Data from: Evolutionary history of chimpanzees inferred from complete mitochondrial genomes

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) MYA for the four proposed
subspecies, with two major lineages. One of these lineages (tMRCA = 0.510
[0.387-0.650] MYA) contains P. t. verus (tMRCA = 0.155 [0.101-0.213] MYA)
and P. t. ellioti (formerly P. t. vellerosus; tMRCA = 0.157 [0.102-0.215]
MYA), both of which are monophyletic. The other major lineage contains P.
t. schweinfurthii (tMRCA = 0.111 [0.077-0.146] MYA), a monophyletic clade
nested within the P. t. troglodytes lineage (tMRCA = 0.380 [0.296-0.476]
¬MYA). 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 sub-sampled alignments.