Publication Cover
Mitochondrial DNA Part A
DNA Mapping, Sequencing, and Analysis
Volume 27, 2016 - Issue 4
309
Views
8
CrossRef citations to date
0
Altmetric
Short Communication

Phylogeography and spatial structure of the lowland tapir (Tapirus terrestris, Perissodactyla: Tapiridae) in South America

, , , , &
Pages 2334-2342 | Received 27 Nov 2014, Accepted 21 Feb 2015, Published online: 22 May 2015

References

  • Ashley MV, Norman JE, Stross L. (1996). Phylogenetic analysis of the periossodactylan family Tapiridae using mitochondrial cytochrome c oxidase (COII) sequences. J Mammal Evol 3:315–26
  • Banguera-Hinestroza E, Cardenas H, Ruiz-García M, Marmontel M, Gaitán E, Vásquez R, García-Vallejo F. (2002). Molecular identification of evolutionarily units in the Amazon River dolphin, Inia sp (Cetacea: Iniidae). J Hered 93:312–22
  • Bertorelle G, Barbujani G. (1995). Analysis of DNA diversity by spatial autocorrelation. Genetics 140:811–19
  • Clapperton C. (1993). Quaternary geology and geomorphology of South America. Amsterdam, The Nederlands: Elsevier. p 1–489
  • Colbert M. (2005). The facial skeleton of the early Oligocene Colodon (Perissodactyla, Tapiroidea). Palaeontol Elect 8:1–27
  • Couzzol MA, Clozato CL, Holanda EC, Rodrigues FHG, Nienow S, Thoisy B, Redondo RAF, Santos FR. (2013). A new species of tapir from the Amazon. J Mammal 94:1331–45
  • Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. (2006). Relaxed phylogenetics and dating with confidence. PLoS Biol 4:e88
  • Drummond AJ, Rambaut A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214
  • Eizirik E, Kim JH, Menotti-Raymond M, Crawshaw P, O'Brien SJ, Johnson W. (2001). Phylogeography, population history and conservation genetics of jaguars (Panthera onca, Mammalia, Felidae). Mol Ecol 10:65–79
  • Felsenstein J. (1981). Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368–76
  • Gabriel KR, Sokal RR. (1969). A new statistical approach to geographic variation analysis. Syst Zool 18:259–78
  • Haffer J. (1969). Speciation in Amazonian forest birds. Science 165:131–7
  • Haffer J. (1997). Alternative models of vertebrate speciation in Amazonia: An overview. Biodivers Conserv 6:451–76
  • Haffer J. (2008). Hypotheses to explain the origin of species in Amazonia. Braz J Biol 68:917–47
  • Hall T. (2004). Bioedit sequence alignment editor. Version 7.0.0. Available at: http://www.genecodes.com/?referrer=20years&gclid=CP2uqo7mkcQCFfLm7AodNioAyQ
  • Hebert PDN, Ratnasingham S, de Waard JR. (2003). Barcoding animal life: Cytochrome c oxidase subunit 1 divergences among closely related species. Proc R Soc Lond B 270:S96–9
  • Hebert PDN, Stoeckle MY, Zemlak T, Francis CM. (2004). Identification of birds through DNA barcodes. PLoS Biol 2:1657–63
  • Hudson RR, Boss DD, Kaplan NL. (1992). A statistical test for detecting population subdivision. Mol Biol Evol 9:138–51
  • Hulbert RC, Wallace SC, Klippel WE, Parmalee PW. (2009). Cranial morphology and systematics of an extraordinary sample of the late Neogene Dwarf Tapir, Tapirus polkensis (Olsen). J Paleontol 83:238–62
  • Hulbert RC, Wallace SC. (2005). Phylogenetic analysis of late Cenozoic Tapirus (Mammalia, Perissodactyla). J Vert Paleontol 25:72A
  • Hulbert RC. (1995). The giant tapir, Tapirus haysii, from Leisey Shell Pit 1A and other Florida Irvingtonian localities. Bull Florida Mus Nat Hist Biol Sci 37:515–51
  • Hulbert RC. (2010). A new early Pleitocene tapir (Mammalia: Perissodactyla) from Florida, with a review of Blancan tapirs from the state. Bull Florida Mus Nat Hist Biol Sci 49:67–126
  • Librado P, Rozas J. (2009). DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–2
  • Martínez-Agüero M, Flores–Ramírez S, Ruiz–García M. (2006). First report for the Major Histocompatibility complex (MHC) Class II loci from the Amazon Pink river dolphin (genus Inia). Genet Mol Res 5:421–31
