Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data
Effect of taxon sampling on recovering the phylogeny of squamate reptiles based on complete mitochondrial genome and nuclear gene sequence data
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DOI：
10.1016/j.gene.2008.05.014
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发表时间：
2009-07-15
期刊：
影响因子：
3.5
通讯作者：
Zardoya, Rafael
中科院分区：
文献类型：
--
作者：
Albert, Eva M.;San Mauro, Diego;Zardoya, Rafael
重新测定了三种有鳞蜥蜴的线粒体（mt）基因组的全序列。将所有13个mt蛋白编码基因的推导氨基酸序列合并为一个数据集，并在最大似然（ML）和贝叶斯推断（BI）下分析主要有鳞动物谱系之间的系统发育关系。在有鳞目中，鬣蜥科，Anguimorpha，Amphisbaenia，Gekkota，Serpentes和Acrodonta的单系性得到了很高的统计支持与两种方法。特别引人注目的是，这是第一个恢复Scincomorpha（包括Scincidae，Xantusiidae，Cordylidae和Lacertidae）单系性的分子分析，尽管它只在贝叶斯分析中得到支持，并且对外群的变化很敏感（见下文）。主要有鳞动物谱系之间的系统发育关系不能解决ML，但得到了强有力的支持BI（95%以上）。新重建的有鳞类的单生发育不支持鬣蜥-硬舌亚目的分裂。端齿亚目和蛇亚目形成一个分支，是其余有鳞类谱系的姐妹群。其中，Gekkota是第一个分支，其次是Amphisbaenia，以及一个分支，包括Anguimorpha作为Scincomorpha + Iguanidae的姐妹群。恢复的拓扑结构与以前报道的有鳞动物关系的假设有很大不同，并探讨了使用不同外群，基因和分类单元采样的相对影响。蛇+ Acrodonta的姐妹群关系，以及它们在有鳞目中的相对基础位置可能是由于长枝吸引人工制品。双鞭螺属Scincomorpha的系统发育关系和Anguimorpha被认为是相当悬而未决。未来有鳞类系统发育关系的改善将依赖于寻找mt进化速度较慢的蛇和端齿类物种，确保有鳞类多样性的完整分类单元覆盖，并在适当的进化速度下整合更多的核基因。(C)2008 Elsevier B. V.保留所有权利。
The complete nucleotide sequences of the mitochondrial (mt) genomes of three species of squamate lizards: Blanus cinereus (Amphisbaenidae), Anguis fragilis (Anguidae), and Tarentola mauritanica (Geckkonidae) were determined anew. The deduced amino acid sequences of all 13 mt protein-coding genes were combined into a single data set and phylogenetic relationships among main squamate lineages were analyzed under maximum likelihood (ML) and Bayesian Inference (BI). Within Squamata, the monophyly of Iguanidae, Anguimorpha, Amphisbaenia, Gekkota, Serpentes, and Acrodonta received high statistical support with both methods. It is particularly striking that this is the first molecular analysis that recovers the monophyly of Scincomorpha (including Scincidae, Xantusiidae, Cordylidae, and Lacertidae), although it is only supported in the Bayesian analysis, and it is sensitive to changes in the outgroup (see below). Phylogenetic relationships among the main squamate lineages could not be resolved with ML but received strong support with BI (above 95%). The newly reconstructed phylogeny of squamates does not support the Iguania-Scleroglossa split. Acrodonta and Serpentes form a clade, which is the sister group of the remaining squamate lineages. Within these, Gekkota were the first branching out, followed by Amphisbaenia, and a clade including Anguimorpha as sister group of Scincomorpha + Iguanidae. The recovered topology differed substantially from previously reported hypotheses on squamate relationships, and the relative effect of using different outgroups, genes, and taxon samplings were explored. The sister group relationship of Serpentes + Acrodonta, and their relative basal position within Squamata could be due to a long-branch attraction artifact. Phylogenetic relationships among Scincomorpha, Amphisbaenia. and Anguimorpha were found to be rather unresolved. Future improving of squamate phylogenetic relationships would rely on finding snake and acrodont species with slower mt evolutionary rates, ensuring thorough taxon coverage of squamate diversity, and incorporating more nuclear genes with appropriate evolutionary rates. (C) 2008 Elsevier B.V. All rights reserved.