Biodiversity Literature Repository
Published August 26, 2015 | Version v1
Journal article Restricted

Exceptional maternal lineage diversity in brown bears (Ursus arctos) from Turkey

Creators

Description

Çilingir, F. Gözde, Pekşen, Çiğdem Akin, Ambarli, Hüseyin, Beerli, Peter, Bilgin, C. Can (2016): Exceptional maternal lineage diversity in brown bears (Ursus arctos) from Turkey. Zoological Journal of the Linnean Society 176 (2): 463-477, DOI: 10.1111/zoj.12322, URL: http://dx.doi.org/10.1111/zoj.12322

Files

Restricted

The record is publicly accessible, but files are restricted to users with access.

Linked records

Additional details

Identifiers

LSID
urn:lsid:plazi.org:pub:E7354C57E123BD1DFFB1FFE0FFA21302

Related works

Cites
Publication: 10.1515/mammalia-2014-0111 (DOI)
Has part
Figure: 10.5281/zenodo.5357918 (DOI)
Figure: 10.5281/zenodo.5357920 (DOI)
Figure: 10.5281/zenodo.5357922 (DOI)

References

  • Allen HD. 2009. Vegetation and ecosystem dynamics. In: Woodward J, ed. The physical geography of the Mediterranean. Oxford: Oxford University Press, 203-227.
  • Allen JRM, Brandt U, Brauer A, Hubberten HW, Huntley B, Kraml M, Mackensen A, Mingram J, Negendank JFW, Nowaczyk NR, Oberhansli H, Watts WA, Wulf S, Zolitschka B. 1999. Rapid environmental changes in southern Europe during the last glacial period. Nature 400: 740- 743.
  • Ambarli H. 2006. Analysis of human-bear conflict at Yusufeli, Artvin, Turkey. Unpublished MSc, Middle East Technical University.
  • Ambarli H. 2010. Marking behavior of brown bear (Ursus arctos) at power poles and trees in the Kackar Mountains range, Artvin, Turkey. International Bear News 19: 14-15.
  • Ambarli H. 2012. Spatio-temporal ecology, habitat use and population size of brown bears (Ursus arctos) in Yusufeli, Turkey. Unpublished PhD, Middle East Technical University.
  • Ambarli H. 2015. Litter size and basic diet of brown bears (Ursus arctos, Carnivora) in northeastern Turkey. Mammalia in press. DOI: 10.1515/mammalia-2014-0111
  • Ambarli H, Bilgin CC. 2008. Human-brown bear conflicts in Artvin, northeastern Turkey: encounters, damage, and attitudes. Ursus (International Association for Bear Research and Management) 19: 146-153.
  • Ambarli H, Kus¸dili Y, Bilgin CC. 2010. Bears are on the air in Artvin, Turkey. International Bear News 19: 12.
  • Bandelt HJ, Forster P, Rohl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution 16: 37-48.
  • Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A. 2002. Dynamics of pleistocene population extinctions in Beringian Brown bears. Science 295: 2267-2270.
  • Beja-Pereira A, Oliveira R, Alves PC, Schwartz MK, Luikart G. 2009. Advancing ecological understandings through technological transformations in noninvasive genetics. Molecular Ecology Resources 9: 1279-1301.
  • Bilgin CC. 2010. Country report on Turkey Large carnivores in the Caucasus, Tbilisi, Georgia.
  • Bojarska K, Selva N. 2012. Spatial patterns in brown bear Ursus arctos diet: the role of geographical and environmental factors. Mammal Review 42: 120-143.
  • Boom R, Sol CJ, Salimans MM, Jansen CL, Wertheimvan Dillen PM, van der Noordaa J. 1990. Rapid and simple method for purification of nucleic acids. Journal of Clinical Microbiology 28: 495-503.
  • Bray SCE, Austin JJ, Metcalf JL, Ostbye K, Ostbye E, Lauritzen S-E, Aaris-Sorensen K, Valdiosera C, Adler CJ, Cooper A. 2013. Ancient DNA identifies post-glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears. Diversity and Distributions 19: 245- 256.
  • Calvignac S, Hughes S, Hanni C. 2009. Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. Diversity and Distributions 15: 742-750.
  • Calvignac S, Hughes S, Tougard C, Michaux J, Thevenot M, Philippe M, Hamdine W, Hanni C. 2008. Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times. Molecular Ecology 17: 1962- 1970.
