Genetics of the Andean bear (Tremarctos ornatus; Ursidae, Carnivora) in Ecuador: when the Andean Cordilleras are not an Obstacle

References

• Akaike H. 1974. A new look at the statistical model identification. IEEE Trans Automat Contr. 19(6):716–723.
   Web of Science ®Google Scholar
• Allendorf FW, Luikart G. 2007. Conservation and the genetics of populations. Malden (MA): Blackwell.
   Google Scholar
• Ameghino F. 1889. Contribución al conocimiento de los mamíferos fósiles de la Republica Argentina. Actas de la Academia Nacional de Ciencias de Córdoba. 6:1–1027.
   Google Scholar
• Amos W, Sawcer SJ, Feakes RW, Rubinsztein DC. 1996. Microsatellite are subject to directional evolution. Nat Genet. 13(4):390–391.
   PubMed Web of Science ®Google Scholar
• Avise JC. 2000. Phylogeography: the history and formation of the species. Cambridge, Massachusetts: Harvard University Press.
   Google Scholar
• Avise JC, Arnold JR, Ball M, Bermingham E, Lamb T, Neigel JE, Reeb CA, Saunders NC. 1987. Intraspecific phylogeographic: the mitochondrial DNA bridge between population genetics and systematics. Annu Rev Ecol Syst. 18(1):489–522.
   Google Scholar
• Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 16(1):37–48.
   PubMed Web of Science ®Google Scholar
• Barton NH, Slatkin M. 1986. A quasi-equilibrium theory of thedistribution of rare alleles in a subdivided population. Heredity. 56(3):409–416.
   PubMedGoogle Scholar
• Beaumont LJ, Pitman A, Perkins S, Zimmermann NE, Yoccoz NG, Thuiller W. 2011. Impacts of climate change on the world’s most exceptional ecoregions. Proc Natl Acad Sci. 108(6):2306–2311.
   PubMed Web of Science ®Google Scholar
• Bebbington A, Humphreys D, Bury J, Lingan L, Muñoz JP, Scurrah M. 2008. Mining and social movements: struggles over livelihood and rural territorial development in the Andes. World Dev. 36(12):2888–2905.
   Web of Science ®Google Scholar
• Brouns G, De Wulf A, Constales D. 2003. Delaunay triangulation algorithms useful for multibeam echosounding. J Surv Eng. 129(2):79–84.
   Web of Science ®Google Scholar
• Cabrera A. 1957. Catálogo de los mamíferos de América del Sur 1 (Metatheria, Unguiculata, Carnivora). Peru: Imprenta y Casa Editorial Conil.
   Google Scholar
• Cueva DF, Gutierrez B, Bruque G, Molina S, Torres ML. 2018. Mitochondrial DNA reveals low genetic diversity in Ecuadorian Andean bears. Ursus. 29(1):43–51.
   Web of Science ®Google Scholar
• Culver M, Johnson WE, Pecon-Slattery J, O’Brien SJ. 2000. Genomic ancestry of the American puma (Puma concolor). J Hered. 91(3):186–197.
   PubMed Web of Science ®Google Scholar
• Cuvier F. 1825. Des Dents des mammifères considérées comme caracteres zoologiques. Monographie. París: Le Normant.
   Google Scholar
• Darriba D, Taboada GL, Doallo R, Posada D. 2012. jModelTest2: more models, new heuristics and parallel computing. Nat Methods. 9(8): 772–772.
   Google Scholar
• Del Moral JF, Bracho AE. 2009. Indicios indirectos de la presencia del oso andino (Tremarctos ornatus Cuvier, 1825) en el noroeste de Argentina. MACN. 11:69–76.
   Google Scholar
• Del Moral JF, Lameda FI. 2011. Registros de ocurrencia del oso andino (Tremarctos ornatus Cuvier, 1825) en sus límites de distribución nororiental y austral. MACN. 13:7–19.
   Google Scholar
• Dollfus O. 1999. Bases ecológicas y paleoambientales de América Latina. In: Murra JV, Rojas Rabiela T, editors. Historia general de América Latina. Las sociedades originarias. Vol. 1. Madrid (España): Editorial Trotta, Ediciones UNESCO; p. 29–40.
   Google Scholar
• Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Mol Ecol. 11(12):2571–2581.
   PubMed Web of Science ®Google Scholar
• Ellegren H, Primmer CR, Sheldon BC. 1995. Microsatellite evolution: directionality or bias? Nat Genet. 11(4):360–362.
