extents or rates of locus-specific introgression), and variable linkage disequilibrium among those outliers. At the same time, correlated genome-wide rates of introgression between zones suggest the presence of processes common to both boundaries. These findings highlight the contrasting population genetic dynamics that can occur at separate frontiers of a single population, while also suggesting that shared patterns may frequently accompany cases of divergence-with-gene-flow that involve a lineage in common. Our results point to potentially complex evolutionary outcomes for populations experiencing multiple sources of gene flow.
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Data from: Repurposing population genetics data to discern genomic architecture: a case study of linkage cohort detection in mountain pine beetle (Dendroctonus ponderosae)
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Trevoy, Stephen A.L.; Janes, Jasmine K.; Muirhead, Kevin; Sperling, Felix A.H. — 2019-02-06 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.
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Data from: Cross-platform compatibility of de novo-aligned SNPs in a non-model butterfly genus
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Campbell, Erin O.; Davis, Corey S.; Dupuis, Julian R.; Muirhead, Kevin; Sperling, Felix A.H.; Sperling, Felix A. H. — 2017-06-20 High-throughput sequencing methods for genotyping genome-wide markers are being rapidly adopted for phylogenetics of non-model organisms in conservation and biodiversity studies. However, the reproducibility of SNP genotyping and degree of marker overlap or compatibility between datasets from different methodologies have not been tested in non-model systems. Using double-digest restriction site associated DNA sequencing, we sequenced a common set of 22 specimens from the butterfly genus Speyeria on two different Illumina platforms, using two variations of library preparation. We then used a de novo approach to bioinformatic locus assembly and SNP discovery for subsequent phylogenetic analyses. We found a high rate of locus recovery despite differences in library preparation and sequencing platforms, as well as overall high levels of data compatibility after data processing and filtering. These results provide the first application of NGS methods for phylogenetic reconstruction in Speyeria, and support the use and long-term viability of SNP genotyping applications in non-model systems.

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(Author: Muirhead, Kevin)

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