Fulton TL, Strobeck C: Molecular phylogeny of the Arctoidea (Carnivora): effect of missing data on supertree and supermatrix analyses of multiple gene data sets. Mol Phylogenet Evol. 2006, 41: 165-181. 10.1016/j.ympev.2006.05.025.
Article
CAS
PubMed
Google Scholar
Talbot SL, Shields GF: A phylogeny of the bears (Ursidae) inferred from complete sequences of three mitochondrial genes. Mol Phylogenet Evol. 1996, 5: 567-575. 10.1006/mpev.1996.0051.
Article
CAS
PubMed
Google Scholar
Waits LP, Sullivan J, O'Brien SJ, Ward RH: Rapid radiation events in the family Ursidae indicated by likelihood phylogenetic estimation from multiple fragments of mtDNA. Mol Phylogenet Evol. 1999, 13: 82-92. 10.1006/mpev.1999.0637.
Article
CAS
PubMed
Google Scholar
Yu L, Li YW, Ryder OA, Zhang YP: Analysis of complete mitochondrial genome sequences increases phylogenetic resolution of bears (Ursidae), a mammalian family that experienced rapid speciation. BMC Evol Biol. 2007, 7: 198-10.1186/1471-2148-7-198.
Article
PubMed Central
PubMed
Google Scholar
McKenna MC, Bell SK: Classification of Mammals above the Species Level. 1997, New York: Columbia University Press
Google Scholar
Cummings MP, Otto SP, Wakeley J: Sampling properties of DNA sequence data in phylogenetic analysis. Mol Biol Evol. 1995, 12: 814-822.
CAS
PubMed
Google Scholar
Krause J, Dear PH, Pollack JL, Slatkin M, Spriggs H, Barnes I, Lister AM, Ebersberger I, Paabo S, Hofreiter M: Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature. 2006, 439: 724-727. 10.1038/nature04432.
Article
CAS
PubMed
Google Scholar
Rogaev EI, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, Chumakov I, Grigorenko AP: Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLoS Biol. 2006, 4: e73-10.1371/journal.pbio.0040073.
Article
PubMed Central
PubMed
Google Scholar
Rohland N, Malaspinas AS, Pollack JL, Slatkin M, Matheus P, Hofreiter M: Proboscidean mitogenomics: chronology and mode of elephant evolution using mastodon as outgroup. PLoS Biol. 2007, 5: e207-10.1371/journal.pbio.0050207.
Article
PubMed Central
PubMed
Google Scholar
Delisle I, Strobeck C: Conserved primers for rapid sequencing of the complete mitochondrial genome from carnivores, applied to three species of bears. Mol Biol Evol. 2002, 19: 357-361.
Article
CAS
PubMed
Google Scholar
Kurten B: The Cave Bear Story, life and death of a vanished animal. 1976, New York: Columbia University Press
Google Scholar
Hunt RMJ: Ursidae. Evolution of Tertiary Mammals of North America. Edited by: Janis CM, Scott KM, Jacobs LL. 1998, Cambridge: Cambridge University Press, 1: 174-195.
Google Scholar
Hofreiter M, Jaenicke V, Serre D, Haeseler AvA, Pääbo S: DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001, 29: 4793-4799. 10.1093/nar/29.23.4793.
Article
PubMed Central
CAS
PubMed
Google Scholar
Delisle I, Strobeck C: A phylogeny of the Caniformia (order Carnivora) based on 12 complete protein-coding mitochondrial genes. Mol Phylogenet Evol. 2005, 37: 192-201. 10.1016/j.ympev.2005.04.025.
Article
CAS
PubMed
Google Scholar
Nash WG, O'Brien SJ: A comparative chromosome banding analysis of the Ursidae and their relationship to other carnivores. Cytogenet Cell Genet. 1987, 45: 206-212. 10.1159/000132455.
Article
CAS
PubMed
Google Scholar
O'Brien SJ, Nash WG, Wildt DE, Bush ME, Benveniste RE: A molecular solution to the riddle of the giant panda's phylogeny. Nature. 1985, 317: 140-144. 10.1038/317140a0.
Article
PubMed
Google Scholar
Yu L, Li QW, Ryder OA, Zhang YP: Phylogenetic relationships within mammalian order Carnivora indicated by sequences of two nuclear DNA genes. Mol Phylogenet Evol. 2004, 33: 694-705. 10.1016/j.ympev.2004.08.001.
