Was the universal common ancestry proved?

Abstract

Arising from D. L. Theobald Nature 465, 219–222 (2010)10.1038/nature09014; Theobald reply

The question of whether or not all life on Earth shares a single common ancestor has been a central problem of evolutionary biology since Darwin¹. Although the theory of universal common ancestry (UCA) has gathered a compelling list of circumstantial evidence, as given in ref. 2, there has been no attempt to test statistically the UCA hypothesis among the three domains of life (eubacteria, archaebacteria and eukaryotes) by using molecular sequences. Theobald² recently challenged this problem with a formal statistical test, and concluded that the UCA hypothesis holds. Although his attempt is the first step towards establishing the UCA theory with a solid statistical basis, we think that the test of Theobald² is not sufficient enough to reject the alternative hypothesis of the separate origins of life, despite the Akaike information criterion (AIC) of model selection³ giving a clear distinction between the competing hypotheses.

Main

Dawkins⁴ argued that even though it may, at first, seem unlikely that such a complex structure as the eye evolved by selection, it could have been realized by a long sequence of small evolutionary steps driven by selection. Theobald² mentions that statistically significant sequence similarity can arise from factors other than common ancestry, such as convergent evolution due to selection, but such factors were not taken into account in his ‘formal’ test to reject the independent origins hypothesis.

Table 1 shows that the formal test provides support for a common origin of two putatively unrelated genes, mitochondrial cytb and nd2, with no homology. However, we believe that this result should not be regarded as evidence of the ultimate common ancestry of cytb and nd2. This raises a question mark as to the effectiveness of the formal test applied by Theobald². It should be noted that, because alignment gives a bias for common ancestry, we did not make an alignment between cytb and nd2. To reject the separate origins hypothesis of the domains of life, it would be indispensable to develop a more ‘biological’ test to show that even by improving the model of the separate origins by taking into account biological factors such as the possibility of convergent evolution due to selection, the UCA hypothesis is still supported by the AIC. To do this, it is necessary to develop an entirely new methodological framework of molecular phylogenetics that is different from the conventional framework that neglects convergent and parallel evolution. Notably, there have been many reported cases of convergent and parallel evolution misleading molecular phylogenetic inference^5,6,7,8,9, and such a method is needed for molecular phylogenetics in general.

Table 1 A formal test of the common ancestry between mitochondrial genes cytb and nd2