Mitogenomics phylogenetic relationships of the current sloth’s genera and species (Bradypodidae and Megalonychidae)

References

• Adam PJ. 1999. Choloepus didactylus. Mammal sp. 621:1–8.
   Google Scholar
• Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automatic Control. 19:716–723.
   Web of Science ®Google Scholar
• Anderson RP, Handley CO. 2001. A new species of three-toed sloth (Mammalia: Xenarthra) from Panama, with a review of the genus Bradypus. Proc Biol Soc Wash. 114:1–33.
   Web of Science ®Google Scholar
• Anderson RP, Handley CO. 2002. Dwarfism in insular sloths: biogeography, selection, and evolutionary rate. Evolution. 56:1045–1058.
   PubMed Web of Science ®Google Scholar
• Arnason U, Adegoke JA, Bodin K, Born EW, Esa YB, Gullberg A, Nilsson M, Short RV, Xu X, Janke A. 2002. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc Natl Acad Sci USA. 99:8151–8156.
   PubMed Web of Science ®Google Scholar
• Arnason U, Gullberg A, Janke A. 2004. Mitogenomic analyses provide new insights into cetacean origin and evolution. Gene. 333:27–34.
   PubMed Web of Science ®Google Scholar
• Arnason U, Adegoke JA, Gullberg A, Harley EH, Janke A, Kullberg M. 2008. Mitogenomic relationships of placental mammals and molecular estimates of their divergences. Gene. 421:37–51.
   PubMed Web of Science ®Google Scholar
• Asher RJ, Lin KH, Kardjilov N, Hautier L. 2011. Variability and constraint in the mammalian vertebral column. J. Evol Biol. 24:1080–1090.
   PubMed Web of Science ®Google Scholar
• Auler AS, Smart PL. 2001. Late quaternary paleoclimate in semiarid northeastern Brazil from U-series dating of travertine and water-table speleothems. Quatern Res. 55:159–167.
   Google Scholar
• Bagley JC, Johnson JB. 2014. Phylogeography and biogeography of the Central American Neotropics: diversification between two continents and between two seas. Biol Rev. 89:767–790.
   PubMed Web of Science ®Google Scholar
• Bandelt H-J, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16:37–48.
   PubMed Web of Science ®Google Scholar
• Barreda V, Palazzesi L. 2007. Patagonian Vegetation Turnovers during the Paleogene-Early Neogene: Origin of Arid-Adapted Floras. Bot Rev. 73:31–50.
   Web of Science ®Google Scholar
• Barros MC, Sampaio I, Schneider H. 2003. Phylogenetic analysis of 16S mitochondrial DNA data in sloths and anteaters. Genet Mol Biol. 26:5–12.
   Web of Science ®Google Scholar
• Barros MC, Sampaio I, Schneider H. 2008. Novel 12S mtDNA findings in sloths (Pilosa, Folivora) and anteaters (Pilosa, Vermilingua) suggest a true case of long branch attraction. Genet Mol Biol. 31:793–799.
   Web of Science ®Google Scholar
• Bensasson D, Zhang D-X, Hartl DL, Hewitt GM. 2001. Mitochondrial pseudogenes: evolution's misplaced witnesses. Trends Ecol Evol (Amst.). 16:314–321.
   PubMed Web of Science ®Google Scholar
• Benton MJ, Donoghue PC. 2007. Paleontological evidence to date the tree of life. Mol Biol Evol. 24:26–53.
   PubMed Web of Science ®Google Scholar
• Billet G, Hautier L, de Muizon C, Valentin X. 2011. Oldest cingulate skulls provide congruence between morphological and molecular scenarios of armadillo evolution. Proc R Soc Lond B. 278:2791–2797.
   PubMed Web of Science ®Google Scholar
• Bloch JI, Woodruff ED, Wood AR, Rincon AF, et al. 2016. First North American fossil monkey and early Miocene tropical biotic interchange. Nature. 533:243–246.
   PubMed Web of Science ®Google Scholar
• Canto J, Salas-Gismondi R, Cozzuol M, Yáñez J. 2008. The aquatic sloth Thalassocnus (Mammalia, Xenarthra) from the late miocene of North-Central Chile: biogeographic and ecological implications. J Vert Paleontol. 28:918–922.
   Web of Science ®Google Scholar
• Carlini AA, Scillato-Yané GJ. 2004. The oldest Megalonychidae (Xenarthra: Tardigrada); phylogenetic relationships and an emended diagnosis of the family. Neu Jb Geol Paläont, Abh. 233:423–443.
   Web of Science ®Google Scholar
• Carroll RL. 1988. Vertebrate paleontology and evolution. New York: Freeman.
