Section: Evolutionary Biology
Topic: Evolution, Genetics/Genomics, Statistics

Probabilities of tree topologies with temporal constraints and diversification shifts

Didier, Gilles1  
1 Univ Montpellier, CNRS, IMAG, Montpellier, France

Corresponding author(s): Didier, Gilles (gilles.didier@umontpellier.fr)

10.24072/pcjournal.73 - Peer Community Journal, Volume 1 (2021), article no. e65.

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Dating the tree of life is a task far more complicated than only determining the evolutionary relationships between species. It is therefore of interest to develop approaches apt to deal with undated phylogenetic trees. The main result of this work is a method to compute probabilities of undated phylogenetic trees under Markovian diversification models by constraining some of the divergence times to belong to given time intervals and by allowing diversification shifts on certain clades. If the diversification models considered are lineage-homogeneous, the time complexity of this computation is quadratic with the number of species of the phylogenetic tree and linear with the number of temporal constraints. The interest of this computation method is illustrated with three applications, namely, to compute the distribution of the divergence times of a tree topology with temporal constraints, to directly sample the divergence times of a tree topology, and to test for a diversification shift at a given clade.

Published online:
DOI: 10.24072/pcjournal.73
Type: Research article

Didier, Gilles 1

1 Univ Montpellier, CNRS, IMAG, Montpellier, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights 
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Didier, Gilles. Probabilities of tree topologies with temporal constraints and diversification shifts. Peer Community Journal, Volume 1 (2021), article  no. e65. doi : 10.24072/pcjournal.73. https://peercommunityjournal.org/articles/10.24072/pcjournal.73/

PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.evolbiol.100088

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

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