Phylogenomic analysis of brachyuran crabs using transcriptome data reveals possible sources of conflicting phylogenetic relationships within the group

Despite extensive morphological and molecular studies, the phylogenetic interrelationships within the infraorder Brachyura and the phylogenetic positions of many taxa remain uncertain. Studies that used a limited number of molecular markers have often failed to provide sufficient resolution and may be susceptible to stochastic errors and incomplete lineage sorting (ILS). Here we reconstructed the phylogenetic relationships within the Brachyura using transcriptome data of 56 brachyuran species, including 14 newly sequenced taxa. Five supermatrices were constructed in order to exclude different sources of systematic error. The results of the phylogenetic analyses indicate that Heterotremata is non-monophyletic and that the two Old World primary freshwater crabs (Potamidae and Gecarcinucidae) and the Hymenosomatoidea form a clade that is sister to the Thoracotremata, and outside the Heterotremata. We also found that ILS is the main cause of the gene-tree discordance of these freshwater crabs. Divergence time estimations indicate that the Brachyura has an ancient origin, probably either in the Triassic or Jurassic, and that the majority of extant families and superfamilies first appeared during the Cretaceous, with a constant increase of diversity in Post-Cretaceous-Palaeogene times. The results support the hypothesis that the two Old World freshwater crab families included in this study (Potamidae and Gecarcinucidae) diverged from their marine ancestors around 120 Ma, in the Cretaceous. In addition, this work provides new insights that may aid in the reclassification of some of the more problematic brachyuran groups.

尽管已有大量形态学与分子生物学研究，但短尾下目（Brachyura）内部的系统发育亲缘关系，以及诸多类群的系统发育位置仍未明确。过往仅使用有限数量分子标记的研究，往往无法提供足够的分辨率，且易受随机误差与不完全谱系分选（ILS）的影响。本研究基于56种短尾类的转录组数据（其中14个类群为本次新测序获得），重建了短尾下目的系统发育关系。本研究构建了5套超级矩阵，以排除不同来源的系统误差。系统发育分析结果显示，异孔亚派（Heterotremata）并非单系群；两支旧大陆原生淡水蟹类群——溪蟹科（Potamidae）与束腹蟹科（Gecarcinucidae），以及膜壳蟹总科（Hymenosomatoidea）共同构成一个演化支，该演化支与胸孔亚派（Thoracotremata）互为姊妹群，且处于异孔亚派之外。本研究同时发现，不完全谱系分选（ILS）是导致这些淡水蟹类基因树冲突的主要原因。分歧时间估算结果显示，短尾下目起源古老，可能可追溯至三叠纪或侏罗纪；绝大多数现生科与总科均首次出现于白垩纪，并在白垩纪-古近纪之后持续经历多样性增长。本研究结果支持如下假说：本次研究涉及的两支旧大陆淡水蟹科——溪蟹科与束腹蟹科，其祖先类群约于白垩纪的120 Ma前从海洋类群分化而来。此外，本研究为部分疑难短尾类类群的重新分类提供了新的理论依据。