Data from: Phylogeny with introgression in Habronattus jumping spiders (Araneae: Salticidae)

Background: Habronattus is a diverse clade of jumping spiders with complex courtship displays and repeated evolution of Y chromosomes. A well-resolved species phylogeny would provide an important framework to study these traits, but has not yet been achieved, in part because of conflicting signals from the few genes available in past studies. Such discordant gene trees could be the result of incomplete lineage sorting (ILS) in recently diverged parts of the phylogeny, but there are indications that introgression could be a source of conflict.
Results: To infer Habronattus phylogeny and investigate the cause of gene tree discordance, we assembled transcriptomes for 34 Habronattus species and 2 outgroups. The concatenated 2.41 Mb of nuclear data (1877 loci) resolved phylogeny by Maximum Likelihood (ML) with high bootstrap support (95-100%) at most nodes, with some uncertainty surrounding the relationships of H. icenoglei, H. cambridgei, H. oregonensis, and Pellenes canadensis. Species tree analyses by ASTRAL and SVDQuartets gave almost completely congruent results. Several nodes in the ML phylogeny from 12.33 kb of mitochondrial data are incongruent with the nuclear phylogeny and indicate possible mitochondrial introgression: the internal relationships of the americanus and the coecatus groups, the relationship between the altanus, decorus, banksi, and americanus group, and between H. clypeatus and the coecatus group. To determine the relative contributions of ILS and introgression, we analyzed gene tree
discordance for loci longer than 1 kb using Bayesian Concordance Analysis (BCA) for the americanus group (679 loci) and the VCCR clade (viridipes/clypeatus/coecatus/roberti groups) (517 loci) and found signals of introgression in both. Finally, we tested specifically for nuclear introgression in the concatenated nuclear matrix with Patterson's D statistics and DFOIL. We found nuclear introgression resulting in substantial admixture between americanus group species, between H. roberti and the clypeatus group, and between the clypeatus and coecatus groups.
Conclusions: Our results indicate that the phylogenetic history of Habronattus is predominantly a diverging tree, but that hybridization may have been common between phylogenetically distant species, especially in subgroups with complex courtship displays.

背景：雅蛛属（Habronattus）是一类物种多样性丰富的跳蛛演化支，其成员具有复杂的求偶行为，且Y染色体存在多次独立演化事件。构建高分辨率的物种系统发育树，将为研究这些特征提供关键框架，但目前尚未实现这一目标，部分原因在于过往研究中基于少量基因得到的系统发育信号存在冲突。这类不一致的基因树可能源于系统发育树中近期分化支系的不完全谱系分选（ILS），但也有迹象表明基因渐渗可能是冲突产生的另一诱因。
结果：为推断雅蛛属的系统发育关系并探究基因树冲突的成因，我们对34个雅蛛属物种及2个外类群进行了转录组组装。通过串联得到的2.41 Mb核基因组数据（包含1877个基因座），经最大似然法（ML）构建的系统发育树在绝大多数节点上获得了较高的自展支持率（95%~100%），仅在H. icenoglei、H. cambridgei、H. oregonensis以及加拿大佩蛛（Pellenes canadensis）的系统发育关系上存在一定不确定性。利用ASTRAL与SVDQuartets进行的物种树分析得到了几乎完全一致的结果。基于12.33 kb线粒体数据构建的最大似然树中，多个节点与核基因组系统发育树不一致，提示可能存在线粒体基因渐渗：包括美洲组（americanus group）与科卡图斯组（coecatus group）的内部亲缘关系、altanus组、decorus组、banksi组与美洲组之间的亲缘关系，以及H. clypeatus与科卡图斯组之间的亲缘关系。为量化不完全谱系分选与基因渐渗的相对贡献，我们针对长度超过1 kb的基因座，分别对美洲组（包含679个基因座）与VCCR演化支（viridipes组/clypeatus组/coecatus组/roberti组，共517个基因座）开展了贝叶斯一致性分析（BCA），结果在两个类群中均检测到了基因渐渗的信号。最后，我们利用帕特森D统计量与DFOIL对串联核矩阵开展了专门的核基因渐渗检测，发现核基因渐渗导致了以下类群间出现了显著的遗传混合：美洲组内部各物种之间、H. roberti与clypeatus组之间，以及clypeatus组与科卡图斯组之间。
结论：本研究结果表明，雅蛛属的系统发育历史整体上呈现为不断分化的树形结构，但不同演化支之间的杂交事件可能较为频繁，尤其是在那些拥有复杂求偶行为的亚类群之间。