   Google Scholar
• Cartelle C. 1994. Tempo passado. Mamíferos do Pleistoceno em Minas Gerais. Belo Horizonte, MG, Brazil: Editora Palco. p. 131.
   Google Scholar
• Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol. 17:540–552.
   PubMed Web of Science ®Google Scholar
• Chiou KL, Pozzi L, Lynch Alfaro JW, Di Fiore A. 2011. Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences. Mol Phylogenet Evol. 59:736–745.
   PubMed Web of Science ®Google Scholar
• Coates AG, Collins LS, Aubry MP, Berggren WA. 2004. The geology of the Darien, Panama, and the late Miocene-Pliocene collision of the Panama arc with northwestern South America. Geo Soc Am Bull. 116:1327–1344.
   Web of Science ®Google Scholar
• Coates AG, Stallard RF. 2013. How old is the Isthmus of Panama? Bull Mar Sci. 89:801–813.
   Web of Science ®Google Scholar
• Condamine FL, Rolland J, Morlon H. 2013. Macroevolutionary perspectives to environmental change. Ecol Lett. 16:72–75.
   PubMed Web of Science ®Google Scholar
• Corin-Frederic J. 1969. Les formules gonosomiques dites aberrantes chez les mammiferes eutheriens. Chromosoma. 27:268–287.
   PubMedGoogle Scholar
• Cortés-Ortiz L, Berminham E, Rico C, Rodriguez-Luna E, Sampaio I, Ruíz-García M. 2003. Molecular systematics and biogeography of the Neotropical monkey genus Alouatta. Mol Phylogenet Evol. 26:64–81.
   PubMed Web of Science ®Google Scholar
• Cracraft J. 1983. Species concepts and speciation analysis. In: Johnston RJ, editor. Current ornithology. Vol I. New York: Plenum Press; p. 159–187.
   Google Scholar
• Cummings MP, Otto SP, Wakeley J. 1995. Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol. 12:814–822.
   PubMed Web of Science ®Google Scholar
• Delsuc F, Catzeflis FM, Stanhope MJ, Douzery EJP. 2001. The evolution of armadillos, anteaters and sloths depicted by nuclear and mitochondrial phylogenies: implications for the status of the enigmatic fossil Eurotamandua. Proc R Soc Lond BS. 268:1605–1615.
   PubMed Web of Science ®Google Scholar
• Delsuc F, Douzery EJP. (2008). Recent advances and future prospects in xenarthran molecular phylogenetics. In: Vizcaíno SF, Loughry WJ, editors. The Biology of the Xenarthra. Gainesville: University Press of Florida; p. 11–23.
   Google Scholar
• Delsuc F, Scally M, Madsen O, Stanhope MJ, De Jong WW, Catzeflis FM, Springer MS, Douzery EJP. 2002. Molecular phylogeny of living xenarthrans and the impact of character and taxon sampling on the placental tree rooting. Mol Biol Evol. 19:1656–1671.
   PubMed Web of Science ®Google Scholar
• Delsuc F, Superina M, Tilak MK, Douzery EJP, Hassanin A. 2012. Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos. Mol Phylogenet Evol. 62:673–680.
   PubMed Web of Science ®Google Scholar
• Delsuc F, Vizcaíno SF, Douzery EJP. 2004. Influence of tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans. BMC Evol Biol. 4:11.
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biol. 4:e88
   PubMed Web of Science ®Google Scholar
• Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. 29:1969–1973.
   PubMed Web of Science ®Google Scholar
• Engelmann GF. 1985. The phylogeny of the Xenarthra. In: Montgomery GG, editor. The evolution and ecology of Armadillos, Sloths and Vermilinguas. Washington and London: Smithsonian Institution Press; p. 51–64.
   Google Scholar
• Erixon P, Svennblad B, Britton T, Oxelman B. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst Biol. 52:665–673.
   PubMed Web of Science ®Google Scholar
• Ferreira LF, Araujo A, Confalonieri U, Chame M. 1989. Acanthocefalan [sic] eggs in animal coprolites from archaeological sites from Brazil. Mem Do Inst Oswaldo Cruz. 84:201–203.
   PubMed Web of Science ®Google Scholar
• Finstermeier K, Zinner D, Brameier M, Meyer M, Kreuz E, Hofreiter M, Roos C. 2013. A mitogenomic phylogeny of living primates. PLoS One. 8:e69504
   PubMed Web of Science ®Google Scholar
• Gardner AL. 2005. Order Pilosa. In: Wilson DE, Reeder, DM editors. Mammal species of the world: a taxonomic and geographic reference.. 3rd ed. Baltimore, Maryland: Johns Hopkins University Press; p. 100–103.
