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Mol Biol Evol. 2018 Jul 1;35(7):1770-1782. doi: 10.1093/molbev/msy044.

Theoretical Foundation of the RelTime Method for Estimating Divergence Times from Variable Evolutionary Rates.

Tamura K1,2, Tao Q3,4, Kumar S3,4,5.

Author information

1
Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
2
Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Hachioji, Tokyo, Japan.
3
Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
4
Department of Biology, Temple University, Philadelphia, PA.
5
Center for Excellence in Genome Medicine and Research, King Abdulaziz University, Jeddah, Saudi Arabia.

Abstract

RelTime estimates divergence times by relaxing the assumption of a strict molecular clock in a phylogeny. It shows excellent performance in estimating divergence times for both simulated and empirical molecular sequence data sets in which evolutionary rates varied extensively throughout the tree. RelTime is computationally efficient and scales well with increasing size of data sets. Until now, however, RelTime has not had a formal mathematical foundation. Here, we show that the basis of the RelTime approach is a relative rate framework (RRF) that combines comparisons of evolutionary rates in sister lineages with the principle of minimum rate change between evolutionary lineages and their respective descendants. We present analytical solutions for estimating relative lineage rates and divergence times under RRF. We also discuss the relationship of RRF with other approaches, including the Bayesian framework. We conclude that RelTime will be useful for phylogenies with branch lengths derived not only from molecular data, but also morphological and biochemical traits.

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