As filogenias de genes ortólogos apoiam realmente o pensamento de árvore?

quarta-feira, março 24, 2010

BMC Evol Biol. 2005; 5: 33.
Published online 2005 May 24. doi: 10.1186/1471-2148-5-33.
PMCID: PMC1156881

Copyright © 2005 Bapteste et al; licensee BioMed Central Ltd.

Do orthologous gene phylogenies really support tree-thinking?

E Bapteste,1,2 E Susko,1,3 J Leigh,1,2 D MacLeod,1,2 RL Charlebois,1,2and WF Doolittle1,2

1GenomeAtlantic, 1721 Lower Water Street, Suite 401, Halifax, NS, B3J 1S5, Canada

2Dalhousie University, Department of Biochemistry & Molecular Biology, 5850 College St., Halifax, NS, B3H 1X5, Canada

3Dalhousie University, Department of Mathematics and Statistics, Halifax, Nova Scotia, Canada

Corresponding author.

E Bapteste: eric.bapteste@dal.ca; E Susko: susko@mathstat.dal.ca; J Leigh: jleigh@dal.ca; D MacLeod:djmacleo@dal.ca; RL Charlebois: rlcharlebois@mac.com; WF Doolittle: ford@dal.ca

Received April 1, 2005; Accepted May 24, 2005.

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.

Background

Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.

Results

Heat map analyses were used to investigate the congruence of orthologues in four datasets (archaeal, bacterial, eukaryotic and alpha-proteobacterial). We conclude that we simply cannot determine if a large portion of the genes have a common history. In addition, none of these datasets can be considered free of lateral gene transfer.

Conclusion

Our phylogenetic analyses do not support tree-thinking. These results have important conceptual and practical implications. We argue that representations other than a tree should be investigated in this case because a non-critical concatenation of markers could be highly misleading.

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