Abstract
BackgroundIt is common belief that all cellular life forms on earth have a common origin. This view is supported by the universality of the genetic code and the universal conservation of multiple genes, particularly those that encode key components of the translation system. A remarkable recent study claims to provide a formal, homology independent test of the Universal Common Ancestry hypothesis by comparing the ability of a common-ancestry model and a multiple-ancestry model to predict sequences of universally conserved proteins.ResultsWe devised a computational experiment on a concatenated alignment of universally conserved proteins which shows that the purported demonstration of the universal common ancestry is a trivial consequence of significant sequence similarity between the analyzed proteins. The nature and origin of this similarity are irrelevant for the prediction of "common ancestry" of by the model-comparison approach. Thus, homology (common origin) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis.ConclusionA formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle. Nevertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming.Reviewersthis article was reviewed by William Martin, Ivan Iossifov (nominated by Andrey Rzhetsky) and Arcady Mushegian. For the complete reviews, see the Reviewers' Report section.
Highlights
It is common belief that all cellular life forms on earth have a common origin
In the Origin of Species, Charles Darwin famously proposed what we may call the Universal Common Ancestry (UCA) hypothesis: “I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.” [1]
In each of the 100 generated alignments, all sequences are highly similar to each other because each alignment column is derived from a single statistical model. These alignments contain no signal of common ancestry whatsoever because each position in each sequence is generated independently from other positions
Summary
To formally demonstrate the independence of Theobald’s test on the common ancestry of the compared sequences, we designed and performed the following computational experiment (Figure 1). In each of the 100 generated alignments, all sequences are highly similar to each other because each alignment column is derived from a single statistical model These alignments contain no signal of common ancestry (in more general terms, no evolutionary signal) whatsoever because each position in each sequence is generated independently from other positions. When unrelated alignments were merged (first half of alignment #1 with the second half of alignment #2 etc), all log likelihoods from combined alignments were substantially lower than the sum of individual log likelihoods (difference ranged from -133 to -45 log likelihood units with the mean of -90) In this case, the lower likelihood of the combined alignment reflects the improbability of a very long tree branch connecting two dissimilar clusters of sequences. Common ancestry (or homology, in the modern, post-Darwinian sense) of the compared proteins remains an inference from sequence similarity rather than an independent property demonstrated by the likelihood analysis
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