Mitogenomic analyses from ancient DNA.

[1]  J. Poulain,et al.  Coprolites as a source of information on the genome and diet of the cave hyena , 2012, Proceedings of the Royal Society B: Biological Sciences.

[2]  Johnf . Thompson,et al.  Improving the performance of true single molecule sequencing for ancient DNA , 2012, BMC Genomics.

[3]  B. Hallström,et al.  Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage , 2012, Science.

[4]  K. Tsangaras,et al.  Museums and disease: using tissue archive and museum samples to study pathogens. , 2012, Annals of anatomy = Anatomischer Anzeiger : official organ of the Anatomische Gesellschaft.

[5]  Natalie M. Myres,et al.  New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing , 2012, Nature Communications.

[6]  S. Ho,et al.  Evaluating the Impact of Post-Mortem Damage in Ancient DNA: A Theoretical Approach , 2011, Journal of Molecular Evolution.

[7]  M. Meyer,et al.  Multilocus Resolution of Phylogeny and Timescale in the Extant Adaptive Radiation of Hawaiian Honeycreepers , 2011, Current Biology.

[8]  Julia T. Vilstrup,et al.  Mitogenome Phylogenetics: The Impact of Using Single Regions and Partitioning Schemes on Topology, Substitution Rate and Divergence Time Estimation , 2011, PloS one.

[9]  J. Ayroles,et al.  Museum genomics: low‐cost and high‐accuracy genetic data from historical specimens , 2011, Molecular ecology resources.

[10]  Matthias Meyer,et al.  A draft genome of Yersinia pestis from victims of the Black Death , 2011, Nature.

[11]  Yong Wang,et al.  An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia , 2011, Science.

[12]  W. Murphy,et al.  Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens. , 2011, Genome research.

[13]  P. Kapranov,et al.  True single-molecule DNA sequencing of a pleistocene horse bone. , 2011, Genome research.

[14]  T. Glenn.  Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.

[15]  David J D Earn,et al.  Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death , 2011, Proceedings of the National Academy of Sciences.

[16]  M. Thomas P. Gilbert,et al.  Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA , 2011, Scientific reports.

[17]  M. Hofreiter,et al.  Discovery of lost diversity of paternal horse lineages using ancient DNA. , 2011, Nature communications.

[18]  John J. Welch,et al.  Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline , 2011, Current Biology.

[19]  Tom H. Pringle,et al.  Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil) , 2011, Proceedings of the National Academy of Sciences.

[20]  Steven L Salzberg,et al.  Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths , 2011, Genome Biology.

[21]  Jon R. Armstrong,et al.  Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue. , 2011, The Journal of molecular diagnostics : JMD.

[22]  G. Bertorelle,et al.  The Complete Mitochondrial Genome of an 11,450-year-old Aurochsen (Bos primigenius) from Central Italy , 2011, BMC Evolutionary Biology.

[23]  Philip L. F. Johnson,et al.  Genetic history of an archaic hominin group from Denisova Cave in Siberia , 2010, Nature.

[24]  Swapan Mallick,et al.  Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants , 2010, PLoS biology.

[25]  S. Pääbo,et al.  Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products , 2010, PloS one.

[26]  M. Hofreiter,et al.  Next Generation Sequencing of Ancient DNA: Requirements, Strategies and Perspectives , 2010, Genes.

[27]  James Haile,et al.  Fossil avian eggshell preserves ancient DNA , 2010, Proceedings of the Royal Society B: Biological Sciences.

[28]  N. Rohland,et al.  Substitutions in woolly mammoth hemoglobin confer biochemical properties adaptive for cold tolerance , 2010, Nature Genetics.

[29]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[30]  Philip L. F. Johnson,et al.  A Draft Sequence of the Neandertal Genome , 2010, Science.

[31]  Philip L. F. Johnson,et al.  Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture , 2010, Science.

[32]  J. Delgado,et al.  Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms. , 2010, Animal genetics.

[33]  Qiaomei Fu,et al.  The complete mitochondrial DNA genome of an unknown hominin from southern Siberia , 2010, Nature.

[34]  W. Miller,et al.  Complete mitochondrial genome of a Pleistocene jawbone unveils the origin of polar bear , 2010, Proceedings of the National Academy of Sciences.

[35]  D. A. Magee,et al.  A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius) , 2010, PloS one.

[36]  A. Krogh,et al.  Ancient human genome sequence of an extinct Palaeo-Eskimo , 2010, Nature.

