The implications of lineage-specific rates for divergence time estimation.
Carruthers T., Sanderson MJ., Scotland RW.
Rate variation adds considerable complexity to divergence time estimation in molecular phylogenies. Here, we evaluate the impact of lineage-specific rates - which we define as among-branch-rate-variation that acts consistently across the entire genome. We compare its impact to residual rates - defined as among-branch-rate-variation that shows a different pattern of rate variation at each sampled locus, and gene-specific rates - defined as variation in the average rate across all branches at each sampled locus. We show that lineage-specific rates lead to erroneous divergence time estimates, regardless of how many loci are sampled. Further, we show that stronger lineage-specific rates lead to increasing error. This contrasts to residual rates and gene-specific rates, where sampling more loci significantly reduces error. If divergence times are inferred in a Bayesian framework, we highlight that error caused by lineage-specific rates significantly reduces the probability that the 95% highest posterior density (HPD) includes the correct value, and leads to sensitivity to the prior. Use of a more complex rate prior - which has recently been proposed to model rate variation more accurately - does not affect these conclusions. Finally, we show that the scale of lineage-specific rates used in our simulation experiments is comparable to that of an empirical dataset for the angiosperm genus Ipomoea. Taken together, our findings demonstrate that lineage-specific rates cause error in divergence time estimates, and that this error is not overcome by analysing genomic scale multi-locus datasets.