References
- Anderson C.N.K. Ramakrishnan U. Chan Y.L. Hadly E.A. Serial SimCoal: A population genetics model for data from multiple populations and points in time Bioinformatics 2005 21 1733 1734 10.1093/bioinformatics/bti154
- Anton M. Galobart A. Turner A. Co-existence of scimitar-toothed cats, lions and hominins in the European Pleistocene. Implications of the post-cranial anatomy of Homotherium latidens (Owen) for comparative palaeoecology Quaternary Sci Rev 2005 24 1287 1301 10.1016/j.quascirev.2004.09.008
- Baele G. Lemey P. Bedford T. Rambaut A. Suchard M.A. Alekseyenko A.V. Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty Mol Biol Evol 2012 29 2157 2167 10.1093/molbev/mss084
- Baele G. Li W.L.S. Drummond A.J. Suchard M.A. Lemey P. Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics Mol Biol Evol 2013 30 239 243 10.1093/molbev/mss243
- Barnes I. Matheus P. Shapiro B. Jensen D. Cooper A. Dynamics of Pleistocene population extinctions in Beringian brown bears Science 2002 295 2267 2270 10.1126/science.1067814
- Barnes I. Shapiro B. Lister A. Kuznetsova T. Sher A. Guthrie D. Thomas M.G. Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius Current Biology 2007 17 1072 1075 10.1016/j.cub.2007.05.035
- Barnett R. Shapiro B. Barnes I. Ho S.Y.W. Burger J. Yamaguchi N. Higham T.F.G. Wheeler H.T. Rosendahl W. Sher A.V. Sotnikova M. Kuznetsova T. Baryshnikov G.F. Martin L.D. Harington C.R. Burns J.A. Cooper A. Phylogeography of lions (Panthera leo ssp.) reveals three distinct taxa and a late Pleistocene reduction in genetic diversity Mol Ecol 2009 18 1668 1677 10.1111/j.1365-294X.2009.04134.x
- Barnosky A.D. Koch P.L. Feranec R.S. Wing S.L. Shabel A.B. Assessing the causes of Late Pleistocene extinctions on the continents Science 2004 306 70 75 10.1126/science.1101476
- Battistuzzi F.U. Filipski A. Hedges S.B. Kumar S. Performance of Relaxed-Clock Methods in Estimating Evolutionary Divergence Times and Their Credibility Intervals Mol Biol Evol 2010 27 1289 1300 10.1093/molbev/msq014
- Bennett K.D. Provan J. What do we mean by ‘refugia? Quaternary Sci Rev 2008 27 2449 2455 10.1016/j.quascirev.2008.08.019
- Björklund M. The risk of inbreeding due to habitat loss in the lion (Panthera leo) Conservation Genetics 2003 4 515 523 10.1023/A:1024737317695
- Bocherens H. Drucker D.G. Bonjean D. Bridault A. Conard N.J. Cupillard C. Germonpre M. Honeisen M. Munzel S.C. Napierala H. Patou-Mathis M. Stephan E. Uerpmann H.P. Ziegler R. Isotopic evidence for dietary ecology of cave lion (Panthera spelaea) in North-Western Europe: Prey choice, competition and implications for extinction Quaternary International 2011 245 249 261 10.1016/j.quaint.2011.02.023
- Burger J. Rosendahl W. Loreille O. Hemmer H. Eriksson T. Gotherstrom A. Hiller J. Collins M.J. Wess T. Alt K.W. Molecular phylogeny of the extinct cave lion Panthera leo spelaea Mol Phylogenet Evol 2004 30 841 849 10.1016/j.ympev.2003.07.020
- Campos P.F. Kristensen T. Orlando L. Sher A. Kholodova M.V. Gotherstrom A. Hofreiter M. Drucker D.G. Kosintsev P. Tikhonov A. Baryshnikov G.F. Willerslev E. Gilbert M.T.P. Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene Mol Ecol 2010a 19 4863 4875 10.1111/j.1365-294X.2010.04826.x
- Campos P.F. Willerslev E. Sher A. Orlando L. Axelsson E. Tikhonov A. Aaris-Sorensen K. Greenwood A.D. Kahlke R.D. Kosintsev P. Krakhmalnaya T. Kuznetsova T. Lemey P. MacPhee R. Norris C.A. Shepherd K. Suchard M.A. Zazula G.D. Shapiro B. Gilbert M.T.P. Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics Proceedings of the National Academy of Sciences of the United States of America 2010b 107 5675 5680 10.1073/pnas.0907189107
