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Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học Journal of Biology đề tài: Search for a ‘Tree of Life’ in the thicket of the phylogenetic forest. | Journal of Biology BioMed Central Research article Open Access Search for a Tree of Life in the thicket of the phylogenetic forest Pere Puigbò Yuri I Wolf and Eugene V Koonin Address National Center for Biotechnology Information National Library of Medicine National Institutes of Health Bethesda MD 20894 USA. Correspondence Eugene V Koonin. Email koonin@ncbi.nlm.nih.gov Published 13 July 2009 Received 25 April 2009 Journal of Biology 2009 8 59 doi 10.1186 jbiol159 RevỈ edjJ.9 MaL2009 Accepted 12 June 2009 The electronic version of this article is the complete one and can be found online at http jbiol.com content 8 6 59 2009 Puigbò et al. 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 genomics has revealed extensive horizontal gene transfer among prokaryotes a development that is often considered to undermine the tree of life concept. However the possibility remains that a statistical central trend still exists in the phylogenetic forest of life . Results A comprehensive comparative analysis of a forest of 6 901 phylogenetic trees for prokaryotic genes revealed a consistent phylogenetic signal particularly among 102 nearly universal trees despite high levels of topological inconsistency probably due to horizontal gene transfer. Horizontal transfers seemed to be distributed randomly and did not obscure the central trend. The nearly universal trees were topologically similar to numerous other trees. Thus the nearly universal trees might reflect a significant central tendency although they cannot represent the forest completely. However topological consistency was seen mostly at shallow tree depths and abruptly dropped at the level of the radiation of archaeal and bacterial phyla suggesting that