[37]  Martin Kircher,et al.  A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia , 2010, Current Biology.

[38]  Emily H Turner,et al.  Target-enrichment strategies for next-generation sequencing , 2010, Nature Methods.

[39]  Volker Deckert,et al.  Recent advances in single-molecule sequencing. , 2010, Current opinion in biotechnology.

[40]  D. Summerer.  Enabling technologies of genomic-scale sequence enrichment for targeted high-throughput sequencing. , 2009, Genomics.

[41]  C. Millar,et al.  High mitogenomic evolutionary rates and time dependency. , 2009, Trends in genetics : TIG.

[42]  U. Stenzel,et al.  Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. , 2009, Genome research.

[43]  M. Hofreiter,et al.  Ecological Change, Range Fluctuations and Population Dynamics during the Pleistocene , 2009, Current Biology.

[44]  Adrian W. Briggs,et al.  Targeted Retrieval and Analysis of Five Neandertal mtDNA Genomes , 2009, Science.

[45]  Arne Röhl,et al.  Correcting for purifying selection: an improved human mitochondrial molecular clock. , 2009, American journal of human genetics.

[46]  Hans-Jürgen Bandelt,et al.  The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome , 2009, PloS one.

[47]  Zhenyu Xuan,et al.  Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing , 2009, Nature Protocols.

[48]  W. Miller,et al.  Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution , 2009, BMC Evolutionary Biology.

[49]  E. Rogaev,et al.  Genomic identification in the historical case of the Nicholas II royal family , 2009, Proceedings of the National Academy of Sciences.

[50]  N. Rohland,et al.  First DNA sequences from Asian cave bear fossils reveal deep divergences and complex phylogeographic patterns , 2009, Molecular ecology.

[51]  J. Maguire,et al.  Solution Hybrid Selection with Ultra-long Oligonucleotides for Massively Parallel Targeted Sequencing , 2009, Nature Biotechnology.

[52]  Yeting Zhang,et al.  The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus). , 2008, Genome research.

[53]  Eric S. Lander,et al.  Sequencing the nuclear genome of the extinct woolly mammoth , 2008, Nature.

[54]  M. Richards,et al.  Complete Mitochondrial Genome Sequence of the Tyrolean Iceman , 2008, Current Biology.

[55]  J. van der Plicht,et al.  Deciphering the complete mitochondrial genome and phylogeny of the extinct cave bear in the Paleolithic painted cave of Chauvet , 2008, Proceedings of the National Academy of Sciences.

[56]  H. McCallum,et al.  Tasmanian devil facial tumour disease: lessons for conservation biology. , 2008, Trends in ecology & evolution.

[57]  A. Drummond,et al.  Bayesian inference of population size history from multiple loci , 2008, BMC Evolutionary Biology.

[58]  Hanlee P. Ji,et al.  Next-generation DNA sequencing , 2008, Nature Biotechnology.

[59]  Edward L. Braun,et al.  Phylogenomic evidence for multiple losses of flight in ratite birds , 2008, Proceedings of the National Academy of Sciences.

[60]  J. Southon,et al.  Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths , 2008, Current Biology.

[61]  Philip L. F. Johnson,et al.  A Complete Neandertal Mitochondrial Genome Sequence Determined by High-Throughput Sequencing , 2008, Cell.

[62]  Svante Pääbo,et al.  Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary , 2008, BMC Evolutionary Biology.

[63]  C. Millar,et al.  New developments in ancient genomics. , 2008, Trends in ecology & evolution.

[64]  M. Metspalu,et al.  Paleo-Eskimo mtDNA Genome Reveals Matrilineal Discontinuity in Greenland , 2008, Science.

[65]  Aakrosh Ratan,et al.  Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes , 2008, Proceedings of the National Academy of Sciences.

[66]  Hans-Jürgen Bandelt,et al.  Mitochondrial genomes of extinct aurochs survive in domestic cattle , 2008, Current Biology.

[67]  J. Hodgson,et al.  No evidence of a Neanderthal contribution to modern human diversity , 2008, Genome Biology.

[68]  S. Ho,et al.  Elevated substitution rates estimated from ancient DNA sequences , 2007, Biology Letters.

[69]  L. Keller,et al.  Back to the future: museum specimens in population genetics. , 2007, Trends in ecology & evolution.

[70]  Z. Xuan,et al.  Genome-wide in situ exon capture for selective resequencing , 2007, Nature Genetics.

[71]  Jaume Bertranpetit,et al.  A Melanocortin 1 Receptor Allele Suggests Varying Pigmentation Among Neanderthals , 2007, Science.