  • Martínez-Agüero M, Flores-Ramirez S, Ruiz-García M. (2010). Amazon river dolphin polymorphism and population differentiation of MHC class II peptides. In: Ruiz-García M, Shostell J, editors. Biology, evolution, and conservation of river Dolphins within South America and Asia. New York: Nova Science Publishers Inc. p 117–30
  • Matula DW, Sokal RR. (1980). Properties of Gabriel graphs relevant to geographic variation research and the clustering of points in the plane. Geogr Anal 12:205–22
  • Moran PAP. (1950). Notes on continuous stochastic phenomena. Biometrika 37:17–23
  • Nores M. (1999). An alternative hypothesis for the origin of Amazonian bird diversity. J Biogeogr 26:475–85
  • Nores M. (2004). The implications of Tertiary and Quaternary sea level rise events for avian distribution patterns in the lowlands of northern South America. Global Ecol Biogeogr 13:149–61
  • Norman J, Ashley M. (2000). Phylogenentics of peryssodactyla and tests of the molecular clock. J Mol Evol 50:11–21
  • Patton JL, da Silva MNF, Malcolm JR. (2000). Mammals of the Rio Jurua and the evolutionary and ecological diversification of Amazonia. Bull Am Mus Nat Hist 244:1–306
  • Ruiz-García M, Caballero S, Martínez-Aguero M, Shostell J. (2008). Molecular differentiation among Inia geoffrensis and Inia boliviensis (Iniidae, Cetacea) by means of nuclear intron sequences. In: Koven VP, editors. Population genetics research progress. New York: Nova Science Publisher, Inc. p 177–223
  • Ruiz-García M, Murillo A, Corrales C, Romero-Aleán N, Alvarez-Prada D. (2007). Genética de Poblaciones Amazónicas: La historia evolutiva del jaguar, ocelote, delfín rosado, mono lanudo y piurí reconstruida a partir de sus genes. Anim Biodivers Conserv 30:115–30
  • Ruiz-García M, Orozco-terWengel P, Castellanos A, Arias L. (2005). Microsatellite analysis of the spectacled bear (Tremarctos ornatus) across its range distribution. Genes Genet Syst 80:57–69
  • Ruiz-García M, Orozco-terWengel P, Payán E, Castellanos A. (2003). Genética de Poblaciones molecular aplicada al estudio de dos grandes carnívoros (Tremarctos ornatus–Oso andino, Panthera onca-jaguar): Lecciones de conservación. Bol Real Soc Esp Hist Nat 98:135–58
  • Ruiz-García M, Payán E, Murillo A, Alvarez D. (2006). DNA microsatellite characterization of the Jaguar (Panthera onca) in Colombia. Genes Genet Syst 81:115–27
  • Ruiz-García M, Vásquez C, Murillo A, Pinedo-Castro M, Alvarez D. (2013). Population genetics and phylogeography of the largest wild cat in the Americas: An analysis of the jaguar by means of microsatellites and mitochondrial gene sequences. In: Ruiz-García M, Shostell JM, editors. Molecular population genetics, evolutionary biology and biological conservation of neotropical carnivores. New York: Nova Science Publishers., Inc. p 413–64 (Chapter 11)
  • Ruiz-García M, Vásquez C, Pinedo-Castro M, Sandoval S, Kaston F, Thoisy B, Shostell JM. (2012). Phylogeography of the mountain tapir (Tapirus pinchaque) and the Central American tapir (Tapirus bairdii) and the molecular origins of the three South-American tapirs. In: Anamthawat-Jónsson K, editors. Current topics in phylogenetics and phylogeography of terrestrial and aquatic systems. Rijeka, Croatia: InTech. p 83–116
  • Ruiz-García M. (2001). Diversidad genética como herramienta de zonificación ambiental: Estudios moleculares (microsatélites) en el caso de Primates y Félidos neotropicales comportan una nueva perspectiva. In: Defler T, Palacios AP, editors. Zonificación ambiental para el ordenamiento territorial en la Amazonía Colombiana: Sinchi-Universidad Nacional de Colombia, Bogotá DC, Colombia. p. 85–108
  • Ruiz-García M. (2003). Molecular population genetic analysis of the spectacled bear (Tremarctos ornatus) in the Northern Andean Area. Hereditas 138:81–93
