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）是当前动物分子多样性研究中最常用的分子标记，其核心优势在于较高的突变率。尽管该标记已被广泛应用二十余年，但学界对于不同物种间线粒体进化速率差异的程度、该差异对序列分析方法的实际影响，以及mtDNA高突变性的根本成因，仍存在诸多未得到充分解决的问题。 本研究依托大规模细胞色素b（cytochrome b）数据集与化石数据，并借助同义替换与非同义替换的解偶联演化动态特征，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对比。本研究发现不同谱系间的线粒体突变率存在出乎意料的两个数量级差异：在进化最快的哺乳动物类群中，细胞色素b基因的密码子第三位平均每1至2百万年（Myr）便会发生一次替换，而进化缓慢的谱系则需要超过100百万年（Myr）才能完成一次替换。该结果对分子系统发育、分子定年以及群体遗传学等领域均具有明确的启示意义。 不同物种间线粒体替换速率的差异，可部分通过体重、寿命以及雌性性成熟年龄进行解释。然而，经典代谢速率与世代时间假说无法完全解释本研究观测到的演化模式，尤其是寿命对长寿命类群的影响显著强于短寿命类群这一现象。 本研究据此提出，自然选择倾向于降低长寿命类群的线粒体突变率，这一结论与线粒体衰老理论的核心观点相一致。