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

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.

Keywords: Adaptive selection; Dendroctonus ponderosae; mountain pine beetle; population genetic structure.

Figure 1

Mountain pine beetle found outside pitch tube of a lodgepole pine.

Figure 2

STRUCTURE and discriminant analysis of principal components plots of North American Dendroctonus ponderosae populations for K = 3–5 using putatively adaptive loci, neutral loci, and both adaptive and neutral loci combined. Regions underlined below represent: (A) northern Canada; (B) southern Canada; (C) Idaho, Montana, and Washington; (D) Oregon, California, and Nevada; (E) Utah and Wyoming; and (F) Arizona and South Dakota. Stars indicate Whistler and Manning Park.

Figure 3

Cluster assignments from discriminant analysis of principal components for three sets of single‐nucleotide polymorphisms at K = 4. The colors in each pie chart correspond to the assignment probability, with the four general regions identified as follows: Red = northern Canada; Green = southern Canada and northern USA; Orange = west coast populations; Blue = outlying southern populations. Mountain pine beetle sampling is overlaid on lodgepole (hatched area) and jack pine (dotted area) distributions.