   Google Scholar
• Gardner AL. 2008. Magnorder Xenarthra. In: Gardner AL, editor. Mammals of South America: Volume 1 Marsupials, Xenarthrans, Shrews, and Bats. Chicago (IL): University of Chicago Press; p. 127–128.
   Google Scholar
• Gardner AL, Naples VL. 2007. Genus Tamandua Gray, 1825. In: Gardner AL, editor. Mammals of South America. Vol. 1. Marsupials, xenarthrans, shrews, and bats. Chicago, IL: University of Chicago Press; p. 173–177.
   Google Scholar
• Garzione CN, Hoke GD, Libarkin JC, Withers S, MacFadden B, Eiler J, Ghosh P, Mulch A. 2008. Rise of the Andes. Science 320:1304–1307.
   PubMed Web of Science ®Google Scholar
• Gaudin TJ. 1995. The ear region of edentates and the phylogeny of the Tardigrada (Mammalia, Xenarthra). J Vert Paleontol. 15:672–705.
   Web of Science ®Google Scholar
• Gaudin TJ. 2004. Phylogenetic relationships among sloths (Mammalia, Xenarthra, Tardigrada): the craniodental evidence. Zool J Linnean Soc. 140:255–305.
   Web of Science ®Google Scholar
• Gibb GC, Condamine FL, Kuch M, Enk J, Moraes-Barros N, Superina M, Poinar HN, Delsuc F. 2016. Shotgun mitogenomics provides a reference phylogenetic framework and timescale for living Xenarthrans. Mol Biol Evol. 33:621–642.
   Google Scholar
• Gissi C, Reyes A, Pesole G, Saccone C. 2000. Lineage-specific evolutionary rate in mammalian mtDNA. Mol Biol Evol. 17:1022–1031.
   PubMed Web of Science ®Google Scholar
• Greenwood AD, Castresana J, Feldmaier-Fuchs G, Pääbo S. 2001. A molecular phylogeny of two extinct sloths. Mol Phylogenet Evol. 18:94–103.
   PubMed Web of Science ®Google Scholar
• Haffer J. 1969. Speciation in Amazonian forest birds. Science. 165:131–137.
   PubMed Web of Science ®Google Scholar
• Haffer J. 1997. Alternative models of vertebrate speciation in Amazonia: an overview. Biodiversity and Evol. 6:451–476.
   Google Scholar
• Haffer J. 2008. Hypotheses to explain the origin of species in Amazonia. Braz J Biol. 68:917–947.
   PubMed Web of Science ®Google Scholar
• Haq BU, Hardenbol J, Vail PR. 1987. Chronology of fluctuating sea levels since the Triassic. Science. 235:1156–1167.
   PubMed Web of Science ®Google Scholar
• Hasegawa M, Kishino H, Yano T. 1985. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 22:160–174.
   PubMed Web of Science ®Google Scholar
• Hautier LG, Eastwood BB, Lane J. 2014. Patterns of morphological variation of extant sloth skulls and their implication for future conservation efforts. Anat Rec. 297:979–1008.
   Google Scholar
• Hautier L, Weisbecker V, Sanchez-Villagra MR, Goswami A, Asher RJ. 2010. Skeletal development in sloths and the evolution of mammalian vertebral patterning. Proc Natl Acad Sci USA.107:18903–18908.
   PubMed Web of Science ®Google Scholar
• Hayssen V. 2011. Tamandua tetradactyla (Pilosa: Myrmecophagidae). Mammal Sp. 43:64–74.
   Google Scholar
• Hillis D, Bull J. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst Biol. 42:182–192.
   Web of Science ®Google Scholar
• Hodgson JA, Sterner KN, Matthews LJ, Burrel AS, Rachana AJ, Raaum RL, Stewart CB, Disotell TR. 2009. Successive radiations, not stasis, in the South American primate fauna. Proc Natl Acad Sci USA. 106:5534–5539.
   PubMed Web of Science ®Google Scholar
• Hoorn C, Wesselingh FP, ter Steege H, Bermudez MA, Mora A, Sevink J, Sanmartín I, Sanchez-Meseguer A, Anderson CL, Figueiredo JP, et al. 2010. Amazonia through time: Andean uplift, climate change, landscape evolution, and biodiversity. Science. 330:927–931.
   PubMed Web of Science ®Google Scholar
• Höss M, Dilling A, Currant A, Pääbo S. 1996. Molecular phylogeny of the extinct ground sloth Mylodon darwinii. Proc Natl Acad Sci USA. 93:181–185.
   PubMed Web of Science ®Google Scholar
• Huelsenbeck JP, Rannala B. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst Biol. 53:904–913.
   PubMed Web of Science ®Google Scholar
• Inoue JG, Miya M, Lam K, Tay BH, Danks JA, Bell J, Walker TI, Venkatesh B. 2010. Evolutionary origin and phylogeny of the modern holocephalans (Chondrichthyes: Chimaeriformes): a mitogenomic perspective. Mol Biol Evol. 27:2576–2586.
