DNA extraction from dry museum beetles without conferring external morphological damageM Thomas P Gilbert
Department of Ecology and Evolutionary Biology, The University of Arizona, Tucson, Arizona, United States of America
PLoS ONE 2:e272. 2007
..This is clearly undesirable when dealing with rare species or otherwise important specimens, such as type specimens...
Multiplex PCR with minisequencing as an effective high-throughput SNP typing method for formalin-fixed tissueMarcus T P Gilbert
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
Electrophoresis 28:2361-7. 2007
..In the light of this evidence, we suggest that the systematic screening of FFPE collections may in the future provide valuable insights into the past...
- Fellow travellers: a concordance of colonization patterns between mice and men in the North Atlantic region
E P Jones
Department of Biology, University of York, PO Box 373, York YO10 5YW, UK
BMC Evol Biol 12:35. 2012
..Here we investigate whether house mouse mtDNA sequences reflect human history in these other regions as well...
- Statistical analysis of post mortem DNA damage-derived miscoding lesions in Neandertal mitochondrial DNA
Sergi Vives
Institut de Biologia Evolutiva CSIC UPF, Dr, Aiguader 88, 08003 Barcelona, Spain
BMC Res Notes 1:40. 2008
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- Mitogenomic phylogenetic analyses of the Delphinidae with an emphasis on the Globicephalinae
Julia T Vilstrup
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
BMC Evol Biol 11:65. 2011
..Further ad hoc tests were then conducted to estimate the support for alternative topologies...
- Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis
M Thomas P Gilbert
Center for Ancient Genetics, Niels Bohr Institute and Biological Institutes, The University of Copenhagen, Juliane Maries Vej 30, DK 2100 Copenhagen Ø, Denmark
Nucleic Acids Res 35:1-10. 2007
..How widespread these implications are for aDNA will become apparent as future studies analyse data recovered from a wider range of substrates...
- The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?
M Thomas P Gilbert
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, United States of America
PLoS ONE 2:e537. 2007
..Our findings recommend that the extraction methodology adopted should be chosen carefully. Here we provide a quick reference table that can be used to determine appropriate protocols for particular aims...
- Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes
M Thomas P Gilbert
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Proc Natl Acad Sci U S A 105:8327-32. 2008
..Modeling of protein structures failed to indicate any important functional difference between genomes belonging to the two clades, suggesting that the loss of clade II more likely is due to genetic drift than a selective sweep...
- mtDNA from hair and nail clarifies the genetic relationship of the 15th century Qilakitsoq Inuit mummies
M Thomas P Gilbert
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
Am J Phys Anthropol 133:847-53. 2007
..The observation of haplogroups A2a and A2b amongst the 550-year-old Inuit puts a lower limit on the age of the two lineages in Greenland...
- Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution
Eske Willerslev
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100, Denmark
BMC Evol Biol 9:95. 2009
..One notable example concerns the rhinoceroses, a group for which several contradictory phylogenies were proposed on the basis of morphology, then apparently resolved using mitochondrial DNA fragments...
- Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics
Paula F Campos
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, DK 1350 Copenhagen, Denmark
Proc Natl Acad Sci U S A 107:5675-80. 2010
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Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the PleistocenePaula F Campos
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5 7, 1350 Copenhagen, Denmark
Mol Ecol 19:4863-75. 2010
..66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition...
- Whole-genome shotgun sequencing of mitochondria from ancient hair shafts
M Thomas P Gilbert
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Science 317:1927-30. 2007
..The method therefore sets the stage for molecular-genetic analysis of museum collections...
- Ancient human genome sequence of an extinct Palaeo-Eskimo
Morten Rasmussen
Centre for GeoGenetics, Natural History Museum of Denmark and Department of Biology, University of Copenhagen, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Nature 463:757-62. 2010
..This provides evidence for a migration from Siberia into the New World some 5,500 years ago, independent of that giving rise to the modern Native Americans and Inuit...
- Paleo-Eskimo mtDNA genome reveals matrilineal discontinuity in Greenland
M Thomas P Gilbert
Center for Ancient Genetics, Department of Biology, Universitetsparken 15, DK 2100 Copenhagen, Denmark
Science 320:1787-9. 2008
..This result suggests that the earliest migrants into the New World's northern extremes derived from populations in the Bering Sea area and were not directly related to Native Americans or the later Neo-Eskimos that replaced them...
- Species-specific responses of Late Quaternary megafauna to climate and humans
Eline D Lorenzen
Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5 7, DK 1350 Copenhagen K, Denmark
Nature 479:359-64. 2011
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- 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
Science 300:791-5. 2003
..Therefore, many sedimentary deposits may contain unique, and widespread, genetic records of paleoenvironments...
- 800,000 year old mammoth DNA, modern elephant DNA or PCR artefact?
