Data from: Body mass-corrected molecular rate for bird mitochondrial DNA

Mitochondrial DNA is still one of the most widely used molecular marker to reconstruct small scale bird phylogeny and phylogeography. It has been proposed that bird mitochondrial genome are evolving under a constant rate of ~0.01 substitution per site per Million years. A large number of studies on bird mitochondrial phylogeny are often associated with molecular dating applying this convenient molecular clock. However, the rate of mitochondrial evolution have repeatedly been shown to vary among species of birds. This variation is not random but is correlated with life-history traits such as body-mass and sexual maturity. As a consequence, the use of a strict molecular clock could systematically biased the molecular dating. In this study, we proposed to used the relationship between body-mass and the rate of molecular evolution to provide a simple method to estimate the substitution rate according to birds body-mass. Using the complete or nearly mitochondrial genome of 475 species, we found a strong relationship between body-mass and neutral substitution rates (R² ~ 0.45 - 0.60). We also report a slight, but significant, variation of the neutral substitution rates among mitochondrial protein-coding genes. Finally, we re-analysed two recently published datasets in order to illustrate the principle of our method. In one case, we obtained molecular dates that are two times older than the estimation obtained using the classical molecular clock. We hope that the corrected molecular clocks we provide will increase the accuracy of future molecular dating studies in birds.线粒体DNA（mitochondrial DNA）仍是目前用于重建小型鸟类系统发育（phylogeny）与系统地理学（phylogeography）的最常用分子标记之一。此前有研究提出，鸟类线粒体基因组（mitochondrial genome）以约0.01次替换/位点/百万年的恒定速率进行演化。大量鸟类线粒体系统发育相关研究，常借助这一便捷的分子钟（molecular clock）开展分子定年（molecular dating）工作。然而，已有多项研究反复证实，鸟类物种间的线粒体演化速率存在差异。这种差异并非随机，而是与体重（body-mass）、性成熟（sexual maturity）等生活史特征（life-history traits）相关。因此，使用严格分子钟可能会对分子定年结果产生系统性偏倚。本研究拟基于体重与分子演化速率的关联关系，提出一种可根据鸟类体重估算替换率的简便方法。我们利用475个物种的完整或近完整线粒体基因组数据，发现体重与中性替换率（neutral substitution rates）之间存在显著关联（决定系数R²约为0.45~0.60）。本研究还发现，线粒体蛋白编码基因（mitochondrial protein-coding genes）间的中性替换率虽存在小幅差异，但该差异具有统计学显著性。最后，我们重新分析了两篇近期发表的数据集，以阐明本研究方法的应用原理。其中一例的分子定年结果是使用经典分子钟得到的估算值的两倍。我们期望本研究提出的校正分子钟方法，能够提升未来鸟类分子定年研究的准确性。