  • Can OE. 2001. The status of gray wolf (Canis lupus L. 1758), brown bear (Ursus arctos L. 1758), and Eurasian lynx (Lynx lynx L. 1758) in Turkey and recommendation for effective conservation programs. Unpublished MSc., Middle East Technical University.
  • Chestin IE, Mikeshina NG. 1998. Variation in skull morphology of brown bears (Ursus arctos) from Caucasus. Journal of Mammology 79: 118-130.
  • Clark JD, Huber D, Servheen C. 2002. Bear reintroductions: lessons and challenges. Ursus (International Association for Bear Research and Management) 13: 335-345.
  • Cowan IM. 1972. The status and conservation of bears (Ursidae) of the world The Second International Conference on Bear Research and Management. Calgary, AB: IUCN Publications New Series. 343-367.
  • Davison J, Ho SYW, Bray SC, Korsten M, Tammeleht E, Hindrikson M, Ostbye K, Ostbye E, Lauritzen S-E, Austin J. 2011. Late-Quaternary biogeographic scenarios for the brown bear (Ursus arctos), a wild mammal model species. Quaternary Science Reviews 30: 418-430.
  • Deecke VB. 2012. Tool-use in the brown bear (Ursus arctos). Animal Cognition 15: 725-730.
  • Drummond AJ, Ho SYW, Phillips MJ, Rambaut A. 2006. Relaxed phylogenetics and dating with confidence. PLoS Biology 4: e88.
  • Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian Phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969-1973.
  • Excoffier L, Lischer HEL. 2010. Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564-567.
  • Gagneux P, Boesch C, Woodruff DS. 1997. Microsatellite scoring errors associated with noninvasive genotyping based on nuclear DNA amplified from shed hair. Molecular Ecology 6: 861-868.
  • Garshelis D, McLellan B. 2011. What's so special about the Syrian bear? International Bear News 20: 5-7.
  • Haig SM, Beever EA, Chambers SM, Draheim HM, Dugger BD, Dunham S, Elliott-Smith E, Fontaine JB, Kesler DC, Knaus BJ, Lopes IE, Loschl P, Mullins T, Sheffield LM. 2006. Taxonomic considerations in listing subspecies under the U.S. Endangered Species Act. Conservation Biology 20: 1584-1594.
  • Hajjar I. 2011. The Syrian bear still lives in Syria. International Bear News 20: 7-11.
  • Hasegawa M, Kishino H, Yano T. 1985. Dating of humanape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution 22: 160-174.
  • Herrero S. 1999. Introduction. In: Servheen C, Herrero S, Peyton B, eds. Status survey and slobal conservation action plan: bears. Gland: IUCN Publications, 1-7.
  • Hewitt G. 2000. The genetic legacy of the Quaternary ice ages. Nature 405: 907-913.
  • Ho SY, Saarma U, Barnett R, Haile J, Shapiro B. 2008. The effect of inappropriate calibration: three case studies in molecular ecology. PLoS ONE 3: e1615.
  • Hofreiter M, Capelli C, Krings M, Waits L, Conard N, Munzel S, Rabeder G, Nagel D, Paunovic M, Jambresic G, Meyer S, Weiss G, Paabo S. 2002. Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of Late Pleistocene cave bears. Molecular Biology and Evolution 19: 1244-1250.
  • Hofreiter M, Serre D, Rohland N, Rabeder G, Nagel D, Conard N, Munzel S, Paabo S. 2004. Lack of phylogeography in European mammals before the last glaciation. Proceedings of the National Academy of Sciences of the United States of America 101: 12963-12968.
  • Jasmine VW, Nelson OL, Robbins CT, Jansen HT. 2012. Temporal organization of activity in the brown bear (Ursus arctos): roles of circadian rhythms, light and food entrainment. American Journal of Physiology - Regulatory Integrative and Comparative Physiology 303: R890- R902.
  • Kitchener AC. 2010. Taxonomic issues in bears: impacts on conservation in zoos and the wild, and gaps in current knowledge. International Zoo Yearbook 44: 33-46.
  • Kocher TD, Thomas WK, Meyer A, Edwards SV, Paabo S, Villablanca FX, Wilson AC. 1989. Dynamics of mitochondrial DNA evolution in animals: amplification and sequencing with conserved primers. Proceedings of the National Academy of Sciences 86: 6196-6200.
