Lopez J V, Culver M, Stephens J C, Johnson W E, O'Brien S J
Intramural Research Support Program, SAIC, Frederick, Maryland, USA.
Mol Biol Evol. 1997 Mar;14(3):277-86. doi: 10.1093/oxfordjournals.molbev.a025763.
Differential rates of nucleotide substitution among different gene segments and between distinct evolutionary lineages is well documented among mitochondrial genes and is likely a consequence of locus-specific selective constraints that delimit mutational divergence over evolutionary time. We compared sequence variation of 18 homologous loci (15 coding genes and 3 parts of the control region) among 10 mammalian mitochondrial DNA genomes which allowed us to describe different mitochondrial evolutionary patterns and to produce an estimation of the relative order of gene divergence. The relative rates of divergence of mitochondrial DNA genes in the family Felidae were estimated by comparing their divergence from homologous counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced "new might"), a genomic fossil that represents an ancient transfer of 7.9 kb of mitochondrial DNA to the nuclear genome of an ancestral species of the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial (mtDNA) sequences with multiple outgroup species were conducted to date the ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes and to calibrate the rate of sequence divergence of mitochondrial genes relative to nuclear homologous counterparts. By setting the fastest substitution rate as strictly mutational, an empirical "selective retardation index" is computed to quantify the sum of all constraints, selective and otherwise, that limit sequence divergence of mitochondrial gene sequences over time.
线粒体基因中不同基因片段之间以及不同进化谱系之间核苷酸替换率的差异已有充分记录，这可能是由于位点特异性选择限制导致的，这种限制在进化时间内界定了突变差异。我们比较了10种哺乳动物线粒体DNA基因组中18个同源位点（15个编码基因和控制区的3个部分）的序列变异，这使我们能够描述不同的线粒体进化模式，并对基因分化的相对顺序进行估计。通过比较猫科动物线粒体DNA基因与包含在核线粒体DNA（Numt，发音为“new might”）中的同源对应基因的差异，估计了猫科动物线粒体DNA基因的相对分化率，核线粒体DNA是一种基因组化石，代表了7.9 kb线粒体DNA向家猫（Felis catus）祖先物种核基因组的古老转移。对多个外群物种的线粒体（mtDNA）序列进行系统发育分析，以确定Numt和细胞质（Cymt）mtDNA基因共有的祖先节点的时间，并校准线粒体基因相对于核同源对应基因的序列分化率。通过将最快的替换率设定为严格的突变率，计算出一个经验性的“选择性延迟指数”，以量化所有限制线粒体基因序列随时间发生序列分化的限制因素（选择性和其他因素）的总和。