   PubMed Web of Science ®Google Scholar
• Ellegren H, Moore S, Robinson N, Byrne K, Ward W, Sheldon BC. 1997. Microsatellite evolution- a reciprocal study of repeat lengths at homologous loci in cattle and sheep. Mol Biol Evol. 14(8):854–860.
   PubMed Web of Science ®Google Scholar
• Excoffier L, Lischer HE. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Res. 10(3):564–567.
   PubMed Web of Science ®Google Scholar
• Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Mol Mar Biol Biotechnol. 3(5):294–299.
   PubMedGoogle Scholar
• Fu YX. 1997. Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 147(2):915–925.
   PubMed Web of Science ®Google Scholar
• Fu YX, Li WH. 1993. Statistical tests of neutrality of mutations. Genetics. 133(3):693–709.
   PubMed Web of Science ®Google Scholar
• Galtier N, Enard D, Radondy Y, Bazin E, Belkhir K. 2005. Mutation hotspots in mammalian mitochondrial DNA. Genome Res. 16(2):215–222.
   PubMed Web of Science ®Google Scholar
• García-Rangel S. 2012. On Andean bear (Tremarctos ornatus) natural history and conservation. Mamm Rev. 42(2):85–119.
   Web of Science ®Google Scholar
• Gervais P. 1855. Tremarctos. Hist Nat Mamm. 2:20.
   Google Scholar
• Goldman D, Giri PR, O’Brien SJ. 1989. Molecular genetic distance estimates among the Ursidae as indicated by one- and two-dimensional protein electrophoresis. Evolution. 43(2):282–295.
   PubMed Web of Science ®Google Scholar
• Harpending H. 1994. Signature of ancient population growth in a low resolution mitochondrial DNA mismatch distribution. Hum Biol. 66:591–600.
   PubMed Web of Science ®Google Scholar
• Harpending HC, Sherry ST, Rogers AR, Stoneking M. 1993. Genetic structure of ancient human populations. Curr Antrophol. 34(4):483–496.
   Web of Science ®Google Scholar
• Hudson RR, Boos DD, Kaplan NL. 1992. A statistical test for detecting population subdivision. Mol Biol Evol. 9(1):138–151.
   PubMed Web of Science ®Google Scholar
• IPCC 2013. Summary for policymakers. Climate change 2013: the physical science basis. Contribution of Working Group I to the Fifth Assessment Report of the Intergovernmental Panel on Climate Change, Intergovernmental Panel on Climate Change. Cambridge University Press, New York.
   Google Scholar
• Kuhry P. 1988. Palaeobotanical-palaeoecological studies of tropical high Andean Peatbog sections (Cordillera Oriental, Colombia). Dissertationes Bot Band. 116:1–241.
   Google Scholar
• Kumar V, Lammers F, Bidon T, Pfenninger M, Kolter L, Nilsson MA, Janke A. 2017. The evolutionary history of bears is characterized by gene flow across species. Sci Rep. 7:46487.
   PubMed Web of Science ®Google Scholar
• Lanfear R, Calcott B, Ho SYW, Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol. 29(6):1695–1701.
   PubMed Web of Science ®Google Scholar
• Librado P, Rozas J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 25(11):1451–1452.
   PubMed Web of Science ®Google Scholar
• Lorenzen ED, Nogués-Bravo D, Orlando L, Weinstock J, Binladen J, Marske KA, Ugan A, Borregaard MK, Gilbert MTP, Nielsen R, et al. 2011. Species-specific responses of Late Quaternary megafauna to climate and humans. Nature. 479(7373):359–364.
   PubMed Web of Science ®Google Scholar
• Manel S, Schwartz ML, Luikart G, Taberlet P. 2003. Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol. 18(4):189–197.
   Web of Science ®Google Scholar
• Manni F, Guerard E, Heyer E. 2004. Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier’s algorithm. Hum Biol. 76(2):173–190.
   PubMed Web of Science ®Google Scholar
• Mantel NA. 1967. The detection of disease clustering and a generalized regression approach. Cancer Res. 27:209–220.
   PubMed Web of Science ®Google Scholar
• Miller MP. 2005. Alleles In Space: Computer software for the joint analysis of interindividual spatial and genetic information. J Hered. 96(6):722–724.
