The Implications of Lineage-Specific Rates for Divergence Time Estimation

Tom Carruthers, Michael J. Sanderson, Robert W. Scotland, Michael Alfaro

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


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 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 data set 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 analyzing genomic scale multilocus data sets. [Divergence time estimation; error; rate variation.].

Original languageEnglish (US)
Pages (from-to)660-670
Number of pages11
JournalSystematic biology
Issue number4
StatePublished - Jul 1 2020

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics


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