[72]  D. Turnbull,et al.  Relative rates of evolution in the coding and control regions of African mtDNAs. , 2007, Molecular biology and evolution.

[73]  Stephan C. Schuster,et al.  Whole-Genome Shotgun Sequencing of Mitochondria from Ancient Hair Shafts , 2007, Science.

[74]  Philip L. F. Johnson,et al.  Patterns of damage in genomic DNA sequences from a Neandertal , 2007, Proceedings of the National Academy of Sciences.

[75]  M. Beaumont,et al.  Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions , 2007, Nucleic acids research.

[76]  M. Hofreiter.  Pleistocene Extinctions: Haunting the Survivors , 2007, Current Biology.

[77]  M. Slatkin,et al.  Proboscidean Mitogenomics: Chronology and Mode of Elephant Evolution Using Mastodon as Outgroup , 2007, PLoS biology.

[78]  James Haile,et al.  Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland , 2007, Science.

[79]  Michael Hofreiter,et al.  Ancient DNA extraction from bones and teeth , 2007, Nature Protocols.

[80]  Mark George Thomas,et al.  Genetic Structure and Extinction of the Woolly Mammoth, Mammuthus primigenius , 2007, Current Biology.

[81]  S. Ho,et al.  Evidence for time dependency of molecular rate estimates. , 2007, Systematic biology.

[82]  N. Rohland,et al.  Comparison and optimization of ancient DNA extraction. , 2007, BioTechniques.

[83]  M. Carling,et al.  Gene Sampling Strategies for Multi-Locus Population Estimates of Genetic Diversity (θ) , 2007, PloS one.

[84]  Feng Chen,et al.  Sequencing and Analysis of Neanderthal Genomic DNA , 2006, Science.

[85]  Adrian W. Briggs,et al.  Analysis of one million base pairs of Neanderthal DNA , 2006, Nature.

[86]  W. Miller,et al.  Recharacterization of ancient DNA miscoding lesions: insights in the era of sequencing-by-synthesis , 2006, Nucleic acids research.

[87]  M. Meyer,et al.  Multiplex amplification of ancient DNA , 2006, Nature Protocols.

[88]  Jaume Bertranpetit,et al.  Nuclear Gene Indicates Coat-Color Polymorphism in Mammoths , 2006, Science.

[89]  P. Taberlet,et al.  The origin of European cattle: evidence from modern and ancient DNA. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[90]  J. Felsenstein.  Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci? , 2006, Molecular biology and evolution.

[91]  Ian Barnes,et al.  Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae , 2006, Nature.

[92]  Alexander F. Auch,et al.  Metagenomics to Paleogenomics: Large-Scale Sequencing of Mammoth DNA , 2006, Science.

[93]  S. O’Brien,et al.  Genomic inferences from Afrotheria and the evolution of elephants. , 2005, Current opinion in genetics & development.

[94]  S. Pääbo,et al.  The population history of extant and extinct hyenas. , 2005, Molecular biology and evolution.

[95]  M. Hofreiter,et al.  Assessing ancient DNA studies. , 2005, Trends in ecology & evolution.

[96]  James R. Knight,et al.  Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.

[97]  Edward M. Rubin,et al.  Genomic Sequencing of Pleistocene Cave Bears , 2005, Science.

[98]  R. Debruyne.  A case study of apparent conflict between molecular phylogenies: the interrelationships of African elephants , 2005, Cladistics : the international journal of the Willi Hennig Society.

[99]  E. Willerslev,et al.  Review Paper. Ancient DNA , 2005, Proceedings of the Royal Society B: Biological Sciences.

[100]  S. Pääbo,et al.  Genetic analyses from ancient DNA. , 2004, Annual review of genetics.

[101]  Michael Bunce,et al.  Ancient mitochondrial DNA from hair , 2004, Current Biology.

[102]  S. Pääbo,et al.  No Evidence of Neandertal mtDNA Contribution to Early Modern Humans , 2004, PLoS biology.

[103]  Svante Pääbo,et al.  Evidence for Reproductive Isolation between Cave Bear Populations , 2004, Current Biology.

[104]  W. Hoppitt,et al.  Extreme reversed sexual size dimorphism in the extinct New Zealand moa Dinornis , 2003, Nature.

[105]  C. Millar,et al.  Nuclear DNA sequences detect species limits in ancient moa , 2003, Nature.

