Molecular Clocks: Determining the Age of the Human–Chimpanzee Divergence


The approximate clocklike nature of the accumulation of nucleotide substitutions (the ‘molecular clock’) allows for the estimation of the time of divergence between modern species, dependent on calibrating the clock with known divergence dates from the fossil record. The use of fossils to calibrate divergence dates must be done thoughtfully, with an understanding that in most cases fossils provide a constraint on the minimal age of, rather than a true estimate of, the species divergence. Although older studies relied on single loci, recent publications have used complete genome sequences to estimate divergence. Although still dependent on assumptions of the model used, most recent estimates using the molecular clock give dates of approximately 5–8 million years ago for the human–chimpanzee divergence, in general agreement with the palaeontological evidence.

Key Concepts:

  • The molecular clock hypothesis proposes that nucleotide changes occur at a regular rate during evolution.

  • Applying the molecular clock to sequence divergence among living species can provide an estimate of the time of the divergence of these species.

  • The conversion from sequence divergence to units of geologic time usually requires calibration from the fossil record, although fossil‐free estimates have also been used.

  • The first appearance in the fossil record of a given lineage provides a minimum age of divergence of taxa that created that lineage, not a point estimate of the divergence.

  • Confidence in the fossil calibration is dependent on the completeness of the fossil record.

  • Estimates of the human–chimpanzee divergence using the molecular clock have ranged from less than 3 million to nearly 12 million years ago (Ma).

  • Most reliable estimates of the human–chimpanzee divergence range from 5 to 8 Ma.

  • Considering the various sources of uncertainty associated with molecular dating, in general the dates are in agreement with palaeontological data.

Keywords: molecular clock; human evolution; hominin; hominid; divergence; chimpanzee

Figure 1.

Estimating the time of divergence between human and chimpanzee typically relies on a calibration based on a known divergence time – in this case either the hominine–pongine split or the hominoid–cercopithecoid split. Note the taxonomy used herein.

Figure 2.

Hypothetical species divergence leading to extant taxa (species 1–3), and fossils used to date the calibration node (A–E).

Figure 3.

The current state of knowledge regarding the early hominin fossil record (left) surrounding the human–chimpanzee divergence, compared with divergence dates from molecular data (right). Fossil species are taken from Wood and Lonergan , and references therein. Molecular dates are largely taken from Steiper and Young (, p. 390, Table 4), removing dates not based on DNA sequence data, and adding the dates from Hasegawa et al. , Patterson et al. and Wilkinson et al. . Small open circles represent divergence dates as estimated in the original publications (or means if ranges were given); closed circles are the same dates standardised by assuming a 30.5 Ma divergence between hominoids and cercopithecoids or an 18.3 Ma divergence between humans and orangutans (Steiper and Young, ). The large open circles represent two recent estimates from complete genome sequence data (Prüfer et al., ; Scally et al., ); large closed circles show dates derived from the same data, revised with new estimates of the mutation rate and hominid generation lengths (Langergraber et al., ).



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Further Reading

Bradley BJ (2008) Reconstructing phylogenies and phenotypes: a molecular view of human evolution. Journal of Anatomy 212: 337–353.

Burgess R and Yang Z (2008) Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Molecular Biology and Evolution 25: 1979–1994.

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Elango N, Thomas JW, NISC Comparative Sequencing Program and Yi SV (2006) Variable molecular clocks in hominoids. Proceedings of the National Academy of Sciences of the USA 103: 1370–1375.

Groves CP (2001) Primate Taxonomy. Washington: Smithsonian Institution Press.

Steiper ME and Seiffert ER (2012) Evidence for a convergent slowdown in primate molecular rates and its implications for the timing of primate evolution. Proceedings of the National Academy of Sciences of the USA 109: 6006–6011.

Steiper ME, Young NM and Sukarna TY (2004) Genomic data support the hominoids slowdown and an Early Oligocene estimate for the hominoid–cercopithecoid divergence. Proceedings of the National Academy of Sciences of the USA 101: 17021–17026.

Yamamichi M, Gojobori J and Innan H (2012) An autosomal analysis gives no genetic evidence for complex speciation of humans and chimpanzees. Molecular Biology and Evolution 29: 145–156.

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Jensen‐Seaman, Michael I, and Hooper‐Boyd, Kathryn A(May 2013) Molecular Clocks: Determining the Age of the Human–Chimpanzee Divergence. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020813.pub2]