Publication Cover
Historical Biology
An International Journal of Paleobiology
Volume 31, 2019 - Issue 4: SI: Cave Bear
436
Views
11
CrossRef citations to date
0
Altmetric
Articles

From a molecules’ perspective – contributions of ancient DNA research to understanding cave bear biology

Pages 442-447 | Received 17 Dec 2017, Accepted 26 Jan 2018, Published online: 31 Jan 2018

References

  • Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego J a, Gilbert MTP, Willerslev E, et al. 2012. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc Biol Sci [Internet]. [accessed 2013 Oct 22];279:4724–4733. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2305506110.1098/rspb.2012.1745
  • Baca M, Popović D, Stefaniak K, Marciszak A, Urbanowski M, Nadachowski A, Mackiewicz P. 2016. Retreat and extinction of the Late Pleistocene cave bear (Ursus spelaeus sensu lato). Sci Nat [Internet]. 103:92. Available from: http://link.springer.com/10.1007/s00114-016-1414-8.10.1007/s00114-016-1414-8
  • Barnosky AD, Koch PL, Feranec RS, Wing SL, Shabel AB. 2004. Assessing the Causes of Late Pleistocene Extinctions on the Continents. Science (80-) [Internet]. 306:70–75. DOI:10.1126/science.1101476
  • Baryshnikov G. 1998. Cave bears from the Paleolithic of the Greater Caucasus. In: Saunders J, Styles B, Baryshnikov G, editors. Quat Paleozoology North Hemisph. Vol. XXVII. Springfield (IL): Illinois State Museum; p. 69–118.
  • Baryshnikov GF, Foronova I. 2001. Pleistocene small cave bear (Ursus rossicus) from the South Siberia, Russia. Cad do Lab Xeol Laxe. 373–398.
  • Baryshnikov GF, Puzachenko AY. 2011. Craniometrical variability in the cave bears (Carnivora, Ursidae): multivariate comparative analysis. Quat Int [Internet]. 245:350–368. DOI:10.1016/j.quaint.2011.02.035
  • Bocherens H, Bridault A, Drucker DG, Hofreiter M, Münzel SC, Stiller M, van der Plicht J. 2014. The last of its kind? Radiocarbon, ancient DNA and stable isotope evidence from a late cave bear (Ursus spelaeus ROSENMÜLLER, 1794) from Rochedane (France). Quat Int [Internet]. 339–340:179–188. DOI:10.1016/j.quaint.2013.05.021
  • Bocherens H, Stiller M, Hobson KA, Pacher M, Rabeder G, Burns JA, Tütken T, Hofreiter M. 2011. Niche partitioning between two sympatric genetically distinct cave bears (Ursus spelaeus and Ursus ingressus) and brown bear (Ursus arctos) from Austria: Isotopic evidence from fossil bones. Quat Int [Internet]. 245:238–248. DOI:10.1016/j.quaint.2010.12.020
  • Bon C, Caudy N, de Dieuleveult M, Fosse P, Philippe M, Maksud F, Beraud-Colomb E, Bouzaid E, Kefi R, Laugier C, et al. 2008. Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet. Proc Natl Acad Sci [Internet]. 105:17447–17452. DOI:10.1073/pnas.0806143105
  • Carbonell E, Bermúdez de Castro JM, Parés JM, Pérez-González A, Cuenca-Bescós G, Ollé A, Mosquera M, Huguet R, van der Made J, Rosas A, et al. 2008. The first hominin of Europe. Nature. 452:465–469.10.1038/nature06815
  • Chang D, Knapp M, Enk J, Lippold S, Kircher M, Lister A, MacPhee RDE, Widga C, Czechowski P, Sommer R, et al. 2017. The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis. Sci Rep [Internet]. 7:44585. Available from: http://www.nature.com/articles/srep44585.10.1038/srep44585
  • Dabney J, Knapp M, Glocke I, Gansauge M-T, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga J-L, et al. 2013. Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci USA [Internet]. [accessed 2013 Sep 16];110:15758–15763. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2401949010.1073/pnas.1314445110
  • Figueirido B, Palmqvist P, Pérez-Claros JA. 2009. Ecomorphological correlates of craniodental variation in bears and paleobiological implications for extinct taxa: an approach based on geometric morphometrics. J Zool. 277:70–80.10.1111/jzo.2009.277.issue-1
  • Fortes GG, Grandal-d’Anglade A, Kolbe B, Fernandes D, Meleg IN, García-Vázquez A, Pinto-Llona AC, Constantin S, de Torres TJ, Ortiz JE, et al. 2016. Ancient DNA reveals differences in behaviour and sociality between brown bears and extinct cave bears. Mol Ecol. 25:4907–4918.10.1111/mec.13800
  • García N. 2004. New results on the remains of Ursidae from Untermassfeld: comparisons with Ursus dolinensis from Atapuerca and other early and middle Pleistocene sites. Late Neogene Quat Biodivers Evol Reg Dev Interreg Correl Conf 18.
