Universal Common Ancestry- A Test

Are Americans, Archaea, Amoeba and bacteria all genetically related? The notion of a 'universal common ancestor' (UCA) is central to evolutionary biology. Much of the traditional arguments have been confined to 'local' common ancestry (of particular phyla) as opposed to the totality of life; let's overcome this assumption and test the hypothesis using probability theory and phylogenetics. The problem of UCA has been compounded by horizontal gene transfer (transduction, transformation and conjugation) where early genetic material passed on between entirely different species is thought by some to challenge the 'tree of life' pattern by creating reticulated lineages. The qualitative evidence for UCA spans the congruence of biogeography and phylogeny; the mutual agreement between the fossil record and  phylogeny, the nested hierarchy of forms and the correspondence between morphology and molecular genetics. Such arguments boil down to 2 premises: (1) the nearly-universal nature of the genetic code and (2) critical similarities on molecular level (L-amino acids, fundamental polymers, metabolic intermediates). Since these arguments are merely qualitative, they do not rule out conclusively, the possibility of multiple independent ancestors. We can examine UCA quantitatively by model selection theory (without the presumption that sequence similarity implies a genealogical relationship) and a set of highly-conserved proteins. Also, we can model our test on Bayesian and likelihoodist probability (as opposed to the classical frequentist null hypotheses). Keep in mind that sequence similarity is the most likely consequence of common ancestry but this alone is not enough to support homology (similarity may be due to convergence). It is the nested, hierarchical relationship between sequences that necessitates the inference of common ancestry (because some similar sequences produce a conflicting phylogenetic structure which forces the conclusion of uncommon descent).

So are the three superkingdoms of life (archaea, bacteria, eukarya) united by a common ancestor? Douglas Theobald recently performed a test where 23 conserved amino-acids across the three domains had evolutionary networks (or trees) build around their sequences. Then contrasting the probability values for a range of ancestry hypotheses. But does this imply that life originated only once around 3.5 BYA? Not at all! It just implies that one of the primordial (original) forms of life has extant descendants; however it is possible for life to arisen more than once but the whole conclusion necessitates that all life has at least once common ancestor: a last universal common ancestor (LUCA). A problem however is that a phylogenetic tree can be build on virtually any set of data; we need to demonstrate an agreement between trees for the exact set of data spanning different datasets. And this agreement can also be explained in terms of other biological processes so the Akaike Information Criterion (AIC) may be applied to compare and contrast a range of hypotheses.So what signature feature of sequence data allows us to give qualitative evidence for UCA? In a nut-shell, the site-specific relationships in the amino-acids across a range of species; such relationships fade away as we go back in time through a lineage and species converge back (but with enough data, the progressive accumulation of relationships becomes statistically significant). On the other hand, if a pair of extant species have absolutely distinct origins, the relationships between the site-specific amino acid correlations (in the two species) disappear.