speciation
Burgess R & Yang Z 2008 Estimation of hominoid ancestral population sizes under Bayesian coalescent models incorporating mutation rate variation and sequencing errors. Mol Biol Evol 25:1979-1994.
- we obtained robust and precise estimates for effective population sizes along the hominoid lineage extending back ~30 Myr to the cercopithecoid divergence
- ancestral populations were 5–10 times larger than modern humans along the entire hominoid lineage
- the unusually low X chromosome divergence between human and chimpanzee could not be explained by variation in the male mutation bias or by current models of hybridization and introgression
- instead, our parameter estimates were consistent with a simple instantaneous process for human–chimpanzee speciation but showed a major reduction in X chromosome effective population size peculiar to the human–chimpanzee common ancestor
- possibly due to selective sweeps on the X prior to separation of the 2 species
- at the major histocompatibility complex (MHC), balancing selection has extended the mean coalescence time for human DRB1 alleles to ~29 Myr
- the diversity and deep coalescence of MHC alleles imply N ≈ 100,000 over this longer timescale
- we calibrated to the human–chimpanzee divergence time (THC), with 2 values used: 4 and 6 Myr
- the generation time was assumed to be g ≈ 15 years
- modern humans have longer generation times, but ancestral species were probably physically smaller, perhaps similar to modern macaques, which have g ≈ 11 years
