Early history of mammals is elucidated with the ENCODE multiple species sequencing data.
Early history of mammals is elucidated with the ENCODE multiple species sequencing data.
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用编码多种物种测序数据阐明了哺乳动物的早期历史。
DOI：
10.1371/journal.pgen.0030002
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发表时间：
2007-01-05
期刊：
影响因子：
4.5
通讯作者：
Antonarakis, Stylianos E.
中科院分区：
文献类型：
--
作者：
Nikolaev, Sergey;Montoya-Burgos, Juan I.;Margulies, Elliott H.;Rougemont, Jacques;Nyffeler, Bruno;Antonarakis, Stylianos E.
了解胎盘哺乳动物的早期进化是哺乳动物进化史上最具挑战性的问题之一。在这里，我们解决了这个问题，使用的序列数据的ENCODE财团，其中包括1%的哺乳动物基因组在18个物种属于所有主要的哺乳动物谱系。基于从218个基因中提取的前所未有数量的编码序列的系统发育重建导致了一个高度支持的树，将胎盘类的根置于非洲兽目和Exafroplacentalia之间（非洲兽目假说）。通过对一类新的基因组系统发育标记--保守的非编码序列的系统发育分析，验证了这种拓扑结构。在编码序列数据集上应用替代拓扑结构的测试导致了对Astratogenata假说（Xenarthra与Afrotheria分组）的拒绝，而当使用非编码序列数据集时，该测试拒绝了第二种替代方案，即Epitheria假说（Xenarthra在基础上）。因此，这两个数据集支持非洲兽亚目假说;然而，没有人可以拒绝剩下的两个拓扑替代方案。分子系统学方法的应用彻底改变了哺乳动物内部关系的概念。最近的分子系统发育研究表明，现存的胎盘哺乳动物属于三个亚群之一：Boreoeutheria，Afrotheria或Xenarthra，但它们之间的关系仍然未知。在之前使用16个基因的分析中，Boreoeutheria和Xenarthra被归为一组。然而，基于LINE插入的研究支持Boreoeutheria和Afrotheria的分组。为了解决这一差异，我们应用了18种哺乳动物亚组中1%基因组的序列数据。我们使用了来自218个基因的串联编码序列数据，包含205千碱基的DNA序列。系统发育分析表明，非洲兽是胎盘动物的一个基本类群，具有很高的统计支持。为了进一步验证这些结果，我们分析了一个新的系统发育标记：保守的非编码序列比对（430个碱基），这导致了胎盘根的相同位置。拓扑测试拒绝了编码序列数据集和Boreoeutheria-Afrotheria分组与非编码序列数据集的可能性。确定哺乳动物之间的亲缘关系对于研究不同功能基因组元件的进化行为具有重要意义。
Understanding the early evolution of placental mammals is one of the most challenging issues in mammalian phylogeny. Here, we addressed this question by using the sequence data of the ENCODE consortium, which include 1% of mammalian genomes in 18 species belonging to all main mammalian lineages. Phylogenetic reconstructions based on an unprecedented amount of coding sequences taken from 218 genes resulted in a highly supported tree placing the root of Placentalia between Afrotheria and Exafroplacentalia (Afrotheria hypothesis). This topology was validated by the phylogenetic analysis of a new class of genomic phylogenetic markers, the conserved noncoding sequences. Applying the tests of alternative topologies on the coding sequence dataset resulted in the rejection of the Atlantogenata hypothesis (Xenarthra grouping with Afrotheria), while this test rejected the second alternative scenario, the Epitheria hypothesis (Xenarthra at the base), when using the noncoding sequence dataset. Thus, the two datasets support the Afrotheria hypothesis; however, none can reject both of the remaining topological alternatives. Application of molecular phylogenetic methods drastically changed the conception of relationships within mammals. Recent molecular phylogenetic studies have shown that living placental mammals belong to one of the three subgroups: Boreoeutheria, Afrotheria, or Xenarthra, but the relations between these are still unknown. In a previous analysis using 16 genes, Boreoeutheria and Xenarthra grouped together. However, a study based on LINE insertions supported the grouping of Boreoeutheria and Afrotheria. To resolve this discrepancy, we applied sequence data from 1% of a genome in a subset of 18 mammalian species. We used concatenated coding sequence data from 218 genes encompassing 205 kilobases of DNA sequence. Phylogenetic analyses have shown Afrotheria as a basal group of Placentalia with high statistical support. To further validate these results, we analyzed a new phylogenetic marker: conserved noncoding sequence alignments (430 kilobases), which resulted in the same position of the placental root. Topological tests rejected the possibility of Afrotheria-Xenarthra grouping with the coding sequence dataset and Boreoeutheria-Afrotheria grouping with the noncoding sequence dataset. Ascertaining the relationships between mammals is of great importance for the investigation of evolutionary behavior of the different functional genomic elements.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
3.4
作者：
Delsuc F;Vizcaíno SF;Douzery EJ
通讯作者：
Douzery EJ
影响因子：
5.8
作者：
Posada, D;Crandall, KA
通讯作者：
Crandall, KA
影响因子：
10.7
作者：
Lin, YH;McLenachan, PA;Penny, D
通讯作者：
Penny, D
影响因子：
10.7
作者：
Dermitzakis, ET;Clark, AG
通讯作者：
Clark, AG