Article
CAS
PubMed
Google Scholar
O'Huigin C, Satta Y, Takahata N, Klein J: Contribution of homoplasy and of ancestral polymorphism to the evolution of genes in anthropoid primates. Mol Biol Evol. 2002, 19: 1501-1513.
Article
PubMed
Google Scholar
Arnason U, Gullberg A, Janke A, Kullberg M: Mitogenomic analyses of caniform relationships. Mol Phylogenet Evol. 2007, 45: 863-874. 10.1016/j.ympev.2007.06.019.
Article
CAS
PubMed
Google Scholar
Shields GF, Adams D, Garner G, Labelle M, Pietsch J, Ramsay M, Schwartz C, Titus K, Williamson S: Phylogeography of mitochondrial DNA variation in brown bears and polar bears. Mol Phylogenet Evol. 2000, 15: 319-326. 10.1006/mpev.1999.0730.
Article
CAS
PubMed
Google Scholar
Talbot SL, Shields GF: Phylogeography of brown bears (Ursus arctos) of Alaska and paraphyly within the Ursidae. Mol Phylogenet Evol. 1996, 5: 477-494. 10.1006/mpev.1996.0044.
Article
CAS
PubMed
Google Scholar
Yang Z, Rannala B: Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds. Mol Biol Evol. 2006, 23: 212-226. 10.1093/molbev/msj024.
Article
CAS
PubMed
Google Scholar
Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R: Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature. 2001, 409: 704-707. 10.1038/35055536.
Article
CAS
PubMed
Google Scholar
Stiller M, Green RE, Ronan M, Simons JF, Du L, He W, Egholm M, Rothberg JM, Keates SG, Ovodov ND, Antipina EE, Baryshnikov GF, Kuzmin YV, Vasilevski AA, Wuenschell GE, Termini J, Hofreiter M, Jaenicke-Despres V, Paabo S: Patterns of nucleotide misincorporations during enzymatic amplification and direct large-scale sequencing of ancient DNA. Proc Natl Acad Sci USA. 2006, 103: 13578-13584. 10.1073/pnas.0605327103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prufer K, Meyer M, Krause J, Ronan MT, Lachmann M, Paabo S: Patterns of damage in genomic DNA sequences from a Neandertal. Proc Natl Acad Sci USA. 2007, 104: 14616-14621. 10.1073/pnas.0704665104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A: Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions. Nucleic Acids Res. 2007, 35: 5717-5728. 10.1093/nar/gkm588.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kurten B, Anderson E: Pleistocene Mammals of North America. 1980, New York: Columbia University Press
Google Scholar
Hall ER: The Mammals of North America. 1981, New York: Ronald Press, 2
Google Scholar
Nowak RM: Walker's Mammals of the World. 1991, Baltimore: Johns Hopkins University Press, 2: 5
Google Scholar
Thenius E: Zur systematischen und phylogenetischen Stellung des Bambusbaeren: Ailuropoda melanoleuca. Z Saugetierk. 1979, 44: 286-305.
Google Scholar
Jin C, Ciochon RL, Dong W, Hunt RM, Liu J, Jaeger M, Zhu Q: The first skull of the earliest giant panda. Proc Natl Acad Sci USA. 2007, 104: 10932-10937. 10.1073/pnas.0704198104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Johnson WE, Eizirik E, Pecon-Slattery J, Murphy WJ, Antunes A, Teeling E, O'Brien SJ: The late Miocene radiation of modern Felidae: a genetic assessment. Science. 2006, 311: 73-77. 10.1126/science.1122277.
Article
CAS
PubMed
Google Scholar
Koepfli KP, Gompper ME, Eizirik E, Ho CC, Linden L, Maldonado JE, Wayne RK: Phylogeny of the Procyonidae (Mammalia: Carnivora): molecules, morphology and the Great American Interchange. Mol Phylogenet Evol. 2007, 43: 1076-1095. 10.1016/j.ympev.2006.10.003.
Article
CAS
PubMed
Google Scholar
Fuchs J, Ohlson JI, Ericson PGP, Pasquet E: Synchronous intercontinental splits between assemblages of woodpeckers suggested by molecular data. Zool Scripta. 2007, 36: 11-25. 10.1111/j.1463-6409.2006.00267.x.
Article
Google Scholar
Van Valkenburgh B: Major patterns in the history of carnivorous mammals. Annu Rev Earth Planet Sci. 1999, 27: 463-493. 10.1146/annurev.earth.27.1.463.
