Dating primate divergences through an integrated analysis of palaeontological and molecular data
Open accessAbstract
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.
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Statistical analyses of fossil stratigraphic data may yield more objective time priors and more informative calibrations.
“Otherwise, statistical analyses of fossil stratigraphic data may yield more objective time priors (e.g., [74, 75, 76]) and more informative calibrations.”
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Phylogenetic principal components analysis of relative brain size and the relative size of 20 brain structures/areas reveals that seven principal components explain up to 90.4 per cent of neural structure variation observed across 17 primate species (spanning more than 40 Myr of evolution).
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From Brain reorganization, not relative brain size, primarily characterizes anthropoid brain evolution (2013) · cites this paper as [26]
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- Authors
- Wilkinson, R. D., Steiper, M. E., Soligo, C., Martin, R. D., Yang, Z., & Tavaré, S.
- Affiliations
- University of Nottingham (GB)
- The Graduate Center, CUNY (US)
- University College London (GB)
- Field Museum of Natural History (US)
- University of Cambridge (GB)
- Corresponding author
- Wilkinson, Richard D.
- Venue
- Systematic Biology
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-11-04
- Volume
- 60
- Issue
- 1
- Pages
- 16-31
- ISSN
- 1063-5157 (ISSN-L)
- 1076-836X
- PMC
- PMC2997628
- OpenAlex
- W2167933455
- Cited by
- 218
- References
- 67
- Citations by year
- 2026: 5 · 2025: 5 · 2024: 6 · 2023: 4 · 2022: 7 · 2021: 5 · 2020: 9 · 2019: 13 · 2018: 8 · 2017: 8 · 2016: 23 · 2015: 21 · 2014: 44 · 2013: 26 · 2012: 20
- FWCI
- 13.48
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Systematic Biology (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Funders
- Cancer Research UK (19556)
- National Institutes of Health
- Directorate for Biological Sciences
- Biotechnology and Biological Sciences Research Council
- National Center for Research Resources (RR-03037)
- Topics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- divergence time estimation, fossil record, fossil preservation, CFTR, CYP7A1, birth-death model, approximate Bayesian computation, primate phylogeny, node age estimation
- MeSH terms
- Animals, Bayes Theorem, Biological Evolution, Fossils, Humans, Markov Chains, Monte Carlo Method, Paleontology, Phylogeny, Primates, Evolution, Molecular
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