Phylogeography of lions (Panthera leo) reveals a Late Pleistocene reduction in genetic diversity
Barnett R, Shapiro B, Ho SYW, Barnes I, Burger J, Yamaguchi N, Higham T, Wheeler HT, Rosendhal W, Sher AV, Baryshnikov G, Cooper A
Molecular Ecology 18: 1668-1677 (2009)
Ancient DNA typing of archaeological pig remains corroborates historical records
Haile J, Larson G, Owens K, Dobney K, Shapiro B
Journal of Archaeological Sciences (in press)
Pleistocene steppe bison (Bison priscus) partial carass from Tsiigehtchic, Northwest Territories, Canada
Zazula GD, MacKay G, Andrews TD, Shapiro B, Letts B, Brock F
Quaternary Science Reviews (in press)
Bison bone collagen isotopic values track climate fluctuations and vegetation change in Late Pleistocene and Early Holocene Northern Eurasia and North America
Richards M, Shapiro B, Ditchfield P, Cooper A
Geological Journal (in press)
Is amino acid racemization a useful tool for screening for ancient DNA in bone?
Collins MJ, Penkman KEH, Rohalnd N, Shapiro B, Dobberstein RC, Rotz-Timme A, Hofretier M
Proceedings of the Royal Society of London - Series B 276: 2971-2977 (2009) pre-publication proof
The Late Pleistocene distribution of vicuñas (Vicugna vicugna) and the “extinction” of the gracile llama (Lama gracilis): New molecular data
Weinstock J. Shapiro B, Prieto A, Martin JC, Gonzáles BA, Gilbert MPT, Willerslev E
Quaternary Science Reviews 28: 15-16 (2009)
Accommodating the effect of ancient DNA damage on inferences of demographic histories
Rambaut A, Ho SYW, Drummond AJ, Shapiro B
Molecular Biology and Evolution 26: 245-248 (2009) pdf
Mid-Holocene vertebrate bone Concentration-Lagerstätte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus)
Rijsdijk KF, Hume JP, Bunnik F, Florens V, Baider C, Shapiro B, van der Plicht J, Janoo A, Griffiths O, van den Hoek Ostende LW, Cremer H, Vernimmen T, De Louw P, Bholah A, Saumtally S, Porch N, Haile J, Buckley M, Collins MC, Gittenberger E
Quaternary Science Reviews 28: 14-24 (2009) pdf
Engineered polymerases amplify the potential of ancient DNA
Shapiro B
Trends in Biotechnology 26: 285-287 (2008) pdf
Late Pleistocene Northward-dispersing Bison antiquus from the Bighill Creek Formation, Gallelli Gravel Pit, Alberta, Canada, and the Fate of Bison occidentalis
Wilson M, Shapiro B, Hills LV
Canadian Journal of Earth Sciences 45: 827-859 (2008) abstract pdf
Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
Ho SYW, Larson G, Edwards CJ, Heupink TH, Lakin KE, Holland PWH, Shapiro B
Biology Letters 274: 1377-1385 (2008) pdf
The effect of inappropriate calibration in molecular ecological studies: evidence from three case studies
Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B
PLoS ONE 3: e1615 (2008) link pdf
Recovery of DNA from footprints in the snow
Dalén L, Götherström A, Shapiro B
Canadian Field Naturalist 12: 321-324 (2008) pdf
Ancient DNA analysis indicates the first English lions originated from North Africa
Barnett R, Yamaguchi N, Shapiro B, Sabin R
Contributions to Zoology 77: 7-16 (2008) pdf
Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
Buckley M, Walker A, Ho SYW, Yang Y, Smith C, Ashton P, Oates JT, Cappellini E, Koon H, Penkman K, Elsworth B, Ashford D, Solazzo C, Andrews P, Strahler J, Shapiro B, Ostrom P, Gandhi H, Miller W, Raney B, Zylber MI, Gilbert MT, Prigodich RV, Ryan M, Rijsdijk KF, Janoo A, Collins MJ
Science 319:33 (2008) abstract pdf supporting material
Using ancient DNA techniques to identify the origin of an unprovenanced museum specimen, as illustrated by the identification of a 19th century lion from Amsterdam
Barnett R, Yamaguchi N, Shapiro B, Nijman VB
Contributions to Zoology 76: 87-94 (2007) abstract pdf
Genetic structure and extinction of the woolly mammoth Mammuthus primigenius (Blum.)
