A phylogenomic study of human, dog, and mouse.
A phylogenomic study of human, dog, and mouse.
复制标题
人类，狗和小鼠的系统基因组研究。
DOI：
10.1371/journal.pcbi.0030002
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发表时间：
2007-01-05
影响因子：
4.3
通讯作者：
Gonnet, Gaston
中科院分区：
文献类型：
--
作者：
Cannarozzi, Gina;Schneider, Adrian;Gonnet, Gaston
近年来，哺乳动物目的系统发育关系已在一些分子研究中得到解决。这些分析经常产生不一致的结果，就一些基本的顺序关系。例如，灵长类动物、啮齿类动物和食肉动物的相对位置在不同的研究中是不同的。在这里，我们试图通过使用完全测序的核基因组的数据来解决这个系统发育问题，以基于尽可能多的数据进行分析。为了最大限度地减少重建伪影的风险，根据不同的标准-距离、简约性和可能性重建树。对于距离树，使用了测量独立现象（氨基酸替换、同义替换和基因重新排序）的距离度量，因为所有树都不太可能受到任何重建伪影的相同影响。与目前流行的分类相反，我们基于人类、狗和小鼠之间系统发育关系的全基因组分析的结果压倒性地支持排除啮齿动物的灵长类-食肉动物分支。在真兽目进化树中的一些基本关系一直难以解决，可能是因为潜在的分歧发生在很短的时间内。在这项研究中，我们特别研究了人类（灵长类动物），狗（食肉动物）和小鼠（啮齿动物）之间的关系。以前的形态学和分子学研究使用不同的数据集和重建方法得出了不同的结论，这些订单的相对位置的哺乳动物树。在这里，我们使用完全测序的核基因组和一些不同的系统发育方法来解决这个难题。直到最近，包括负鼠在内的几种完整哺乳动物基因组的测序才使这种方法成为可能。我们的研究结果强烈表明灵长类动物和食肉动物之间存在姐妹关系。
In recent years the phylogenetic relationship of mammalian orders has been addressed in a number of molecular studies. These analyses have frequently yielded inconsistent results with respect to some basal ordinal relationships. For example, the relative placement of primates, rodents, and carnivores has differed in various studies. Here, we attempt to resolve this phylogenetic problem by using data from completely sequenced nuclear genomes to base the analyses on the largest possible amount of data. To minimize the risk of reconstruction artifacts, the trees were reconstructed under different criteria—distance, parsimony, and likelihood. For the distance trees, distance metrics that measure independent phenomena (amino acid replacement, synonymous substitution, and gene reordering) were used, as it is highly improbable that all of the trees would be affected the same way by any reconstruction artifact. In contradiction to the currently favored classification, our results based on full-genome analysis of the phylogenetic relationship between human, dog, and mouse yielded overwhelming support for a primate–carnivore clade with the exclusion of rodents. Some basal relationships in the eutherian tree have been difficult to resolve, probably because the underlying divergences took place within a very short period of time. In this study we examine particularly the relationship between human (primates), dog (carnivores), and mouse (rodents). Previous morphological and molecular studies using different datasets and reconstruction methods have come to different conclusions about the relative placement of these orders on the mammalian tree. Here, we use completely sequenced nuclear genomes and a number of different phylogenetic methods to address this difficult problem. An approach of this kind has only recently become possible with the sequencing of several complete mammalian genomes including the opossum as a relevant outgroup. Our results strongly suggest a sister relationship between primates and carnivores.
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通讯作者：
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