Performance of a phylogenetic independent contrast method and an improved pairwise comparison under different scenarios of trait evolution after speciation and duplication

Despite the importance of gene function to evolutionary biology, the applicability of comparative methods to gene function is poorly known. A specific case which has crystalized methodological questions is the ortholog conjecture, the hypothesis that function evolves faster after duplication (i.e., in paralogs), and conversely conserved between orthologs. Since the mode of functional evolution after duplication is not well known, we investigate under what reasonable evolutionary scenarios phylogenetic independent contrasts or pairwise comparisons can recover a putative signal of different functional evolution between orthologs and paralogs. We investigate three different simulation models, which represent reasonable but simplified hypotheses about gene function (our trait) evolution. These are time dependent trait acceleration, correlated changes in rates of both sequence and trait evolution, and asymmetric trait jump. For each model we tested phylogenetic independent contrasts and an improved pairwise comparison method which accounts for interactions between events and node age. Both approaches loose power to detect the trend of functional evolution when the functional trait accelerates for a long time following duplication, with better power of phylogenetic contrasts under intermediate scenarios. Concomitant increase in evolutionary rates of sequence and of trait after duplication can lead to both an incorrect rejection of the null under null simulations of trait evolution, and a false rejection of the ortholog conjecture under ortholog conjecture simulations by phylogenetic independent contrasts. Improved pairwise comparisons are robust to this bias. Both approaches perform equally well to trace rapid shift in traits. Considering our ignorance of gene function evolution, and the potential for bias under simple models, we recommend methodological pluralism in studying gene family evolution. Functional phylogenomics is complex and results supported by only one method should be treated with caution.