Beth Shapiro

Summary

Affiliation: Pennsylvania State University
Country: USA

Publications

  1. pmc A Bayesian phylogenetic method to estimate unknown sequence ages
    Beth Shapiro
    Department of Biology, The Pennsylvania State University, PA, USA
    Mol Biol Evol 28:879-87. 2011
  2. pmc Improving the performance of true single molecule sequencing for ancient DNA
    Aurélien Ginolhac
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5 7 Øster Voldgade, København, 1350, Denmark
    BMC Genomics 13:177. 2012
  3. doi request reprint Engineered polymerases amplify the potential of ancient DNA
    Beth Shapiro
    Department of Biology, 326 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16801, USA
    Trends Biotechnol 26:285-7. 2008
  4. doi request reprint Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon
    Tara L Fulton
    Department of Biology, The Pennsylvania State University, 320 Mueller Laboratory, University Park, PA 16802, USA
    Methods Mol Biol 840:29-35. 2012
  5. pmc Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses
    Cadhla Firth
    Department of Biology, The Pennsylvania State University, USA
    Mol Biol Evol 27:2038-51. 2010
  6. pmc Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2
    Cadhla Firth
    Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 83:12813-21. 2009
  7. pmc Multiple losses of flight and recent speciation in steamer ducks
    Tara L Fulton
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Proc Biol Sci 279:2339-46. 2012
  8. doi request reprint Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons
    Tara L Fulton
    Department of Biology, Pennsylvania State University, University Park, 16801, United States
    Ann Anat 194:52-7. 2012
  9. doi request reprint Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the last glacial maximum
    Tara L Fulton
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 22:2540-8. 2013
  10. doi request reprint Case study: ancient DNA recovered from pleistocene-age remains of a Florida armadillo
    Brandon Letts
    Department of Biology, The Pennsylvania State University, 320 Mueller Laboratory, University Park, PA 16802, USA
    Methods Mol Biol 840:87-92. 2012

