Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

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Serval ID
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Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
Journal
Systematic biology
Author(s)
Antonelli A., Hettling H., Condamine F.L., Vos K., Nilsson R.H., Sanderson M.J., Sauquet H., Scharn R., Silvestro D., Töpel M., Bacon C.D., Oxelman B., Vos R.A.
ISSN
1076-836X (Electronic)
ISSN-L
1063-5157
Publication state
Published
Issued date
01/03/2017
Peer-reviewed
Oui
Volume
66
Number
2
Pages
152-166
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
Rapidly growing biological data-including molecular sequences and fossils-hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a "Dated Tree of Life" where all node ages are directly comparable. [Bayesian phylogenetics; data mining; divide-and-conquer methods; GenBank; multilocus multispecies coalescent; next-generation sequencing; palms; primates; tree calibration.].

Keywords
Age Factors, Animal Migration, Animals, Arecaceae/classification, Bayes Theorem, Classification/methods, Fossils, Phylogeny, Primates/classification, Reproducibility of Results, Time
Pubmed
Web of science
Open Access
Yes
Create date
23/09/2016 18:30
Last modification date
20/08/2019 15:02
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