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
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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DOI：
10.1016/j.gene.2012.12.093
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发表时间：
2013-03-15
期刊：
影响因子：
3.5
通讯作者：
Grant, Allison R.
中科院分区：
文献类型：
--
作者：
Marshall, H. Dawn;Baker, Allan J.;Grant, Allison R.
我们描述了全线粒体基因组序列从四个亚种的共同苍头燕雀（Fringilla coelebs），并比较它们的31个公开的线粒体基因组序列从其他雀形目。线粒体基因进化的速率和模式进行了分析，在不同的分类水平，在这个鸟类的顺序，和证据是引证和反对的近中性理论的分子进化和积极的选择在塑造这个小，但关键的基因组的遗传变异的作用。我们在鸟类和其他脊椎动物中发现了线粒体速率异质性的证据，这可能是由于基因组中突变压力的差异。不像在鳕和一些人类线粒体的工作，我们没有观察到强有力的支持近中性理论的分子进化;相反，来自分子钟的证据，dN/dS比率在分类层次的不同水平和不同谱系中的分布，Fringillidae内的McDonald-Kreitman测试，以及Passeriformes内选择的位点特异性测试，都指向正选择的作用，特别是对于复合物I NADH脱氢酶基因。雀形目的蛋白质编码的有丝分裂基因组同源性与以前报道的分子研究结果大致一致，但提供了支持的姐妹关系之间的超家庭Muscicapoidea和Passeroidea短基部节间的Passerida的关系一直难以解决。在Muscicapoidea中观察到了一个意想不到的Paridae（以Hume's groundpecker为代表）的位置。与其他分子生物学研究一致的是，mtDNA同源性揭示了蝇总科中的并系关系，并且燕雀与雀属而不是Emberiza的姐妹关系。(c)2013爱思唯尔有限公司版权所有。
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. (c) 2013 Elsevier B.V. All rights reserved.