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

Artikel i vetenskaplig tidskrift
Författare 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
Publicerad i Systematic biology
Volym 66
Nummer/häfte 2
Sidor 152-166
ISSN 1076-836X
Publiceringsår 2017
Publicerad vid Institutionen för marina vetenskaper
Institutionen för biologi och miljövetenskap
Sidor 152-166
Språk en
Länkar dx.doi.org/10.1093/sysbio/syw066
www.ncbi.nlm.nih.gov/entrez/query.f...
Ämneskategorier Biologisk systematik, Evolutionsbiologi, Bioinformatik och systembiologi, Bioinformatik (beräkningsbiologi)

Sammanfattning

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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