Department of Zoology, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
Department of Botany and Beaty Biodiversity Museum, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
BMC Evol Biol. 2018 Feb 22;18(1):24. doi: 10.1186/s12862-018-1137-x.
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.
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 D. 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.
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.
哈布罗纳图斯是一个多样化的跳蛛属，具有复杂的求偶行为和 Y 染色体的反复进化。一个解决得很好的物种系统发育将为研究这些特征提供一个重要的框架，但尚未实现，部分原因是过去研究中可用的少数基因给出了相互矛盾的信号。这种不一致的基因树可能是系统发育中最近分化部分不完全谱系分选（ILS）的结果，但有迹象表明基因渗入可能是冲突的一个来源。
为了推断哈布罗纳图斯的系统发育，并研究基因树分歧的原因，我们为 34 种哈布罗纳图斯物种和 2 个外群组装了转录组。通过最大似然法（ML）对拼接的 2.41 Mb 核数据（1877 个基因座）进行分析，得到了高 bootstrap 支持（95-100%）的大多数节点的系统发育，而 H.icenoglei、H.cambridgei、H.oregonensis 和 Pellenes canadensis 的关系存在一些不确定性。ASTRAL 和 SVDQuartets 的种系树分析几乎完全一致。从 12.33 kb 的线粒体数据中得到的 ML 系统发育中的几个节点与核系统发育不一致，表明可能存在线粒体基因渗入：americana 和 coecatus 组的内部关系、altanus、decorus、banksi 和 americana 组之间的关系，以及 H.clypeatus 和 coecatus 组之间的关系。为了确定 ILS 和基因渗入的相对贡献，我们使用贝叶斯一致分析（BCA）对核基因座（大于 1 kb）进行了分析，结果显示 americana 组（679 个基因座）和 VCCR 分支（viridipes/clypeatus/coecatus/roberti 组）（517 个基因座）存在基因渗入的信号。最后，我们使用 Patterson 的 D 统计量和 D 专门测试了拼接核矩阵中的基因渗入，结果发现 americana 组物种之间、H.roberti 与 clypeatus 组之间以及 clypeatus 组与 coecatus 组之间存在大量的基因混合。
我们的研究结果表明，哈布罗纳图斯的进化历史主要是一个分歧的树，但在进化上遥远的物种之间可能存在杂交，尤其是在具有复杂求偶行为的亚群中。
