To estimate these numbers, we used the reconciled tree method [37] [39], in which the topology of a gene tree is reconciled with that of a species tree.
If we accept that the evidence constrains us to look for a positive answer to the first question (at least as regards the recommendation of epochê), the second question is how to reconcile Arcesilaus' method with his commitment to these doctrines.
The reconciled tree method was applied to the 35 phylogenetic trees.
We used Class I gene clade and 34 Class II gene clades (A S, AA AJ, AT, BA BD) to apply the reconciled tree method.
Our negative result highlights the challenge of reconciling such methods, which have advanced without explicitly addressing how essential genes impact performance, with principles of molecular evolution.
It should be mentioned that the number of genes in common ancestors is likely to be underestimated using the reconciled-tree method.
Gene tree parsimony [ 32] is the most commonly used reconciled tree method, and the only approach practical for even moderately sized phylogenies at this time.
Here, we did not use the reconciled-tree method (Goodman et al. 1979; Nam and Nei 2005; Niimura and Nei 2007) because the nucleotide sequences of miRNA genes were too short to make reliable gene trees.
To estimate the number of OR genes in ancestral species and gains and losses of genes during primate evolution, we used the modified reconciled tree method as described by Nam and Nei (2005).
We then surveyed the evolutionary history of OR genes in primates using a widely used reconciled tree method (Nam and Nei 2005; Nozawa and Nei 2007; Dong et al. 2009).
