1. Bayesian inference reveals ancient origin of simian foamy virus in orangutans.
- Author
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Reid MJC, Switzer WM, Schillaci MA, Klegarth AR, Campbell E, Ragonnet-Cronin M, Joanisse I, Caminiti K, Lowenberger CA, Galdikas BMF, Hollocher H, Sandstrom PA, and Brooks JI
- Subjects
- Animals, Bayes Theorem, Biological Coevolution, Borneo epidemiology, DNA, Mitochondrial genetics, Electron Transport Complex IV genetics, Fossils, Gene Expression, History, Ancient, Indonesia epidemiology, Pongo classification, Pongo genetics, Retroviridae Infections epidemiology, Retroviridae Infections history, Retroviridae Infections virology, Simian foamy virus classification, Volcanic Eruptions history, Genes, Viral, Genome, Viral, Host-Pathogen Interactions genetics, Pongo virology, Retroviridae Infections veterinary, Simian foamy virus genetics
- Abstract
Simian foamy viruses (SFVs) infect most nonhuman primate species and appears to co-evolve with its hosts. This co-evolutionary signal is particularly strong among great apes, including orangutans (genus Pongo). Previous studies have identified three distinct orangutan SFV clades. The first of these three clades is composed of SFV from P. abelii from Sumatra, the second consists of SFV from P. pygmaeus from Borneo, while the third clade is mixed, comprising an SFV strain found in both species of orangutan. The existence of the mixed clade has been attributed to an expansion of P. pygmaeus into Sumatra following the Mount Toba super-volcanic eruption about 73,000years ago. Divergence dating, however, has yet to be performed to establish a temporal association with the Toba eruption. Here, we use a Bayesian framework and a relaxed molecular clock model with fossil calibrations to test the Toba hypothesis and to gain a more complete understanding of the evolutionary history of orangutan SFV. As with previous studies, our results show a similar three-clade orangutan SFV phylogeny, along with strong statistical support for SFV-host co-evolution in orangutans. Using Bayesian inference, we date the origin of orangutan SFV to >4.7 million years ago (mya), while the mixed species clade dates to approximately 1.7mya, >1.6 million years older than the Toba super-eruption. These results, combined with fossil and paleogeographic evidence, suggest that the origin of SFV in Sumatran and Bornean orangutans, including the mixed species clade, likely occurred on the mainland of Indo-China during the Late Pliocene and Calabrian stage of the Pleistocene, respectively., (Copyright © 2017 Elsevier B.V. All rights reserved.)
- Published
- 2017
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