title: Evolutionary history of chimpanzees inferred from complete mitochondrial genomes.
abstract: Investigations into the evolutionary history of the common chimpanzee, Pan troglodytes, have produced inconsistent results due to differences in the types of molecular data considered, the model assumptions employed, and the quantity and geographical range of samples used. We amplified and sequenced 24 complete P. troglodytes mitochondrial genomes from fecal samples collected at multiple study sites throughout sub-Saharan Africa. Using a "relaxed molecular clock," fossil calibrations, and 12 additional complete primate mitochondrial genomes, we analyzed the pattern and timing of primate diversification in a Bayesian framework. Our results support the recognition of four chimpanzee subspecies. Within P. troglodytes, we report a mean (95% highest posterior density [HPD]) time since most recent common ancestor (tMRCA) of 1.026 (0.811-1.263) Ma for the four proposed subspecies, with two major lineages. One of these lineages (tMRCA = 0.510 [0.387-0.650] Ma) contains P. t. verus (tMRCA = 0.155 [0.101-0.213] Ma) and P. t. ellioti (formerly P. t. vellerosus; tMRCA = 0.157 [0.102-0.215] Ma), both of which are monophyletic. The other major lineage contains P. t. schweinfurthii (tMRCA = 0.111 [0.077-0.146] Ma), a monophyletic clade nested within the P. t. troglodytes lineage (tMRCA = 0.380 [0.296-0.476] Ma). We utilized two analysis techniques that may be of widespread interest. First, we implemented a Yule speciation prior across the entire primate tree with separate coalescent priors on each of the chimpanzee subspecies. The validity of this approach was confirmed by estimates based on more traditional techniques. We also suggest that accurate tMRCA estimates from large computationally difficult sequence alignments may be obtained by implementing our novel method of bootstrapping smaller randomly subsampled alignments.
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Arizona, USA. acbjork@gmail.com
authors.forename: Adam
authors.initials: A
authors.lastname: Bjork
authors.forename: Weimin
authors.initials: W
authors.lastname: Liu
authors.forename: Joel O
authors.initials: JO
authors.lastname: Wertheim
authors.forename: Beatrice H
authors.initials: BH
authors.lastname: Hahn
authors.forename: Michael
authors.initials: M
authors.lastname: Worobey
mesh_terms: D017954:Africa South of the Sahara; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D005243:Feces / Q000737:chemistry; D054629:Genome, Mitochondrial; D006801:Humans; D008969:Molecular Sequence Data; D002679:Pan troglodytes / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: J Mol Evol. 2004 Oct;59(4):478-87
references.pmid: 15638459
references.citation: Mol Biol Evol. 2006 Jan;23(1):7-9
references.pmid: 16177232
references.citation: PLoS Genet. 2007 Apr 20;3(4):e66
references.pmid: 17447846
references.citation: PLoS Genet. 2007 Feb 23;3(2):e7
references.pmid: 17319744
references.citation: Syst Biol. 2010 Jan;59(1):1-8
references.pmid: 20525616
references.citation: Bioinformatics. 2001 Aug;17(8):754-5
references.pmid: 11524383
references.citation: Nature. 2006 Nov 9;444(7116):164
references.pmid: 17093443
references.citation: BMC Evol Biol. 2007 Nov 08;7:214
references.pmid: 17996036
references.citation: Science. 2006 Jul 28;313(5786):523-6
references.pmid: 16728595
references.citation: Primates. 2009 Jan;50(1):78-80
references.pmid: 19034382
references.citation: Mol Biol Evol. 2003 Mar;20(3):424-34
references.pmid: 12644563
references.citation: PLoS Pathog. 2008 Jul 04;4(7):e1000097
references.pmid: 18604273
references.citation: Genetics. 2003 Aug;164(4):1511-8
references.pmid: 12930756
references.citation: Nature. 1997 Jul 24;388(6640):337
references.pmid: 9237749
references.citation: J Mol Evol. 1992 Jul;35(1):32-43
references.pmid: 1518083
references.citation: J Virol. 2003 Jul;77(13):7545-62
references.pmid: 12805455
references.citation: PLoS Biol. 2006 May;4(5):e88
references.pmid: 16683862
references.citation: Mol Phylogenet Evol. 1992 Jun;1(2):97-135
references.pmid: 1342932
references.citation: Mol Biol Evol. 2010 Apr;27(4):921-33
references.pmid: 19955478
references.citation: J Hum Evol. 2006 Dec;51(6):646-62
references.pmid: 16965803
references.citation: J Hum Evol. 2005 Mar;48(3):237-57
references.pmid: 15737392
references.citation: Philos Trans R Soc Lond B Biol Sci. 2001 Jun 29;356(1410):889-97
references.pmid: 11405936
references.citation: Mol Phylogenet Evol. 2006 Nov;41(2):384-94
references.pmid: 16815047
references.citation: Biol Lett. 2008 Aug 23;4(4):370-4
references.pmid: 18426745
references.citation: Science. 1999 Nov 5;286(5442):1159-62
references.pmid: 10550054
references.citation: Proc Biol Sci. 1992 Sep 22;249(1326):293-7
references.pmid: 1359560
references.citation: Nature. 2004 Apr 22;428(6985):820
references.pmid: 15103367
references.citation: Mol Biol Evol. 2005 Feb;22(2):297-307
references.pmid: 15483319
references.citation: Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):43-8
references.pmid: 11756656