Data from: Testing for Universal Common Ancestry

A phylogenetic model selection test to quantify the evidence for the Universal Common Ancestry (UCA) of life forms was proposed recently and applied in the confirmation of the common origin of a data set of universally conserved proteins spanning the three domains of life (Theobald 2010). While there is no question of the common ancestry of the particular set of aligned sequences analyzed, the UCA test has been criticized on several grounds (Koonin and Wolf 2010; Yonezawa and Hasegawa 2010, Martins and Posada 2012). In our simulations, the original UCA test showed bias towards common ancestry even for data sets simulated under independent origins, but this bias almost disappeared when we coestimated alignment and phylogeny for each competing hypothesis.