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

Mitochondrial DNA remains one of the most widely used molecular markers to reconstruct the phylogeny and phylogeography of closely related birds. It has been proposed that bird mitochondrial genomes evolve at a constant rate of ~0.01 substitution per site per million years, that is that they evolve according to a strict molecular clock. This molecular clock is often used in studies of bird mitochondrial phylogeny and molecular dating. However, rates of mitochondrial genome evolution vary among bird species and correlate with life history traits such as body mass and generation time. These correlations could cause systematic biases in molecular dating studies that assume a strict molecular clock. In this study, we overcome this issue by estimating corrected molecular rates for birds. Using complete or nearly complete mitochondrial genomes of 475 species, we show that there are strong relationships between body mass and substitution rates across birds. We use this information to build models that use bird species’ body mass to estimate their substitution rates across a wide range of common mitochondrial markers. We demonstrate the use of these corrected molecular rates on two recently published data sets. In one case, we obtained molecular dates that are twice as old as the estimates obtained using the strict molecular clock. We hope that this method to estimate molecular rates will increase the accuracy of future molecular dating studies in birds.线粒体DNA（mitochondrial DNA）仍是目前用于重构近缘鸟类系统发育与系统地理学的最常用分子标记之一。此前研究认为，鸟类线粒体基因组以约0.01次替换/位点/百万年的恒定速率演化，即遵循严格分子钟假说。该分子钟常被应用于鸟类线粒体系统发育与分子定年研究中。然而，鸟类线粒体基因组的演化速率在不同物种间存在差异，且与体重、世代时间等生活史性状相关。这种相关性可能会在采用严格分子钟假设的分子定年研究中引入系统性偏差。本研究通过估算鸟类校正后的分子演化速率，解决了这一问题。我们利用475个物种的完整或近乎完整线粒体基因组数据，证实鸟类体重与替换速率之间存在强相关性。基于这一发现，我们构建了以鸟类物种体重为参数的模型，可用于估算其在多种常见线粒体标记下的替换速率。我们将这些校正后的分子速率应用于两套新近发表的数据集以验证其效果。其中一套数据集的分子定年结果较采用严格分子钟得到的估算值高出一倍。我们期望该分子速率估算方法能够提升未来鸟类分子定年研究的准确性。