   PubMed Web of Science ®Google Scholar
• Jorge W, Meritt DA, Benirschke K. 1978. Chromosome studies in Edentata. Cytobios. 18:157–172.
   PubMedGoogle Scholar
• Jorge W, Orsi-Souza A, Best R. 1985. The somatic chromosomes of Xenarthra. In: Montgomery GG, editor. The evolution and ecology of armadillos, sloths and vermilinguas. Washington and London: Smithsonian Institution Press; p. 121–129.
   Google Scholar
• Jorge W, Pereira HRJ. 2008. Chromosomal studies in the Xenarthra. In: Vizcaíno SF, Loughry WJ, editors. The Biology of the Xenarthra. Miami: University Press of Florida; p. 196–204.
   Google Scholar
• Katzourakis A, Gifford RJ, Tristem M, Gilbert TP, Pybus OG. 2009. Macroevolution of complex retroviruses. Science. 325:1512.
   PubMed Web of Science ®Google Scholar
• Kimura M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 16:111–120.
   PubMed Web of Science ®Google Scholar
• Kovacs A, Revay T, Tardy P, Mezosi L. 2001. 2n =  65 karyotype in a two-toed sloth (Choloepus didactylus, L.). Ann Genet. 44:43.
   Google Scholar
• Lara-Ruiz P, Chiarello A, Santos F. 2008. Extreme population divergence and conservation implications for the rare endangered Atlantic Forest sloth, Bradypus torquatus (Pilosa: Bradypodidae). Biol Cons. 141:1332–1342.
   Web of Science ®Google Scholar
• Ledru MP, Bertaux J, Sifeddine A, Suguio K. 1998. Absence of last glacial records in lowland tropical forests. Quatern Res. 49:233–237.
   Web of Science ®Google Scholar
• Lessa EP, Cook JA, Patton JL. 2003. Genetic footprints of demographic expansion in North America, but not Amazonia, during the Late Quaternary. Proc Natl Acad Sci. 100:10331–10334.
   PubMed Web of Science ®Google Scholar
• Lewis H. 1966. Speciation in flowering plants. Science. 152:167–172.
   PubMed Web of Science ®Google Scholar
• Long A, Martin PS. 1974. Death of American ground sloths. Science. 186:638–640.
   PubMed Web of Science ®Google Scholar
• Mackensen A, Ehrmann WU. 1992. Middle Eocene through early oligocene climate history and paleoceanography in the Southern Ocean: stable oxygen and carbon isotopes from ODP sites on Maud Rise and Kerguelen Plateau. Marine Geol. 108:1–27.
   Web of Science ®Google Scholar
• MacPhee RDE, Iturralde Vinent M. 1995. Origin of the greater Antillean land mammal fauna. 1, New tertiary fossils from Cuba and Puerto Rico. Amer Mus Novitates. 3141:1–31.
   Google Scholar
• MacPhee RD, Iturralde-Vinent MA, Gaffney ES. 2003. Domo de Zaza, an early Miocene vertebrate locality in South-Central Cuba, with notes on the tectonic evolution of Puerto Rico and the Mona passage. Amer Mus Novitates. 3394:1–42.
   Web of Science ®Google Scholar
• Marshall LG, Sempere T. 1993. Evolution of the Neotropical land mammal fauna in its geochronologic, stratigraphic and tectonic context. In: Goldblatt P, editor. Biological relationships between Africa and South America. New Heaven and London: Yale University Press; p. 329–392.
   Google Scholar
• Marshall LG, Webb SD, Sepkoski JJ, Raup DM. 1982. Mammalian evolution and the great American interchange. Science. 215:1351–1357.
   PubMed Web of Science ®Google Scholar
• Maslin A, Stepien C, Buchholtz E. 2007. Morphological and molecular analysis of vertebral variants in the two-toed sloths Choloepus hoffmanni and Choloepus didactylus. J Vert Paleontol. 27:113A.
   Web of Science ®Google Scholar
• Matsui A, Rakotondraparany F, Hasegawa M, Horai S. 2007. Determination of a complete lemur mitochondrial genome from feces. Mammal Study. 32:7–16.
   Google Scholar
• Mayr E. (1942). Systematics and the Origin of Species. NY: Columbia University Press. p. 1–334.
   Google Scholar
• McDonald HG, Rincón AD, Gaudin TJ. 2013. A new genus of megalonychid sloth (Mammalia, Xenarthra) from the Late Pleistocene (Lujanian) of Sierra de Perija, Zulia State, Venezuela. J Vert Paleontol. 33:1226–1238.
