Data from: Mitochondrial DNA as a tool for reconstructing past life-history traits in mammals

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生物学与比较生物学的核心研究目标之一。然而，化石材料往往并非总能获取且信息量不足，而基于特征演化模型的系统发育方法也常难以令人满意。基因组数据则为祖先特征状态的估算提供了新的可能途径：一是依托DNA演化过程与物种生活史性状之间的关联，二是借助现有可靠的祖先序列推断方法。
本研究以鲸偶蹄目（Cetartiodactyla）作为基准类群，评估作为动物界最常用分子标记的线粒体DNA（mitochondrial DNA）能否作为哺乳动物祖先生活史性状的预测指标。我们基于13个线粒体蛋白编码基因的完整数据集，发现鲸偶蹄类中，谱系特异性非同义替换与同义替换速率比值（dN/dS）与物种体重、寿命及性成熟年龄显著相关；若能合理处理短分支引入的噪声，该比值即可作为祖先特征的预测标记。
基于祖先dN/dS的估算结果，我们预测首批鲸偶蹄类动物体型相对较小（约20千克）。这一发现符合科普法则（Cope's rule）与化石记录，但通过连续特征演化方法却无法得到该结论。