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

Journal article
Authors Alexandre Antonelli
Hannes Hettling
Fabien L. Condamine
Karin Vos
R. Henrik Nilsson
Michael J Sanderson
Hervé Sauquet
Ruud Scharn
Daniele Silvestro
Mats H. Töpel
Christine D. Bacon
Bengt Oxelman
Rutger A Vos
Published in Systematic biology
Volume 66
Issue 2
Pages 152-166
ISSN 1076-836X
Publication year 2017
Published at Department of marine sciences
Department of Biological and Environmental Sciences
Pages 152-166
Language en
Links dx.doi.org/10.1093/sysbio/syw066
www.ncbi.nlm.nih.gov/entrez/query.f...
Subject categories Biological Systematics, Evolutionary Biology, Bioinformatics and Systems Biology, Bioinformatics (Computational Biology)

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.].

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