Gilbert MT, Drautz DI, Lesk AM, Ho SY, Qi J, Ratan A, Hsu CH, Sher A, Dalen L, Gotherstrom A, et al: Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes. Proc Natl Acad Sci USA. 2008, 105 (24): 8327-8332. 10.1073/pnas.0802315105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hofreiter M, Munzel S, Conard NJ, Pollack J, Slatkin M, Weiss G, Paabo S: Sudden replacement of cave bear mitochondrial DNA in the late Pleistocene. Curr Biol. 2007, 17 (4): R122-123. 10.1016/j.cub.2007.01.026.
Article
CAS
PubMed
Google Scholar
Hofreiter M, Serre D, Rohland N, Rabeder G, Nagel D, Conard N, Munzel S, Paabo S: Lack of phylogeography in European mammals before the last glaciation. Proc Natl Acad Sci USA. 2004, 101 (35): 12963-12968. 10.1073/pnas.0403618101.
Article
PubMed Central
CAS
PubMed
Google Scholar
Larson G, Albarella U, Dobney K, Rowley-Conwy P, Schibler J, Tresset A, Vigne JD, Edwards CJ, Schlumbaum A, Dinu A, et al: Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proc Natl Acad Sci USA. 2007, 104 (39): 15276-15281. 10.1073/pnas.0703411104.
Article
PubMed Central
PubMed
Google Scholar
Van Vuure C: Retracing the Aurochs: History, Morphology and Ecology of an extinct Wild Ox. Pensoft. 2005
Google Scholar
Hewitt G: The genetic legacy of the Quaternary ice ages. Nature. 2000, 405 (6789): 907-913. 10.1038/35016000.
Article
CAS
PubMed
Google Scholar
Hewitt GM: Genetic consequences of climatic oscillations in the Quaternary. Philos Trans R Soc Lond B Biol Sci. 2004, 359 (1442): 183-195. 10.1098/rstb.2003.1388. discussion 195.
Article
PubMed Central
CAS
PubMed
Google Scholar
Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF: Comparative phylogeography and postglacial colonization routes in Europe. Mol Ecol. 1998, 7 (4): 453-464. 10.1046/j.1365-294x.1998.00289.x.
Article
CAS
PubMed
Google Scholar
Petit RJ, Aguinagalde I, de Beaulieu JL, Bittkau C, Brewer S, Cheddadi R, Ennos R, Fineschi S, Grivet D, Lascoux M, et al: Glacial refugia: hotspots but not melting pots of genetic diversity. Science (New York, NY). 2003, 300 (5625): 1563-1565.
Article
CAS
Google Scholar
Hewitt G: Post-glacia re-colonization of European biota. Biological Journal of the Linnean Society. 1999, 68: 87-112. 10.1111/j.1095-8312.1999.tb01160.x.
Article
Google Scholar
Schmitt T: Molecular biogeography of Europe: Pleistocene cycles and postglacial trends. Front Zool. 2007, 4: 11-10.1186/1742-9994-4-11.
Article
PubMed Central
PubMed
Google Scholar
Hansson B, Hasselquist D, Tarka M, Zehtindjiev P, Bensch S: Postglacial colonisation patterns and the role of isolation and expansion in driving diversification in a passerine bird. PLoS ONE. 2008, 3 (7): e2794-10.1371/journal.pone.0002794.
Article
PubMed Central
PubMed
Google Scholar
Tougard C, Renvoise E, Petitjean A, Quere JP: New insight into the colonization processes of common voles: inferences from molecular and fossil evidence. PLoS ONE. 2008, 3 (10): e3532-10.1371/journal.pone.0003532.
Article
PubMed Central
PubMed
Google Scholar
Valdiosera CE, Garcia-Garitagoitia JL, Garcia N, Doadrio I, Thomas MG, Hanni C, Arsuaga JL, Barnes I, Hofreiter M, Orlando L, et al: Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos). Proc Natl Acad Sci USA. 2008, 105 (13): 5123-5128. 10.1073/pnas.0712223105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Canestrelli D, Cimmaruta R, Nascetti G: Population genetic structure and diversity of the Apennine endemic stream frog, Rana italica--insights on the Pleistocene evolutionary history of the Italian peninsular biota. Mol Ecol. 2008, 17 (17): 3856-3872. 10.1111/j.1365-294X.2008.03870.x.
Article
PubMed
Google Scholar
Excoffier L, Ray N: Surfing during population expansions promotes genetic revolutions and structuration. Trends Ecol Evol. 2008, 23 (7): 347-351. 10.1016/j.tree.2008.04.004.