Barnes I, Shapiro B, Kuznetsova T, Sher A, Guthrie D, Lister A, Thomas MG
Current Biology 17: 1072-1075 (2007) abstract pdf
Bayesian estimation of sequence damage in ancient DNA
Ho SYW, Heupink, TH, Rambaut, A, Shapiro B
Molecular Biology and Evolution 24:1416-1422 (2007) abstract pdf
Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs
Edwards CJ, Bollongino R, Scheu A, Chamberlain A, Tresset A, Vigne J-D, Baird JF, Larson G, Ho SYW, Heupink TH, Shapiro B, Freeman AR, Thomas MG, Arbogast R-M, Arndt B, Bartosiewicz L, Benecke N, Budja M, Chaix L, Choyke AM, Coqueugniot E, Dohle H-J, Goldner H, Hartz S, Helmer D, Herzig B, Hongo H, Mashkour M, Ozdogan M, Pucher E, Roth G, Schade-Lindig S, Schmolcke U, Schulting RJ, Stephan E, Uerpmann H-P, Voros I, Voytek B, Bradley DG, Burger J
Proceedings of the Royal Society B 274: 1377-1385 (2007) abstract pdf
Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
Haile J, Holdaway R, Oliver K, Bunce M, Gilbert MTP, Nielsen R, Munch K, Ho, SYW, Shapiro B, Willerslev E
Molecular Biology and Evolution 24: 982-989 (2007) abstract pdf
No proof that typhoid caused the Plague of Athens
Shapiro B, Rambaut A, Gilbert MTP
International Journal of Infectious Disease 10:334-335 (2006) abstract
Metagenomics to paleogenomics: large scale sequencing of mammoth DNA
Poinar HN, Schwartz C, Qi J, Shapiro B, MacPhee RD, Biogues B, Tikhonov A, Huson D, Tonsho LP, Auch A, Rampp M, Miller W, Schuster SC
Science 311: 392-394 (2006) abstract pdf
Bayesian coalescent inference of past population dynamics from molecular sequences
Drummond AJ, Pybus OG, Shapiro B, Rambaut A
Molecular Biology and Evolution 22: 1185-1192 (2005) full text
Post-mortem DNA damage hotspots in Bison (Bison bison and B. bonasus) provide supporting evidence for mutational hotspots in human mitochondria
Gilbert MTP, Shapiro B, Drummond A, Cooper A
Journal of Archaeological Sciences 32:1053-1060 (2005) abstract
Ancient DNA provides new insights into the evolutionary history of New Zealand’s extinct giant eagle
Bunce M, Szulkin M, Lerner HRL, Barnes I, Shapiro B, Cooper A, Holdaway RN
PLoS Biology 3(1) e20 (2005) abstract pdf
Rise and fall of the Beringian steppe bison
Shapiro B, Drummond AJ, Rambaut A, Wilson MC, Matheus P, Sher AV, Pybus OG, Gilbert MTP, Barnes I, Binladen J, Willerslev E, Hansen A, Baryshnikov GF, Burns JA, Davydov S, Driver JC, Froese D, Harington CR, Keddie G, Kosintsev P, Kunz ML, Martin LD, Stephenson RO, Storer J, Tedford R, Zimov S, Cooper A
Science 306: 1561-1565 (2004) abstract pdf
Ancient mitochondrial DNA from hair
Gilbert MTP, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, Higham TFG, Richards MP, O’Connell TC, Tobin DJ, Janaway RC, Cooper A
Current Biology 14: R463-464 (2004) abstract
Beringia as an Ice Age genetic museum
Shapiro B, Cooper A
Quaternary Research 60 (1): 94-100 (2003) abstract
Diverse plant and animal genetic records from Holocene and Pleistocene sediments
Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A
Science 300: 791-795 (2003) abstract pdf
Exceptional preservation in bison bones older than 55 ka demonstrated by protein and DNA sequences
Nielsen-Marsh, CM, Ostrom PH, Gandhi H, Shapiro B, Cooper A, Collins MJ
Geology 30: 1099-1102 (2002) pdf
Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus
Lalueza-Fox, C, Shapiro B, Bover P, Alcover JA, Bertranpetit J
Molecular Phylogenetics and Evolution 25 (3): 501-510 (2002) abstract
Flight of the Dodo
Shapiro B, Sibthorpe D, Austin J, Wragg G, Lee PLM, Bininda-Emonds ORP, and Cooper A
Science 295: 1683 (2002) abstract pdf
Dynamics of mammal population extinctions in eastern Beringia during the last glaciation
Barnes I, Matheus P, Shapiro B, Jensen D, Cooper A
Science 295: 2267-2270 (2002) abstract pdf
BOOK CHAPTERS
Using DNA to investigate human evolution
Shapiro B, Gilbert MTP, Barnes I
In H Schutkowski, Ed. Between Biology and Culture. Cambridge University Press (in press).
