Speciation and intrasubspecific variation of Bornean orangutans, Pongo pygmaeus pygmaeus

Mitochondrial DNA control region sequences of orangutans (Pongo pygmaeus) from six different populations on the island of Borneo were determined and analyzed for evidence of regional diversity and were compared separately with orangutans from the island of Sumatra. Within the Bornean population, four distinct subpopulations were identified. Furthermore, the results of this study revealed marked divergence, supportive evidence of speciation between Sumatran and Bornean orangutans. This study demonstrates that, as an entire population, Bornean orangutans have not experienced a serious genetic bottleneck, which has been suggested as the cause of low diversity in humans and east African chimpanzees. Based on these new data, it is estimated that Bornean and Sumatran orangutans diverged approximately 1.1 MYA and that the four distinct Bornean populations diverged 860,000 years ago. These findings have important implications for management, breeding, and reintroduction practices in orangutan conservation efforts

Analysis of two genomic variants of orang-utan hepadnavirus and their relationship to other primate hepatitis B-like viruses

We recently described orang-utan hepadnavirus (OuHV) (Warren et al., Journal of Virology, 73, 7860–7865, 1999). Phylogenetic analyses indicated that the various isolates of OuHV can be divided into two genomic variants. Two representatives from each genomic cluster were analysed both molecularly and phylogenetically. Their genome organization was highly similar to other hepadnaviruses of apes and humans. The complete genome sequences of the two OuHV types had an overall 5% sequence difference. Research on 25 seropositive Bornean orang-utans showed that, of the 19 animals infected with one variant, 12 originated from East Kalimantan. Phylogenetic analysis was performed using the full-length genomes of various primate hepadnaviruses. The tree topology revealed one cluster of Old World hepadnaviruses that is divided into two subclusters, one consisting of the ape viruses, and the other comprising the human genotypes A–E. These data suggest that the great apes and gibbons have been infected with a common ancestor hepadnavirus

Divergence of hepatitis B virus-like infections in orangutans

A high prevalence of hepatitis B virus (HBV) infection was suspected in 195 ex-captive orang-utans due to sera that cross-reacted with human HBV antigens. Initially, it was assumed that such viral infections were contracted from humans during captivity. However, two wild-caught orang-utans were identified which were HBV surface antigen-positive, indicating that HBV or related viruses may be naturally circulating in wild orang-utan populations. Sequence analyses of 7 isolates revealed that orang-utans were infected with hepadnaviruses, but that these were clearly divergent from the known 6 human HBV genotypes and other nonhuman primate hepadnaviruses reported. Phylogenetic analyses of the sequences encoding the pre-S and small S proteins indicated that the various isolates of the orang-utan hepadnavirus (OHV) could be divided in two types, OHV-1 and -2. Two representative isolates (OU-Somad and OU-Papa) from the types of OHV were analyzed both molecularly and phylogenetically. OHV-1 and OHV-2 were highly similar in their the genome organisation to other primate hepadnaviruses. The complete genome sequences of both OHV types had an overall 5% sequence. Using a PCR-RFLP assay on sera of twenty-five OHV-positive Bornean orang-utans we found 19 OHV-1-infected individuals, while the remaining were infected with OHV-2. Phylogenetic analysis was performed using the full-length genomes of various hepadnaviruses. The tree topology showed a bifurcation, with one branch to the ape viruses and the other to the human genotypes A to E. These data suggest an ancient transmission event with a common ancestor virus and subsequent coevolution of this virus in different orang-utan populations

Structural and evolutionary analysis of an orangutan foamy virus

The full-length proviral genome of a foamy virus infecting a Bornean orangutan was amplified, and its sequence was analyzed. Although the genome showed a clear resemblance to other published foamy virus genomes from apes and monkeys, phylogenetic analysis revealed that simian foamy virus SFVora was evolutionarily equidistant from foamy viruses from other hominoids and from those from Old World monkeys. This finding suggests an independent evolution within its host over a long period of time

Structural and Evolutionary Analysis of an Orangutan Foamy Virus

The full-length proviral genome of a foamy virus infecting a Bornean orangutan was amplified, and its sequence was analyzed. Although the genome showed a clear resemblance to other published foamy virus genomes from apes and monkeys, phylogenetic analysis revealed that simian foamy virus SFVora was evolutionarily equidistant from foamy viruses from other hominoids and from those from Old World monkeys. This finding suggests an independent evolution within its host over a long period of time

The Phylogeography of Orangutan Foamy Viruses Supports the Theory of Ancient Repopulation of Sumatra

Phylogenetic analysis of foamy virus sequences obtained from Bornean and Sumatran orangutans showed a distinct clustering pattern. One subcluster was represented by both Bornean and Sumatran orangutan simian foamy viruses (SFV). Combined analysis of host mitochondrial DNA and SFV phylogeny provided evidence for the hypothesis of the repopulation of Sumatra by orangutans from Borneo