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 crab）作为活化石类群，在过去1.5亿年间其形态几乎未发生显著改变。鲎类群间微弱的形态分化，使得现存鲎物种间的系统发育关系存在极大争议，其中尤以印度-太平洋区域的3个物种为甚。既往研究表明，这3个物种构成了系统发育上无法解析的三分群，该三分群是一次短地质时间尺度内的分支演化事件的产物，此事件造就了印度-太平洋区域的全部3个鲎物种。本研究针对4种鲎及外类群物种，获取了2个线粒体基因（分别编码16S核糖体RNA（16S rRNA）与细胞色素氧化酶亚基I（cytochrome oxidase subunit I））以及1个核基因（编码凝固素（coagulogen））的序列数据，并采用多种替换模型开展系统发育分析。三个基因均得到了一致的系统发育树拓扑结构：巨鲎（Tachypleus gigas）与圆尾鲎（Carcinoscorpius rotundicauda）聚为一支单系类群。采用RELL（重采样估计对数似然，resampling estimated log-likelihood）方法进行检验时，该拓扑结构显著优于所有其他备选拓扑结构。