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

Philip D Batista,Felix A H Sperling,Jasmine K Janes,Celia K Boone,Brent W Murray

doi:10.1002/ece3.2367

Philip D Batista, Felix A H Sperling + Show 3 more

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https://doi.org/10.1002/ece3.2367

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Abstract

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.

Highlights

Neutral genetic markers have been considered essential to research on population structure (Luikart et al 2003; SotoCerda and Cloutier 2013), and numerous methods have been developed to identify and potentially remove outlier markers that may be under selection (Seeb et al 2011)
At K = 4 in the neutral and combined data sets, beetles from Manning Park and Whistler in British Columbia clustered with MPB populations along the west coast USA (Oregon, California, and Nevada: orange)
For adaptive single-nucleotide polymorphisms (SNPs), population groupings are less distinct in each plot, and some genetic differentiation of west coast US populations can be seen, adaptive SNPs did not identify the Manning Park and Whistler populations as a separate cluster

Summary

Introduction

Neutral genetic markers have been considered essential to research on population structure (Luikart et al 2003; SotoCerda and Cloutier 2013), and numerous methods have been developed to identify and potentially remove outlier markers that may be under selection (Seeb et al 2011). Adaptive markers may help to identify populations experiencing different ecological conditions, such as temperature or salinity (Nosil et al 2009; Heylar et al 2011; Milano et al 2014). It should be useful to include markers under selection in surveys of population structure, to allow greater understanding of evolutionary processes and support more effective management of populations, especially in nonmodel organisms.

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