Data from: Reproductive isolation and environmental adaptation shape the phylogeography of mountain pine beetle (Dendroctonus ponderosae)

Chromosomal rearrangement can be an important mechanism driving population differentiation and incipient speciation. In the mountain pine beetle (MPB, Dendroctonus ponderosae), deletions on the Y chromosome that are polymorphic among populations are associated with reproductive incompatibility. Here we used RAD sequencing across the entire MPB range in western North America to reveal the extent of the phylogeographic differences between Y haplotypes compared to autosomal and X-linked loci. Clustering and gene flow analyses revealed three distinct Y haplogroups geographically positioned within and on either side of the Great Basin Desert. Despite close geographic proximity between populations on the boundaries of each Y haplogroup, there was extremely low Y haplogroup mixing among populations, and gene flow on the autosomes was reduced across Y haplogroup boundaries. These results are consistent with a previous study suggesting that independent degradation of a recently evolved neo-Y chromosome in previously isolated populations causes male sterility or inviability among Y haplotype lineages. Phylogeographic results supported historic contraction of MPB into three separate Pleistocene glacial refugia followed by post-glacial range expansion and secondary contact. Distinct sets of SNPs were statistically associated with environmental data among the most genetically distinct sets of geographic populations. This finding suggests that the process of adaptation to local climatic conditions is influenced by population genetic structure, with evidence for largely independent evolution in the most genetically isolated Y haplogroup.

染色体重排可作为推动种群分化与初期物种形成的重要机制。在山松甲虫（MPB，*Dendroctonus ponderosae*）中，种群间具多态性的Y染色体缺失与生殖不兼容性相关联。本研究依托覆盖北美西部山松甲虫全分布范围的限制性位点关联测序（RAD sequencing）数据，解析了Y染色体单倍型相较于常染色体与X连锁位点的系统地理学差异程度。聚类与基因流分析结果显示，存在3个地理分布分别位于大盆地沙漠内部及其两侧的Y染色体单倍群。尽管各Y单倍群边界的种群地理毗邻性极高，但种群间的Y单倍群混合程度极低，且常染色体的基因流在Y单倍群边界处受到阻滞。本研究结果与此前一项研究的结论相符：此前研究提出，先前处于隔离状态的种群中，新近演化出的新Y染色体（neo-Y chromosome）发生独立退化，会导致不同Y单倍型谱系间出现雄性不育或个体致死现象。系统地理学分析结果支持山松甲虫曾在地质历史上收缩至3个独立的更新世冰期避难所，随后经历冰期后种群扩张与二次接触的演化历程。在遗传分化程度最高的地理种群组中，存在与环境数据呈显著统计关联的独特单核苷酸多态性（SNPs）位点集。该结果表明，本地气候适应过程受到种群遗传结构的调控，且遗传隔离程度最高的Y单倍群呈现出显著独立的演化路径。