Figure 10

Example of a tree with substantial disagreement in inferred duplication events, and corresponding orthologs, between TreeBeST (A) and GIGA (B), TreeFam family TF105095. The sequence alignment is of high quality according to PredictedSP, so this disagreement is due to algorithm differences rather than a problematic alignment. The main differences are in the inference of gene duplication events (orange nodes) in the CYP17A1 lineage (other than the recent duplications in the bovine lineage). (A) TreeBeST infers two duplication events (dup 1 and dup 2), both prior to the ray-finned fish-tetrapod divergence, followed by at least five separate deletion events: one prior to the frog-amniote divergence (del 1), one prior to the chicken-mammal divergence (del 2), one prior to the fish radiation (del 3), one following the divergence of the frog lineage (del 4), and one following the divergence of the chicken lineage (del 5). Note that according to this tree, there are no orthologs of human CYP17A1 in chicken, frog, or fish. (B) GIGA infers one duplication event, before the fish radiation (dup 1') and no deletion events. Note that according to this tree, there is one ortholog of human CYP17A1 in frog, one in chicken, and two in each fish species. Note also that tree (B) infers two periods of accelerated (potentially adaptive) molecular evolutionary rates, which may account for why a molecular evolution model would favor a topology with longer divergence times such as in (A).