Collaborators

Detail Information

Publications25

  1. pmc A Bayesian phylogenetic method to estimate unknown sequence ages
    Beth Shapiro
    Department of Biology, The Pennsylvania State University, PA, USA
    Mol Biol Evol 28:879-87. 2011
    ....
  2. pmc Improving the performance of true single molecule sequencing for ancient DNA
    Aurélien Ginolhac
    Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen University, 5 7 Øster Voldgade, København, 1350, Denmark
    BMC Genomics 13:177. 2012
    ..Here, we aim at improving even further the performance of tSMS for ancient DNA by testing two novel tSMS template preparation methods for Pleistocene bone fossils, namely oligonucleotide spiking and treatment with DNA phosphatase...
  3. doi request reprint Engineered polymerases amplify the potential of ancient DNA
    Beth Shapiro
    Department of Biology, 326 Mueller Laboratory, The Pennsylvania State University, University Park, PA 16801, USA
    Trends Biotechnol 26:285-7. 2008
    ..Recent work has shown that it is possible to engineer a polymerase capable of using even highly damaged fragments as template sequences...
  4. doi request reprint Case study: recovery of ancient nuclear DNA from toe pads of the extinct passenger pigeon
    Tara L Fulton
    Department of Biology, The Pennsylvania State University, 320 Mueller Laboratory, University Park, PA 16802, USA
    Methods Mol Biol 840:29-35. 2012
    ..We describe simple modifications to both protocols that we employed during the DNA extraction process...
  5. pmc Using time-structured data to estimate evolutionary rates of double-stranded DNA viruses
    Cadhla Firth
    Department of Biology, The Pennsylvania State University, USA
    Mol Biol Evol 27:2038-51. 2010
    ....
  6. pmc Insights into the evolutionary history of an emerging livestock pathogen: porcine circovirus 2
    Cadhla Firth
    Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, PA 16802, USA
    J Virol 83:12813-21. 2009
    ..This high rate of evolution may allow PCV2 to maintain evolutionary dynamics closer to those of single-stranded RNA viruses than to those of double-stranded DNA viruses, further facilitating the rapid emergence of PCV2 worldwide...
  7. pmc Multiple losses of flight and recent speciation in steamer ducks
    Tara L Fulton
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Proc Biol Sci 279:2339-46. 2012
    ..Their phylogenetic relationships suggest multiple losses of flight and/or long-term persistence of mixed-flight capability. As such, steamer ducks may provide a model system to study the evolution of flightlessness...
  8. doi request reprint Nuclear DNA from the extinct Passenger Pigeon (Ectopistes migratorius) confirms a single origin of New World pigeons
    Tara L Fulton
    Department of Biology, Pennsylvania State University, University Park, 16801, United States
    Ann Anat 194:52-7. 2012
    ..These findings have implications for the colonization of North America by pigeons and doves...
  9. doi request reprint Ancient DNA supports southern survival of Richardson's collared lemming (Dicrostonyx richardsoni) during the last glacial maximum
    Tara L Fulton
    Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
    Mol Ecol 22:2540-8. 2013
    ..While more data are required to determine whether or not the LGM southern population is ancestral to extant D. richardsoni, it seems most probable that the species survived the LGM in a southern refugium...
  10. doi request reprint Case study: ancient DNA recovered from pleistocene-age remains of a Florida armadillo
    Brandon Letts
    Department of Biology, The Pennsylvania State University, 320 Mueller Laboratory, University Park, PA 16802, USA
    Methods Mol Biol 840:87-92. 2012
    ....
  11. doi request reprint Analysis of ancient human genomes: using next generation sequencing, 20-fold coverage of the genome of a 4,000-year-old human from Greenland has been obtained
    Beth Shapiro
    Department of Biology, The Pennsylvania State University, University Park, PA, USA
    Bioessays 32:388-91. 2010
    ....
  12. pmc Correlating Bayesian date estimates with climatic events and domestication using a bovine case study
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, UK
    Biol Lett 4:370-4. 2008
    ..The divergence age estimates support domestication-associated expansion times (less than 12 kyr) for the major haplogroups of cattle. We compare the molecular and palaeontological estimates for the Bison-Bos divergence...
  13. pmc The effect of inappropriate calibration: three case studies in molecular ecology
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    PLoS ONE 3:e1615. 2008
    ..Collectively, the results emphasise the importance of judicious selection of calibrations for analyses of recent evolutionary events...
  14. pmc Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry"
    Mike Buckley
    BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK
    Science 319:33; author reply 33. 2008
    ..rex does not...
  15. ncbi request reprint Diverse plant and animal genetic records from Holocene and Pleistocene sediments
    Eske Willerslev
    Department of Evolutionary Biology, Zoological Institute, University of Copenhagen, Universitetsparken 15, Denmark DK 2100 Ø
    Science 300:791-5. 2003
    ..Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments...
  16. ncbi request reprint Ancient mitochondrial DNA from hair
    M Thomas P Gilbert
    Curr Biol 14:R463-4. 2004
  17. ncbi request reprint Rise and fall of the Beringian steppe bison
    Beth Shapiro
    Henry Wellcome Ancient Biomolecules Centre, Oxford University, South Parks Road, Oxford OX13PS, UK
    Science 306:1561-5. 2004
    ....
  18. pmc Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle
    Michael Bunce
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology University of Oxford, United Kingdom
    PLoS Biol 3:e9. 2005
    ..This spectacular evolutionary change illustrates the potential speed of size alteration within lineages of vertebrates, especially in island ecosystems...
  19. ncbi request reprint Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA
    Hendrik N Poinar
    McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada
    Science 311:392-4. 2006
    ..The sample includes a surprisingly small diversity of environmental DNAs. The high percentage of endogenous DNA recoverable from this single mammoth would allow for completion of its genome, unleashing the field of paleogenomics...
  20. ncbi request reprint No proof that typhoid caused the Plague of Athens (a reply to Papagrigorakis et al.)
    Beth Shapiro
    Int J Infect Dis 10:334-5; author reply 335-6. 2006
  21. ncbi request reprint Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor?
    James Haile
    Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
    Mol Biol Evol 24:982-9. 2007
    ..Our study indicates that DNA from sediments can still offer a rich source of information on past environments, provided that the risk from vertical migration can be controlled for...
  22. ncbi request reprint Bayesian estimation of sequence damage in ancient DNA
    Simon Y W Ho
    Department of Zoology, University of Oxford, Oxford, United Kingdom
    Mol Biol Evol 24:1416-22. 2007
    ....
  23. pmc Ancient papillomavirus-host co-speciation in Felidae
    Annabel Rector
    Laboratory of Clinical and Epidemiological Virology, Rega Institute for Medical Research, University of Leuven, Leuven, Belgium
    Genome Biol 8:R57. 2007
    ....
  24. ncbi request reprint Genetic structure and extinction of the woolly mammoth, Mammuthus primigenius
    Ian Barnes
    School of Biological Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, United Kingdom
    Curr Biol 17:1072-5. 2007
    ..The most marked change in diversity at this time is the loss of one of two major mitochondrial lineages...
  25. ncbi request reprint Molecular phylogeny and evolution of the extinct bovid Myotragus balearicus
    Carles Lalueza-Fox
    Laboratori d Antropologia, Facultat de Biologia, Universitat de Barcelona, Avda Diagonal 645, Spain
    Mol Phylogenet Evol 25:501-10. 2002
    ....