Ancestral Population Sizes and Species Divergence Times in the Primate Lineage on the Basis of Intron and BAC End Sequences Yoko Satta, 1 Michael Hickerson, 1,2 Hidemi Watanabe, 3 Colm O’hUigin, 4 Jan Klein 5 1 Department of Biosystems Science, Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan 2 Department of Biology, Duke University, Durham, NC 90338, USA 3 Department of Bioinformatics and Genomics, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan 4 National Cancer Institute, National Institutes of Health, Bethesda, MD, USA 5 Abteilung Immungenetik, Max-Planck-Institut fuer Biologie, Corrensstrasse 42, D-72076, Tuebingen, Germany Received: 5 October 2003 / Accepted: 14 April 2004 [Reviewing Editor: Dr. Magnus Nordborg] Abstract. The effective sizes of ancestral popula- tions and species divergence times of six primate species (humans, chimpanzees, gorillas, orangutans, and representatives of Old World monkeys and New World monkeys) are estimated by applying the two- species maximum likelihood (ML) method to intron sequences of 20 different loci. Examination of rate heterogeneity of nucleotide substitutions and intra- genic recombination identifies five outrageous loci (ODC1, GHR, HBE, INS, and HBG). The estimated ancestral polymorphism ranges from 0.21 to 0.96% at major divergences in primate evolution. One excep- tionally low polymorphism occurs when African and Asian apes diverged. However, taking into consider- ation the possible short generation times in primate ancestors, it is concluded that the ancestral popula- tion size in the primate lineage was no smaller than that of extant humans. Furthermore, under the as- sumption of 6 million years (myr) divergence between humans and chimpanzees, the divergence time of humans from gorillas, orangutans, Old World mon- keys, and New World monkeys is estimated as 7.2, 18, 34, and 65 myr ago, respectively, which are gen- erally older than traditional estimates. Beside the in- tron sequences, three other data sets of orthologous sequences are used between the human and the chimpanzee comparison. The ML application to these data sets including 58,156 random BAC end sequences (BES) shows that the nucleotide substitu- tion rate is as low as 0.6–0.8 · 10 )9 per site per year and the extent of ancestral polymorphism is 0.33– 0.51%. With such a low substitution rate and short generation time, the relatively high extent of poly- morphism suggests a fairly large effective population size in the ancestral lineage common to humans and chimpanzees. Key words: Ancestral population size — Nucleo- tide substitution rate heterogeneity — Primate phy- logeny — Species divergence time Introduction Molecular genetic techniques, combined with rigor- ous statistical methods based on population genetic models that incorporate inherent stochasticity of nucleotide substitution processes or coalescence processes of genes in a population (Kingman 1982; Tajima 1983), allow us to answer questions regarding species divergence times and extents of ancestral polymorphism. Since orthologous genes from two species must have diverged before the divergence of the species, the divergence time of genes always ex- ceeds that of the species. Hence, if we use the gene divergence as a representative of the species diver- Correspondence to: Yoko Satta; email: satta@soken.ac.jp J Mol Evol (2004) 59:478–487 DOI: 10.1007/s00239-004-2639-2