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 |