   Web of Science ®Google Scholar
• McDonald HG, Vizcaíno SF, Bargo MS. 2008. Skeletal anatomy and the fossil history of the Vermilingua. In: Vizcaíno SF, Loughry WJ, editors. The biology of the Xenarthra. Gainesville: University Press of Florida; p. 64–78.
   Google Scholar
• McKenna MC, Bell SK. 1997. Classification of mammals above the species level. New York: Columbia University Press.
   Google Scholar
• MacKenna MC, Wyss AR, Flynn JJ. 2006. Paleogene Pseudoglyptodont xenarthrans from Central Chile and Central Patagonia. Am Mus Novitates. 3536:1–18.
   Google Scholar
• Meireles CM, Czelusniak J, Schneider MP, Muniz JAPC, Brigido MC, Ferreira HS, Goodman M. 1999. Molecular phylogeny of Ateline new world monkeys (Platyrrhini, Atelinae) based on γ-globin gene sequences: evidence that Brachyteles is the sister group of Lagothrix. Mol Phyl Evol. 12:10–30.
   PubMed Web of Science ®Google Scholar
• Meritt M. 2008. Choloepus hoffmanni. In International Union for Conservation of Nature and Natural Resources 2009. International Union for Conservation of Nature and Natural Resources Red list of threatened species. Version 2009.1. www.iucnredlist.org/details/4778/0.
   Google Scholar
• Michaux JR, Chevret P, Filippucci MG, Macholan M. 2002. Phylogeny of the genus Apodemus with a special emphasis on the subgenus Sylvaemus using the nuclear IRBP gene and two mitochondrial markers: cytochrome b and 12S rRNA. Mol Phylogenet Evol. 23:123–136.
   PubMed Web of Science ®Google Scholar
• Miller MJ, et al. 2008. Out of Amazonia again and again: episodic crossing of the Andes promotes diversification in a lowland forest flycatcher. Proc R Soc Lond B Biol Sci. 275:1133–1142.
   PubMed Web of Science ®Google Scholar
• Miya M, Takeshima H, Endo H, Ishiguro NB, Inoue JG, Mukai T, Satoh TP, Yamaguchi M, Kawaguchi A, Mabuchi K, et al. 2003. Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences. Mol Phylogenet Evol. 26:121–138.
   PubMed Web of Science ®Google Scholar
• Moore W. 1995. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution. 49:718–726.
   PubMed Web of Science ®Google Scholar
• Moraes-Barros N, Arteaga MC. 2015. Genetic diversity in Xenarthra and its relevance to patterns of Neotropical biodiversity. J Mammal. 96:690–702.
   Web of Science ®Google Scholar
• Moraes-Barros N, Miyaki CY, Morgante JS. 2007. Identifying management units in non-endangered species: the example of the sloth Bradypus variegatus Schinz, 1825. Braz J Biol. 6:829–837.
   Google Scholar
• Moraes-Barros N, Silva JA, Morgante JS. 2011. Morphology, molecular phylogeny, and taxonomic inconsistencies in the study of Bradypus sloths (Pilosa: Bradypodidae). J Mammal. 92:86–100.
   Web of Science ®Google Scholar
• Morral N, Bertrantpetit J, Estivill X, et al. 1994. The origin of the major cystic fibrosis mutation (delta F508) in European populations. Nat Genet. 7:169–175.
   PubMed Web of Science ®Google Scholar
• Murphy WJ, Eizirik E, Johnson WJ, Zhang YP, Ryder OA, O’Brien SJ. 2001a. Molecular phylogenetics and the origins of placental mammals. Nature. 409:614–618.
   PubMed Web of Science ®Google Scholar
• Murphy WJ, Eizirik E, O’Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ, de Jong WW, et al. 2001b. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science. 294:2348–2351.
   PubMed Web of Science ®Google Scholar
• Nabholz B, Glemin S, Galtier N. 2008. Strong variations of mitochondrial mutation rate across mammals-the longevity hypothesis. Mol Biol Evol. 25:120–130.
   PubMed Web of Science ®Google Scholar
• Nabholz B, Glémin S, Galtier N. 2009. The erratic mitochondrial clock: variations of mutations rate, not population size, affect mtDNA diversity across birds and mammals. BMC Evol Biol. 9:54. doi:10.1186/1471-2148-9-54.
   PubMed Web of Science ®Google Scholar
• Noble DC, Mckee EH, Mégard F. 1979. Early Tertiary “Incaic” tectonism, uplift, and volcanic activity, Andes of central Perú. GSA Bull. 90:903–907.
   Web of Science ®Google Scholar
• Nyakatura JA. 2012. The convergent evolution of suspensory posture and locomotion in tree sloths. J Mammal Evol. 19:225–234.
