Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
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.].
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.|Gothenburg Botanical Garden, Carl Skottsbergs Gata 22A, SE-41319 Göteborg, Sweden.
Alexandre
A
Antonelli
Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands.
Hannes
H
Hettling
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.|CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugéne Bataillon, 34095 Montpellier, France.
Fabien L
FL
Condamine
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.
Karin
K
Vos
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.
R Henrik
RH
Nilsson
Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell, Tucson, AZ 85721, USA.
Michael J
MJ
Sanderson
Université Paris-Sud, Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, 91405 Orsay, France.
Hervé
H
Sauquet
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.
Ruud
R
Scharn
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.|Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland.
Daniele
D
Silvestro
Swedish Bioinformatics Infrastructure for Life Sciences, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.|Department of Marine Sciences, University of Gothenburg, Box 460, SE-405 30 Göteborg, Sweden.
Mats
M
Töpel
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.
Christine D
CD
Bacon
Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.
Bengt
B
Oxelman
Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands.
Rutger A
RA
Vos
D000367:Age Factors; D025041:Animal Migration; D000818:Animals; D028023:Arecaceae / Q000145:classification; D001499:Bayes Theorem; D002965:Classification / Q000379:methods*; D005580:Fossils; D010802:Phylogeny; D011323:Primates / Q000145:classification; D015203:Reproducibility of Results; D013995:Time