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

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 a...

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Published inPLoS computational biology Vol. 17; no. 2; p. e1008322
Main Authors Douglas, Jordan, Zhang, Rong, Bouckaert, Remco
Format Journal Article
LanguageEnglish
Published United States Public Library of Science 01.02.2021
Public Library of Science (PLoS)
Subjects
Approximation
Biology and Life Sciences
Clocks & watches
Computer and Information Sciences
Correlation
COVID-19
Expected values
Nucleic acids
Operators
Parameterization
Phylogenetics
Phylogeny
Physical Sciences
Proposals
Real numbers
Research and Analysis Methods
Substitutes
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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 ).
AbstractList 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).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).
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 ). Biological sequences, such as DNA, accumulate mutations over generations. By comparing such sequences in a phylogenetic framework, the evolutionary tree of lifeforms can be inferred and historic divergence dates can be estimated. With the overwhelming availability of biological sequence data, and the increasing affordability of collecting new data, the development of fast and efficient phylogenetic algorithms is more important than ever. In this article we focus on the relaxed clock model, which is very popular in phylogenetics. We explored how a range of optimisations can improve the statistical inference of the relaxed clock. This work has produced a phylogenetic setup which can infer parameters related to the relaxed clock up to 65 times faster than previous setups, depending on the dataset. The methods introduced adapt to the dataset during computation and are highly efficient when processing long biological sequences.
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 ).
[...]molecular substitution rates are known to vary over time, over population sizes, over evolutionary pressures, and over nucleic acid replicative machineries [14–16]. [...]any given dataset could be clock-like (where substitution rates have a small variance across lineages) or non clock-like (a large variance). [...]although not the focus of this article, the class of correlated clock models assumes some form of auto-correlation between rates over time. In this article, we systematically evaluate how the relaxed clock model can benefit from i) adaptive operator weighting, ii) substitution rate parameterisation, iii) Bactrian proposal kernels [31], iv) tree operators which account for correlations between substitution rates and times, and v) adaptive multivariate operators [30]. [...]rates can be parameterised as real numbers describing the rate’s quantile with respect to some underlying clock model distribution [18].
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).
[...]molecular substitution rates are known to vary over time, over population sizes, over evolutionary pressures, and over nucleic acid replicative machineries [14–16]. [...]any given dataset could be clock-like (where substitution rates have a small variance across lineages) or non clock-like (a large variance). [...]although not the focus of this article, the class of correlated clock models assumes some form of auto-correlation between rates over time. In this article, we systematically evaluate how the relaxed clock model can benefit from i) adaptive operator weighting, ii) substitution rate parameterisation, iii) Bactrian proposal kernels [31], iv) tree operators which account for correlations between substitution rates and times, and v) adaptive multivariate operators [30]. [...]rates can be parameterised as real numbers describing the rate’s quantile with respect to some underlying clock model distribution [18].
Author Bouckaert, Remco
Douglas, Jordan
Zhang, Rong
AuthorAffiliation 3 Max Planck Institute for the Science of Human History, Jena, Germany
2 School of Computer Science, University of Auckland, Auckland, New Zealand
University of Zurich, SWITZERLAND
1 Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
AuthorAffiliation_xml – name: 2 School of Computer Science, University of Auckland, Auckland, New Zealand
– name: University of Zurich, SWITZERLAND
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– name: 1 Centre for Computational Evolution, University of Auckland, Auckland, New Zealand
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  surname: Douglas
  fullname: Douglas, Jordan
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  surname: Zhang
  fullname: Zhang, Rong
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  givenname: Remco
  orcidid: 0000-0001-6765-3813
  surname: Bouckaert
  fullname: Bouckaert, Remco
BackLink https://www.ncbi.nlm.nih.gov/pubmed/33529184$$D View this record in MEDLINE/PubMed
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SSID ssj0035896
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Snippet Relaxed clock models enable estimation of molecular substitution rates across lineages and are widely used in phylogenetics for dating evolutionary divergence...
[...]molecular substitution rates are known to vary over time, over population sizes, over evolutionary pressures, and over nucleic acid replicative...
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SubjectTerms Approximation
Biology and Life Sciences
Clocks & watches
Computer and Information Sciences
Correlation
COVID-19
Expected values
Nucleic acids
Operators
Parameterization
Phylogenetics
Phylogeny
Physical Sciences
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Real numbers
Research and Analysis Methods
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Title Adaptive dating and fast proposals: Revisiting the phylogenetic relaxed clock model
URI https://www.ncbi.nlm.nih.gov/pubmed/33529184
https://www.proquest.com/docview/2501880301
https://www.proquest.com/docview/2486147799
https://pubmed.ncbi.nlm.nih.gov/PMC7880504
https://doaj.org/article/6b2600c3dd5f46c8b8c69cb8c9cbc78a
http://dx.doi.org/10.1371/journal.pcbi.1008322
Volume 17
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