Article
CAS
Google Scholar
Marincovich L, Gladenkov AY: Evidence for an early opening of the Bering Strait. Nature. 1999, 397: 149-151. 10.1038/16446.
Article
CAS
Google Scholar
Hsü KJ, Montadert L, Bernoulli D, Cita MB, Erickson A, Garrison RE, Kidd RB, Mélières F, Müller C, Wright RH: History of the Mediterranean salinity crisis. Nature. 1977, 267: 399-403. 10.1038/267399a0.
Article
Google Scholar
Fortelius M, Eronen J, Liu L, Pushkina D, Tesakov A, Vislobokova I, Zhang Z: Late Miocene and Pliocene large land mammals and climatic changes in Eurasia. Palaeogeogr Palaeoclimatol Palaeoecol. 2006, 238:
Google Scholar
Janis CM: Tertiary mammal evolution in the context of changing climates, vegetation and tectonic events. Annu Rev Ecol Syst. 1993, 24: 467-500. 10.1146/annurev.es.24.110193.002343.
Article
Google Scholar
Cerling TE, Ehleringer JR, Harris JM: Carbon dioxide starvation, the development of C4 ecosystems, and mammalian evolution. Philos Trans R Soc Lond B Biol Sci. 1998, 353: 159-170. 10.1098/rstb.1998.0198. discussion 170–151
Article
PubMed Central
CAS
PubMed
Google Scholar
Gustafson PE: The vertebrate faunas of the Pliocene Ringold Formation, south-central Washington. Univ OR Mus Nat Hist Bull. 1978, 23: 1-62.
Google Scholar
Kumar S, Filipski A, Swarna V, Walker A, Hedges SB: Placing confidence limits on the molecular age of the human-chimpanzee divergence. Proc Natl Acad Sci USA. 2005, 102: 18842-18847. 10.1073/pnas.0509585102.
Article
PubMed Central
CAS
PubMed
Google Scholar
Potts R: Environmental hypotheses of hominin evolution. Am J Phys Anthropol. 1998, 93-136. 10.1002/(SICI)1096-8644(1998)107:27+<93::AID-AJPA5>3.0.CO;2-X. Suppl 27
Loreille O, Orlando L, Patou-Mathis M, Philippe M, Taberlet P, Hanni C: Ancient DNA analysis reveals divergence of the cave bear, Ursus spelaeus, and brown bear, Ursus arctos, lineages. Curr Biol. 2001, 11: 200-203. 10.1016/S0960-9822(01)00046-X.
Article
CAS
PubMed
Google Scholar
Taberlet P, Bouvet J: Mitochondrial DNA polymorphism, phylogeography, and conservation genetics of the brown bear Ursus arctos in Europe. Proc R Soc Lond B Biol Sci. 1994, 255: 195-200. 10.1098/rspb.1994.0028.
Article
CAS
Google Scholar
Vigilant L, Stoneking M, Harpending H, Hawkes K, Wilson AC: African populations and the evolution of human mitochondrial DNA. Science. 1991, 253: 1503-1507. 10.1126/science.1840702.
Article
CAS
PubMed
Google Scholar
Neogene of the Old World – Database of Fossil Mammals (NOW). [http://www.helsinki.fi/science/now]
Jansen E, Fronval T, Rack F, Channel JET: Pliocene-Pleistocene ice rafting history and cyclicity in the Nordic Seas during the last 3.5 Myr. Paleoceanography. 2000, 15: 709-721. 10.1029/1999PA000435.
Article
Google Scholar
Hofreiter M, Rabeder G, Jaenicke-Despres V, Withalm G, Nagel D, Paunovic M, Jambresic G, Pääbo S: Evidence for reproductive isolation between cave bear populations. Curr Biol. 2004, 14: 40-43. 10.1016/j.cub.2003.12.035.
Article
CAS
PubMed
Google Scholar
Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N: Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet. 1999, 23: 147-10.1038/13779.
Article
CAS
PubMed
Google Scholar
Rompler H, Dear PH, Krause J, Meyer M, Rohland N, Schoneberg T, Spriggs H, Stiller M, Hofreiter M: Multiplex amplification of ancient DNA. Nat Protoc. 2006, 1: 720-728. 10.1038/nprot.2006.84.
Article
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004, 32: 1792-1797. 10.1093/nar/gkh340.
