Rooting the eutherian tree the power and pitfalls of phylogenomics 英文参考文献.docVIP

Open Access Re rch 2007NishiharaetVoal.lumesea8, Issue 9, Article R199 Rooting the eutherian tree: the power and pitfalls of phylogenomics Hidenori Nishihara*?, Norihiro Okada* and Masami Hasegawa?? Addresses: *Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B-21 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan. ?Department of Statistical Modeling, Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, Tokyo 106-8569, Japan. ?School of Life Sciences, Fudan University, Handan Road 220#, Shanghai 200433, China. Correspondence: Norihiro Okada. Email: nokada@bio.titech.ac.jp Published: 21 September 2007 Received: 15 December 2006 Revised: 2 July 2007 Accepted: 21 September 2007 Genome Biology 2007, 8:R199 (doi:10.1186/gb-2007-8-9-r199) The electronic version of this article is the complete one and can be found online at /2007/8/9/R199 ? 2007 Nishihara et al.; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Pitfallsa ppuItantaiofvnealphylogenomicsyttemptwrongtotrrootee, wthereutherianeas separatreet ausingnalysegenome-scales of different gdataeneswithreduthec dmaximumthe bias.likelihood/p method, a concatenate analysis supports Abstract Background: Ongoing genome sequencing projects have led to a phylogenetic approach based on genome-scale data (phylogenomics), which is beginning to shed light on longstanding unresolved phylogenetic issues. The use of large datasets in phylogenomic analysis results in a global increase in resolution due to a decrease in sampling error. However, a fully resolved tree can still be wrong if the phylogenetic inference is biased. Results: Here, in an attempt to root the eutherian tree using genome-scale data with