Calibrations used for divergence time estimates.

Pagurus lanuginosus (De Haan, 1833–1850) and Pagurus maculosus (Komai and Imafuku, 1996) are two closely related species of the genus Pagurus, generally referred to as “right-handed hermit crabs”. Previously thought to be color morphs of the same species, recent studies have itemized their unique features. To investigate the molecular and gene expression evolution that have followed the divergence of these two species, we performed transcriptome sequencing and de novo transcriptome assembly using cephalothorax (head) and pereopod (leg) of the two species. Synonymous and nonsynonymous divergence between the two species was estimated to be 0.0246 and 0.0066, respectively. About 5% of the protein-coding transcripts had signatures of positive selection. The phylogenetic analyses showed that the two species are indeed closely related and diverged about 6.24 million years ago. Comparison of tissue expression showed that head expressions were more conserved, and that more genes were upregulated in the legs of P. maculosus leg; while more pigmentation genes were found to be upregulated in the legs of P. lanuginosus. Genes associated with the extracellular matrix and space, chitin binding and chitin-based larval cuticles were found to have higher expression in the legs of P. maculosus, suggesting the roles in morphological differences. This study sheds light on the evolutionary history of the two species at the molecular level.柔毛寄居蟹（Pagurus lanuginosus, De Haan, 1833–1850）与斑寄居蟹（Pagurus maculosus, Komai and Imafuku, 1996）是寄居蟹属（Pagurus）下两个亲缘关系极近的物种，通常被称为“右螯寄居蟹”。此前二者曾被认为是同一物种的色型变种，近期研究已详细梳理了二者各自的独有特征。为探究这两个物种分化后所经历的分子与基因表达演化历程，本研究以二者的头胸部（cephalothorax）与步足（pereopod）为材料，开展了转录组测序及从头转录组组装（de novo transcriptome assembly）。经估算，两物种间的同义替换速率（synonymous divergence）与非同义替换速率（nonsynonymous divergence）分别为0.0246和0.0066。约5%的蛋白编码转录本（protein-coding transcripts）呈现正选择（positive selection）信号。系统发育分析（phylogenetic analyses）结果显示，两物种确实亲缘关系紧密，其分化时间约为624万年前。组织表达比较分析表明，头部组织的基因表达模式更为保守；斑寄居蟹的步足中上调基因更多，而柔毛寄居蟹的步足中上调的色素沉着基因更多。与细胞外基质（extracellular matrix）及空间、几丁质结合（chitin binding）以及几丁质基幼虫表皮（chitin-based larval cuticles）相关的基因在斑寄居蟹的步足中表达量更高，这提示这些基因参与了二者的形态差异形成。本研究从分子层面揭示了这两个物种的演化历程。