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）的核苷酸替换速率通常比核DNA快得多，这使得mtDNA可用于检测密切相关物种之间的差异。然而，由于祖先的多态性和地理种群的划分，线粒体DNA的系统发育关系往往与种间关系发生冲突。例如，在同域条件下，近缘物种间的线粒体渐渗现象已被反复报道，它完全破坏了mtDNA与物种间的亲缘关系，为了阐明物种形成和渐渗对mtDNA进化的相互作用，线粒体DNA序列差异（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）进行了研究，在物种形成过程中，包括几个密切相关的种和亚种，并根据地理位置的不同，在不同的条件下从完全异地分布到同域分布。结果表明，栖息地的地理距离和线粒体DNA的序列分歧之间有很强的相关性，而不是核DNA的情况。此外，在D.nasuta亚组进化过程中频繁的线粒体渐渗的证据被指出。因此，在线粒体DNA系统发育研究中，考虑地理分布格局和渐渗的可能性是非常重要的，而且，为了更好地进行分子系统发育分析，理论研究是为了发展在密码子选择下估计蛋白质编码序列的中性核苷酸取代率的统计方法和用于重构大的用邻接法构建系统发育树。

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.