Jonas Binladen
Centre for Ancient Genetics, Niels Bohr Institute and Biological Institute, University of Copenhagen, Juliane Maries Vej 30, 2100 Copenhagen, Denmark
Biol Lett 3:55-6; discussion 60-3. 2007
..Finally, we demonstrate using a simple BLAST search in GenBank that the claimed 'uniquely derived character state' for mammoths is in fact also found within modern elephants...
- Non-destructive sampling of ancient insect DNA
Philip Francis Thomsen
Centre for Ancient Genetics and Environments, Natural History Museum and Institute of Biology, University of Copenhagen, Copenhagen, Denmark
PLoS ONE 4:e5048. 2009
..Finally, we test the possibility of obtaining ancient insect DNA directly from non-frozen sediments deposited 3280-1800 years ago -- an alternative approach that also does not involve destruction of valuable material...
- Ancient biomolecules from deep ice cores reveal a forested southern Greenland
Eske Willerslev
Centre for Ancient Genetics, University of Copenhagen, Denmark
Science 317:111-4. 2007
..The results provide direct evidence in support of a forested southern Greenland and suggest that many deep ice cores may contain genetic records of paleoenvironments in their basal sections...
- Genetic differentiation among North Atlantic killer whale populations
Andrew D Foote
Institute of Biological and Environmental Sciences, University of Aberdeen, School of Biological Sciences, Tillydrone Avenue, Aberdeen, UK
Mol Ecol 20:629-41. 2011
..These results demonstrate that genetic differentiation can arise through resource specialization in the absence of physical barriers to gene flow...
- Authenticity in ancient DNA studies
M Thomas P Gilbert
Center for Ancient Genetics, Niels Bohr and Biological Institutes, University of Copenhagen
Med Secoli 18:701-23. 2006
..In this paper we outline first the problems associated with aDNA studies, and secondly present potential guidelines designed so as to enable non-specialist readers the opportunity to critically assess the quality of aDNA publications...
- The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing
Jonas Binladen
Center for Ancient Genetics, Institute of Biology, University of Copenhagen, Copenhagen, Denmark
PLoS ONE 2:e197. 2007
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- Positive selection on the killer whale mitogenome
Andrew D Foote
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5 7, 1350 Copenhagen, Denmark
Biol Lett 7:116-8. 2011
..Both substitutions were associated with changes in local polarity, increased steric constraints and α-helical tendencies that could influence overall metabolic performance, suggesting a functional change...
- Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna--protocols, problems, and prospects
Morten E Allentoft
Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
PLoS ONE 6:e16670. 2011
..The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research...
- Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960
Michael Worobey
Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA
Nature 455:661-4. 2008
..The recovery of viral gene sequences from decades-old paraffin-embedded tissues opens the door to a detailed palaeovirological investigation of the evolutionary history of HIV-1 that is not accessible by other methods...
- Assessing the fidelity of ancient DNA sequences amplified from nuclear genes
Jonas Binladen
Ancient DNA and Evolution Group, Centre for Ancient Genetics, Niels Bohr Institute, University of Copenhagen, Denmark
Genetics 172:733-41. 2006
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- Ancient DNA reveals late survival of mammoth and horse in interior Alaska
James Haile
Centre for GeoGenetics, University of Copenhagen, Copenhagen 2100, Denmark
Proc Natl Acad Sci U S A 106:22352-7. 2009
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- mtDNA analysis of human remains from an early Danish Christian cemetery
Lars Rudbeck
Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, 2100 Copenhagen, Denmark
Am J Phys Anthropol 128:424-9. 2005
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- DNA from pre-Clovis human coprolites in Oregon, North America
M Thomas P Gilbert
Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, 2100 Copenhagen, Denmark
Science 320:786-9. 2008
..The mtDNA corresponds to Native American founding haplogroups A2 and B2. The dates of the coprolites are >1000 14C years earlier than currently accepted dates for the Clovis complex...
- Evaluating Neanderthal genetics and phylogeny
Martin B Hebsgaard
Centre for Ancient Genetics, Niels Bohr Institute and Biological Institute, University of Copenhagen, Juliane Maries Vej 30, Copenhagen DK 2100, Denmark
J Mol Evol 64:50-60. 2007
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- 5'-tailed sequencing primers improve sequencing quality of PCR products
Jonas Binladen
University of Copenhagen, Denmark
Biotechniques 42:174, 176. 2007
- The emergence of HIV/AIDS in the Americas and beyond
M Thomas P Gilbert
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
Proc Natl Acad Sci U S A 104:18566-70. 2007
..Our results suggest that HIV-1 circulated cryptically in the United States for approximately 12 years before the recognition of AIDS in 1981...
- 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...
- 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...
