Log Transformation Improves Dating of Phylogenies.
Phylogenetic trees inferred from sequence data often have branch lengths measured in the expected number of substitutions and therefore, do not have divergence times estimated. These trees give an incomplete view of evolutionary histories since many applications of phylogenies require time trees. Many methods have been developed to convert the inferred branch lengths from substitution unit to time unit using calibration points, but none is universally accepted as they are challenged in both scalability and accuracy under complex models. Here, we introduce a new method that formulates dating as a nonconvex optimization problem where the variance of log-transformed rate multipliers is minimized across the tree. On simulated and real data, we show that our method, wLogDate, is often more accurate than alternatives and is more robust to various model assumptions.
['Mai|Uyen|U|', 'Mirarab|Siavash|S|']
D000465:Algorithms D029043:Ebolavirus D005821:Genetic Techniques D053118:Influenza A Virus, H1N1 Subtype D059645:Mutation Rate D010802:Phylogeny
divergence time estimation time tree nonconvex optimization molecular dating phylogenetic dating