   Web of Science ®Google Scholar
• Nylander JA. 2004. MrModeltest v2. Evolutionary Biology Center, Uppsala University.
   Google Scholar
• Nylander J, Wilgenbusch JC, Warren DL, Swofford DL. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics. 24:581–583.
   PubMed Web of Science ®Google Scholar
• Pascual R, Ortiz Jaureguizar E. 1990. Evolving climates and mammal faunas in Cenozoic South America. J Hum Evol. 19:23–60.
   Web of Science ®Google Scholar
• Patterson B, Pascual R. 1968. The fossil mammal fauna of South America. Q Rev Biol. 43:409–451.
   Web of Science ®Google Scholar
• Patterson B, Pascual R. 1972. The fossil mammal fauna of South-America. In: Keast A, Erk FC, Glass BP, editors. Evolution, mammals and southern continents. Albany: State University of New-York Press; p. 247–309.
   Google Scholar
• Paula-Couto C. 1979. Tratado de paleomastozoologia. Academia Brasileira de Ciencias: Rio de Janeiro; p. 590.
   Google Scholar
• Pereira SL, Baker AJ. 2006. A mitogenomic timescale for birds detects variable phylogenetic rates of molecular evolution and refutes the standard molecular clock. Mol Biol Evol. 23:1731–1740.
   PubMed Web of Science ®Google Scholar
• Perrier X, Jacquemoud-Collet JP. 2006. DARwin software http://darwin.cirad.fr/.
   Google Scholar
• Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol. 53:793–808.
   PubMed Web of Science ®Google Scholar
• Pozzi L, Hodgson JA, Burrell AS, Sterner KN, Raaum RL, Disotell TR. 2014. Primate phylogenetic relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogent Evol. 75:165–183.
   PubMed Web of Science ®Google Scholar
• Pujos F, De Iuliis G. 2007. Late Oligocene Megatherioidea fauna (Mammalia: Xenarthra) from Salla-Luribay (Bolivia): new data on basal sloth radiation and Cingulata-Tardigrada split. J Vert Paleontol. 27:132–144.
   Web of Science ®Google Scholar
• Pujos F, De Iullis G, Argot C, Werdelin L. 2007. A peculiar climbing Megalonychidae from the Pleistocene of Peru and its implication for sloth history. Zool J Linnean Soc. 149:179–235.
   Web of Science ®Google Scholar
• Raaum RL, Sterner KN, Noviello CM, Stewart CB, Disotell TR. 2005. Catarrhine primate divergence dates estimated from complete mitochondrial genomes: concordance with fossil and nuclear DNA evidence. J Hum Evol. 48:237–257.
   PubMed Web of Science ®Google Scholar
• Rambaut A. 2012. FigTree v1.4. [cited 2016 Jun 7]. Available from: http://tree.bio.ed.ac.uk/software/figtree/.
   Google Scholar
• Rambaut A, Drummond AJ. (2013a). LogCombiner v1.8.0. [cited 2016 Jun 7]. Available from: http://beast.bio.ed.ac.uk/.
   Google Scholar
• Rambaut A, Drummond AJ. (2013b). TreeAnnotator v1.8.0. [cited 2016 Jun 7]. Available from: http://beast.bio.ed.ac.uk/.
   Google Scholar
• Rambaut A, Suchard MA, Xie W, Drummond AJ. (2013). Tracer v1.6. [cited 2016 Jun 7]. Available from: http://tree.bio.ed.ac.uk/software/tracer/.
   Google Scholar
• Reig O. 1980. Modelos de especiación cromosómica en las casiraguas (Género Proechimys) de Venezuela. In: Reig O, editor. Ecología y Genética de la especiación animal. Caracas, Venezuela: Equinoccio, Editorial de la Universidad Simón Bolívar; p. 149–190.
   Google Scholar
• Rothlisberger F. 1987. 10,000 jahre gletschergeschichte der erde. Aarau, Switzerland: Verlag Sauerlander; p. 1–225.
   Google Scholar
• Ruiz-García M, Chacón D, Plese T, Shostell JM. 2016a. Molecular phylogenetics of Bradypus (three-toed sloth, Pilosa: Bradypodidae, Mammalia) and phylogeography of Bradypus variegatus (brown-throated three-toed sloth) by means of the mitochondrial control region sequences and mitogenomics. Mol Phylogenet Evol. (in press).
   Google Scholar
• Ruiz-García M, Castellanos A, Bernal LA, Pinedo-Castro M, Kaston F, Shostell JM. 2016b. Mitogenomics of the mountain tapir (Tapirus pinchaque, Tapiridae, Perissodactyla, Mammalia) in Colombia and Ecuador: phylogeography and insights into the origins and systematics of the South American tapirs. Mammal Biol. 81:163–175.
