Data from: Genome-wide SNPs resolve phylogenetic relationships in the North American spruce budworm (Choristoneura fumiferana) species complex

High throughput sequencing technologies have revolutionized the potential to reconcile incongruence between gene and species trees, and numerous approaches have been developed to take advantage of these advances. Genotyping-by-sequencing is becoming a regular tool for gathering phylogenetic data, yet comprehensive evaluations of phylogenetic methods using these data are sparse. Here we use multiple phylogenetic and population genetic methods for genotyping-by-sequencing data to assess species relationships in a group of forest insect pests, the spruce budworm (Choristoneura fumiferana) species complex. With few exceptions, all methods agree on the same relationships, most notably placing C. pinus as basal to the remainder of the group, rather than C. fumiferana as previously suggested. We found strong support for the monophyly of C. pinus, C. fumiferana, and C. retinana, but more ambiguous relationships and signatures of introgression in a clade of western lineages, including C. carnana, C. lambertiana, C. occidentalis occidentalis, C. occidentalis biennis, and C. orae. This represents the most taxonomically comprehensive genomic treatment of the spruce budworm species group, which is further supported by the broad agreement among multiple methodologies.高通量测序技术（High throughput sequencing）彻底革新了解决基因树与物种树之间冲突的研究潜能，诸多依托该技术进展的分析方法已被开发出来。测序分型（Genotyping-by-sequencing）正逐步成为获取系统发育数据的常规手段，但针对基于此类数据的系统发育分析方法的全面评估仍较为稀缺。本研究以一类森林害虫——云杉卷叶蛾（Choristoneura fumiferana）物种复合体为研究对象，采用多种系统发育及群体遗传分析方法对其测序分型数据进行物种亲缘关系解析。除极少数例外情况外，所有分析方法均得到了一致的物种亲缘关系拓扑结构，最显著的结论是将松色卷蛾（C. pinus）确定为该类群其余物种的基部类群，而非此前研究所提出的云杉卷叶蛾（C. fumiferana）。本研究为松色卷蛾、云杉卷叶蛾以及网卷色卷蛾（C. retinana）的单系群属性提供了强力支持，但在包含C. carnana、C. lambertiana、C. occidentalis occidentalis、C. occidentalis biennis及C. orae的西部支系中，则发现了更多亲缘关系模糊的类群以及基因渐渗信号。本研究是目前针对云杉卷叶蛾物种类群的分类学覆盖范围最全面的基因组学研究，且该结论得到了多种分析方法广泛一致性结果的进一步佐证。