  • Kocijan I, Galov A, Cetkovic´ H, Kusak J, Gomercic T, Huber D. 2011. Genetic diversity of Dinaric brown bears (Ursus arctos) in Croatia with implications for bear conservation in Europe. Mammalian Biology 76: 615-621.
  • Kohn M, Knauer F, Stoffella A, Schroder W, Paabo S. 1995. Conservation genetics of the European brown bear - a study using excremental PCR of nuclear and mitochondrial sequences. Molecular Ecology 4: 95-104.
  • Korsten M, Ho SYW, Davison J, Pahn B, Vulla E, Roht M, Tumanov IL, Kojola I, Andersone-Lilley Z, Ozolins J, Pilot M, Mertzanis Y, Giannakopoulos A, Vorobiev AA, Markov NI, Saveljev AP, Lyapunova EA, Abramov AV, Mannil P, Valdmann H, Pazetnov SV, Pazetnov VS, Rokov AM, Saarma U. 2009. Sudden expansion of a single brown bear maternal lineage across northern continental Eurasia after the last ice age: a general demographic model for mammals? Molecular Ecology 18: 1963-1979.
  • Kurten B. 1968. Pleistocene mammals of Europe. Chicago, IL: Aldine Publishing Company.
  • Leonard JA, Wayne RK, Cooper A. 2000. Population genetics of ice age brown bears. Proceedings of the National Academy of Sciences of the United States of America 97: 1651- 1654.
  • Lorenzini R, Posillico M, Lovari S, Petrella A. 2004. Noninvasive genotyping of the endangered Apennine brown bear: a case study not to let one's hair down. Animal Conservation 7: 199-209.
  • Martin J, Basille M, Van Moorter B, Kindberg J, Allaine D, Swenson JE. 2010. Coping with human disturbance: spatial and temporal tactics of the brown bear (Ursus arctos). Canadian Journal of Zoology 88: 875-883.
  • Masuda R, Murata K, Aiurzaniin A, Yoshida MC. 1998. Phylogenetic status of brown bears Ursus arctos of Asia: a preliminary result inferred from mitochondrial DNA control region sequences. Hereditas 128: 277-280.
  • Matsuhashi T, Masuda R, Mano T, Murata K, Aiurzaniin A. 2001. Phylogenetic relationships among worldwide populations of the brown bear Ursus arctos. Zoological Science 18: 1137-1143.
  • Matsuhashi T, Masuda R, Mano T, Yoshida MC. 1999.
  • McLellan BN, Servheen C, Huber D. 2008. Ursus arctos the IUCN red list of threatened species. Version 2014.2. International Union for Conservation of Nature. Available at http://www.iucnredlist.org
  • Miller CR, Waits LP, Joyce P. 2006. Phylogeography and mitochondrial diversity of extirpated brown bear (Ursus arctos) populations in the contiguous United States and Mexico. Molecular Ecology 15: 4477-4485.
  • Murphy M, Waits L, Kendall K, Wasser S, Higbee J, Bogden R. 2002. An evaluation of long-term preservation methods for brown bear (Ursus arctos) faecal DNA samples. Conservation Genetics 3: 435-440.
  • Murtskhvaladze M, Gavashelishvili A, Tarkhnishvili D. 2010. Geographic and genetic boundaries of brown bear (Ursus arctos) population in the Caucasus. Molecular Ecology 19: 1829-1841.
  • Nei M, Kumar S. 2000. Molecular evolution and phylogenetics. Oxford: Oxford University Press.
  • Okay S, Junipet B, Lericolais G, Ciftci G, Morigi C. 2011. Morphological and stratigraphic investigation of a Holocene subaqueous shelf fan, north of the Istanbul Strait in the Black Sea. Turkish Journal of Earth Sciences 20: 287- 305.
  • Pasitschniak-Arts M. 1993. Mammalian species, Ursus arctos. American Journal of Mammologists 439: 1-10.
  • Poole KG, Mowat G, Fear DA. 2001. DNA-based population estimate for grizzly bears Ursus arctos in northeastern British Columbia, Canada. Wildlife Biology 7: 105-115.
  • Rambaut A, Drummond AJ. 2009. Tracer v1.5. Available at http://beast.bio.ed.ac.uk/Tracer
  • Randi E, Gentile L, Boscagli G, Huber D, Roth HU. 1994. Mitochondrial DNA sequence divergence among some west European brwon bear (Ursus arctos L.) populations. lessons for conservation. Heredity 73: 480-489.
