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首页> 外文期刊>Gene: An International Journal Focusing on Gene Cloning and Gene Structure and Function >Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity, neutral theory, and phylogenetic relationships within the order Passeriformes
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Complete mitochondrial genomes from four subspecies of common chaffinch (Fringilla coelebs): New inferences about mitochondrial rate heterogeneity, neutral theory, and phylogenetic relationships within the order Passeriformes

机译：来自四个常见花鸡亚种的完整线粒体基因组（Fringilla coelebs）：关于线形目异质性，中性理论和Passeriformes顺序内系统发育关系的新推论

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We describe whole mitochondrial genome sequences from four subspecies of the common chaffinch (Fringilla coelebs), and compare them to 31 publicly available mitochondrial genome sequences from other Passeriformes. Rates and patterns of mitochondrial gene evolution are analyzed at different taxonomic levels within this avian order, and evidence is adduced for and against the nearly neutral theory of molecular evolution and the role of positive selection in shaping genetic variation of this small but critical genome. We find evidence of mitochondrial rate heterogeneity in birds as in other vertebrates, likely due to differences in mutational pressure across the genome. Unlike in gadine fish and some of the human mitochondrial work we do not observe strong support for the nearly neutral theory of molecular evolution; instead evidence from molecular clocks, distribution of dN/dS ratios at different levels of the taxonomic hierarchy and in different lineages, McDonald-Kreitman tests within Fringillidae, and site-specific tests of selection within Passeriformes, all point to a role for positive selection, especially for the complex I NADH dehydrogenase genes. The protein-coding mitogenome phylogeny of the order Passeriformes is broadly consistent with previously-reported molecular findings, but provides support for a sister relationship between the superfamilies Muscicapoidea and Passeroidea on a short basal internode of the Passerida where relationships have been difficult to resolve. An unexpected placement of the Paridae (represented by Hume's groundpecker) within the Muscicapoidea was observed. Consistent with other molecular studies the mtDNA phylogeny reveals paraphyly within the Muscicapoidea and a sister relationship of Fringilla with Carduelis rather than Emberiza. ? 2013 Elsevier B.V.
机译：我们描述了常见的花鸡（Fringilla coelebs）的四个亚种的整个线粒体基因组序列，并将它们与其他Passeriformes的31个可公开获得的线粒体基因组序列进行比较。在该鸟类秩序的不同分类学水平上分析了线粒体基因进化的速率和模式，并为近乎中立的分子进化理论和正选择在塑造这个小而关键的基因组的遗传变异中的作用提供了证据和证据。我们发现与其他脊椎动物一样，鸟类线粒体速率异质性的证据可能是由于整个基因组中突变压力的差异。与普通鱼和某些人类线粒体工作不同，我们没有观察到对分子进化近乎中立的理论的有力支持。取而代之的是来自分子钟的证据，不同分类层次和不同谱系中dN / dS比率的分布，Fringillidae内的McDonald-Kreitman测试以及Passeriformes内特定地点的选择测试，这些都表明了积极选择的作用，特别是对于复杂的I NADH脱氢酶基因。 Passeriformes顺序的蛋白质编码有丝分裂基因组系统发育与先前报道的分子发现大致一致，但是为超家族Muscicapoidea和Passeroidea之间在Passerida的短基底节间的姐妹关系提供了支持，这些关系很难解决。在Muscicapoidea中发现了鹦鹉科（由休姆的啄木鸟代表）的意外放置。与其他分子研究一致，mtDNA的系统发育揭示了Muscicapoidea内的属植物，以及Fringilla与Carduelis而非Emberiza的姐妹关系。 ？ 2013 Elsevier B.V.

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