Abstract

BackgroundThe evidence for universal common ancestry (UCA) is vast and persuasive. A phylogenetic test has been proposed for quantifying its odds against independently originated sequences based on the comparison between one versus several trees. This test was successfully applied to a well-supported homologous sequence alignment, which was however criticized on the basis of simulations showing that alignments without any phylogenetic structure could mislead its conclusions.ResultsHere we present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We also present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. Finally, we present a class of frequentist tests that perform better than the purportedly formal UCA test.ConclusionDespite claims to the contrary, we show that the counterexamples successfully detected a drawback of the original UCA test, of relying on sequence similarity. In light of our own simulations, we therefore conclude that the UCA test as originally proposed should not be trusted unless convergence has already been ruled out a priori.ReviewersThis article was reviewed by Professor Eugene Koonin, Dr. Yuri I. Wolf and Professor William Martin.Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-016-0120-y) contains supplementary material, which is available to authorized users.

Highlights

  • The evidence for universal common ancestry (UCA) is vast and persuasive

  • To claim otherwise would defeat, by the way, the whole phylogenetic model selection framework developed in [1]: if, for each alignment column, sampling the state from a common distribution renders the data related by common ancestry, the idea that two independent trees can represent independent origins (IO) would be wrong since their root positions might be two such ancestral sequences, whose columns came from an “ancestral soup” of amino acids – as we show in the (Additional file 1: Appendix)

  • We have argued that even summary statistics contain information about the likeliness of UCA, and any common ancestry test should take this information into account [6]

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Summary

Results

We present a simplified version of this same counterexample, which can be interpreted as a tree with arbitrarily long branches, and where the UCA test fails again. We present another case whereby any sufficiently similar alignment will favour UCA irrespective of the true independent origins for the sequences. We present a class of frequentist tests that perform better than the purportedly formal UCA test

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