Article
PubMed
Google Scholar
Rowe KC, Heske EJ, Brown PW, Paige KN: Surviving the ice: Northern refugia and postglacial colonization. Proc Natl Acad Sci USA. 2004, 101 (28): 10355-10359. 10.1073/pnas.0401338101.
Article
PubMed Central
CAS
PubMed
Google Scholar
Beja-Pereira A, Caramelli D, Lalueza-Fox C, Vernesi C, Ferrand N, Casoli A, Goyache F, Royo LJ, Conti S, Lari M, et al: The origin of European cattle: evidence from modern and ancient DNA. Proc Natl Acad Sci USA. 2006, 103 (21): 8113-8118. 10.1073/pnas.0509210103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P, Chamberlain AT, Sykes BC, Bradley DG: Genetic evidence for Near-Eastern origins of European cattle. Nature. 2001, 410 (6832): 1088-1091. 10.1038/35074088.
Article
CAS
PubMed
Google Scholar
Helmer D, Gourichon L, Monchot H, Peters J, Saña Segui M: Identifying early domestic cattle from prepottery Neolithic sites on the middle Euphrates using sexual dimorphism. The First Steps of Animal Domestication. Edited by: Vigne JD, Peters J, D H. 2005, Oxford: Oxbow Books, 86-95.
Google Scholar
Bailey JF, Richards MB, Macaulay VA, Colson IB, James IT, Bradley DG, Hedges RE, Sykes BC: Ancient DNA suggests a recent expansion of European cattle from a diverse wild progenitor species. Proc Biol Sci. 1996, 263 (1376): 1467-1473. 10.1098/rspb.1996.0214.
Article
CAS
PubMed
Google Scholar
Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne JD, Baird JF, Larson G, Ho SY, Heupink TH, et al: Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proc Biol Sci. 2007, 274 (1616): 1377-1385. 10.1098/rspb.2007.0020.
Article
PubMed Central
CAS
PubMed
Google Scholar
Achilli A, Olivieri A, Pellecchia M, Uboldi C, Colli L, Al-Zahery N, Accetturo M, Pala M, Kashani BH, Perego UA, et al: Mitochondrial genomes of extinct aurochs survive in domestic cattle. Curr Biol. 2008, 18 (4): R157-158. 10.1016/j.cub.2008.01.019.
Article
CAS
PubMed
Google Scholar
Negrini R, Nijman IJ, Milanesi E, Moazami-Goudarzi K, Williams JL, Erhardt G, Dunner S, Rodellar C, Valentini A, Bradley DG, et al: Differentiation of European cattle by AFLP fingerprinting. Anim Genet. 2007, 38 (1): 60-66. 10.1111/j.1365-2052.2007.01554.x.
Article
CAS
PubMed
Google Scholar
Pellecchia M, Negrini R, Colli L, Patrini M, Milanesi E, Achilli A, Bertorelle G, Cavalli-Sforza LL, Piazza A, Torroni A, et al: The mystery of Etruscan origins: novel clues from Bos taurus mitochondrial DNA. Proc Biol Sci. 2007, 274 (1614): 1175-1179. 10.1098/rspb.2006.0258.
Article
PubMed Central
CAS
PubMed
Google Scholar
Achilli A, Bonfiglio S, Olivieri A, Malusa A, Pala M, Kashani BH, Perego UA, Ajmone-Marsan P, Liotta L, Semino O, et al: The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS One. 2009, 4 (6): e5753-10.1371/journal.pone.0005753.
Article
PubMed Central
PubMed
Google Scholar
Willerslev E, Cooper A: Ancient DNA. Proc Biol Sci. 2005, 272 (1558): 3-16. 10.1098/rspb.2004.2813.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bollongino R, Elsner J, Vigne JD, Burger J: Y-SNPs do not indicate hybridisation between European aurochs and domestic cattle. PLoS ONE. 2008, 3 (10): e3418-10.1371/journal.pone.0003418.
Article
PubMed Central
PubMed
Google Scholar
Paabo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M: Genetic analyses from ancient DNA. Annu Rev Genet. 2004, 38: 645-679. 10.1146/annurev.genet.37.110801.143214.
Article
PubMed
Google Scholar
Poinar HN, Hoss M, Bada JL, Paabo S: Amino acid racemization and the preservation of ancient DNA. Science. 1996, 272 (5263): 864-866. 10.1126/science.272.5263.864.
