Evolutionary history of chimpanzees inferred from complete mitochondrial genomes

Adam Bjork, Weimin Liu, Joel O. Wertheim, Beatrice H. Hahn, Michael Worobey

Research output: Contribution to journalArticle

36 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)615-623
Number of pages9
JournalMolecular Biology and Evolution
Volume28
Issue number1
DOIs
StatePublished - Jan 2011

Fingerprint

Mitochondrial Genome
Pan troglodytes
common ancestry
ancestry
genome
history
primate
Primates
subspecies
Troglodytes
bootstrapping
Fossils
Sequence Alignment
Africa South of the Sahara
sequence alignment
Sub-Saharan Africa
mitochondrial genome
Calibration
calibration
fossils

Keywords

  • chimpanzee
  • coalescent
  • evolution
  • phylogeny
  • relaxed molecular clock
  • Yule

ASJC Scopus subject areas

  • Genetics
  • Molecular Biology
  • Ecology, Evolution, Behavior and Systematics

Cite this

Evolutionary history of chimpanzees inferred from complete mitochondrial genomes. / Bjork, Adam; Liu, Weimin; Wertheim, Joel O.; Hahn, Beatrice H.; Worobey, Michael.

In: Molecular Biology and Evolution, Vol. 28, No. 1, 01.2011, p. 615-623.

Research output: Contribution to journalArticle

Bjork, Adam ; Liu, Weimin ; Wertheim, Joel O. ; Hahn, Beatrice H. ; Worobey, Michael. / Evolutionary history of chimpanzees inferred from complete mitochondrial genomes. In: Molecular Biology and Evolution. 2011 ; Vol. 28, No. 1. pp. 615-623.
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