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

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.

传统上，种群遗传结构与种群历史动态的评估多依托中性分子标记（neutral markers），且会刻意排除适应性标记（adaptive markers）。本研究针对推定适应性与中性的单核苷酸多态性（Single-Nucleotide Polymorphisms, SNPs）在山松甲虫（mountain pine beetle）全地理分布范围内种群遗传结构推断中的应用效能展开对比分析。无论是适应性SNPs、中性SNPs，还是二者的组合，均能区分全分布区的种群遗传结构，并划定出近期在不列颠哥伦比亚省北部与阿尔伯塔省境内完成种群扩张的种群。当采用等量的适应性与中性SNPs开展分析时，结果显示适应性SNPs可在采样种群与推断得到的聚类结果之间建立更强的相关性。本研究结果表明，分析前无需将适应性SNPs从中性SNPs中剔除；相较于单独使用任一标记集，联合两类标记可更清晰地解析种群间的遗传分化程度。上述结果证实了适应性基因座在解析非模式生物（nonmodel organism）种群遗传结构方面的应用价值。