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）的核苷酸替代率通常比核DNA快得多，这使得mtDNA对检测近亲物种之间的差异非常有用。然而，由于祖先多态性和地理种群细分，mtDNA的系统发育关系经常与物种关系发生冲突。例如，在同域条件下，在密切相关的物种之间反复报道了线粒体渗入，它完全破坏了mtDNA与物种系统发育之间的对应关系。为了阐明物种形成和基因渗入对mtDNA进化的交互作用，研究了纳苏塔果蝇亚群的mtDNA（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。纳苏塔果蝇亚群包括几个在物种形成过程中关系密切的物种和亚种，根据地理位置的不同，分布在从完全异种到同属的不同条件下。结果表明，生境的地理距离与mtDNA的序列差异有较强的相关性，而核DNA则不是如此。此外，在d.a nasuta亚群的进化过程中，有证据表明频繁的线粒体渗入。综上所述，建议在mtDNA的系统发育研究中考虑地理分布格局和基因渗入的可能性。此外，为了更好地进行分子系统发育分析，我们进行了理论研究，开发了基于密码子选择的蛋白质编码序列中性核苷酸替代率的统计方法，以及基于邻居连接法重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.