Article
PubMed Central
CAS
PubMed
Google Scholar
Wyman SK, Jansen RK, Boore JL: Automatic annotation of organellar genomes with DOGMA. Bioinformatics. 2004, 20: 3252-3255. 10.1093/bioinformatics/bth352.
Article
CAS
PubMed
Google Scholar
Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13: 555-556.
CAS
PubMed
Google Scholar
Lanave C, Preparata G, Saccone C, Serio G: A new method for calculating evolutionary substitution rates. J Mol Evol. 1984, 20: 86-93. 10.1007/BF02101990.
Article
CAS
PubMed
Google Scholar
Rodriguez F, Oliver JL, Marin A, Medina JR: The general stochastic model of nucleotide substitution. J Theor Biol. 1990, 142: 485-501. 10.1016/S0022-5193(05)80104-3.
Article
CAS
PubMed
Google Scholar
Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol. 1993, 10: 1396-1401.
CAS
PubMed
Google Scholar
Goloboff P, Farris J, Nixon K: TNT, a free program for phylogenetic analysis. Cladistics. 2008, 24: 1-13. 10.1111/j.1096-0031.2008.00217.x.
Article
Google Scholar
Stamatakis A: RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006, 22: 2688-2690. 10.1093/bioinformatics/btl446.
Article
CAS
PubMed
Google Scholar
Ronquist F, Huelsenbeck JP: MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19: 1572-1574. 10.1093/bioinformatics/btg180.
Article
CAS
PubMed
Google Scholar
Sarkar IN, Egan MG, Coruzzi G, Lee EK, DeSalle R: Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phylogenomics. BMC Bioinformatics. 2008, 9: 103-10.1186/1471-2105-9-103.
Article
PubMed Central
PubMed
Google Scholar
Farris JS, Källersjö M, Kluge AG, Bult C: Testing significance of incongruence. Cladistics. 1994, 10: 315-319. 10.1111/j.1096-0031.1994.tb00181.x.
Article
Google Scholar
Gatesy J, O'Grady P, Baker RH: Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics. 1999, 15: 271-313. 10.1111/j.1096-0031.1999.tb00268.x.
Article
Google Scholar
Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol. 2002, 51: 492-508. 10.1080/10635150290069913.
Article
PubMed
Google Scholar
Shimodaira H, Hasegawa M: CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics. 2001, 17: 1246-1247. 10.1093/bioinformatics/17.12.1246.
Article
CAS
PubMed
Google Scholar
Clark J, Guensburg TE: Arctoid genetic characters as related to the genus Parictis. Fieldiana: Geology. 1972, 26: 1-76.
Google Scholar
Clark J, Beerbower JR, Kietze KK: Oligocene sedimentation, stratigraphy, paleoecology, and paleoclimatology in the Big Badlands of South Dakota. Fieldiana Geol. 1967, 5: 1-158.
Google Scholar
Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981, 17: 368-376. 10.1007/BF01734359.
Article
CAS
PubMed
Google Scholar
Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186/1471-2148-7-214.
Article
PubMed Central
PubMed
Google Scholar
Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985, 160-174. 10.1007/BF02101694.
Google Scholar
Rambaut A, Drummond AJ: Tracer v1.3. 2004, [http://tree.bio.ed.ac.uk/software/tracer]
Google Scholar
Eisenberg JF: The Mammalian Radiations. 1981, Chicago: University of Chicago Press
Google Scholar
Ewer RF: The Carnivora. 1973, Ithaca: Cornell University Press
Google Scholar
Corbet GB, Hill JE: A World List of Mammalian Species. 1991, London: Oxford University Press
Google Scholar
Zhang YP, Ryder OA: Phylogenetic relationships of bears (the Ursidae) inferred from mitochondrial DNA sequences. Mol Phylogenet Evol. 1994, 3: 351-359. 10.1006/mpev.1994.1041.
Article
CAS
PubMed
Google Scholar
Thenius E: Carnivores: phylogeny. Grizmek's encyclopedia of mammals. Edited by: Grizmek B. 1990, New York: McGraw Hill, 3: 370-464.
Google Scholar
Wozencraft WC: Order Carnivora. Mammal Species of the World: A taxonomic and geographic reference. Edited by: Wilson DE, Reeder DM. 2005, Baltimore: Johns Hopkins University Press, 3: 532-628. 3
Google Scholar
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