Birth-death prior on phylogeny and speed dating |
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Authors: | Örjan Åkerborg Bengt Sennblad Jens Lagergren |
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Institution: | (1) Stockholm Bioinformatics Centre (SBC), Albanova, Stockholm University, SE-10691 Stockholm, Sweden;(2) School for Computer Science and Communication (CSC), Royal Institute of Technology (KTH), SE-10044 Stockholm, Sweden |
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Abstract: | Background In recent years there has been a trend of leaving the strict molecular clock in order to infer dating of speciations and other
evolutionary events. Explicit modeling of substitution rates and divergence times makes formulation of informative prior distributions
for branch lengths possible. Models with birth-death priors on tree branching and auto-correlated or iid substitution rates among lineages have been proposed, enabling simultaneous inference of substitution rates and divergence
times. This problem has, however, mainly been analysed in the Markov chain Monte Carlo (MCMC) framework, an approach requiring
computation times of hours or days when applied to large phylogenies. |
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