  • García N, Arsuaga J-L. 2001. Ursus dolinensis: a new species of early Pleistocene ursid from Trinchera Dolina, Atapuerca (Spain) = Ursus dolinensis: une nouvelle espèce d’ursidé du Pléistocène inférieur de Trinchera Dolina, Atapuerca (Espagne). Comptes rendus l’Académie des Sci Série 2 Sci la terre des planètes [Internet]. 332:717–725. Available from: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VJ3-43C5CVK-9&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=cb10d66d5eed4688dc9cf6406cb39308
  • García N, Arsuaga JL. 2011. The Sima de los Huesos (Burgos, northern Spain): palaeoenvironment and habitats of Homo heidelbergensis during the Middle Pleistocene. Quat Sci Rev [Internet]. 30:1413–1419. DOI:10.1016/j.quascirev.2010.11.008
  • García N, Arsuaga JL, Torres T. 1997. The carnivore remains from the Sima de los Huesos Middle Pleistocene site (Sierra de Atapuerca, Spain). J Hum Evol. 33:155–174.10.1006/jhev.1997.0154
  • Grandal-d’Anglade A. 2010. Bite force of the extinct Pleistocene Cave bear Ursus spelaeus Rosenmuller from Europe. Comptes Rendus Palevol. 9:31–37.10.1016/j.crpv.2009.10.003
  • Grayson DK, Delpech F. 2003. Ungulates and the middle-to-upper Paleolithic transition at Grotte XVI (Dordogne, France). J Archaeol Sci. 30:1633–1648.10.1016/S0305-4403(03)00064-5
  • Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH-Y, et al. 2010. A draft sequence of the Neandertal genome. Science [Internet]. [accessed 2013 Sep 17];328:710–722. Available from: http://www.ncbi.nlm.nih.gov/pubmed/20448178
  • Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B, Brandt G, Nordenfelt S, Harney E, Stewardson K, et al. 2015. Massive migration from the steppe was a source for Indo-European languages in Europe. Nature [Internet]. [accessed 2017 Nov 24];522:207–211. DOI:10.1038/nature14317
  • Hänni C, Laudet V, Stehelin D, Taberlet P, Fourier J. 1994. Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing. Proc Nat Acad Sci. 91:12336–12340.10.1073/pnas.91.25.12336
  • Hofreiter M, Münzel S, Conard NJ, Pollack J, Slatkin M, Weiss G, Pääbo S. 2007. Sudden replacement of cave bear mitochondrial DNA in the late Pleistocene. Curr Biol. 17:122–123.10.1016/j.cub.2007.01.026
  • Hofreiter M, Rabeder G, Jaenicke-Després V, Withalm G, Nagel D, Paunovic M, Jambrěsić G, Pääbo S. 2004. Evidence for reproductive isolation between cave bear populations. Curr Biol. 14:40–43.10.1016/j.cub.2003.12.035
  • Jacoby ME, Hilderbrand GV, Servheen C, Charles C, Arthur SM, Hanley TA, Robbins CT. 1999. Trophic relations of brown and black bears in several western North American ecosystems. J Wildl Manage. 63:921–929.10.2307/3802806
  • Kahlke R-D. 2006. Untermassfeld: a late early Pleistocene (Epivillafranchian) fossil site near Meiningen (Thuringia, Germany) and its position in the development of the European Mammal Fauna. Oxford: Archaeopress.