- Christiansen P. Phylogeny of the great cats (Felidae: Pantherinae), and the influence of fossil taxa and missing characters Cladistics 2008 24 977 992 10.1111/j.1096-0031.2008.00226.x
- Dalen L. Nystrom V. Valdiosera C. Germonpre M. Sablin M. Turner E. Angerbjorn A. Arsuaga J.L. Gotherstrom A. Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox Proceedings of the National Academy of Sciences of the United States of America 2007 104 6726 6729 10.1073/pnas.0701341104
- de Bruyn M. Hoelzel A.R. Carvalho G.R. Hofreiter M. Faunal histories from Holocene ancient DNA Trends in Ecology & Evolution 2011 26 405 413 10.1016/j.tree.2011.03.021
- Depaulis F. Orlando L. Hanni C. Using Classical Population Genetics Tools with Heterochroneous Data: Time Matters! Plos One 4 2009
- Drummond A.J. Ho S.Y.W. Phillips M.J. Rambaut A. Relaxed phylogenetics and dating with confidence Plos Biol 2006 4 699 710 10.1371/journal.pbio.0040088
- Drummond A.J. Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees BMC evolutionary biology 2007 7
- Drummond A.J. Rambaut A. Shapiro B. Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences Mol Biol Evol 2005 22 1185 1192 10.1093/molbev/msi103
- Fox-Dobbs K. Leonard J.A. Koch P.L. Pleistocene megafauna from eastern Beringia: Paleoecological and paleoenvironmental interpretations of stable carbon and nitrogen isotope and radiocarbon records Palaeogeography Palaeoclimatology Palaeoecology 2008 261 30 46 10.1016/j.palaeo.2007.12.011
- Fu Q. Li H. Moorjani P. Jay F. Slepchenko S.M. Bondarev A.A. Johnson P.L. Aximu-Petri A. Prufer K. de Filippo C. Meyer M. Zwyns N. Salazar-Garcia D.C. Kuzmin Y.V. Keates S.G. Kosintsev P.A. Razhev D.I. Richards M.P. Peristov N.V. Lachmann M. Douka K. Higham T.F. Slatkin M. Hublin J.J. Reich D. Kelso J. Viola T.B. Paabo S. Genome sequence of a 45,000-year-old modern human from western Siberia Nature 2014 514 445 449 10.1038/nature13810
- Gilbert M.T.P. Drautz D.I. Lesk A.M. Ho S.Y.W. Qi J. Ratan A. Hsu C.H. Sher A. Dalen L. Gotherstrom A. Tomsho L.P. Rendulic S. Packard M. Campos P.F. Kuznetsova T.V. Shidlovskiy F. Tikhonov A. Willerslev E. Iacumin P. Buigues B. Ericson P.G.P. Germonpre M. Kosintsev P. Nikolaev V. Nowak-Kemp M. Knight J.R. Irzyk G.P. Perbost C.S. Fredrikson K.M. Harkins T.T. Sheridan S. Miller W. Schuster S.C. Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes Proceedings of the National Academy of Sciences of the United States of America 2008 105 8327 8332 10.1073/pnas.0802315105
- Goebel T. Pleistocene human colonization of Siberia and peopling of the Americas: An ecological approach Evol Anthropol 1999 8 208 227 10.1002/(SICI)1520-6505(1999)8:6<;208::AID-EVAN2>3.0.CO;2-M
- Grootes P.M. Steig E.J. Stuiver M. Waddington E.D. Morse D.L. The Taylor dome antarctic O-18 record and globally synchronous changes in climate Quaternary Res 2001 56 289 298 10.1006/qres.2001.2276
-
Guthrie
R.D.
Frozen Fauna of the Mammoth Steppe: The story of Blue Babe 1990 Chicago University of Chicago - Guthrie R.D. Rapid body size decline in Alaskan Pleistocene horses before extinction Nature 2003 426 169 171 10.1038/nature02098
- Guthrie R.D. Radiocarbon evidence of mid-Holocene mammoths stranded on an Alaskan Bering Sea island Nature 2004 429 746 749 10.1038/nature02612
-
Guthrie
R.D.