Insights into the evolutionary history of an emerging livestock pathogen: Porcine Circovirus 2
Ramsden C, Charleston MA, Duffy S, Shapiro B, Holmes EC
Journal of Virology (in press)
Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
Kapoor A, Shapiro B, Shafer RW, Rhee S-Y, Delwart EL
Retrovirology 5: 7 (2008) full text
Estimating the relative contribution of dNTP pool imbalance and APOBEC3G/3F editing to HIV evolution in vivo
Deforche K, Camacho R, Laethem KV, Shapiro B, Moreau Y, Rambaut A, Vandamme A-M, Lemey P
Journal of Computational Biology 14:1105-14 (2007) abstract
Recombination is confounding the early evolutionary history of HIV-1: subtype G is a circulating recombinant form
Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme A-M
Journal of Virology 81: 8543-51 (2007) abstract
Ancient papillomavirus-host co-speciation in Felidae
Rector A, Lemey P, Tachezy R, Mostmans S, Ghim S-G, Van Doorslaer K, Roelke M, Bush M, Montali RJ, Joslin J, Burk RD, Jenson AB, Sundberg JP, Shapiro B, Van Ranst M
Genome Biology 8:R57 (2007) full text
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics
Lemey P. Kosakovsky-Pond SL, Drummond AJ, Pybus OG, Shapiro B, Barroso H, Taveira N, Rambaut A
PLoS Computational Biology 3:e29 (2007) full text
A phylogenetic method to detect positive epistasis and its application to RNA virus evolution
Shapiro B, Drummond AJ, Rambaut A, Pybus OJ, Holmes EC
Molecular Biology and Evolution 23: 1724-1730 (2006) full text
Accommodating the effect of ancient DNA damage on inferences of demographic histories
Rambaut A, Ho SYW, Drummond AJ, Shapiro B
Molecular Biology and Evolution (in press)
The effect of inappropriate calibration in molecular ecological studies: evidence from three case studies
Ho SYW, Saarma U, Barnett R, Haile J, Shapiro B
PLoS ONE 3: e1615 (2008)
Evidence for time dependency of molecular rate estimates
Ho SYW, Shapiro B, Phillips MJ, Cooper A, Drummond AJ
Systematic Biology 56: 515-522 (2007) pdf
Bayesian estimation of sequence damage in ancient DNA
Ho SYW, Heupink, TH, Rambaut, A, Shapiro B
Molecular Biology and Evolution 24:1416-1422 (2007) abstract pdf
Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences
Shapiro B, Rambaut A, Drummond AJ
Molecular Biology and Evolution 23: 7-9 (2006) full text
Bayesian coalescent inference of past population dynamics from molecular sequences
Drummond AJ, Pybus OG, Shapiro B, Rambaut A
Molecular Biology and Evolution 22: 1185-1192 (2005) full text
Is the endangered Grevy’s zebra threatened by hybridization?
Cordingly JE, Sundarisan SR, Fischhoff IR, Shapiro B, Ruskey J, Rubenstein DI
Animal Conservation (in press) abstract pdf
BOOK CHAPTERS
Natural selection and adaptation of molecular sequences
Pybus OG, Shapiro B
In Lemey P, Salemi M, Vandamme A-M, Eds., The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing (2nd Edition). Cambridge University Press (in press).
Using DNA to investigate human evolution
Shapiro B, Gilbert MTP, Barnes I
In Schutkowski H, Ed., Between Biology and Culture. Cambridge University Press (2008)
Ancient DNA from vertebrate fossils
Barnett R, Shapiro B, Barnes I
In Elias SA, Ed., Encyclopedia of Quaternary Science. Elsevier (2006)
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