   Web of Science ®Google Scholar
• Ruiz-García M, Vallejo A, Camargo E, Alvarez D, Leguizamon N, Gálvez H. 2016c. Can mitochondrial DNA, nuclear microsatellite DNA and cranial morphometrics accurately discriminate different Aotus species (Cebidae)? Some insights on population genetics parameters and the phylogeny of the night monkeys. In: Ruiz-García M, Shostell JM, editors. Phylogeny, molecular population genetics, evolutionary biology and conservation of the Neotropical Primates. New York: Nova Science Publishers, Inc., Chapter 9.
   Google Scholar
• Rull V. 2011. Neotropical biodiversity: timing and potential drivers. Trends Ecol Evol (Amst.). 26:508–513.
   PubMed Web of Science ®Google Scholar
• Saillard J, Forster P, Lynnerup N, Bandelt H-J, Norby S. 2000. mtDNA variation among Greenland Eskimos: the edge of the Beringian expansion. Am J Hum Genet. 67:718–726.
   PubMed Web of Science ®Google Scholar
• Salazar- Bravo J, Dragoo JW, Tinnin DS, Yates TL. 2001. Phylogeny and evolution of the Neotropical rodent genus Calomys: inferences from mitochondrial DNA sequence data. Mol Phylogenet Evol. 20:173–184.
   PubMed Web of Science ®Google Scholar
• Santos TMS. 1977. Osteologia craniana de Bradypus Linnaeus, 1758 e reavaliacao do genero Scaeopus Peters, 1865 [Master Thesis]. Porto Alegre: Universidade Federal Do Rio Grande Do Sul. 178.
   Google Scholar
• Sarich VM. (1985). Xenarthran systematics: albumin immunological evidence. In: Montgomery G, editor. The evolution and ecology of Armadillos, Sloths and Vermilinguas. Washington DC: Smithsonian Institution Press; p. 77–81.
   Google Scholar
• Schwarz GE. 1978. Estimating the dimension of a model. Ann Stat. 6:461–464.
   Web of Science ®Google Scholar
• Sempere T, Marshall L, Rivano S, Godoy E. 1994. Late Oligocene-Early Miocene compressional tecto-sedimentary episode and associated land-mammal faunas in the Andes of central Chile and adjacent Argentina (32-37°S). Tecthonophysics. 229:251–264.
   Web of Science ®Google Scholar
• Silva SM, Moraes-Barros N, Ribas CC, Ferrand N, Morgante JS. 2012. Divide to conquer: a complex pattern of biodiversity depicted by vertebrate components in the Brazilian Atlantic Forest. Biol J Linnean Soc. 107:39–55.
   Web of Science ®Google Scholar
• Simon MF, Grether R, de Queiroz LP, Skema C, Pennington RT, Hughes CE. 2009. Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. Proc Natl Acad Sci USA. 108:20359–20364.
   Google Scholar
• Simpson GG. 1945. The principles of classification and a classification of mammals. Bull Am Mus Nat His. 85:1–350.
   Web of Science ®Google Scholar
• Slack KE, Delsuc F, McLenachan P, Arnason U, Penny D. 2007. Resolving the root of the avian mitogenomic tree by breaking up long branches. Mol Phylogenet Evol. 42:1–13.
   PubMed Web of Science ®Google Scholar
• Slater G, Cui P, Forasiepi AM, Lenz D, Tsangaras K, Voirin B, Moraes N, MacPhee RDE, Greenwood AD. 2016. Evolutionary relationships among extinct and extant sloths: the evidence of mitogenomes and retroviruses. Genome Biol Evol. 8:607–621.
   PubMed Web of Science ®Google Scholar
• Smith AB, Peterson KJ. 2002. Dating the time of origin of major clades: molecular clocks and the fossil record. Ann Rev Earth Planetary Sci. 30:65–88.
   Web of Science ®Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688–1243.
   PubMed Web of Science ®Google Scholar
• Steadman DW, Martin PS, MacPhee RDE, Jull AJT, McDonald HG, Woods CA, Iturralde-Vinent M, Hoodgins GWL. (2005). Asynchronous extinction of late Quaternary sloths on continents and islands. Proc Natl Acad Sci USA. 102:11763–11768.
   Google Scholar
• Steiner CC, Houck ML, Ryder OA. 2011. Species identification and chromosome variation of captive two-toed sloths. Zoo Biol. 29:1–13.
   Google Scholar
• Svartman M. 2012. Chromosome evolution in Xenarthra: new insights from an ancient group. Cytogenet. Genome Res.137:130–143.
   PubMed Web of Science ®Google Scholar
• Talavera G, Castresana J. 2007. Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol. 56:564–577.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 30:2725–2729.
