Chair in Zoology and Evolutionary Biology, Department of Biology, University of Konstanz, Konstanz, Germany.
PLoS One. 2013 Jun 25;8(6):e66400. doi: 10.1371/journal.pone.0066400. Print 2013.
Cartilaginous fishes, divided into Holocephali (chimaeras) and Elasmoblanchii (sharks, rays and skates), occupy a key phylogenetic position among extant vertebrates in reconstructing their evolutionary processes. Their accurate evolutionary time scale is indispensable for better understanding of the relationship between phenotypic and molecular evolution of cartilaginous fishes. However, our current knowledge on the time scale of cartilaginous fish evolution largely relies on estimates using mitochondrial DNA sequences. In this study, making the best use of the still partial, but large-scale sequencing data of cartilaginous fish species, we estimate the divergence times between the major cartilaginous fish lineages employing nuclear genes. By rigorous orthology assessment based on available genomic and transcriptomic sequence resources for cartilaginous fishes, we selected 20 protein-coding genes in the nuclear genome, spanning 2973 amino acid residues. Our analysis based on the Bayesian inference resulted in the mean divergence time of 421 Ma, the late Silurian, for the Holocephali-Elasmobranchii split, and 306 Ma, the late Carboniferous, for the split between sharks and rays/skates. By applying these results and other documented divergence times, we measured the relative evolutionary rate of the Hox A cluster sequences in the cartilaginous fish lineages, which resulted in a lower substitution rate with a factor of at least 2.4 in comparison to tetrapod lineages. The obtained time scale enables mapping phenotypic and molecular changes in a quantitative framework. It is of great interest to corroborate the less derived nature of cartilaginous fish at the molecular level as a genome-wide phenomenon.
软骨鱼类分为全头亚纲（鲟鱼）和板鳃亚纲（鲨鱼、鳐鱼和魟鱼），在重建其进化过程中，在现存脊椎动物中占据着关键的进化位置。它们准确的进化时间尺度对于更好地理解软骨鱼类的表型和分子进化之间的关系是不可或缺的。然而，我们目前对软骨鱼类进化时间尺度的认识在很大程度上依赖于使用线粒体 DNA 序列进行的估计。在这项研究中，我们充分利用软骨鱼类仍然部分但大规模的测序数据，利用核基因估计主要软骨鱼类谱系之间的分歧时间。通过基于可用的软骨鱼类基因组和转录组序列资源进行严格的同源性评估，我们选择了核基因组中的 20 个蛋白编码基因，跨越 2973 个氨基酸残基。我们基于贝叶斯推断的分析得出的结果是，全头亚纲-板鳃亚纲的分歧时间为 421 Ma，即晚志留世；鲨鱼和鳐鱼/魟鱼的分歧时间为 306 Ma，即晚石炭世。通过应用这些结果和其他有记录的分歧时间，我们测量了软骨鱼类谱系中 Hox A 簇序列的相对进化率，与四足动物谱系相比，其取代率至少低了 2.4 倍。所得到的时间尺度使我们能够在定量框架中映射表型和分子变化。证实软骨鱼类在分子水平上作为一个全基因组现象的衍生程度较低，这是非常有趣的。
