How the Mountain Pine Beetle (Dendroctonus ponderosae) Breached the Canadian Rocky Mountains

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Assessments of population genetic structure and demographic history have traditionally been based on neutral markers while explicitly excluding adaptive markers. In this study, we compared the utility of putatively adaptive and neutral single‐nucleotide polymorphisms (SNPs) for inferring mountain pine beetle population structure across its geographic range. Both adaptive and neutral SNPs, and their combination, allowed range‐wide structure to be distinguished and delimited a population that has recently undergone range expansion across northern British Columbia and Alberta. Using an equal number of both adaptive and neutral SNPs revealed that adaptive SNPs resulted in a stronger correlation between sampled populations and inferred clustering. Our results suggest that adaptive SNPs should not be excluded prior to analysis from neutral SNPs as a combination of both marker sets resulted in better resolution of genetic differentiation between populations than either marker set alone. These results demonstrate the utility of adaptive loci for resolving population genetic structure in a nonmodel organism.

“…() and Janes et al. () found that Whistler was genetically different from other Canadian populations, but each provided slightly different explanations for the pattern. Janes et al.…”

Section: Discussionmentioning

confidence: 97%

Section: Introductionmentioning

confidence: 89%

“…Selection of adaptive SNPs for this study was based on the panel of 1546 SNPs previously developed using markers with potentially important physiological functions (Janes et al. ).…”

Section: Methodsmentioning

confidence: 99%

“…Based on their identification as outliers by Janes et al. () using BayeScan (Foll and Gaggiotti ) and Lositan (Antao et al. ), we grouped the SNPs into two sets – adaptive and neutral.…”

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Adaptive and neutral markers both show continent‐wide population structure of mountain pine beetle (Dendroctonus ponderosae)

Batista

Janes

Boone

et al. 2016

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Selection of the sex‐linked inhibitor of apoptosis in mountain pine beetle (Dendroctonus ponderosae) driven by enhanced expression during early overwintering

Horianopoulos

Boone

Samarasekera

et al. 2018

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The mountain pine beetle (Dendroctonus ponderosae) is an insect native to western North America; however, its geographical range has recently expanded north in BC and east into Alberta. To understand the population structure in the areas of expansion, 16 gene‐linked microsatellites were screened and compared to neutral microsatellites using outlier analyses of F st and F ct values. One sex‐linked gene, inhibitor of apoptosis (IAP), showed a strong signature of positive selection for neo‐X alleles and was analyzed for evidence of adaptive variation. Alleles of IAP were sequenced, and differences between the neo‐X and neo‐Y alleles were consistent with neutral evolution suggesting that the neo‐Y allele may not be under functional constraints. Neo‐Y alleles were amplified from gDNA, but not effectively from cDNA, suggesting that there was little IAP expression from neo‐Y alleles. There were no differences in overall IAP expression between males and females with the common northern neo‐X allele suggesting that the neo‐X allele in males compensates for the reduced expression of neo‐Y alleles. However, males lacking the most common northern neo‐X allele thought to be selected for in northern populations had reduced overall IAP expression in early October—at a time when beetles are preparing for overwintering. This suggests that the most common allele may have more rapid upregulation. The reduced function of neo‐Y alleles of IAP suggested by both sequence differences and lower levels of expression may foster a highly selective environment for neo‐X alleles such as the common northern allele with more efficient upregulation.

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

Trevoy

Janes

Muirhead

et al. 2018

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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.