The Nature of Palaeolithic Art 2005 Chicago University of Chicago press - Heinrich H. Origin and Consequences of Cyclic Ice Rafting in the Northeast Atlantic-Ocean during the Past 130,000 Years Quaternary Res 1988 29 142 152 10.1016/0033-5894(88)90057-9
- Hemming S.R. Heinrich events: Massive late pleistocene detritus layers of the North Atlantic and their global climate imprint Rev Geophys 2004 42
- Higham T. Compton T. Stringer C. Jacobi R. Shapiro B. Trinkaus E. Chandler B. Groning F. Collins C. Hillson S. O’Higgins P. FitzGerald C. Fagan M. The earliest evidence for anatomically modern humans in northwestern Europe Nature 2011 479 521 524 10.1038/nature10484
- Ho S.Y.W. Shapiro B. Skyline-plot methods for estimating demographic history from nucleotide sequences Molecular Ecology Resources 2011 11 423 434 10.1111/j.1755-0998.2011.02988.x
- Ho S.Y.W. Shapiro B. Phillips M.J. Cooper A. Drummond A.J. Evidence for time dependency of molecular rate estimates Systematic Biology 2007 56 515 522 10.1080/10635150701435401
- Hofreiter M. Pleistocene extinctions: Haunting the survivors Current Biology 2007 17 R609 R611 10.1016/j.cub.2007.06.031
- Hofreiter M. Jaenicke V. Serre D. von Haeseler A. Paabo S. DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA Nucleic Acids Research 2001 29 4793 4799 10.1093/nar/29.23.4793
- Hofreiter M. Stewart J. Ecological Change, Range Fluctuations and Population Dynamics during the Pleistocene Current Biology 2009 19 R584 R594 10.1016/j.cub.2009.06.030
- Huelsenbeck J.P. Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees Bioinformatics 2001 17 754 755 10.1093/bioinformatics/17.8.754
- Kim J.H. Antunes A. Luo S.J. Menninger J. Nash W.G. O’Brien S.J. Johnson W.E. Evolutionary analysis of a large mtDNA translocation (numt) into the nuclear genome of the Panthera genus species Gene 2006 366 292 302 10.1016/j.gene.2005.08.023
- Librado P. Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data Bioinformatics 2009 25 1451 1452 10.1093/bioinformatics/btp187
- Lister A.M. Stuart A.J. The impact of climate change on large mammal distribution and extinction: Evidence from the last glacial/interglacial transition Cr Geosci 2008 340 615 620 10.1016/j.crte.2008.04.001
- Lorenzen E.D. Nogues-Bravo D. Orlando L. Weinstock J. Binladen J. Marske K.A. Ugan A. Borregaard M.K. Gilbert M.T.P. Nielsen R. Ho S.Y.W. Goebel T. Graf K.E. Byers D. Stenderup J.T. Rasmussen M. Campos P.F. Leonard J.A. Koepfli K.P. Froese D. Zazula G. Stafford T.W. Aaris-Sorensen K. Batra P. Haywood A.M. Singarayer J.S. Valdes P.J. Boeskorov G. Burns J.A. Davydov S.P. Haile J. Jenkins D.L. Kosintsev P. Kuznetsova T. Lai X.L. Martin L.D. McDonald H.G. Mol D. Meldgaard M. Munch K. Stephan E. Sablin M. Sommer R.S. Sipko T. Scott E. Suchard M.A. Tikhonov A. Willerslev R. Wayne R.K. Cooper A. Hofreiter M. Sher A. Shapiro B. Rahbek C. Willerslev E. Species-specific responses of Late Quaternary megafauna to climate and humans Nature 2011 479 359 U195 10.1038/nature10574
-
Martin
P.S.
Steadman
D. W.
MacPhee
R.D.E.