Article
CAS
PubMed
Google Scholar
Collins MJ, Penkman KE, Rohland N, Shapiro B, Dobberstein RC, Ritz-Timme S, Hofreiter M: Is amino acid racemization a useful tool for screening for ancient DNA in bone?. Proc Biol Sci. 2009, 276: 2971-2977. 10.1098/rspb.2009.0563.
Article
PubMed Central
CAS
PubMed
Google Scholar
Schwarz C, Debruyne R, Kuch M, McNally E, Schwarcz H, Aubrey AD, Bada J, Poinar H: New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains. Nucleic acids research. 2009, 37 (10): 3215-3229. 10.1093/nar/gkp159.
Article
PubMed Central
CAS
PubMed
Google Scholar
Hofreiter M, Jaenicke V, Serre D, Haeseler Av A, Paabo S: DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. Nucleic Acids Res. 2001, 29 (23): 4793-4799. 10.1093/nar/29.23.4793.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kass R, Raftery A: Bayes factors. Journal of the American Statistical Association. 1995, 90: 773-795. 10.2307/2291091.
Article
Google Scholar
Gautier M, Faraut T, Moazami-Goudarzi K, Navratil V, Foglio M, Grohs C, Boland A, Garnier JG, Boichard D, Lathrop GM, et al: Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics. 2007, 177 (2): 1059-1070. 10.1534/genetics.107.075804.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tajima F: Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989, 123 (3): 585-595.
PubMed Central
CAS
PubMed
Google Scholar
Fu YX: Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics. 1997, 147 (2): 915-925.
PubMed Central
CAS
PubMed
Google Scholar
Depaulis F, Orlando L, Hanni C: Using classical population genetics tools with heterochroneous data: time matters!. PLoS One. 2009, 4 (5): e5541-10.1371/journal.pone.0005541.
Article
PubMed Central
PubMed
Google Scholar
Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A: Dynamics of Pleistocene population extinctions in Beringian brown bears. Science. 2002, 295 (5563): 2267-2270. 10.1126/science.1067814.
Article
CAS
PubMed
Google Scholar
Belle EM, Ramakrishnan U, Mountain JL, Barbujani G: Serial coalescent simulations suggest a weak genealogical relationship between Etruscans and modern Tuscans. Proc Natl Acad Sci USA. 2006, 103 (21): 8012-8017. 10.1073/pnas.0509718103.
Article
PubMed Central
CAS
PubMed
Google Scholar
Dalen L, Nystrom V, Valdiosera C, Germonpre M, Sablin M, Turner E, Angerbjorn A, Arsuaga JL, Gotherstrom A: Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox. Proc Natl Acad Sci USA. 2007, 104 (16): 6726-6729. 10.1073/pnas.0701341104.
Article
PubMed Central
CAS
PubMed
Google Scholar
Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus PE, Sher AV, Pybus OG, Gilbert MT, Barnes I, Binladen J, et al: Rise and fall of the Beringian steppe bison. Science. 2004, 306 (5701): 1561-1565. 10.1126/science.1101074.
Article
CAS
PubMed
Google Scholar
Haak W, Forster P, Bramanti B, Matsumura S, Brandt G, Tanzer M, Villems R, Renfrew C, Gronenborn D, Alt KW, et al: Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science. 2005, 310 (5750): 1016-1018.
CAS
PubMed
Google Scholar
Leonard JA, Vila C, Fox-Dobbs K, Koch PL, Wayne RK, Van Valkenburgh B: Megafaunal extinctions and the disappearance of a specialized wolf ecomorph. Curr Biol. 2007, 17 (13): 1146-1150. 10.1016/j.cub.2007.05.072.
Article
CAS
PubMed
Google Scholar
Leonard JA, Wayne RK, Cooper A: Population genetics of ice age brown bears. Proc Natl Acad Sci USA. 2000, 97 (4): 1651-1654. 10.1073/pnas.040453097.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bökönyi S: History of domestic mammals in central and eastern Europe. 1974, Budapest: Akadémiai Kiadó
Google Scholar
Ho SY, Larson G, Edwards CJ, Heupink TH, Lakin KE, Holland PW, Shapiro B: Correlating Bayesian date estimates with climatic events and domestication using a bovine case study. Biol Lett. 2008, 4 (4): 370-374. 10.1098/rsbl.2008.0073.
Article
PubMed Central
PubMed
Google Scholar
Slatkin M, Hudson RR: Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics. 1991, 129 (2): 555-562.
PubMed Central
CAS
PubMed
Google Scholar
Valdiosera CE, Garcia N, Anderung C, Dalen L, Cregut-Bonnoure E, Kahlke RD, Stiller M, Brandstrom M, Thomas MG, Arsuaga JL, et al: Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears. Mol Ecol. 2007, 16 (24): 5140-5148. 10.1111/j.1365-294X.2007.03590.x.