  • Riddle A, Pilgrim K, Mills LS, McKelvey K, Ruggiero LF. 2003. Identification of mustelids using mitochondrial DNA and non-invasive sampling. Conservation Genetics 4: 241- 243.
  • Robinson SJ, Waits LP, Martin ID. 2007. Evaluating population structure of black bears on the Kenai Peninsula using mitochondrial and nuclear DNA analyses. Journal of Mammalogy 88: 1288-1299.
  • Schwarz G. 1978. Estimating the dimension of a model. Annals of Statistics 6: 461-464.
  • Shields GF, Kocher TD. 1991. Phylogenetic relationships of North American ursids based on analysis of mitochondrial DNA. Evolution 45: 218-221.
  • Steyaert SM, Endrestol A, Hacklaender K, Swenson JE, Zedrosser A. 2012. The mating system of the brown bear Ursus arctos. Mammal Review 42: 12-34.
  • Stiller M, Baryshnikov G, Bocherens H, Grandal d'Anglade A, Hilpert B, Munzel SC, Pinhasi R, Rabeder G, Rosendahl W, Trinkaus E, Hofreiter M, Knapp M. 2010. Withering away - 25,000 years of genetic decline preceded cave bear extinction. Molecular Biology and Evolution 27: 975-978.
  • Stoen OG, Bellemain E, Saebo S, Swenson J. 2005. Kinrelated spatial structure in brown bears (Ursus arctos). Behavioral Ecology and Sociobiology 59: 191-197.
  • Sukumaran J, Holder MT. 2010. DendroPy: a Python library for phylogenetic computing. Bioinformatics (Oxford, England) 26: 1569-1571.
  • Swenson JE, Taberlet P, Bellemain E. 2011. Genetics and conservation of European brown bears Ursus arctos. Mammal Review 41: 87-98.
  • Taberlet P, Bouvet J. 1994. Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proceedings of the Royal Society of London. Series B: Biological Sciences 255: 195-200.
  • Taberlet P, Fumagalli L, Wust-Saucy A-G, Cosson J-F. 1998. Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology 7: 453-464.
  • Taberlet P, Swenson JE, Sandegren F, Bjarvall A. 1995. Localization of a contact zone between two highly divergent mitochondrial DNA lineages of the brown bear Ursus arctos in Scandinavia. Conservation Biology 9: 1255-1261.
  • Talbot SL, Shields GF. 1996. A phylogeny of the bears (Ursidae) inferred from complete sequences of three mitochondrial genes. Molecular Phylogenetics and Evolution 5: 567-575.
  • Tamura K. 1992. Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G+C content biases. Molecular Biology and Evolution 9: 678- 687.
  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular Biology and Evolution 28: 2731-2739.
  • Turan N. 1984. Mammals and game animals of Turkey. Ankara: Self-published.
  • Valdiosera CE, Garcia N, Anderung C, Dalen L, Cregut- Bonnoure E, Kahlke RD, Stiller M, Brandstrom M, Thomas MG, Arsuaga JL, Gotherstrom A, Barnes I. 2007. Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Molecular Ecology 16: 5140-5148.
  • Valdiosera CE, Garcia-Garitagoitia JL, Garcia N, Doadrio I, Thomas MG, Hanni C, Arsuaga JL, Barnes I, Hofreiter M, Orlando L, Gotherstrom A. 2008. Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proceedings of the National Academy of Sciences of the United States of America 105: 5123-5128.
  • Waits LP, Talbot SL, Ward RH, Shields GF. 1998. Mitochondrial DNA phylogeography of the North American brown bear and implications for conservation. Conservation Biology 12: 408-417.
  • Wick L, Lemcke G, Sturm M. 2003. Evidence of Lateglacial and Holocene climatic change and human impact in eastern Anatolia: high-resolution pollen, charcoal, isotopic and geochemical records from the laminated sediments of Lake Van, Turkey. The Holocene 13: 665-675.
  • Woods JG, Paetkau D, Lewis D, McLellan BN, Proctor M, Strobeck C. 1999. Genetic tagging of free-ranging black and brown bears. Wildlife Society Bulletin 27: 616-627.
  • Zachos F, Otto M, Unici R, Lorenzini R, Hartl G. 2008. Evidence of a phylogeographic break in the Romanian brown bear (Ursus arctos) population from the Carpathians. Mammalian Biology 73: 93-101.