Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada.
Mol Biol Evol. 2012 Feb;29(2):763-9. doi: 10.1093/molbev/msr243. Epub 2011 Oct 13.
Despite the great utility of mitochondrial DNA (mtDNA) sequence data in population genetics and phylogenetics, key parameters describing the process of mitochondrial mutation (e.g., the rate and spectrum of mutational change) are based on few direct estimates. Furthermore, the variation in the mtDNA mutation process within species or between lineages with contrasting reproductive strategies remains poorly understood. In this study, we directly estimate the mtDNA mutation rate and spectrum using Daphnia pulex mutation-accumulation (MA) lines derived from sexual (cyclically parthenogenetic) and asexual (obligately parthenogenetic) lineages. The nearly complete mitochondrial genome sequences of 82 sexual and 47 asexual MA lines reveal high mtDNA mutation rate of 1.37 × 10(-7) and 1.73 × 10(-7) per nucleotide per generation, respectively. The Daphnia mtDNA mutation rate is among the highest in eukaryotes, and its spectrum is dominated by insertions and deletions (70%), largely due to the presence of mutational hotspots at homopolymeric nucleotide stretches. Maximum likelihood estimates of the Daphnia mitochondrial effective population size reveal that between five and ten copies of mitochondrial genomes are transmitted per female per generation. Comparison between sexual and asexual lineages reveals no statistically different mutation rates and highly similar mutation spectra.
尽管线粒体 DNA（mtDNA）序列数据在群体遗传学和系统发育学中具有很大的用途，但描述线粒体突变过程的关键参数（例如，突变率和突变谱）基于少数直接估计。此外，物种内部或具有不同繁殖策略的谱系之间的 mtDNA 突变过程的变化仍然知之甚少。在这项研究中，我们使用源自有性（周期性孤雌生殖）和无性（专性孤雌生殖）谱系的 Daphnia pulex 突变积累（MA）系直接估计 mtDNA 突变率和突变谱。82 条有性 MA 系和 47 条无性 MA 系的近乎完整的线粒体基因组序列揭示了高达 1.37×10(-7)和 1.73×10(-7)的 mtDNA 突变率，分别为每个核苷酸每代。Daphnia 的 mtDNA 突变率在真核生物中属于最高之列，其突变谱主要由插入和缺失（70%）主导，这主要是由于同源多核苷酸序列存在突变热点。对 Daphnia 线粒体有效种群大小的最大似然估计表明，每个雌性每代传递五到十个线粒体基因组拷贝。有性和无性谱系之间的比较显示，突变率没有统计学上的差异，且突变谱非常相似。