   PubMed Web of Science ®Google Scholar
• Tchaicka L, Eizirik E, De Oliveira TG, Candido JF, Jr, Freitas TRO. 2007. Phylogeography and population history of the crab-eating fox (Cerdocyon thous). Mol Ecol. 16:819–838.
   PubMed Web of Science ®Google Scholar
• Thalmann O, Hebler J, Poinar HN, Paabo S, Vigilant L. 2004. Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes. Mol Ecol. 13:321–335.
   PubMed Web of Science ®Google Scholar
• Thorne JL, Kishino H, Painter IS. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol Biol Evol. 15:1647–1657.
   PubMed Web of Science ®Google Scholar
• Turcq B, Pressinotti MMN, Martin L. 1997. Paleohydrology and paleoclimate of the past 33,000 years at the Tamanduá River, central Brazil. Quatern Res. 47:284–294.
   Web of Science ®Google Scholar
• Vaidya G, Lohman DJ, Meier R. 2011. SequenceMatrix: concatenation software for the fast assembly of multi-gene datasets with character set and codon information. Cladistics. 27:171–180.
   PubMed Web of Science ®Google Scholar
• Vanzolini PE, Williams EE. 1970. South American anoles: Geographic differentiation and evolution of the Anolis chrysolepis species group (Sauria, Iguanidae). Arq Zoolog. 19:1–298.
   Google Scholar
• Vizcaíno SF, Scillato-Yané GJ. 1995. An Eocene Tardigrada (Mammalia, Xenarthra) from Seymour Island, Antarctica. Antarctic Sci. 7:407–408.
   Google Scholar
• Wayne RK, Geffen E, Girman D, Koepfli K, Lau L, Marshal C. 1997. Molecular systematics of the Canidae. Syst Biol. 46:622–653.
   PubMed Web of Science ®Google Scholar
• Webb SD. 1976. Mammalian faunal dynamics of the great American interchange. Paleobiology. 2:216–234.
   Google Scholar
• Webb SD. (1985). The interrelationships of tree sloths and ground sloths. In: Montgomery GG, editor. The evolution and ecology of Armadillos, Sloths and Vermilinguas. Washington: Smithsonian Institution; p. 105–112.
   Google Scholar
• Wetzel RM. (1982). Systematics, distribution, ecology, and conservation of South American edentates. In: Mares MA, Genoways HH, editors. Mammalian biology in South America. Pittsburgh, Pennsylvania: Pymantuning Laboratory of Ecology, University of Pittsburgh; p. 345–375.
   Google Scholar
• Wetzel RM. 1985. The identfication and distribution of recent Xenarthra (= Edentata). In: Montgomery GG, editor. The evolution and ecology of armadillos, sloths, and vermilinguas. Washington and London: Smithsonian Institution Press; p. 5–21.
   Google Scholar
• Wetzel RM, Avila-Pires FD. 1980. Identification and distribution of the recent sloths of Brazil (Edentata). Brazil J Biol. 40:831–836.
   Google Scholar
• White MJD. 1968. Models of speciation. New concepts suggest that the classical sympatric and allopatric models are not the only alternatives. Science. 159:1065–1070.
   PubMed Web of Science ®Google Scholar
• White MJD. 1978. Modes of speciation. San Francisco: W. H. Freeman.
   Google Scholar
• White JL, MacPhee RDE. 2001. The sloths of the West Indies: a systematic and phylogenetic review. In: Woods CA, Sergile FE, editors. Biogeography of the West Indies: Patterns and Perspective. Boca Raton LA: CRC Press; p. 201–236.
   Google Scholar
• Whithmore RT, Prance GT. 1987. Biogeography and quaternary history in tropical America. Oxford: Clarendon Press. (Monography on Biogeography, 3).
   Google Scholar
• Wilcox TP, Zwickl DJ, Heath TA, Hillis DM. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol Phylogenet Evol. 25:361–371.
   PubMed Web of Science ®Google Scholar
• Wilgenbusch JC, Warren DL, Swofford DL. 2004. AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. Available from: <http://ceb.csit.fsu.edu/awty>.
   Google Scholar
• Zachos J, Pagani M, Sloan L, Thomas E, Billups K. 2001. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science. 292:686–693.
   PubMed Web of Science ®Google Scholar
• Zhang P, Wake DB. 2009. Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes. Mol Phylogenet Evol. 53:492–508.
   PubMed Web of Science ®Google Scholar
• Zhang P, Zhou H, Liang D, Liu Y-F, Chen Y-Q, Qu L-H. 2005. The complete mitochondrial genome of a tree frog, Polypedates megacephalus (Amphibia: Anura: Rhacophoridae), and a novel gene organization in living amphibians. Gene. 346:133–143.
   PubMed Web of Science ®Google Scholar