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Open Access Highly Accessed Research article

Estimating the phylogeny and divergence times of primates using a supermatrix approach

Helen J Chatterjee1*, Simon YW Ho23, Ian Barnes4 and Colin Groves5

Author Affiliations

1 Research Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK

2 Department of Zoology, University of Oxford, Oxford OX1 3PS, UK

3 Centre for Macroevolution and Macroecology, Research School of Biology, Australian National University, Canberra, ACT 0200, Australia

4 School of Biological Sciences, Royal Holloway University of London, Egham, Surrey, TW20 0EX, UK

5 School of Archaeology and Anthropology, Australian National University, Canberra, ACT 0200, Australia

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BMC Evolutionary Biology 2009, 9:259  doi:10.1186/1471-2148-9-259

Published: 27 October 2009



The primates are among the most broadly studied mammalian orders, with the published literature containing extensive analyses of their behavior, physiology, genetics and ecology. The importance of this group in medical and biological research is well appreciated, and explains the numerous molecular phylogenies that have been proposed for most primate families and genera. Composite estimates for the entire order have been infrequently attempted, with the last phylogenetic reconstruction spanning the full range of primate evolutionary relationships having been conducted over a decade ago.


To estimate the structure and tempo of primate evolutionary history, we employed Bayesian phylogenetic methods to analyze data supermatrices comprising 7 mitochondrial genes (6,138 nucleotides) from 219 species across 67 genera and 3 nuclear genes (2,157 nucleotides) from 26 genera. Many taxa were only partially represented, with an average of 3.95 and 5.43 mitochondrial genes per species and per genus, respectively, and 2.23 nuclear genes per genus. Our analyses of mitochondrial DNA place Tarsiiformes as the sister group of Strepsirrhini. Within Haplorrhini, we find support for the primary divergence of Pitheciidae in Platyrrhini, and our results suggest a sister grouping of African and non-African colobines within Colobinae and of Cercopithecini and Papionini within Cercopthecinae. Date estimates for nodes within each family and genus are presented, with estimates for key splits including: Strepsirrhini-Haplorrhini 64 million years ago (MYA), Lemuriformes-Lorisiformes 52 MYA, Platyrrhini-Catarrhini 43 MYA and Cercopithecoidea-Hominoidea 29 MYA.


We present an up-to-date, comprehensive estimate of the structure and tempo of primate evolutionary history. Although considerable gaps remain in our knowledge of the primate phylogeny, increased data sampling, particularly from nuclear loci, will be able to provide further resolution.