Island Biogeography Reveals the Deep History of SIV

The ubiquity of simian immunodeficiencyvirus (SIV) in African nonhuman primatesand the discovery of ancient endogenous lentiviruses (1) suggest that SIV is very old. Con-versely, molecular clock methods calibrated by using modern sequences indicate a time scale of just centuries (2, 3).To resolve this conundrum, we sampled monkeys on Bioko Island, Equatorial Guinea, which was isolated from Africa as sea levels rose 10,000 to 12,000 years before the pres-ent (yr B.P.) (fig. S1) (4). Bushmeat specimens were screened by SIV serological tests and reverse transcription polymerase chain reaction (RT-PCR) and sequencing of conserved viral pol gene frag-ments [472 to 633 base pairs (bp)], followed by phylogenetic analyses. Of 79 individuals from six species, we de-tected 22 sequence-confirmed SIV positives in four species, with a prevalence of 22 to 33 % (table S1). Phylogenetic analyses (Fig. 1 and figs. S2 and S3) revealed previously uncharacterized species-specific SIV lineages in Cercopithecus erythrotis erythrotis (SIVreg-Bioko),Colobus satanas satanas (SIVblc-Bioko), andCercopithecus preussi insularis (SIVprg-Bioko). The fourth, the Bioko drill, Mandrillus leucophaeus poensis, is infected with SIVdrl-Bioko and has a mainland conspecific counterpart,Mandrillus leucophaeus leucophaeus, infectedwith SIVdrl (fig. S1). These viruses form a monophyletic group with SIVmnd-2 from the mandrill, the closest relative of the drill (Fig. 1). Each Bioko SIV lineage shares ancestry with a mainland virus found in a monkey of the same genus (Fig. 1). Barring the possibility that hu-mans introduced multiple species-specific SIV lineages to the wild monkey populations of Bioko, the mainland and island SIVdrl variants must have been evolving independently since Biokobecame isolated~10,000yrB.P., and perhaps longer given the high levels of genetic diversity seen within local SIV populations. We used the SIVdrl/SIVdrl-Bioko ancestor dated ~10,000 yr B.P. to calibrate our molecular clock phylogenetic analysis. From amino acid sequences, the mean estimate of the time of the most recent commo