Filipi Karolína, Marková Silvia, Searle Jeremy B, Kotlík Petr
Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, Viničná 5, 12844 Prague 2, Czech Republic.
Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 27721 Liběchov, Czech Republic.
Mol Phylogenet Evol. 2015 Jan;82 Pt A:245-57. doi: 10.1016/j.ympev.2014.10.016. Epub 2014 Oct 30.
We have revisited the mtDNA phylogeny of the bank vole Clethrionomys glareolus based on Sanger and next-generation Illumina sequencing of 32 complete mitochondrial genomes. The bank vole is a key study species for understanding the response of European fauna to the climate change following the Last Glacial Maximum (LGM) and one of the most convincing examples of a woodland mammal surviving in cryptic northern glacial refugia in Europe. The genomes sequenced included multiple representatives of each of the eight bank vole clades previously described based on cytochrome b (cob) sequences. All clades with the exception of the Basque - likely a misidentified pseudogene clade - were highly supported in all phylogenetic analyses and the relationships between the clades were resolved with high confidence. Our data extend the distribution of the Carpathian clade, the marker of a northern glacial refugium in the Carpathian Mountains, to include Britain and Fennoscandia (but not adjacent areas of continental Europe). The Carpathian sub-clade that colonized Britain and Fennoscandia had a somewhat different history from the sub-clade currently found in or close to the Carpathians and may have derived from a more north-westerly refugial area. The two bank vole populations that colonized Britain at the end of the last glaciation are for the first time linked with particular continental clades, the first colonists with the Carpathian clade and the second colonists with the western clade originating in a more southerly refugium in the vicinity of the Alps. We however found no evidence that a functional divergence of proteins encoded in the mitochondrial genome promoted the partial genetic replacement of the first colonists by the second colonists detected previously in southern Britain. We did identify one codon site that changed more often and more radically in the tree than expected and where the observed amino acid change may affect the reductase activity of the cytochrome bc1 complex, but the change was not specific to a particular clade. We also found an excess of radical changes to the primary protein structure for geographically restricted clades from southern Italy and Norway, respectively, possibly related to stronger selective pressure at the latitudinal extremes of the bank vole distribution. However, overall, we find little evidence of pervasive effects of deviation from neutrality on bank vole mtDNA phylogeography.
我们基于对32个完整线粒体基因组的桑格测序和新一代Illumina测序，重新审视了棕色田鼠（Clethrionomys glareolus）的线粒体DNA系统发育。棕色田鼠是了解末次盛冰期（LGM）后欧洲动物群对气候变化响应的关键研究物种，也是欧洲林地哺乳动物在隐秘的北方冰川避难所中生存的最有说服力的例子之一。测序的基因组包括先前基于细胞色素b（cob）序列描述的八个棕色田鼠分支中每个分支的多个代表。除了巴斯克分支（可能是一个错误识别的假基因分支）之外，所有分支在所有系统发育分析中都得到了高度支持，并且分支之间的关系得到了高度置信度的解析。我们的数据将喀尔巴阡山脉分支（喀尔巴阡山脉北方冰川避难所的标志）的分布扩展到包括英国和斯堪的纳维亚半岛（但不包括欧洲大陆的相邻地区）。在英国和斯堪的纳维亚半岛定居的喀尔巴阡山脉亚分支与目前在喀尔巴阡山脉或其附近发现的亚分支历史有所不同，可能源自更偏西北的避难区。在上次冰期末期定居英国的两个棕色田鼠种群首次与特定的大陆分支联系起来，第一批殖民者与喀尔巴阡山脉分支相关，第二批殖民者与起源于阿尔卑斯山附近更南端避难所的西部分支相关。然而，我们没有发现证据表明线粒体基因组中编码的蛋白质的功能差异促进了先前在英国南部检测到的第一批殖民者被第二批殖民者的部分基因替代。我们确实确定了一个密码子位点，其在树中的变化比预期更频繁、更剧烈，并且观察到的氨基酸变化可能会影响细胞色素bc1复合物的还原酶活性，但这种变化并非特定于某个特定分支。我们还分别在来自意大利南部和挪威的地理分布受限的分支中发现了对一级蛋白质结构的大量激进变化，这可能与棕色田鼠分布纬度极端处更强的选择压力有关。然而，总体而言，我们几乎没有发现偏离中性对棕色田鼠线粒体DNA系统地理学产生普遍影响的证据。
