Inferring the Process of Human–Chimpanzee Speciation


Although the fossil record around the times of the key speciation events that splits humans from orangutans, gorillas and chimpanzees is sparse, genetic comparisons of the extant apes enable us to analyse the process of speciation that lead to modern humans. Deoxyribonucleic acid (DNA) sequencing technology has improved greatly over the last decade and the complete genomes of all great apes have now been mapped. Analysis of this rich data has enabled the inference of key parameters of their speciation events. Though inference of the speciation events has so far focussed on simple models it is an active area of research to develop better models and understand the processes involved in the speciation and divergence of the great apes. Of the speciations along the human lineage, the split between ourselves and our closest living relatives, the chimpanzees and bonobos, naturally receives special attention.

Key Concepts:

  • Population genetics modelling of speciation events informs us of the timing and mode of ancient speciations from present day genomic data.

  • A strong source of information about speciation is found in the changing gene trees along a genomic alignment.

  • By studying great ape genomes we learn about the speciations along the human lineage, where the human–chimpanzee speciation is of special interest.

  • It is still an open question if this speciation was a clean (allopatric) split or if occurred in the presence of gene flow or was followed by admixture events.

  • If the speciation happened in the presence of gene flow it might have left signals of which genes first became incompatible and drove the speciation.

Keywords: coalescent; genome; hybridisation; speciation; speciation genes; gene trees and species trees; incomplete lineage sorting; ancient gene flow

Figure 1.

Illustrations of three speciation models: (a) instantaneous speciation model, which posits a sudden loss of gene flow at t=Ts; (b) prolonged gene flow model, which posits a gradual formation of isolating barriers to gene flow before t=Ts; and (c) hybridisation model, which involves a period of admixture following temporal isolation during TIe<t<TIs.

Figure 2.

The probability density distributions of TMRCA under the three speciation models. For each model, the distribution is derived by setting Ts=1. The thick line represents the distribution under the null model of instantaneous speciation. The dashed line is for the prolonged gene flow model, and the grey line is for the hybridisation model with TIs=3 and TIe=1.2. The three situations correspond to Figure a, b and c, respectively.

Figure 3.

Genealogical trees showing (HC)G and H(CG) relationships, presented by solid and grey lines, respectively. Only the mutations that occurred on the internal branch between the first coalescent event and the MRCA of the three species (represented by circles) are useful in resolving the trispecies relationship.



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Mailund, Thomas, Munch, Kasper, and Schierup, Mikkel Heide(May 2014) Inferring the Process of Human–Chimpanzee Speciation. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0020833.pub2]