title: Detailed phylogenetic analysis of primate T-lymphotropic virus type 1 (PTLV-1) sequences from orangutans (Pongo pygmaeus) reveals new insights into the evolutionary history of PTLV-1 in Asia.
abstract: While human T-lymphotropic virus type 1 (HTLV-1) originates from ancient cross-species transmission of simian T-lymphotropic virus type 1 (STLV-1) from infected nonhuman primates, much debate exists on whether the first HTLV-1 occurred in Africa, or in Asia during early human evolution and migration. This topic is complicated by a lack of representative Asian STLV-1 to infer PTLV-1 evolutionary histories. In this study we obtained new STLV-1 LTR and tax sequences from a wild-born Bornean orangutan (Pongo pygmaeus) and performed detailed phylogenetic analyses using both maximum likelihood and Bayesian inference of available Asian PTLV-1 and African STLV-1 sequences. Phylogenies, divergence dates and nucleotide substitution rates were co-inferred and compared using six different molecular clock calibrations in a Bayesian framework, including both archaeological and/or nucleotide substitution rate calibrations. We then combined our molecular results with paleobiogeographical and ecological data to infer the most likely evolutionary history of PTLV-1. Based on the preferred models our analyses robustly inferred an Asian source for PTLV-1 with cross-species transmission of STLV-1 likely from a macaque (Macaca sp.) to an orangutan about 37.9-48.9kya, and to humans between 20.3-25.5kya. An orangutan diversification of STLV-1 commenced approximately 6.4-7.3kya. Our analyses also inferred that HTLV-1 was first introduced into Australia ~3.1-3.7kya, corresponding to both genetic and archaeological changes occurring in Australia at that time. Finally, HTLV-1 appears in Melanesia at ~2.3-2.7kya corresponding to the migration of the Lapita peoples into the region. Our results also provide an important future reference for calibrating information essential for PTLV evolutionary timescale inference. Longer sequence data, or full genomes from a greater representation of Asian primates, including gibbons, leaf monkeys, and Sumatran orangutans are needed to fully elucidate these evolutionary dates and relationships using the model criteria suggested herein.
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: MJ
authors.lastname: Reid
authors.affiliation: Laboratory Branch, Division of HIV/AIDS Prevention, Center for Disease Control and Prevention, Atlanta, GA, USA 30329. 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; Department of Anthropology, University of Toronto, 19 Russell Street, Toronto, Ontario M5S 2S2, Canada. Electronic address: schillaci@utsc.utoronto.ca.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Schillaci
authors.affiliation: Institute of Evolutionary Biology, University of Edinburgh, Ashworth Laboratories, West Mains Road, Edinburgh EH9 3JT, United Kingdom. Electronic address: manonragonnet@gmail.com.
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, 745 Logan Avenue, Winnipeg, Manitoba, R3E 3L5, 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, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada. Electronic address: clowenbe@sfu.ca.
authors.forename: Carl A
authors.initials: CA
authors.lastname: Lowenberger
authors.affiliation: Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5A 1S6, Canada; Orangutan Foundation International, 824 S. Wellesley Ave., Los Angeles, CA 90049, USA. Electronic address: drbirute@gmail.com.
authors.forename: Birute Mary F
authors.initials: BM
authors.lastname: Galdikas
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, 745 Logan Avenue, Winnipeg, Manitoba, R3E 3L5, Canada. Electronic address: james.brooks@phac-aspc.gc.ca.
authors.forename: James I
authors.initials: JI
authors.lastname: Brooks
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D005075:Biological Evolution; D006800:Deltaretrovirus Infections / Q000453:epidemiology / Q000266:history / Q000635:transmission* / Q000821:virology; D016356:Gene Products, tax / Q000235:genetics; D049690:History, Ancient; D015368:Human T-lymphotropic virus 1 / Q000145:classification / Q000235:genetics*; D006801:Humans; D008251:Macaca / Q000821:virology; D059645:Mutation Rate; D010163:Paleontology; D010802:Phylogeny; D011148:Pongo pygmaeus / Q000821:virology; D030261:Primate T-lymphotropic virus 1 / Q000145:classification / Q000235:genetics*; D015303:Simian T-lymphotropic virus 1 / Q000145:classification / Q000235:genetics*; D020079:Terminal Repeat Sequences
chemical_list: D016356:Gene Products, tax
keywords: Australasia; Cross-species transmission; HTLV-1; Orangutans; PTLV-1; Paleovirology; Pongo; STLV-1