Data from: Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses

The horseshoe crabs, known as living fossils, have maintained their morphology almost unchanged for the past 150 million years. The little morphological differentiation among horseshoe crab lineages has resulted in substantial controversy concerning the phylogenetic relationship among the extant species of horseshoe crabs, especially among the three species in the Indo-Pacific region. Previous studies suggest that the three species constitute a phylogenetically unresolvable trichotomy, the result of a cladogenetic process leading to the formation of all three Indo-Pacific species in a short geological time. Data from two mitochondrial genes (for 16S ribosomal rRNA and cytochrome oxidase subunit I) and one nuclear gene (for coagulogen) in the four species of horseshoe crabs and outgroup species were used in a phylogenetic analysis with various substitution models. All three genes yield the same tree topology, with Tachypleus-gigas and Carcinoscorpius-rotundicauda grouped together as a monophyletic taxon. This topology is significantly better than all the alternatives when evaluated with the RELL (resampling estimated log-likelihood) method.

鲎（horseshoe crabs）素有活化石（living fossils）之称，在过去1.5亿年间其形态几乎未发生改变。鲎类支系间的形态分化程度极低，这使得现存鲎类物种间的系统发育关系（phylogenetic relationship）存在极大争议，尤以印度-太平洋区域的三个物种间的系统发育关系为甚。既往研究表明，该三个物种构成了系统发育上无法解析的三分支（trichotomy），三者均是在极短的地质时间内通过分支演化过程（cladogenetic process）形成的。本研究针对4种鲎及外类群物种（outgroup species），获取了2个线粒体基因（分别编码16S核糖体RNA（16S ribosomal rRNA）和细胞色素氧化酶亚基I（cytochrome oxidase subunit I））以及1个核基因（编码凝固原（coagulogen））的序列数据，并采用多种替换模型（substitution models）开展系统发育分析。结果显示，三个基因均得到一致的树拓扑结构（tree topology）：巨鲎（Tachypleus gigas）与圆尾鲎（Carcinoscorpius rotundicauda）聚为一支单系类群（monophyletic taxon）。通过重采样估计对数似然法（RELL，resampling estimated log-likelihood）评估，该拓扑结构显著优于所有其他备选拓扑结构。