183

Title

Probabilities of tree topologies with temporal constraints and diversification shiftsuse asterix (*) to get italics

Authors

Gilles DidierPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

Year

2019

Picture

Abstract

<p>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.</p>

Indicate the full web address (DOI or URL) giving public access to these data (if you have any problems with the deposit of your data, please contact contact@evolbiol.peercommunityin.org). In case all raw data are included in the preprint, indicate the DOI or URL of the preprint.

You should fill this box only if you chose 'All or part of the results presented in this preprint are based on data'. URL must start with http:// or https://

Indicate the full web address (DOI or URL) giving public access to these scripts (if you have any problems with the deposit of your scripts, please contact contact@evolbiol.peercommunityin.org). In case all raw scripts are included in the preprint, indicate the DOI or URL of the preprint.

You should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

Indicate the full web address (DOI, SWHID or URL) giving public access to these codes (if you have any problems with the deposit of your codes, please contact contact@evolbiol.peercommunityin.org). In case all raw codes are included in the preprint, indicate the DOI or URL of the preprint.

You should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Keywords

Phylogenetics, Datation, Shift Detection, Diversification, Birth-death process

Methods that require specific expertise (optional)

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Thematic fields

Bioinformatics & Computational Biology, Macroevolution

Suggested reviewers - Suggest up to 10 reviewers (provide names and Email addresses). (Optional)

No need for them to be recommenders of PCIEvolBiol. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

Opposed reviewers - Suggest up to 5 people not to invite as reviewers. (Optional)

e.g. John Doe [john@doe.com]

Submission date

2019-01-30 11:28:58

Recommender

Nicolas Lartillot

Reviewers

or Register
Submit a preprint

MANAGING BOARD

Guillaume Achaz
Juan Arroyo
Trine Bilde
Dustin Brisson
Marianne Elias
Inês Fragata
Matteo Fumagalli
Tatiana Giraud
Frédéric Guillaume
Ruth Hufbauer
Sara Magalhaes
Caroline Nieberding
Michael David Pirie
Tanja Pyhäjärvi

Fernando Racimo
Tanja Schwander
Alejandro Gonzalez Voyer

RECOMMENDERS

MANAGING BOARD

MEMBER OF

INDEXED BY