Dataset Information

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

ABSTRACT: 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).

SUBMITTER: Douglas J

PROVIDER: S-EPMC7880504 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

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

Douglas Jordan J Zhang Rong R Bouckaert Remco R

PLoS computational biology 20210202 2

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 com ...[more]

PMID: 33529184

Similar Datasets

Project description:Understanding the processes that give rise to quantitative measurements associated with molecular sequence data remains an important issue in statistical phylogenetics. Examples of such measurements include geographic coordinates in the context of phylogeography and phenotypic traits in the context of comparative studies. A popular approach is to model the evolution of continuously varying traits as a Brownian diffusion process acting on a phylogenetic tree. However, standard Brownian diffusion is quite restrictive and may not accurately characterize certain trait evolutionary processes. Here, we relax one of the major restrictions of standard Brownian diffusion by incorporating a nontrivial estimable mean into the process. We introduce a relaxed directional random walk (RDRW) model for the evolution of multivariate continuously varying traits along a phylogenetic tree. Notably, the RDRW model accommodates branch-specific variation of directional trends while preserving model identifiability. Furthermore, our development of a computationally efficient dynamic programming approach to compute the data likelihood enables scaling of our method to large data sets frequently encountered in phylogenetic comparative studies and viral evolution. We implement the RDRW model in a Bayesian inference framework to simultaneously reconstruct the evolutionary histories of molecular sequence data and associated multivariate continuous trait data, and provide tools to visualize evolutionary reconstructions. We demonstrate the performance of our model on synthetic data, and we illustrate its utility in two viral examples. First, we examine the spatiotemporal spread of HIV-1 in central Africa and show that the RDRW model uncovers a clearer, more detailed picture of the dynamics of viral dispersal than standard Brownian diffusion. Second, we study antigenic evolution in the context of HIV-1 resistance to three broadly neutralizing antibodies. Our analysis reveals evidence of a continuous drift at the HIV-1 population level towards enhanced resistance to neutralization by the VRC01 monoclonal antibody over the course of the epidemic. [Brownian Motion; Diffusion Processes; Phylodynamics; Phylogenetics; Phylogeography; Trait Evolution.].

Project description:Relaxation of selective strength, manifested as a reduction in the efficiency or intensity of natural selection, can drive evolutionary innovation and presage lineage extinction or loss of function. Mechanisms through which selection can be relaxed range from the removal of an existing selective constraint to a reduction in effective population size. Standard methods for estimating the strength and extent of purifying or positive selection from molecular sequence data are not suitable for detecting relaxed selection, because they lack power and can mistake an increase in the intensity of positive selection for relaxation of both purifying and positive selection. Here, we present a general hypothesis testing framework (RELAX) for detecting relaxed selection in a codon-based phylogenetic framework. Given two subsets of branches in a phylogeny, RELAX can determine whether selective strength was relaxed or intensified in one of these subsets relative to the other. We establish the validity of our test via simulations and show that it can distinguish between increased positive selection and a relaxation of selective strength. We also demonstrate the power of RELAX in a variety of biological scenarios where relaxation of selection has been hypothesized or demonstrated previously. We find that obligate and facultative ?-proteobacteria endosymbionts of insects are under relaxed selection compared with their free-living relatives and obligate endosymbionts are under relaxed selection compared with facultative endosymbionts. Selective strength is also relaxed in asexual Daphnia pulex lineages, compared with sexual lineages. Endogenous, nonfunctional, bornavirus-like elements are found to be under relaxed selection compared with exogenous Borna viruses. Finally, selection on the short-wavelength sensitive, SWS1, opsin genes in echolocating and nonecholocating bats is relaxed only in lineages in which this gene underwent pseudogenization; however, selection on the functional medium/long-wavelength sensitive opsin, M/LWS1, is found to be relaxed in all echolocating bats compared with nonecholocating bats.

Dataset Information

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

Publications

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

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets