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Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Critical Care giúp cho các bạn có thêm kiến thức về ngành y học đề tài: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. | Open Access Bias in phylogenetic tree reconciliation methods implications for vertebrate genome evolution Matthew W Hahn Address Department of Biology and School of Informatics E. 3rd Street Indiana University Bloomington IN 47405 USA. Email mwh@indiana.edu Published 16 July 2007 Received 15 May 2007 Genome Biology 2007 8 R141 doi 10.1186 gb-2007-8-7-r141 Accepted 16 July 2007 The electronic version of this article is the complete one and can be found online at http genomebiology.com 2007 8 7 R141 2007 Hahn licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License http creativecommons.org licenses by 2.0 which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract Background Comparative genomic studies are revealing frequent gains and losses of whole genes via duplication and pseudogenization. One commonly used method for inferring the number and timing of gene gains and losses reconciles the gene tree for each gene family with the species tree of the taxa considered. Recent studies using this approach have found a large number of ancient duplications and recent losses among vertebrate genomes. Results I show that tree reconciliation methods are biased when the inferred gene tree is not correct. This bias places duplicates towards the root of the tree and losses towards the tips of the tree. I demonstrate that this bias is present when tree reconciliation is conducted on both multiple mammal and Drosophila genomes and that lower bootstrap cut-off values on gene trees lead to more extreme bias. I also suggest a method for dealing with reconciliation bias although this method only corrects for the number of gene gains on some branches of the species tree. Conclusion Based on the results presented it is likely that most tree reconciliation analyses show biases unless the gene trees used are exceptionally well-resolved and .
