Mais arbustos na Árvore da Vida

Artigo interessante sobre os atuais problemas em filogenética você encontra neste artigo intitulado "Bushes in the Tree of Life". Como se encontra no PLOS,pode baixar que é de graça. Para desespero da Nomenklatura científica,o artigo é assinado por Sean B. Carroll...

Vou destacar aqui algumas citações interessantes deste artigo:

Rokas A, Carroll SB (2006) Bushes in the tree of life. PLoS Biol 4(11): e352. DOI: 10.1371/journal.pbio.0040352

Quotes of note:
"Here we discuss how and why certain critical parts of the TOL [Tree of Life] may be difficult to resolve, regardless of the quantity of conventional data available. We do not mean this essay to be a comprehensive review of molecular systematics. Rather, we have focused on the emerging evidence from genome-scale studies on several branches of the TOL that sharply contrasts with viewpoints—such as that in the opening quotation [a quote by Dawkins that implies we'll get the TOL correct eventually]—which imply that the assembly of all branches of the TOL will simply be a matter of data collection. We view this difficulty in obtaining full resolution of particular clades—when given substantial data—as both biologically informative and a pressing methodological challenge. The recurring discovery of persistently unresolved clades (bushes) should force a re-evaluation of several widely held assumptions of molecular systematics. Now, as the field is transformed from a data-limited to an analysis-limited discipline, it is an opportune time to do so."

Three observations generally hold true across metazoan datasets that indicate the pervasive influence of homoplasy at these evolutionary depths. First, a large fraction of single genes produce phylogenies of poor quality. For example, Wolf and colleagues [9] omitted 35% of single genes from their data matrix, because those genes produced phylogenies at odds with conventional wisdom (Figure 2D). Second, in all studies, a large fraction of characters—genes, PICs or RGCs—disagree with the optimal phylogeny, indicating the existence of serious conflict in the DNA record. For example, the majority of PICs conflict with the optimal topology in the Dopazo and Dopazo study [10]. Third, the conflict among these and other studies in metazoan phylogenetics [11,12] is occurring at very “high” taxonomic levels—above or at the phylum level.

For instance, theory [34] and simulation analyses [8] predict that a small fraction of substitutions will be homoplastic by chance (about 2–5%, depending upon model assumptions and evolutionary distances). However, analysis of the elephant/sirenian/hyrax dataset and the coelacanth/lungfish/ tetrapod dataset indicates that the actual level of homoplasy is ~10% of amino acid substitutions in the first case (178 homoplastic/1,743 total substitutions) and ~15% in the second case (588 homoplastic/3,800 total substitutions), several times greater than expected [8,34]. Similar high levels of homoplasy exist in datasets from other bushy clades [35] (unpublished data) and hold irrespective of analytical methodology [8].

"Although it may be heresy to say so, it could be argued that knowing that strikingly different groups form a clade and that the time spans between the branching of these groups must have been very short, makes the knowledge of the branching order among groups potentially a secondary concern."

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E agora como é que fica a especulação transformista da ancestralidade comum? A teoria geral da evolução não é um fato, Fato, FATO,assim como a Terra gira em torno do Sol?