   PubMed Web of Science ®Google Scholar
• Mitchell KJ, Bray SC, Bover P, Soibelzon L, Schubert BW, Prevosti F, Prieto A, Martin F, Austin JJ, Cooper A. 2016. Ancient mitochondrial DNA reveals convergent evolution of giant short-faced bears (Tremarctinae) in North and South America. Biol Lett. 12(4):20160062.
   PubMed Web of Science ®Google Scholar
• Monmonier MS. 2010. Maximum-difference barriers: an alternative numerical regionalization method. Geogr Anal. 5(3):245–261.
   Google Scholar
• Moore W. 1995. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution. 49(4):718–726.
   PubMed Web of Science ®Google Scholar
• Morral N, Bertranpetit J, Estivill X, Nunes V, Casals T, Giménez J, Reis A, Varon-Mateeva R, Macek M, Kalaydjieva L, et al. 1994. The origin of the major cystic fibrosis mutation (delta F508) in European populations. Nat Genet. 7(2):169–175.
   PubMed Web of Science ®Google Scholar
• Nabholz B, Ellegren H, Wolf JB. 2013. High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes. Mol Biol Evol. 30(2):272–284.
   PubMed Web of Science ®Google Scholar
• Nash WG, O’Brien SJ. 1987. A comparative chromosome banding analysis of the Ursidae and their relationship to other Carnivores. Cytogenet Cell Genet. 45(3-4):206–212.
   PubMedGoogle Scholar
• O’Brien SJ, Knight K. 1987. The future of the Giand panda. Nature. 325(6107):758–759.
   Web of Science ®Google Scholar
• Orejuela J, Jorgenson J. 1999. Status and management of the Spectacled bear in Colombia. In: Servheen C, Herrero S, Peyton B, editors. Bears. Status survey and conservation action plan. Gland (Switzerland); Cambridge (UK): IUCN/SSC Bear and Polar Bear Specialist Groups; p. 168–179.
   Google Scholar
• Pennington RT, Dick CW. 2010. Diversification of the Amazonian flora and its relation to key geological and environmental events: a molecular perspective. In Hoorn C, Wesselingh F, editors. Amazonia, landscape and species evolution: a look into the past. Oxford (UK): Wiley-Blackwell; p. 373–385.
   Google Scholar
• Paetkau D, Strobeck C. 1994. Microsatellite analysis of genetic variation in black bear populations. Mol Ecol. 3(5):489–495.
   PubMed Web of Science ®Google Scholar
• Paetkau D, Calvert W, Stirling S, Strobeck C. 1995. Microsatellite analysis of population structure in Canadian polar bears. Mol Ecol. 4(3):347–354.
   PubMed Web of Science ®Google Scholar
• Paetkau D, Waits LP, Clarkson PL, Craighead L, Vyse E, Ward R, Strobeck C. 1998. Variation in genetic diversity across the range of North American brown bears. Conserv Biol. 12(2):418–429.
   Web of Science ®Google Scholar
• Peyton B. 1999. Spectacled bear conservation action plan. In: Servheen C, Herrero S, Peyton B, editors. Bears. Status survey and conservation action plan. Gland (Switzerland); Cambridge (UK): IUCN/SSC Bear and Polar Bear Specialist Groups; p. 157–164.
   Google Scholar
• Peyton B, Yerena E, Rúmiz DI. 1998. Status of wild Andean bears and policies for their management. Ursus. 10:87–100.
   Google Scholar
• Portillo-Quintero C, Larreal J, González I, Sánchez A, Valbuena C. 2012. Forest Cover and deforestation patterns in the northern Andes (Lake Maracaibo Basin): a synoptic assessment using MODIS and Landsat imagery. Appl Geogr. 35(1–2):152–163.
   Web of Science ®Google Scholar
• Posada D, Crandall KA. 2001. Intraspecific gene genealogies: trees grafting into networks. Trends Ecol Evol (Amst). 16(1):37–45.
   PubMed Web of Science ®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(5):793–808.
   PubMed Web of Science ®Google Scholar
• Ramos-Onsins SE, Rozas J. 2002. Statistical properties of new neutrality tests against population growth. Mol Biol Evol. 19(12):2092–2100.
   PubMed Web of Science ®Google Scholar
• Raymond M, Rousset F. 1995. An exact test for population differentiation. Evolution. 49(6):1280–1283.
