(A) Probability of (in)congruence as a function of difference in speciation time τ. Consider the human–chimpanzee–gorilla triplet. With a speciation time difference of 2 million years (Myr), a generation time of 20 yr, and an effective human–chimpanzee population size of 50,000, we obtain an incongruence probability of 25%. Assuming a speciation time difference of 8 Myr for the human–chimpanzee–orangutan triplet, we obtain a congruence probability of 98.8%. Thus, the coalescent process predicts 1.2% lineage sorting between human, chimpanzee, and orangutan. (B) If the number of generations r between the speciation time of the three species and the speciation time of human and chimpanzee is small compared to the ancestral (effective) population size N of the human–chimpanzee common ancestor, then a gene from human and chimpanzee does not necessarily find common ancestry within the human–chimpanzee common ancestors. Here τ = t/(2Ng), where g is the generation time in years. (C) Average parameter estimates for the global analysis. (D) The mean time estimates for speciation for 21 autosomal chromosomes.