  • Ruiz-García M. (2007). Genética de Poblaciones: Teoría y aplicación a la conservación de mamíferos neotropicales (Oso andino y delfín rosado). Bol Real Soc Esp Hist Nat 102:99–126
  • Ruiz-García M. (2010a). Micro-geographical genetic structure of Inia geoffrensis in the Napo-Curaray River basin by means of Chesser’s models. In: Ruiz-García M, Shostell J, editors. Biology, evolution, and conservation of river Dolphins within South America and Asia. New York: Nova Science Publishers., Inc. p 131–60
  • Ruiz-García M. (2010b). Changes in the demographic trends of pink river dolphins (Inia) at the micro-geographical level in Peruvian and Bolivian rivers and within the Upper Amazon: Microsatellites and mtDNA analyses and insights into Inia's origin. In: Ruiz-García M, Shostell J, editors. Biology, evolution, and conservation of river Dolphins within South America and Asia. New York: Nova Science Publishers., Inc. p 161–92
  • Ruiz-García M. (2013). The genetic demography history and phylogeography of the Andean bear (Tremarctos ornatus) by means of microsatellites and mtDNA markers. In: Ruiz-García M, Shostell J, editors. Molecular population genetics, evolutionary biology and conservation of neotropical carnivores. New York: Nova Science Publishers. p 129–58
  • Sambrock J, Fritsch E, Maniatis T. (1989). Molecular cloning: A laboratory manual. 2nd ed. V1. New York: Cold Spring Harbor Laboratory Press
  • Sokal RR, Oden NL. (1978a). Spatial autocorrelation in biology. 1. Methodology. Biol J Linnean Soc 10:199–228
  • Sokal RR, Oden NL. (1978b). Spatial autocorrelation in biology. 2. Some biological implications and four applications of evolutionary and ecological interest. Biol J Linnean Soc 10:229–49
  • Sokal RR, Wartenberg DE. (1983). A test of spatial autocorrelation using and isolation by distance model. Genetics 105:219–37
  • Thoisy B, Goncalves da Silva A, Ruiz-García M, Tapia A, Ramirez O, Arana M, Quse V, et al. (2010). Population history, phylogeography, and conservation genetics of the last Neotropical mega-herbivore, the Lowland tapir (Tapirus terrestris). BMC Evol Biol 10:278–95
  • Thompson LG, Mosley E, Davies ME, Lin PN, Henderson KA, Coledal J, Bolzan JF, Liu KB. (1995). Huascarán, Perú. Science 269:46–50
  • Tougard C, Delefosse T, Hänni F, Montgelard C. (2001). Phylogenetics relationships of the five extant rhinoceros species (Rhinocerotidae, Perissodactyla) based on mitochondrial Cytochrome b and 12S rRNA genes. Mol Phylogenet Evol 19:34–44
  • Van der Hammen T, Cleff AM. (1992). Holocene changes of rainfall and river discharge in northern South America and the El Niño phenomenon. Erdkunde 46:252–6
  • Van der Hammen T. (1992). Historia, ecología y vegetación. Araracuara, Bogotá DC: Editorial Corporación Colombiana para la Amazonía. p 1–411
  • Van der Hammen T. (2001). Paleoecology of Amazonia. In: Guimaraes Vieira IC, Silva JMC, Oren DC, D'Incao MAD, editors. Diversidade biológica e cultural da Amazonia. Belem, Brazil: Museu Paraense Emilio Goeldi. p 19–44
  • Voss RS, Helgen KM, Jansa SA. (2014). Extraordinary claims require extraordinary evidence: A comment on Cozzuol et al. (2013). J Mammal 95:893–8
  • Walsh PS, Metzger DA, Higuchi R. (1991). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. BioTechniques 10:506–13
  • White MJD. (1968). Models of speciation. New concepts suggest that the classical sympatric and allopatric models are not the only alternatives. Science 159:1065–70
  • White MJD. (1978). Modes of speciation. San Francisco: W. H. Freeman
  • Whithmore RT, Prance GT. (1987). Biogeography and quaternary history in tropical America. Oxford: Clarendon Press. (Monograpy on Biogeography, 3)

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.