The interactive effects of speciation and introgression on the mitochondrial DNA evolution in Drosophila

在高等动物中，线粒体DNA(MtDNA)的核苷酸替换率通常比核DNA快得多，这使得mtDNA有助于检测近缘物种之间的差异。然而，由于祖先的多态和地理种群的分化，线粒体DNA的系统发育关系往往与物种关系发生冲突。例如，线粒体内渗完全破坏了线粒体DNA和物种系统发育之间的对应关系，在共域条件下密切相关的物种之间反复报道。为了阐明物种形成和导入对线粒体DNA进化的交互作用，研究了果蝇亚群物种和亚种的线粒体DNA(细胞色素c氧化酶亚基1基因)和核DNA(黄嘌呤脱氢酶和白色基因)的序列差异，该亚种包括几个物种形成方式上的密切相关物种和亚种，并根据地理位置从完全异位分布到共生。结果表明，栖息地的地理距离与线粒体DNA的序列差异有很强的相关性，而核DNA则不是这样。此外，有证据表明，在鼻甲亚群的进化过程中，线粒体的插入频繁。此外，为了更好地进行分子系统发育分析，从理论上研究了密码子选择下蛋白质编码序列的中性核苷酸替换率的估计方法和邻接法构建大型系统发育树的距离矩阵。

The nucleotide substitution rate for mitochondrial DNA (mtDNA) is generally much faster than that for nuclear DNA in higher animals, which makes mtDNA useful to detect a difference between closely related species. However, phylogenetic relationships of mtDNA often show conflicts with the species relationships due to ancestral polymorphisms and geographic population subdivisions. For instance, the mitochondrial introgression, which totally disrupts the correspondence between mtDNA and species phylogenies, has been reported repeatedly between closely related species in a sympatric condition.To clarify the interactive effects of speciation and introgression on the mtDNA evolution, the sequence divergences of mtDNA (cytochrome c oxidase subunit 1 gene) and nuclear DNA (xanthine dehydrogenase and white genes) were investigated for species and subspecies of the Drosophila nasuta subgroup, which includes several closely related species and subspecies on the way of speciation and distributes in various condition from complete allopatry to sympatry depending on the geographic locations. The results show a strong correlation between geographic distances of habitats and sequence divergences of mtDNA, whereas it was not the case of nuclear DNA. Furthermore, evidence of frequent mitochondrial introgressions in the course of the D.nasuta subgroup evolution was indicated. In conclusion, the importance of taking geographic distribution pattern and the potential of introgression into consideration in the phylogenetic studies of mtDNA was suggested.Furthermore, for better performance of molecular phylogenetic analyses, theoretical studies were conducted to develop the statistical methods for estimating a neutral nucleotide substitution rate from protein coding sequences under a codon selection and a distance matrix for the reconstruction of large phylogenetic trees with the neighbor-joining method.