Contrasting demographic histories of the neighboring bonobo and chimpanzee
The Pleistocene epoch was a period of dramatic climate change that had profound impacts on the population sizes of many animal species. How these species were shaped by past events is often unclear, hindering our understanding of the population dynamics resulting in present day populations. We analyzed complete mitochondrial genomes representing all four recognized chimpanzee subspecies and the bonobo to infer the recent demographic history and used simulations to exclude a confounding effect of population structure. Our genus-wide Bayesian coalescent-based analysis revealed surprisingly dissimilar demographic histories of the chimpanzee subspecies and the bonobo, despite their overlapping habitat requirements. Whereas the central and eastern chimpanzee subspecies were inferred to have expanded tenfold between around 50,000 and 80,000 years ago and today, the population size of the neighboring bonobo remained constant. The changes in population size are likely linked to changes in habitat area due to climate oscillations during the late Pleistocene. Furthermore, the timing of population expansion for the rainforest-adapted chimpanzee is concurrent with the expansion of the savanna-adapted human, which could suggest a common response to changed climate conditions around 50,000–80,000 years ago.
KeywordsPan Mitochondrial genome Bayesian inference Demography MCMC
For generously providing samples, we thank Professor Dr. Werner Schempp (University of Freiburg), Ronald Bontrop (Biomedical Primate Research Centre), and Furuviksparken, Sweden. Thanks to Sandra Abel Nielsen for sharing her research protocol and to Amal Al Chaer and Tanja Normann Gade for their invaluable assistance. For financial support we thank 15. Juni Fund, Torben & Alice Frimodts Fund, H.R. & Grete S. Frederiksens Fund, the Danish Council for Independent Research | Natural Sciences, as well as the Industrial PhD program, Danish Agency for Science, Technology and Innovation.
- Becquet C, Patterson N, Stone AC, Przeworski M, Reich D (2007) Genetic structure of chimpanzee populations. PLoS Genet 3:617–626Google Scholar
- Chan Y, Anderson CNK, Hadly EA (2006) Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. PLoS Genet 2:451–460Google Scholar
- Clark PU, Dyke AS, Shakun JD, Carlson AE, Clark J, Wohlfarth B, Mitrovica JX, Hostetler SW, McCabe AM (2009) The Last Glacial Maximum. Science 325:710–714Google Scholar
- Heller R, Brüniche-Olsen A, Siegismund HR (2012) Cape Buffalo mitogenomics reveals a Holocene shift in the African human-megafauna dynamics. Mol Ecol 21:3947–3959Google Scholar
- Hill WCO (1969) The nomenclature, taxonomy and distribution of chimpanzees. In: Bourne GH (ed) The chimpanzee, vol 1. Karger, Basel, pp 22–49Google Scholar
- Kawamoto Y, Takemoto H, Higuchi S, Sakamaki T, Hart JA, Hart TB, Tokuyama N, Reinartz GE, Guislain P, Dupain J, Cobden AK, Mulavwa MN, Yangozene K, Darroze S, Devos C, Furuichi T (2013) Genetic structure of wild bonobo populations: diversity of mitochondrial DNA and geographical distribution. PLoS One 8:e59660PubMedCentralPubMedCrossRefGoogle Scholar
- Langergraber K, Prüfer K, Rowney C, Boesch C, Crockford C, Fawcett K, Inoue E, Inoue-Muruyama M, Mitani JC, Muller MN, Robbins MM, Schubert G, Stoinski TS, Viola B, Watts D, Wittig RM, Wrangham RW, Zuberbühler K, Pääbo S, Vigilant L (2012) Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution. PNAS 109:15716–15721PubMedCrossRefGoogle Scholar
- Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New YorkGoogle Scholar
- Scholz CA, Johnson TC, Cohen AS, King JW, Peck JA, Overpeck JT, Talbot MR, Brown ET, Kalindekafe L, Amoako PYO, Lyons RP, Shanahan TM, Castaneda IS, Heil CW, Forman SL, McHargue LR, Beuning KR, Gomez J, Pierson J (2007) East African megadroughts between 135 and 75 thousand years ago and bearing on early-modern human origins. Proc Natl Acad Sci USA 104:16416–16421PubMedCrossRefGoogle Scholar
- Suchard MA, Weiss RE, Sinsheimer JS (2001) Bayesian selection of continuous-time Markov chain evolutionary models. Mol Biol Evol 18:1001–1013Google Scholar
- Wegmann D, Leuenberger C, Excoffier L (2009) Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics 182:1207–1218Google Scholar