  • Knapp M, Hofreiter M. 2010. Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes (Basel) [Internet]. [accessed 2013 Sep 17];1:227–243. Available from: http://www.mdpi.com/2073-4425/1/2/227/10.3390/genes1020227
  • Knapp M, Lalueza-Fox C, Hofreiter M. 2015. Re-inventing ancient human DNA. Investig Genet [Internet]. 6:4. Available from: http://www.investigativegenetics.com/content/6/1/4
  • Knapp M, Rohland N, Weinstock J, Baryshnikov G, Sher A, Nagel D, Rabeder G, Pinhasi R, Schmidt HA, Hofreiter M. 2009. First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns. Mol Ecol [Internet]. [accessed 2013 Sep 17];18:1225–1238. Available from: http://www.ncbi.nlm.nih.gov/pubmed/1922632110.1111/mec.2009.18.issue-6
  • Kurtén B. 1976. The cave bear story. New York (NY): Columbia University Press.
  • Lazaridis I, Patterson N, Mittnik A, Renaud G, Mallick S, Kirsanow K, Sudmant PH, Schraiber JG, Castellano S, Lipson M, et al. 2014. Ancient human genomes suggest three ancestral populations for present-day Europeans. Nature [Internet]. [accessed 2014 Sep 17];513:409–413. DOI:10.1038/nature13673
  • 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 [Internet]. [accessed 2013 Sep 17];479:359–364. DOI:10.1038/nature10574
  • Meyer M, Fu Q, Aximu-Petri A, Glocke I, Nickel B, Arsuaga J-L, Martínez I, Gracia A, de Castro JMB, Carbonell E, et al. 2014. A mitochondrial genome sequence of a hominin from Sima de los Huesos. Nature [Internet]. [accessed 2014 Jan 20];505:403–406. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2430505110.1038/nature12788
  • Meyer M, Kircher M, Gansauge M-T, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, et al. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science [Internet]. [accessed 2014 Jul 15];338:222–226. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3617501&tool=pmcentrez&rendertype=abstract
  • Murray GGR, Soares AER, Novak BJ, Schaefer NK, Gilbert MTP, Heintzman PD, Letts B. 2017. Natural selection shaped the rise and fall of passenger pigeon genomic diversity. Science (80-). 954:1–14.
  • Noonan JP, Hofreiter M, Smith D, Priest JR, Rohland N, Rabeder G. 2005. Genomic sequencing of Pleistocene cave bears. Science. 309:597–600.10.1126/science.1113485
  • Orlando L, Bonjean D, Bocherens H, Thenot A, Argant A, Otte M, Hänni C. 2002. Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. Mol Biol Evol. 19:1920–1933.10.1093/oxfordjournals.molbev.a004016
  • Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, et al. 2013. Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature [Internet]. [accessed 2014 Jul 9];499:74–78. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2380376510.1038/nature12323
  • Pacher M, Stuart AJ. 2009. Extinction chronology and palaeobiology of the cave bear (Ursus spelaeus). Boreas. 38:189–206.10.1111/bor.2009.38.issue-2
  • Palkopoulou E, Dalén L, Lister AM, Vartanyan S, Sablin M, Sher A, Edmark VN, Brandström MD, Germonpré M, Barnes I, et al. 2013. Holarctic genetic structure and range dynamics in the woolly mammoth Holarctic genetic structure and range dynamics in the woolly mammoth. Proc R Soc B. 280:20131910.
