Data from: The emergence of the lobsters: phylogenetic relationships, morphological evolution and divergence time comparisons of an ancient group (Decapoda: Achelata, Astacidea, Glypheidea, Polychelida)

Lobsters are a ubiquitous and economically important group of decapod crustaceans that includes the infraorders Polychelida, Glypheidea, Astacidea and Achelata. They include familiar forms such as the spiny, slipper, clawed lobsters and crayfish and unfamiliar forms such as the deep-sea and “living fossil” species. The high degree of morphological diversity among these infraorders has led to a dynamic classification and conflicting hypotheses of evolutionary relationships. In this study, we estimated phylogenetic relationships amongst the major groups of all lobster families and 94% of the genera using 6 genes (mitochondrial and nuclear) and 195 morphological characters across 173 species of lobsters for the most comprehensive sampling to date. Lobsters were recovered as a non-monophyletic assemblage in the combined (molecular + morphology) analysis. All families were monophyletic, with the exception of Cambaridae, and 7 of 79 genera were recovered as poly- or paraphyletic. A rich fossil history coupled with dense taxon coverage allowed us to estimate and compare divergence times and origins of major lineages using two drastically different approaches. Age priors were constructed and/or included based on fossil age information or fossil discovery, age, and extant species count data. Results from the two approaches were largely congruent across deep to shallow taxonomic divergences across major lineages. The origin of the first lobster-like decapod (Polychelida) was estimated in the Devonian (~409-372 million years ago (Ma)) with all infraorders present in the Carboniferous (~353-318 Ma). Fossil calibration subsampling studies examined the influence of sampling density (number of fossils) and placement (deep, middle, shallow) on divergence time estimates. Results from our study suggest including at least 1 fossil per 10 operational taxonomic units (OTUs) in divergence dating analyses.

龙虾是一类分布广泛且具有重要经济价值的十足目甲壳动物类群，涵盖多螯虾下目（Polychelida）、雕虾下目（Glypheidea）、螯虾下目（Astacidea）和无螯下目（Achelata）四个下目。该类群包含广为人知的物种，如棘龙虾、蝉虾、螯龙虾以及螯虾，也包括鲜为人知的类群，例如深海龙虾与“活化石”类物种。这些下目之间存在极高的形态多样性，这使得其分类系统处于动态调整中，且学界对其演化关系存在诸多相悖的假说。本研究针对173种龙虾展开采样，这是目前为止最全面的龙虾类群采样方案；研究依托6个基因（线粒体及核基因）与195个形态学特征，对所有龙虾科类群以及94%的龙虾属开展了系统发育关系推断。在分子+形态学的联合数据分析中，龙虾类群被恢复为一个非单系群集合。除美螯虾科（Cambaridae）外，所有龙虾科均为单系群；79个龙虾属中有7个被恢复为多系群或并系群。依托丰富的化石记录与高密度的类群采样，本研究采用两种截然不同的分析方法，对主要演化支的分化时间与起源时间进行了估算与对比。年龄先验信息的构建与引入，基于化石年代数据，或结合化石发现记录、化石年代以及现生物种数量数据完成。两种分析方法的结果在主要演化支的深层至浅层分类分化事件中均保持高度一致。首个类似龙虾的十足类动物（多螯虾下目，Polychelida）的起源时间被估算为泥盆纪（约4.09亿~3.72亿年前，Ma），而所有龙虾下目类群均出现于石炭纪（约3.53亿~3.18亿年前）。本研究开展了化石校准子采样分析，以检验采样密度（化石数量）与化石校准位点（深层、中层、浅层）对分化时间估算结果的影响。本研究结果表明，在分化时间定年分析中，每10个操作分类单元（OTUs）至少应纳入1个化石校准点。