Article
CAS
PubMed
Google Scholar
Provan J, Bennett KD: Phylogeographic insights into cryptic glacial refugia. Trends in ecology & evolution (Personal edition). 2008, 23 (10): 564-571.
Article
Google Scholar
Sommer RS, Fahlke JM, Schmolcke U, Beneke N, Zachos FE: Quaternary history of the European roe deer Capreolus capreolus . Mammal Rev. 2009, 39: 1-16. 10.1111/j.1365-2907.2008.00137.x.
Article
Google Scholar
Liew P-M, Kuo C-M, Huang S, Tseng M-H: Vegetation change and terrestrial carbon storage in eastern Asia during the Last Glacial Maximum as indicated by a new pollen record from central Taiwan. Global and Planetary Change. 1998, 16-17: 85-94. 10.1016/S0921-8181(98)00014-9.
Article
Google Scholar
Stock F, Edwards CJ, Bollongino R, Finlay EK, Burger J, Bradley DG: Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations. Anim Genet. 2009, 40 (5): 694-700. 10.1111/j.1365-2052.2009.01905.x.
Article
CAS
PubMed
Google Scholar
Gotherstrom A, Anderung C, Hellborg L, Elburg R, Smith C, Bradley DG, Ellegren H: Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe. Proc Biol Sci. 2005, 272 (1579): 2345-2350. 10.1098/rspb.2005.3243.
Article
PubMed Central
PubMed
Google Scholar
Boscato P: Vado all'Arancio (Massa Marittima, GR), studio delle faune. Rassegna di Archeologia. 1996, 13: 159-176.
Google Scholar
Calattini M: Il livello finale di Grotta delle Mura- Area A. Rivista di Scienze Preistoriche, Supplemento 1: Askategi, miscellanea in memoria di Georges Laplace. 2005, 305-320.
Google Scholar
Palma di Cesnola A: Il Paleolitico Superiore in Italia. Garlatti e Razzai Editori, Firenze, Italy. 1993, 38: 645-679.
Google Scholar
Poinar HN, Stankiewicz BA: Protein preservation and DNA retrieval from ancient tissues. Proc Natl Acad Sci USA. 1999, 96 (15): 8426-8431. 10.1073/pnas.96.15.8426.
Article
PubMed Central
CAS
PubMed
Google Scholar
Cooper A, Poinar HN: Ancient DNA: do it right or not at all. Science. 2000, 289 (5482): 1139-10.1126/science.289.5482.1139b.
Article
CAS
PubMed
Google Scholar
Caramelli D, Milani L, Vai S, Modi A, Pecchioli E, Girardi M, Pilli E, Lari M, Lippi B, Ronchitelli A, et al: A 28,000 years old Cro-Magnon mtDNA sequence differs from all potentially contaminating modern sequences. PLoS ONE. 2008, 3 (7): e2700-10.1371/journal.pone.0002700.
Article
PubMed Central
PubMed
Google Scholar
Bandelt HJ, Forster P, Rohl A: Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999, 16 (1): 37-48.
Article
CAS
PubMed
Google Scholar
Excoffier L, Smouse PE, Quattro JM: Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992, 131 (2): 479-491.
PubMed Central
CAS
PubMed
Google Scholar
Excoffier L, Laval G, Schneider S: Arlequin (version 3.0): An integrated software package for population genetics data analysis. Evolutionary Bioinformatics. 2005, 1: 47-50.
CAS
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
Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14 (9): 817-818. 10.1093/bioinformatics/14.9.817.
Article
CAS
PubMed
Google Scholar
Rambaut A, Drummond AJ: TRACER. Version 1.3. 2004, [http://beast.bio.ed.ac.uk/Tracer]
Google Scholar
Ho SY, Phillips MJ, Cooper A, Drummond AJ: Time dependency of molecular rate estimates and systematic overestimation of recent divergence times. Mol Biol Evol. 2005, 22 (7): 1561-1568. 10.1093/molbev/msi145.
Article
CAS
PubMed
Google Scholar
Anderson CN, Ramakrishnan U, Chan YL, Hadly EA: Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics. 2005, 21 (8): 1733-1734. 10.1093/bioinformatics/bti154.
Article
CAS
PubMed
Google Scholar
Drummond AJ, Rambaut A, Shapiro B, Pybus OG: Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005, 22 (5): 1185-1192. 10.1093/molbev/msi103.
Article
CAS
PubMed
Google Scholar