UMR 5554, ISEM, CNRS, Université Montpellier 2, Montpellier, France.
J Evol Biol. 2014 May;27(5):899-910. doi: 10.1111/jeb.12361. Epub 2014 Apr 10.
Reconstructing the ancestral characteristics of species is a major goal in evolutionary and comparative biology. Unfortunately, fossils are not always available and sufficiently informative, and phylogenetic methods based on models of character evolution can be unsatisfactory. Genomic data offer a new opportunity to estimate ancestral character states, through (i) the correlation between DNA evolutionary processes and species life-history traits and (ii) available reliable methods for ancestral sequence inference. Here, we assess the relevance of mitochondrial DNA--the most popular molecular marker in animals--as a predictor of ancestral life-history traits in mammals, using the order of Cetartiodactyla as a benchmark. Using the complete set of 13 mitochondrial protein-coding genes, we show that the lineage-specific nonsynonymous over synonymous substitution rate ratio (dN/dS) is closely correlated with the species body mass, longevity and age of sexual maturity in Cetartiodactyla and can be used as a marker of ancestral traits provided that the noise introduced by short branches is appropriately dealt with. Based on ancestral dN/dS estimates, we predict that the first cetartiodactyls were relatively small animals (around 20 kg). This finding is in accordance with Cope's rule and the fossil record but could not be recovered via continuous character evolution methods.
重建物种的祖先特征是进化和比较生物学的主要目标。不幸的是，化石并不总是可用且信息量充足，并且基于字符进化模型的系统发育方法可能并不令人满意。基因组数据通过（i）DNA 进化过程与物种生活史特征之间的相关性和（ii）可用于祖先序列推断的可靠方法，为估计祖先特征状态提供了新的机会。在这里，我们使用偶蹄目作为基准，评估了动物中最流行的分子标记线粒体 DNA 作为哺乳动物祖先生活史特征预测因子的相关性。使用完整的 13 个线粒体蛋白质编码基因集，我们表明特定于谱系的非同义替换与同义替换率比（dN/dS）与偶蹄目物种的体重，寿命和性成熟年龄密切相关，并且可以作为标记使用祖先的特征，只要适当处理短分支引入的噪声即可。基于祖先 dN/dS 的估计，我们预测第一批偶蹄目动物是相对较小的动物（约 20 公斤）。这一发现与科佩法则和化石记录相符，但无法通过连续的特征进化方法恢复。
