Data from: Strong variations of mitochondrial mutation rate across mammals--the longevity hypothesis.

Mitochondrial DNA (mtDNA) is the most popular marker of molecular diversity in animals, primarily because of its elevated mutation rate. After >20 years of intensive usage, the extent of mitochondrial evolutionary rate variations across species, their practical consequences on sequence analysis methods, and the ultimate reasons for mtDNA hypermutability are still largely unresolved issues. Using an extensive cytochrome b data set, fossil data, and taking advantage of the decoupled dynamics of synonymous and nonsynonymous substitutions, we measure the lineage-specific mitochondrial mutation rate across 1,696 mammalian species and compare it with the nuclear rate. We report an unexpected 2 orders of magnitude mitochondrial mutation rate variation between lineages: cytochrome b third codon positions are renewed every 1-2 Myr, in average, in the fastest evolving mammals, whereas it takes >100 Myr in slow-evolving lineages. This result has obvious implications in the fields of molecular phylogeny, molecular dating, and population genetics. Variations of mitochondrial substitution rate across species are partly explained by body mass, longevity, and age of female sexual maturity. The classical metabolic rate and generation time hypothesis, however, do not fully explain the observed patterns, especially a stronger effect of longevity in long-lived than in short-lived species. We propose that natural selection tends to decrease the mitochondrial mutation rate in long-lived species, in agreement with the mitochondrial theory of aging.

线粒体DNA（mtDNA）是动物分子多样性研究中最常用的分子标记，这主要源于其较高的突变率。经过二十余年的广泛应用，跨物种间线粒体进化速率的差异程度、其对序列分析方法的实际影响，以及mtDNA高突变性的根本原因，仍在很大程度上属于未解决的问题。本研究借助大规模细胞色素b（cytochrome b）数据集与化石数据，并利用同义替换（synonymous substitution）与非同义替换（nonsynonymous substitution）的解耦动力学特征，对1696个哺乳动物物种的谱系特异性线粒体突变率进行了测算，并将其与核基因组突变率进行了对比。我们观测到不同谱系间的线粒体突变率存在高达两个数量级的意外差异：在进化最快的哺乳动物类群中，细胞色素b基因第三密码子位点的平均更新周期为100万至200万年，而在进化缓慢的谱系中，该周期则超过1亿年。该研究结果对分子系统发育学、分子定年学以及群体遗传学领域均具有重要的启示意义。跨物种间线粒体替换速率的差异，可部分由体质量、寿命以及雌性性成熟年龄予以解释。然而，经典的代谢速率与世代时间假说，并不能完全阐释观测到的进化模式，尤其在长寿类群中，寿命对突变率的抑制作用相较于短寿类群更为显著。结合线粒体衰老理论，我们提出自然选择倾向于降低长寿物种的线粒体突变率。