Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes
Revealing Less Derived Nature of Cartilaginous Fish Genomes with Their Evolutionary Time Scale Inferred with Nuclear Genes
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DOI：
10.1371/journal.pone.0066400
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发表时间：
2013-06-25
期刊：
影响因子：
3.7
通讯作者：
Kuraku, Shigehiro
中科院分区：
文献类型：
--
作者：
Renz, Adina J.;Meyer, Axel;Kuraku, Shigehiro
软骨鱼类在现存脊椎动物中占有重要的系统发育地位，在重建其进化过程中占有重要地位。它们准确的进化时间尺度对于更好地理解软骨鱼类表型和分子进化之间的关系是必不可少的。然而，我们目前对软骨鱼类进化时间尺度的了解在很大程度上依赖于使用线粒体DNA序列的估计。在这项研究中，我们充分利用仍然部分但大规模的软骨鱼类物种的测序数据，估计了使用核基因的主要软骨鱼类物种之间的分歧时间。通过对已有的软骨鱼类基因组和转录序列资源进行严格的正交学评估，我们在核基因组中选择了20个蛋白质编码基因，涉及2973个氨基酸残基。基于贝叶斯推断的分析结果表明，全头-以拉莫支裂带的平均发散时间为421 Ma，而鲨鱼和鲨鱼/溜冰鲨的平均发散时间为306 Ma。通过应用这些结果和其他文献记载的分歧时间，我们测量了软骨鱼类谱系中Hox A簇序列的相对进化速度，这导致了与四足动物谱系相比替换率较低，替换率至少为2.4倍。所获得的时间尺度使得能够在定量框架内绘制表型和分子变化的图谱。在分子水平上证实软骨鱼类较少起源的本质是一种全基因组现象，这是非常有意义的。
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.