title: Bayesian inference reveals ancient origin of simian foamy virus in orangutans.
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.
authors.affiliation: Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada. Electronic address: mj.reid@utoronto.ca.
authors.forename: Michael J C
authors.initials: MJC
authors.lastname: Reid
authors.affiliation: Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: bis3@cdc.gov.
authors.forename: William M
authors.initials: WM
authors.lastname: Switzer
authors.affiliation: Department of Anthropology, University of Toronto Scarborough, 1265 Military Trail, Scarborough, Ontario M1C 1A4, Canada. Electronic address: schillaci@utsc.utoronto.ca.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Schillaci
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Department of Anthropology, University of Washington, Seattle, WA 98105, USA. Electronic address: klegarth@uw.edu.
authors.forename: Amy R
authors.initials: AR
authors.lastname: Klegarth
authors.affiliation: Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA 30329, USA. Electronic address: ykk7@cdc.gov.
authors.forename: Ellsworth
authors.initials: E
authors.lastname: Campbell
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
authors.forename: Manon
authors.initials: M
authors.lastname: Ragonnet-Cronin
authors.affiliation: National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Joanisse
authors.affiliation: Centre for Biosecurity, Public Health Agency of Canada, 100 Colonnade Road, Ottawa, Ontario, Canada. Electronic address: kyna.caminiti@phac-aspc.gc.ca.
authors.forename: Kyna
authors.initials: K
authors.lastname: Caminiti
authors.affiliation: Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada. Electronic address: clowenbe@sfu.ca.
authors.forename: Carl A
authors.initials: CA
authors.lastname: Lowenberger
authors.affiliation: Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA.
authors.forename: Birute Mary F
authors.initials: BMF
authors.lastname: Galdikas
authors.affiliation: Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA. Electronic address: Hope.Hollocher.1@nd.edu.
authors.forename: Hope
authors.initials: H
authors.lastname: Hollocher
authors.affiliation: National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Ottawa, Ontario, Canada. Electronic address: paul_sandstrom@phac-aspc.gc.ca.
authors.forename: Paul A
authors.initials: PA
authors.lastname: Sandstrom
authors.affiliation: National HIV & Retrovirology Laboratories, JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada; The Ottawa Hospital, Division of Infectious Diseases, Department of Medicine, University of Ottawa, 1053 Carling Ave., Ottawa, ONK1Y 4E9, Canada.
authors.forename: James I
authors.initials: JI
authors.lastname: Brooks
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D000073930:Biological Coevolution; D001893:Borneo / Q000453:epidemiology; D004272:DNA, Mitochondrial / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D005580:Fossils; D015870:Gene Expression; D005814:Genes, Viral; D016679:Genome, Viral; D049690:History, Ancient; D054884:Host-Pathogen Interactions / Q000235:genetics*; D007214:Indonesia / Q000453:epidemiology; D057079:Pongo / Q000145:classification / Q000235:genetics / Q000821:virology*; D012192:Retroviridae Infections / Q000453:epidemiology / Q000266:history / Q000662:veterinary* / Q000821:virology; D053150:Simian foamy virus / Q000145:classification / Q000235:genetics*; D018707:Volcanic Eruptions / Q000266:history
chemical_list: D004272:DNA, Mitochondrial; D003576:Electron Transport Complex IV
keywords: Co-evolution; Mt. Toba; Orangutans; Paleobiogeography; Paleovirology; Pongo; SFV