Prehistoric Extinctions on Islands and Continents Extinctions in Near Time 1999 New York Kluwer Academic/Plenum Publishers 17 55 10.1007/978-1-4757-5202-1_2 - Mazak J.H. Geographical variation and phylogenetics of modern lions based on craniometric data Journal of Zoology 2010 281 194 209
- Mourier T. Ho S. Y. Gilbert M. T. Willerslev E. Orlando L. Statistical guidelines for detecting past population shifts using ancient DNA Mol. Biol. Evol. 2012 10.1093/molbev/mss094
- Pitulko V.V. Nikolsky P.A. Girya E.Y. Basilyan A.E. Tumskoy V.E. Koulakov S.A. Astakhov S.N. Pavlova E.Y. Anisimov M.A. The Yana RHS site: Humans in the Arctic before the Last Glacial Maximum Science 2004 303 52 56 10.1126/science.1085219
- Reumer J.W.F. Rook L. van der Borg K. Post K. Mol D. de Vos J. Late Pleistocene survival of the saber-toothed cat Homotherium in northwestern Europe Journal of Vertebrate Paleontology 2003 23 260 262 10.1671/0272-4634(2003)23[260:LPSOTS]2.0.CO;2
- Sandoval-Castellanos E. Testing temporal changes in allele frequencies: a simulation approach Genet Res 2010 92 309 320 10.1017/S0016672310000339
- Sandoval-Castellanos E. Palkopoulou E. Dalén L. Back to BaySICS: A User-Friendly Program for Bayesian Statistical Inference from Coalescent Simulations PloS one 2014 9 e98011 10.1371/journal.pone.0098011
- Shapiro B. Drummond A.J. Rambaut A. Wilson M.C. Matheus P.E. Sher A.V. Pybus O.G. Gilbert M.T.P. Barnes I. Binladen J. Willerslev E. Hansen A.J. Baryshnikov G.F. Burns J.A. Davydov S. Driver J.C. Froese D.G. Harington C.R. Keddie G. Kosintsev P. Kunz M.L. Martin L.D. Stephenson R.O. Storer J. Tedford R. Zimov S. Cooper A. Rise and fall of the Beringian steppe bison Science 2004 306 1561 1565 10.1126/science.1101074
- Shapiro B. Ho S.Y.W. Ancient hyaenas highlight the old problem of estimating evolutionary rates Mol Ecol 2014 23 499 501 10.1111/mec.12621
- Sotnikova M. Nikolskiy P. Systematic position of the cave lion Panthera spelaea (Goldfuss) based on cranial and dental characters Quaternary International 2006 142 218 228 10.1016/j.quaint.2005.03.019
-
Staden
R.
Beal
K.F.
Bonfield
J.K.
Misener
S.
Krawetz
S. A.
The Staden Package, 1998 Methods in Molecular Biology 1999 Totowa, NJ Bioinformatics Methods and Protocols. Humana Press 132 115 130 - Stewart J.R. The progressive effect of the individualistic response of species to Quaternary climate change: an analysis of British mammalian faunas Quaternary Sci Rev 2008 27 2499 2508 10.1016/j.quascirev.2008.08.003
- Stewart J.R. Lister A.M. Barnes I. Dalen L. Refugia revisited: individualistic responses of species in space and time Proceedings of the Royal Society B-Biological Sciences 2010 277 661 671 10.1098/rspb.2009.1272
-
Stuart
A.J.
MacPhee
R.D.E.
Late Pleistocene Megafaunal Extinctions Extinctions in Near Time 1999 New York Kluwer Academic/Plenum Publishers 257 269 10.1007/978-1-4757-5202-1_11 - Stuart A.J. Kosintsev P.A. Higham T.F.G. Lister A.M. Pleistocene to Holocene extinction dynamics in giant deer and woolly mammoth Nature 2004 431 684 689 10.1038/nature02890
- Stuart A.J. Lister A.M. Extinction chronology of the cave lion Panthera spelaea Quaternary Sci Rev 2011 30 2329 2340 10.1016/j.quascirev.2010.04.023
- Suchard M.A. Weiss R.E. Sinsheimer J.S. Bayesian selection of continuous-time Markov chain evolutionary models Mol Biol Evol 2001 18 1001 1013 10.1093/oxfordjournals.molbev.a003872
-
Turner
A.
Antón
M.
The Big Cats and Their Fossil Relatives 1997 New York Columbia University Press - Vartanyan S.L. Garutt V.E. Sher A.V. Holocene Dwarf Mammoths from Wrangel-Island in the Siberian Arctic Nature 1993 362 337 340 10.1038/362337a0
- Voelker A.H.L. Global distribution of centennial-scale records for Marine Isotope Stage (MIS) 3: a database Quaternary Sci Rev 2002 21 1185 1212 10.1016/S0277-3791(01)00139-1
- Yang D.Y. Eng B. Waye J.S. Dudar J.C. Saunders S.R. Technical note: Improved DNA extraction from ancient bones using silica-based spin columns American Journal of Physical Anthropology 1998 105 539 543 10.1002/(SICI)1096-8644(199804)105:4<;539::AID-AJPA10>3.0.CO;2-1