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 the few genes available in past studies gave conflicting signals. 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 nuclear 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 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：哈氏跳蛛属（Habronattus）是一类物种多样性极高的跳蛛演化支，兼具复杂的求偶展示行为，且Y染色体经历了多次独立演化事件。构建高分辨率的哈氏跳蛛属物种系统发育树，将为研究上述性状提供关键框架，但目前学界尚未实现这一目标，部分原因在于过往研究仅使用少量基因，导致不同基因得到的系统发育信号相互矛盾。这类基因树不一致的现象，可能源于系统发育树近期分化支系中的不完全谱系分选（incomplete lineage sorting, ILS），但也有迹象表明基因渐渗可能是引发系统发育冲突的另一诱因。
结果：为推断哈氏跳蛛属的系统发育关系并探究基因树冲突的成因，本研究组装了34个哈氏跳蛛物种及2个外类群的转录组数据。合并后的核基因组数据总长2.41 Mb，涵盖1877个基因座，通过最大似然法（Maximum Likelihood, ML）构建的系统发育树在绝大多数节点上获得了95%~100%的高自展支持率，仅在H. icenoglei、H. cambridgei、H. oregonensis以及Pellenes canadensis的系统发育关系上存在一定不确定性。采用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系统发育树，其多个节点与核基因组系统发育树存在冲突，提示可能存在线粒体基因渐渗：具体涉及americanus类群的内部亲缘关系、altanus、decorus、banksi类群与americanus类群之间的系统发育关系，以及H. clypeatus与coecatus类群之间的亲缘关系。为评估不完全谱系分选与基因渐渗的相对贡献，本研究针对长度超过1 kb的核基因座，分别对americanus类群（含679个基因座）和VCCR演化支（viridipes/clypeatus/coecatus/roberti类群，含517个基因座）开展了贝叶斯一致性分析（Bayesian Concordance Analysis, BCA），结果在两个类群中均检测到了基因渐渗的信号。最后，本研究使用帕特森D统计（Patterson’s D statistics）与DFOIL方法，针对合并后的核基因组矩阵专门检测了基因渐渗事件，结果发现americanus类群内部物种间、H. roberti与clypeatus类群之间、以及clypeatus类群与coecatus类群之间均存在显著的核基因渐渗与基因交流。
结论：本研究结果表明，哈氏跳蛛属的系统发育历史整体呈现为分化的树形结构，但系统发育距离较远的物种间可能存在频繁的杂交事件，尤其是在那些具有复杂求偶行为的类群亚支中。