Desafiando a Nomenklatura Científica: Bapteste et al 'falaram e disseram': as filogenias de genes ortólogos não apoiam a Árvore da Vida de Darwin

domingo, maio 16, 2010

Do orthologous gene phylogenies really support tree-thinking?

E Bapteste1,2 , E Susko1,3 , J Leigh1,2 , D MacLeod1,2 , RL Charlebois1,2 and WF Doolittle1,2

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

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

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

author email corresponding author email

BMC Evolutionary Biology 2005, 5:33doi:10.1186/1471-2148-5-33

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2148/5/33

Received: 1 April 2005
Accepted: 24 May 2005
Published: 24 May 2005

© 2005 Bapteste 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

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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FREE PDF GRÁTIS: OPEN ACCESS

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NOTA CAUSTICANTE DESTE BLOGGER:

Estou republicando aqui o artigo de Bapteste et al. porque estão exagerando demais com a pesquisa de Douglas L. Theobald sobre o Ancestral comum Universal, especialmente a Nature, uma publicação científica de renome, mas que ultimamente está mais ideologizada do que científica, que não leva em conta pesquisas contrárias sobre o tal de ancestral comum [seja lá o que isso signifique].

Editor's Summary

13 May 2010
One big family

Universal common ancestry (UCA), the idea that all terrestrial life is genetically related, from some “warm little pond” as Darwin put it, has become central to modern evolutionary theory. The classic evidence for UCA is extensive, but largely qualitative, and the theory is rarely subjected to a formal, quantitative test. And the UCA view has been called into question by the existence of extensive horizontal gene transfer in many organisms. Douglas Theobald has framed the UCA view as a formal hypothesis and put it to the test using Bayesian statistical analysis of the sequences of universally conserved proteins and contrasting the results with alternative models where genetic similarity is not assumed to reflect phylogenetic relatedness. The UCA view wins out: a single origin of life is overwhelmingly more likely than any competing hypothesis.

NEWS AND VIEWS:Origins of life: Common ancestry put to the test

The question of whether or not all life on Earth has an ultimate common origin is a subtle one, complicated by the phenomenon of lateral gene transfer. It has now been tackled with a formal statistical analysis.

Mike Steel & David Penny

doi:10.1038/465168a

LETTER:A formal test of the theory of universal common ancestry

Douglas L. Theobald

doi:10.1038/nature09014

A formal test of the theory of universal common ancestry

Douglas L. TheobaldNature 465, 219–222 (13 May 2010) doi:10.1038/nature09014Received 28 August 2009 Accepted 17 March 2010

Universal common ancestry (UCA) is a central pillar of modern evolutionary theory1. As first suggested by Darwin2, the theory of UCA posits that all extant terrestrial organisms share a common genetic heritage, each being the genealogical descendant of a single species from the distant past3, 4, 5, 6. The classic evidence for UCA, although massive, is largely restricted to ‘local’ common ancestry—for example, of specific phyla rather than the entirety of life—and has yet to fully integrate the recent advances from modern phylogenetics and probability theory. Although UCA is widely assumed, it has rarely been subjected to formal quantitative testing7, 8, 9, 10, and this has led to critical commentary emphasizing the intrinsic technical difficulties in empirically evaluating a theory of such broad scope1, 5, 8, 9, 11, 12, 13, 14, 15. Furthermore, several researchers have proposed that early life was characterized by rampant horizontal gene transfer, leading some to question the monophyly of life11, 14, 15. Here I provide the first, to my knowledge, formal, fundamental test of UCA, without assuming that sequence similarity implies genetic kinship. I test UCA by applying model selection theory5, 16, 17 to molecular phylogenies, focusing on a set of ubiquitously conserved proteins that are proposed to be orthologous. Among a wide range of biological models involving the independent ancestry of major taxonomic groups, the model selection tests are found to overwhelmingly support UCA irrespective of the presence of horizontal gene transfer and symbiotic fusion events. These results provide powerful statistical evidence corroborating the monophyly of all known life.

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NOTA CAUSTICANTE DESTE BLOGGER:

Sumário do artigo de Theobal pode ser visto aqui na Scientific American:

By plugging these sequences into various relational and evolutionary models, he found that a universal common ancestor is at least 102,860 more likely to have produced the modern-day protein sequence variances than even the next most probable scenario (involving multiple separate ancestors).