   PubMed Web of Science ®Google Scholar
• Rodríguez ED, Cuesta F, Goldstein I, Bracho AE, Naranjo LG, Hernández OL. 2003. Ecoregional strategy for the conservation of the spectacled bear (Tremarctos ornatus) in the northern Andes. WWF Colombia, Fundación Wii, EcoCiencia, Wildlife Conservation Society, and Red Tremarctos.
   Google Scholar
• Rodriguez ED, Poveda FE, Rivera D. 1986. Distribución preliminar del oso andino (Tremarctos ornatus) en Colombia. MANABA. 2:1–16.
   Google Scholar
• Rogers AR, Fraley AE, Bamshad MJ, Watkins WS, Jorde LB. 1996. Mitochondrial mismatch analysis is insensitive to the mutational process. Mol Biol Evol. 13(7):895–902.
   PubMed Web of Science ®Google Scholar
• Rogers AR, Harpending HC. 1992. Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol. 9:552–569.
   PubMed Web of Science ®Google Scholar
• Rostworowski M. 1981. Recursos naturales renovables y pesca, siglos XVI y XVII. Colección Historia Andina 8. Lima (Peru): Instituto de Estudios Peruanos.
   Google Scholar
• Ruiz-García M. 2003. Molecular population genetic analysis of the spectacled bear (Tremarctos ornatus) in the northern Andean Area. Hereditas. 138:81–93.
   PubMed Web of Science ®Google Scholar
• Ruiz-García M. 2006. El oso andino, evolución y conservación: una sorprendente historia contenida en sus genes. In: Avances del Programa Nacional para la conservación en Colombia del oso andino (Tremarctos ornatus). Plan de acción 2002–2016. Dirección General de Ecosistemas. Bogotá (CO): Ministerio de Ambiente, Vivienda y desarrollo territorial; p. 19–27.
   Google Scholar
• 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.
   Google Scholar
• 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 JM, editors. Molecular population genetics, evolutionary biology and conservation of Neotropical carnivores. New York: Nova Science Publishers; p. 129–158.
   Google Scholar
• Ruiz-García M, Arias JY, Restrepo H, Cáceres-Martínez CH, Shostell JM. 2020b. The genetic structure of the Andean bear (Tremarctos ornatus; Ursidae, Carnivora) in Colombia by means of mitochondrial and microsatellite markers. J Mammal. (in press).
   Google Scholar
• 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. 98:135–158.
   Google Scholar
• 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(1):57–69.
   PubMed Web of Science ®Google Scholar
• Ruiz-García M, Arias Vásquez JY, Castellanos A, Költer L, Shostell JM. 2020a. Molecular evolution (mitochondrial and nuclear microsatellites markers). In: Ortega J, Maldonado JE, editors. The Andean bear (Tremarctos ornatus; Ursidae, Carnivora): how many ESUs are there? In conservation genomics of mammals. New York: Springer-Verlag; p. 165–194.
   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. Amer J Human Genet. 67:718–726.
   Google Scholar
• Sambrook J, Fritsch EF, Maniatis T. 1989. Molecular cloning: a laboratory manual. 2nd ed. New York: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Sánchez-Mercado A, Ferrer-Paris JR, Yerena E, García-Rangel S, Rodríguez-Clark KM. 2008. Factors affecting poaching risk to Vulnerable Andean bears Tremarctos ornatus in the Cordillera de Mérida, Venezuela: space, parks and people. ORX. 42(03):437–447.
   Google Scholar
• Schwarz GE. 1978. Estimating the dimension of a model. Ann Statist. 6(2):461–464.
   Web of Science ®Google Scholar
• Slatkin M. 1985. Rare alleles as indicators of gene flow. Evolution. 39(1):53–65.
   PubMed Web of Science ®Google Scholar
• Smouse PE, Long JC, Sokal RR. 1986. Multiple regression and correlation extension of the Mantel test of matrix corresponde. Syst Zool. 35(4):627–632.
   Google Scholar
• Sokal RR, Oden NL 1978. Spatial autocorrelation in biology. 2. Some biological implications and four applications of evolutionary and ecological interest. Biol J Linn Soc 10: 229–249.
   Google Scholar
• Soibelzon LH. 2004. Revisión sistemática de los Tremarctinae (Carnivora, Ursidae) fósiles de América del Sur. Revista Museo Argentino Ciencias Naturales. 6:107–133.
