Schöniger M, von Haeseler A
Technical University Munich, Germany.
Mol Phylogenet Evol. 1994 Sep;3(3):240-7. doi: 10.1006/mpev.1994.1026.
Currently used stochastic models of DNA sequence evolution assume independent and identically distributed nucleotide sites. They are too simple to account for dependence structures obviously present in molecular data. Up to now more realistic stochastic models for nucleotide substitutions have been considered intractable. In this paper a procedure that accounts for non-overlapping correlations among pairs of sites of a DNA sequence is developed. We show that currently used models that ignore correlated sites underestimate distances inferred from observed sequence dissimilarities. For the analyzed mitochondrial sequence data this underestimation is not drastic in contrast to paired regions (stems) of bacterial 23S rRNA sequences.
目前使用的DNA序列进化随机模型假定核苷酸位点是独立同分布的。它们过于简单，无法解释分子数据中明显存在的依赖结构。到目前为止，更现实的核苷酸替换随机模型一直被认为难以处理。本文开发了一种考虑DNA序列位点对之间非重叠相关性的方法。我们表明，目前忽略相关位点的模型低估了从观察到的序列差异推断出的距离。与细菌23S rRNA序列的配对区域（茎）相比，对于所分析的线粒体序列数据，这种低估并不严重。
