TY - JOUR
T1 - Toward a self-updating platform for estimating rates of speciation and migration, ages, and relationships of Taxa
AU - Antonelli, Alexandre
AU - Hettling, Hannes
AU - Condamine, Fabien L.
AU - Vos, Karin
AU - Nilsson, R. Henrik
AU - Sanderson, Michael J.
AU - Sauquet, Hervé
AU - Scharn, Ruud
AU - Silvestro, Daniele
AU - Töpel, Mats
AU - Bacon, Christine D.
AU - Oxelman, Bengt
AU - Vos, Rutger A.
N1 - Publisher Copyright:
© The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.
PY - 2017/3/1
Y1 - 2017/3/1
N2 - 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.
AB - 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.
KW - Bayesian phylogenetics
KW - Data mining
KW - Divide-and-conquer methods
KW - GenBank
KW - Multilocus multispecies coalescent
KW - Next-generation sequencing
KW - Palms
KW - Primates
KW - Tree calibration
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U2 - 10.1093/sysbio/syw066
DO - 10.1093/sysbio/syw066
M3 - Article
C2 - 27616324
AN - SCOPUS:84992032330
SN - 1063-5157
VL - 66
SP - 153
EP - 166
JO - Systematic biology
JF - Systematic biology
IS - 2
ER -