Jan 31, 2019

Molecular dating for phylogenies containing a mix of populations and species

BioRxiv : the Preprint Server for Biology
Beatriz MelloSudhir Kumar

Abstract

Concurrent molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics, and species delimitation studies. Multiple sequence alignments used in these investigations frequently consist of both intra- and inter-species samples (mixed samples). As a result, the phylogenetic trees contain inter-species, inter-population, and within population divergences. To date these sequence divergences, Bayesian relaxed clock methods are often employed, but they assume the same tree prior for both inter- and intra-species branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of using the same tree prior on the Bayesian divergence time estimates by analyzing computer-simulated datasets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with Skyline-coalescent tree priors generally produced excellent molecular dates, with some tree priors (e.g., Yule) performing the best when evolutionary rates were autocorrelated, and lineage sorting was incomplete. We c...Continue Reading

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Mentioned in this Paper

Study
Trees (plant)
Divergence
Evaluation
Simulation
Species
Approach
Branching (Qualifier Value)
Population Group
Branched-chain Amino Acid Metabolic Process

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