Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model.

PLoS Comput Biol

Centre for Computational Evolution, University of Auckland, Auckland, New Zealand.

Published: February 2021

Relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence times. Under the (uncorrelated) relaxed clock model, tree branches are associated with molecular substitution rates which are independently and identically distributed. In this article we delved into the internal complexities of the relaxed clock model in order to develop efficient MCMC operators for Bayesian phylogenetic inference. We compared three substitution rate parameterisations, introduced an adaptive operator which learns the weights of other operators during MCMC, and we explored how relaxed clock model estimation can benefit from two cutting-edge proposal kernels: the AVMVN and Bactrian kernels. This work has produced an operator scheme that is up to 65 times more efficient at exploring continuous relaxed clock parameters compared with previous setups, depending on the dataset. Finally, we explored variants of the standard narrow exchange operator which are specifically designed for the relaxed clock model. In the most extreme case, this new operator traversed tree space 40% more efficiently than narrow exchange. The methodologies introduced are adaptive and highly effective on short as well as long alignments. The results are available via the open source optimised relaxed clock (ORC) package for BEAST 2 under a GNU licence (https://github.com/jordandouglas/ORC).

Download full-text PDF

Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7880504PMC
http://dx.doi.org/10.1371/journal.pcbi.1008322DOI Listing

Publication Analysis

Top Keywords

relaxed clock
32
clock model
20
relaxed
8
clock
8
molecular substitution
8
substitution rates
8
introduced adaptive
8
narrow exchange
8
model
5
adaptive dating
4

Similar Publications

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!