Saitou N, Ueda S
Laboratory of Evolutionary Genetics, National Institute of Genetics, Mishima Japan.
Mol Biol Evol. 1994 May;11(3):504-12. doi: 10.1093/oxfordjournals.molbev.a040130.
Insertions and deletions are responsible for gaps in aligned nucleotide sequences, but they have been usually ignored when the number of nucleotide substitutions was estimated. We compared six sets of nuclear and mitochondrial noncoding DNA sequences of primates and obtained the estimates of the evolutionary rate of insertion and deletion. The maximum-parsimony principle was applied to locate insertions and deletions on a given phylogenetic tree. Deletions were about twice as frequent as insertions for nuclear DNA, and single-nucleotide insertions and deletions were the most frequent in all events. The rate of insertion and deletion was found to be rather constant among branches of the phylogenetic tree, and the rate (approximately 2.0/kb/Myr) for mitochondrial DNA was found to be much higher than that (approximately 0.2/kb/Myr) for nuclear DNA. The rates of nucleotide substitution were about 10 times higher than the rate of insertion and deletion for both nuclear and mitochondrial DNA.
插入和缺失是导致比对后的核苷酸序列出现缺口的原因，但在估计核苷酸替换数量时，它们通常被忽略。我们比较了六组灵长类动物的核DNA和线粒体非编码DNA序列，并获得了插入和缺失的进化速率估计值。应用最大简约原则在给定的系统发育树上定位插入和缺失。对于核DNA，缺失的频率约为插入的两倍，并且单核苷酸插入和缺失在所有事件中最为频繁。发现在系统发育树的各分支中，插入和缺失的速率相当恒定，并且线粒体DNA的速率（约2.0/千碱基/百万年）远高于核DNA的速率（约0.2/千碱基/百万年）。对于核DNA和线粒体DNA，核苷酸替换的速率都比插入和缺失的速率高约10倍。
