Document Detail


Dating primate divergences through an integrated analysis of palaeontological and molecular data.
MedLine Citation:
PMID:  21051775     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Estimation of divergence times is usually done using either the fossil record or sequence data from modern species. We provide an integrated analysis of palaeontological and molecular data to give estimates of primate divergence times that utilize both sources of information. The number of preserved primate species discovered in the fossil record, along with their geological age distribution, is combined with the number of extant primate species to provide initial estimates of the primate and anthropoid divergence times. This is done by using a stochastic forwards-modeling approach where speciation and fossil preservation and discovery are simulated forward in time. We use the posterior distribution from the fossil analysis as a prior distribution on node ages in a molecular analysis. Sequence data from two genomic regions (CFTR on human chromosome 7 and the CYP7A1 region on chromosome 8) from 15 primate species are used with the birth-death model implemented in mcmctree in PAML to infer the posterior distribution of the ages of 14 nodes in the primate tree. We find that these age estimates are older than previously reported dates for all but one of these nodes. To perform the inference, a new approximate Bayesian computation (ABC) algorithm is introduced, where the structure of the model can be exploited in an ABC-within-Gibbs algorithm to provide a more efficient analysis.
Authors:
Richard D Wilkinson; Michael E Steiper; Christophe Soligo; Robert D Martin; Ziheng Yang; Simon Tavaré
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2010-11-04
Journal Detail:
Title:  Systematic biology     Volume:  60     ISSN:  1076-836X     ISO Abbreviation:  Syst. Biol.     Publication Date:  2011 Jan 
Date Detail:
Created Date:  2010-12-07     Completed Date:  2011-02-17     Revised Date:  2013-07-03    
Medline Journal Info:
Nlm Unique ID:  9302532     Medline TA:  Syst Biol     Country:  England    
Other Details:
Languages:  eng     Pagination:  16-31     Citation Subset:  IM    
Affiliation:
School of Mathmatical Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK. r.d.wilkinson@nottingham.ac.uk
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MeSH Terms
Descriptor/Qualifier:
Animals
Bayes Theorem
Biological Evolution*
Evolution, Molecular
Fossils*
Humans
Markov Chains
Monte Carlo Method
Paleontology / methods
Phylogeny
Primates / classification*,  genetics*
Grant Support
ID/Acronym/Agency:
RR03037/RR/NCRR NIH HHS; //Biotechnology and Biological Sciences Research Council
Comments/Corrections

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