  • Palkopoulou E, Mallick S, Skoglund P, Enk J, Rohland N, Li H, Omrak A, Vartanyan S, Poinar H, Götherström A, et al. 2015. Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth. Curr Biol. 25:1395–1400.10.1016/j.cub.2015.04.007
  • Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, et al. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature [Internet]. [accessed 2014 Jan 21];505:43–49. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2435223510.1038/nature12886
  • Rabeder G, Hofreiter M. 2004. Der neue Stammbaum der alpinen Höhlenbären [The new phylogeny of alpine cave bears], German. Die Höhle [Internet]. 55:1–19. Available from: http://en.scientificcommons.org/41418343
  • Richards MP, Pacher M, Stiller M, Quilès J, Hofreiter M, Constantin S, Zilhão J, Trinkaus E. 2008. Isotopic evidence for omnivory among European cave bears: Late Pleistocene Ursus spelaeus from the Peştera cu Oase, Romania. Proc Natl Acad Sci USA [Internet]. 105:600–604. Available from: http://www.scopus.com/inward/record.url?eid=2-s2.0-38649134134&partnerID=tZOtx3y1.10.1073/pnas.0711063105
  • Sánchez-Quinto F, Schroeder H, Ramirez O, Avila-Arcos MC, Pybus M, Olalde I, Velazquez AM, Marcos MEP, Encinas JMV, Bertranpetit J, et al. 2012. Genomic affinities of two 7000-year-old Iberian hunter-gatherers. Curr Biol [Internet]. [accessed 2014 Sep 8];22:1494–1499. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2274831810.1016/j.cub.2012.06.005
  • Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MTP, Barnes I, Binladen J, et al. 2004. Rise and Fall of the Beringian Steppe Bison. Science (80-) [Internet]. [accessed 2013 Sep 17];306:1561–1565. DOI:10.1126/science.1101074
  • Skoglund P, Malmström H, Raghavan M, Storå J, Hall P, Willerslev E, Gilbert MTP, Götherström A, Jakobsson M. 2012. Origins and genetic legacy of Neolithic farmers and hunter-gatherers in Europe. Science [Internet]. [accessed 2014 Aug 29];336:466–469. Available from: http://www.ncbi.nlm.nih.gov/pubmed/22539720
  • Stiller M, Baryshnikov G, Bocherens H, Grandal d’Anglade A, Hilpert B, Münzel SC, Pinhasi R, Rabeder G, Rosendahl W, Trinkaus E, et al. 2010. Withering Away–25,000 years of genetic decline preceded cave bear extinction. Mol Biol Evol [Internet]. [accessed 2013 Sep 17];27:975–978. Available from: http://www.ncbi.nlm.nih.gov/pubmed/2033527910.1093/molbev/msq083
  • Stiller M, Knapp M, Stenzel U, Hofreiter M, Meyer M. 2009. Direct multiplex sequencing (DMPS) – a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res [Internet]. [accessed 2013 Sep 17];19:1843–1848. Available from: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2765274&tool=pmcentrez&rendertype=abstract10.1101/gr.095760.109
  • Stiller M, Molak M, Prost S, Rabeder G, Baryshnikov G, Rosendahl W, Münzel S, Bocherens H, Grandal-d’Anglade A, Hilpert B, et al. 2014. Mitochondrial DNA diversity and evolution of the Pleistocene cave bear complex. Quat Int [Internet]. 339–340:224–231. DOI:10.1016/j.quaint.2013.09.023
  • van Andel T. 2003. Glacial environment I: the Weichselian climate in Europe between the end of the OIS-5 and the LGM. In: van Andel T, Davies W, editors. Neanderthals Mod humans Eur Landsc Dur last Glaciat. Cambridge: Mc Donald Institute Monographs; p. 9–19.
  • van Heteren AH, MacLarnon A, Soligo C, Rae TC. 2014. Functional morphology of the cave bear (Ursus spelaeus) cranium: a three-dimensional geometric morphometric analysis. Quat Int [Internet]. 339–340:209–216. DOI:10.1016/j.quaint.2013.10.056
  • van Heteren AH, MacLarnon A, Soligo C, Rae TC. 2016. Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis. Org Divers Evol. 16:299–314.10.1007/s13127-015-0238-2

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.