Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data

@article{nikolaev07tree, abstract = {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\&\#37; 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.}, author = {Nikolaev, Sergey and Juan and Margulies, Elliott H. and Program, Nisc C. and Rougemont, Jacques and Nyffeler, Bruno and Antonarakis, Stylianos E. }, citeulike-article-id = {1031700}, doi = {http://dx.doi.org/10.1371/journal.pgen.0030002}, journal = {PLoS Genetics}, keywords = {mammal, phylogenetics, phylogenomics, root\_eutheria, tree, zooseq}, month = {January}, number = {1}, pages = {e2+}, posted-at = {2007-01-09 17:20:39}, priority = {0}, title = {Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data}, url = {http://dx.doi.org/10.1371/journal.pgen.0030002}, volume = {3}, year = {2007} }

TY - JOUR ID - nikolaev07tree L3 - citeulike-article-id:1031700 N2 - 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. IS - 1 JF - PLoS Genetics TI - Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data VL - 3 SP - e2 KW - mammal KW - phylogenetics KW - phylogenomics KW - root_eutheria KW - tree KW - zooseq AU - Nikolaev, Sergey AU - Juan AU - Margulies, Elliott AU - Program, Nisc AU - Rougemont, Jacques AU - Nyffeler, Bruno AU - Antonarakis, Stylianos PY - 2007/January/01/ UR - http://dx.doi.org/10.1371/journal.pgen.0030002 ER -