Data from: microRNAs reveal the interrelationships of hagfish, lampreys, and gnathostomes and the nature of the ancestral vertebrate

Hagfish and lampreys are the only living representatives of the jawless vertebrates (agnathans), and compared with jawed vertebrates (gnathostomes), they provide insight into the embryology, genomics, and body plan of the ancestral vertebrate. However, this insight has been obscured by controversy over their interrelationships. Morphological cladistic analyses have identified lampreys and gnathostomes as closest relatives, whereas molecular phylogenetic studies recover a monophyletic Cyclostomata (hagfish and lampreys as closest relatives). Here, we show through deep sequencing of small RNA libraries, coupled with genomic surveys, that Cyclostomata is monophyletic: hagfish and lampreys share 4 unique microRNA families, 15 unique paralogues of more primitive microRNA families, and 22 unique substitutions to the mature gene products. Reanalysis of morphological data reveals that support for cyclostome paraphyly was based largely on incorrect character coding, and a revised dataset is not decisive on the mono- vs. paraphyly of cyclostomes. Furthermore, we show fundamental conservation of microRNA expression patterns among lamprey, hagfish, and gnathostome organs, implying that the role of microRNAs within specific organs is coincident with their appearance within the genome and is conserved through time. Together, these data support the monophyly of cyclostomes and suggest that the last common ancestor of all living vertebrates was a more complex organism than conventionally accepted by comparative morphologists and developmental biologists.

盲鳗与七鳃鳗是现存仅存的无颌脊椎动物（agnathans）类群。相较于有颌脊椎动物（gnathostomes），二者可为探究脊椎动物祖先的胚胎学、基因组学以及躯体构型提供关键研究视角。然而，二者的演化亲缘关系长期存在争议，这一争议一度阻碍了相关研究的推进。形态学分支分类分析曾将七鳃鳗与有颌脊椎动物认定为亲缘关系最近的姊妹群，而分子系统发育研究则支持单系的圆口纲（Cyclostomata）假说——即盲鳗与七鳃鳗为彼此亲缘关系最近的类群。本研究通过对小RNA文库的深度测序结合基因组筛查，证实圆口纲为单系类群：盲鳗与七鳃鳗共享4个独特的微小RNA（microRNA）家族、15个源自更古老微小RNA家族的独特旁系同源拷贝，以及22个成熟基因产物的独有碱基替换。对形态学数据的重新分析显示，此前支持圆口纲为并系类群的结论，主要源于特征编码错误；经修正后的形态学数据集，仍无法明确判定圆口纲属于单系还是并系类群。此外，本研究证实七鳃鳗、盲鳗与有颌脊椎动物的器官中，微小RNA的表达模式存在高度保守性，这意味着微小RNA在特定器官中的功能角色，与其在基因组中出现的演化时间相契合，并随演化历程得以保留。综上，上述数据支持圆口纲的单系性，并表明所有现存脊椎动物的最后共同祖先，其复杂程度远超比较形态学家与发育生物学家此前的普遍认知。