Inferring the mode of speciation from genomic data: a study of the great apes

Abstract

The strictly allopatric model of speciation makes definable predictions on the pattern of divergence, one of which is the uniformity in the divergence time across genomic regions. Using 345 coding and 143 intergenic sequences from the African great apes, we were able to reject the null hypothesis that the divergence time in the coding sequences (CDSs) and intergenic sequences (IGSs) is the same between human and chimpanzee. The conclusion is further supported by the analysis of whole-genome sequences between these species. The difference suggests a prolonged period of genetic exchange during the formation of these two species. Because the analysis should be generally applicable, collecting DNA sequence data from many genomic regions between closely related species should help to settle the debate over the prevalence of the allopatric mode of speciation.

Figure 1.—

(A) Allopatric speciation. In strict allopatry, there is no gene flow beyond the time of separation. All genes hence have diverged for a fixed time t and further coalesce with an average length of 2N_e generations. (B) Parapatric speciation. Under the parapatric model, there is a period of time when gene flow between nascent species is possible. The intensity of shade indicates the strength of the barrier to gene flow. For genomic regions (such as CDSs) associated with reproductive incompatibility, early cessation of gene flow is likely. For regions free of such association (including most IGSs), gene flow may continue until relatively late. (C) Segregation of polymorphisms (m for the ancestral and M for the derived variant) under the allopatric model. The two speciation events, denoted a and b, were separated by t′, during which time the effective population size is N_e^′.