- 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
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- Most of the extant mtDNA boundaries in south and southwest Asia were likely shaped during the initial settlement of Eurasia by anatomically modern humans
Mait Metspalu
Institute of Molecular and Cell Biology, Tartu University, Tartu, Estonia
BMC Genet 5:26. 2004
..The results were integrated and analyzed together with published data from South, Southeast Asia and West Eurasia...
- Ancient mitochondrial DNA from hair
M Thomas P Gilbert
Curr Biol 14:R463-4. 2004
- Characterization of genetic miscoding lesions caused by postmortem damage
M Thomas P Gilbert
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, Oxford, United Kingdom
Am J Hum Genet 72:48-61. 2003
..Last, a significant correlation between archaeological site and sample-specific level of DNA damage was detected...
- Distribution patterns of postmortem damage in human mitochondrial DNA
M Thomas P Gilbert
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, Oxford, United Kingdom
Am J Hum Genet 72:32-47. 2003
..Finally, a simple method for the identification of incorrect archaeological haplogroup designations is introduced, on the basis of the observed spectrum of postmortem damage...
- More on contamination: the use of asymmetric molecular behavior to identify authentic ancient human DNA
Helena Malmström
Evolutionary Biology, Uppsala University, Uppsala, Sweden
Mol Biol Evol 24:998-1004. 2007
..This asymmetrical behavior of authentic and contaminant DNA can be used to identify authentic haplotypes in human aDNA studies...
- The effect of ancient DNA damage on inferences of demographic histories
Erik Axelsson
Department of Biology, Evolutionary Biology, Copenhagen University, Copenhagen, Denmark
Mol Biol Evol 25:2181-7. 2008
..Our results suggest that population genetic analyses of aDNA sequences, which do not accurately account for damage, should be interpreted with great caution...
- Rescuing ancient DNA
M Thomas P Gilbert
Nat Biotechnol 25:872-4. 2007
- Tracking down human contamination in ancient human teeth
Maria Lourdes Sampietro
Unitat de Biologia Evolutiva, Departament de Ciencies Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Spain
Mol Biol Evol 23:1801-7. 2006
..We argue therefore that the typing of those involved in the manipulation of the ancient human specimens is critical in order to ensure that generated results are accurate...
- The genetic origins of the Andaman Islanders
Phillip Endicott
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, Oxford, OX1 3PS England
Am J Hum Genet 72:178-84. 2003
..The results demonstrate that Victorian anthropological collections can be used to study extinct, or seriously admixed populations, to provide new data about early human origins...
- Barking up the wrong tree: modern northern European dogs fail to explain their origin
Helena Malmström
Department of Evolutionary Biology, Uppsala University, SE 752 36 Uppsala, Sweden
BMC Evol Biol 8:71. 2008
..This has been suggested to indicate a possible origin of the haplogroup (perhaps even a separate domestication) in central or northern Europe...
- A preliminary analysis of the DNA and diet of the extinct Beothuk: a systematic approach to ancient human DNA
Melanie Kuch
McMaster Ancient DNA Center, McMaster University, Hamilton, ON L8S 4L9, Canada
Am J Phys Anthropol 132:594-604. 2007
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- 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
- Stable isotope and DNA evidence for ritual sequences in Inca child sacrifice
Andrew S Wilson
Archaeological Sciences School of Life Sciences, University of Bradford, Bradford BD7 1DP, United Kingdom
Proc Natl Acad Sci U S A 104:16456-61. 2007
..Such direct information amplifies, yet also partly contrasts with, Spanish historical accounts...
- Reply to Pape et al.: the phylogeography of HIV-1 group M subtype B
Michael Worobey
Proc Natl Acad Sci U S A 105:E16. 2008
- Absence of Yersinia pestis-specific DNA in human teeth from five European excavations of putative plague victims
M Thomas P Gilbert
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
Microbiology 150:341-54. 2004
..In addition, the utility of the published tooth-based ancient DNA technique used to diagnose fatal bacteraemias in historical epidemics still awaits independent corroboration...
- Resistance of degraded hair shafts to contaminant DNA
M Thomas P Gilbert
Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, University of Oxford, South Parks Rd, Oxford OX1 3PS, UK
Forensic Sci Int 156:208-12. 2006
..Therefore, hair samples represent an important and underestimated source of DNA in both forensic and ancient DNA studies...
- Beringian paleoecology inferred from permafrost-preserved fungal DNA
Magnus C Lydolph
Microbial Discovery, Novozymes A S, Smørmosevej 25 1B1, DK 2880 Bagsvaerd, Denmark
Appl Environ Microbiol 71:1012-7. 2005
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- Long-term survival of ancient DNA in Egypt: response to Zink and Nerlich (2003)
M Thomas P Gilbert
Department of Zoology, Oxford University, Oxford, OX1 3PS United Kingdom
Am J Phys Anthropol 128:110-4; discussion 115-8. 2005