   Google Scholar
• Soibelzon LH, Prevosti F. 2013. Fossils of South American land carnivores (Carnivora, Mammalia). In: Ruiz-García M, Shostell JM, editors. Molecular population genetics, evolutionary biology and biological conservation of neotropical carnivores. New York: Nova Science Publisher; p. 509–530.
   Google Scholar
• Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22(21):1243–2688.
   Web of Science ®Google Scholar
• Stamatakis A, Hoover P, Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol. 57(5):758–771.
   PubMed Web of Science ®Google Scholar
• Stirling I. 1993. Bears: majestic creatures of the wild. Emmaus (PA): Rodale Press; p. 240.
   Google Scholar
• Tajima F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 123(3):585–595.
   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(12):2725–2729.
   PubMed Web of Science ®Google Scholar
• Tovar C, Arnillas CA, Cuesta F, Buytaert W. 2013. Diverging responses of tropical Andean Biomes under future climate conditions. PloS ONE. 8(5):e63634.
   PubMed Web of Science ®Google Scholar
• Van Der Hammen T. 1985. The Plio-Pleistocene climatic record of the Tropical Andes. J Geol Soc Lond. 142:561–580.
   Web of Science ®Google Scholar
• Viteri MP, Waits LP. 2009. Identifying polymorphic microsatellite loci for Andean bear research. Ursus. 20(2):102–108.
   Web of Science ®Google Scholar
• Waits LP, Sullivan J, O’Brien SJ, Ward RH. 1999. Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA. Mol Phylogenet Evol. 13(1):82–92.
   PubMed Web of Science ®Google Scholar
• Waits L, Taberlet P, Swenson JE, Sandegren F, Franzén R. 2000. Nuclear DNA microsatellite analysis of genetic diversity and gene flow in the Scandinavian brown bear (Ursus arctos). Mol Ecol. 9(4):421–431.
   PubMed Web of Science ®Google Scholar
• 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(4):506–513.
   PubMed Web of Science ®Google Scholar
• Watson DF. 1992. Contouring: a guide to the analysis and display of spatial data. New York: Pergamon Press.
   Google Scholar
• Weber JL, May PE. 1989. Abundant class of human DNA polymorphisms which can be typed using the polymerase chain reaction. Am J Hum Genet. 44(3):388–396.
   PubMed Web of Science ®Google Scholar
• Wijmstra TA, Van Der Hammen T. 1974. The last interglacial cycle: state of affairs of correlation between data obtained from the land and from the ocean. Geologie en Mijnbouw. 53:386–392.
   Google Scholar
• Wright S. 1943. Isolation by distance. Genetics. 28:114–138.
   PubMedGoogle Scholar
• Wright S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution. 19(3):395–420.
   Web of Science ®Google Scholar
• Yerena E. 1987. Distribución pasada y contemporánea de los úrsidos en América del Sur. Universidad Simón Bolívar, Departamento de Estudios Ambientales, Seminario EA-7154, Caracas, Venezuela, 32 pp.
   Google Scholar
• Yerena E. 1998. Protected areas for the Andean bear in South America. Ursus. 10:101–106.
   Google Scholar
• Yerena E, Monsalve Dam D, Torres D, Sánchez A, García-Rangel S, Bracho A, Martínez Z, Gómez I. 2007. Plan de Acción para la Conservación del Oso Andino (Tremarctos ornatus) en Venezuela (2006–2016). Fundación Andígena, FUDENA, Universidad Simón Bolívar, Mérida, Venezuela, Mérida, Venezuela.
   Google Scholar
• Yu L, Li QW, Ryder OA, Zhang YP. 2004. Phylogeny of the bears (Ursidae) based on nuclear and mitochondrial genes. Mol Phylogenet Evol. 32(2):480–494.
   PubMed Web of Science ®Google Scholar
• Zhang YP, Ryder OA. 1993. Mitochondrial DNA sequence evolution in the Arctoidea. Proc Natl Acad Sci USA. 90(20):9557–9561.
   PubMed Web of Science ®Google Scholar
• Zhang YP, Ryder OA. 1994. Phylogenetic relationships of bears (the Ursidae) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol. 3(4):351–359.
   PubMed Web of Science ®Google Scholar
• Zukowski B, Ormsby A. 2016. Andean bear livestock depredation and community perceptions in northern Ecuador. Hum Dimens Wildl. 21(2):111–126.
   Web of Science ®Google Scholar