RRC ID 54311
著者 Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA.
タイトル Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.
ジャーナル Syst Biol
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.].
巻・号 66(2)
ページ 152-166
公開日 2016-8-16
DOI 10.1093/sysbio/syw066
PII syw066
PMID 27616324
PMC PMC5410925
MeSH Age Factors Animal Migration Animals Arecaceae / classification Bayes Theorem Classification / methods* Fossils* Phylogeny* Primates / classification Reproducibility of Results Time
IF 8.523
引用数 23
リソース情報
GBIF Vascular Plant Specimen database of Kanagawa Prefectural Museum of Natural History Plant specimens in the Museum of Nature and Human Activities, Hyogo Prefecture, Japan Plant Specimens of Kurashiki Museum of Natural History Herbarium Specimens of Tokushima Prefectural Museum, Japan Vascular Plant Specimens of Kochi Prefectural Makino Botanical Garden Angiospermatatophytina Collection of Saitama Museum of Natural History Vascular plants collection of Hiratsuka City Museum Vascular Plant Collection of Natural History Museum and Institute, Chiba