title: Evolutionary Relationships among Extinct and Extant Sloths: The Evidence of Mitogenomes and Retroviruses.
abstract: Macroevolutionary trends exhibited by retroviruses are complex and not entirely understood. The sloth endogenized foamy-like retrovirus (SloEFV), which demonstrates incongruence in virus-host evolution among extant sloths (Order Folivora), has not been investigated heretofore in any extinct sloth lineages and its premodern history within folivorans is therefore unknown. Determining retroviral coevolutionary trends requires a robust phylogeny of the viral host, but the highly reduced modern sloth fauna (6 species in 2 genera) does not adequately represent what was once a highly diversified clade (∼100 genera) of placental mammals. At present, the amount of molecular data available for extinct sloth taxa is limited, and analytical results based on these data tend to conflict with phylogenetic inferences made on the basis of morphological studies. To augment the molecular data set, we applied hybridization capture and next-generation Illumina sequencing to two extinct and three extant sloth species to retrieve full mitochondrial genomes (mitogenomes) from the hosts and the polymerase gene of SloEFV. The results produced a fully resolved and well-supported phylogeny that supports dividing crown families into two major clades: 1) The three-toed sloth, Bradypus, and Nothrotheriidae and 2) Megalonychidae, including the two-toed sloth, Choloepus, and Mylodontidae. Our calibrated time tree indicates that the Miocene epoch (23.5 Ma), particularly its earlier part, was an important interval for folivoran diversification. Both extant and extinct sloths demonstrate multiple complex invasions of SloEFV into the ancestral sloth germline followed by subsequent introgressions across different sloth lineages. Thus, sloth mitogenome and SloEFV evolution occurred separately and in parallel among sloths.
authors.affiliation: Department of Paleobiology & Division of Mammals, National Museum of Natural History, Smithsonian Institution, Washington, DC Department of the Geophysical Sciences, University of Chicago.
authors.forename: Graham J
authors.initials: GJ
authors.lastname: Slater
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
authors.forename: Pin
authors.initials: P
authors.lastname: Cui
authors.affiliation: CCT-Mendoza, IANIGLA, Mendoza, Argentina.
authors.forename: Analía M
authors.initials: AM
authors.lastname: Forasiepi
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
authors.forename: Dorina
authors.initials: D
authors.lastname: Lenz
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany.
authors.forename: Kyriakos
authors.initials: K
authors.lastname: Tsangaras
authors.affiliation: Max Planck Institute for Ornithology, Seewiesen, Germany.
authors.forename: Bryson
authors.initials: B
authors.lastname: Voirin
authors.affiliation: Cibio/Inbio - Centro De Investigação Em Biodiversidade E Recursos Genéticos, Universidade Do Porto, Vairão, Portugal.
authors.forename: Nadia
authors.initials: N
authors.lastname: de Moraes-Barros
authors.affiliation: Department of Mammalogy and Division of Vertebrate Zoology, American Museum of Natural History, New York, NY macphee@amnh.org;greenwood@izw-berlin.de.
authors.forename: Ross D E
authors.initials: RD
authors.lastname: MacPhee
authors.affiliation: Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany macphee@amnh.org;greenwood@izw-berlin.de.
authors.forename: Alex D
authors.initials: AD
authors.lastname: Greenwood
mesh_terms: D000818:Animals; D019143:Evolution, Molecular; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D054884:Host-Pathogen Interactions / Q000235:genetics; D008322:Mammals / Q000235:genetics; D010802:Phylogeny; D012190:Retroviridae / Q000235:genetics*; D012896:Sloths / Q000235:genetics*
keywords: ancient DNA; foamy virus; hybridization capture; mitogenomes; retrovirus–host coevolution; sloth