[106]  L. Orlando,et al.  Ancient DNA analysis reveals woolly rhino evolutionary relationships. , 2003, Molecular phylogenetics and evolution.

[107]  Chris Stringer,et al.  University of Birmingham The thermal history of human fossils and the likelihood of successful DNA amplification , 2003 .

[108]  S. Pääbo,et al.  Nuclear Gene Sequences from a Late Pleistocene Sloth Coprolite , 2003, Current Biology.

[109]  U. Gyllensten,et al.  Mitochondrial genome variation and evolutionary history of Australian and New Guinean aborigines. , 2003, Genome research.

[110]  V. Barriel,et al.  Mitochondrial cytochrome b of the Lyakhov mammoth (Proboscidea, Mammalia): new data and phylogenetic analyses of Elephantidae. , 2003, Molecular phylogenetics and evolution.

[111]  Svante Pääbo,et al.  The mosaic that is our genome , 2003, Nature.

[112]  E. Braun,et al.  Examining Basal avian divergences with mitochondrial sequences: model complexity, taxon sampling, and sequence length. , 2002, Systematic biology.

[113]  C. Millar,et al.  Rates of Evolution in Ancient DNA from Adélie Penguins , 2002, Science.

[114]  B. Shapiro,et al.  Dynamics of Pleistocene Population Extinctions in Beringian Brown Bears , 2002, Science.

[115]  A. von Haeseler,et al.  DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA. , 2001, Nucleic acids research.

[116]  N. Georgiadis,et al.  Genetic Evidence for Two Species of Elephant in Africa , 2001, Science.

[117]  K. Field,et al.  Methods for the Study of Ancient Hair: Radiocarbon Dates and Gene Sequences from Individual Hairs , 2001 .

[118]  A. Baker,et al.  Complete mitochondrial DNA genome sequences of extinct birds: ratite phylogenetics and the vicariance biogeography hypothesis. , 2001, Proceedings. Biological sciences.

[119]  C. Hänni,et al.  Phylogenetic relationships of the five extant Rhinoceros species (Rhinocerotidae, Perissodactyla) based on mitochondrial cytochrome b and 12S rRNA genes. , 2001, Molecular phylogenetics and evolution.

[120]  R. Ward,et al.  Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution , 2001, Nature.

[121]  C. Wiuf,et al.  Statistical evidence for miscoding lesions in ancient DNA templates. , 2001, Molecular biology and evolution.

[122]  E. Hagelberg,et al.  Molecular and morphological evidence on the phylogeny of the Elephantidae , 2000, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[123]  W. G. Spaulding,et al.  A molecular analysis of ground sloth diet through the last glaciation , 2000, Molecular ecology.

[124]  Stephen Wroe,et al.  CLADISTIC ANALYSIS OF DASYUROMORPHIAN (MARSUPIALIA) PHYLOGENY USING CRANIAL AND DENTAL CHARACTERS , 2000 .

[125]  M. Westerman,et al.  DNA Sequence Analysis of Familial Relationships Among Dasyuromorphian Marsupials , 2000, Journal of Mammalian Evolution.

[126]  M. Ramsay,et al.  Phylogeography of mitochondrial DNA variation in brown bears and polar bears. , 2000, Molecular Phylogenetics and Evolution.

[127]  W. Goodwin,et al.  Molecular analysis of Neanderthal DNA from the northern Caucasus , 2000, Nature.

[128]  V. Barriel,et al.  Molecular phylogeny of Elephantidae. Extreme divergence of the extant forest African elephant. , 1999, Comptes rendus de l'Academie des sciences. Serie III, Sciences de la vie.

[129]  S. Pääbo,et al.  Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis. , 1998, Science.

[130]  R. Masuda,et al.  Molecular Phylogenetic Inference of the Woolly Mammoth Mammuthus primigenius, Based on Complete Sequences of Mitochondrial Cytochrome b and 12S Ribosomal RNA Genes , 1998, Journal of Molecular Evolution.

[131]  M. Stoneking,et al.  Neandertal DNA Sequences and the Origin of Modern Humans , 1997, Cell.

[132]  M. Westerman,et al.  DNA phylogeny of the marsupial wolf resolved , 1997, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[133]  T. Ozawa,et al.  Phylogenetic Position of Mammoth and Steller's Sea Cow Within Tethytheria Demonstrated by Mitochondrial DNA Sequences , 1997, Journal of Molecular Evolution.

[134]  S. Talbot,et al.  A phylogeny of the bears (Ursidae) inferred from complete sequences of three mitochondrial genes. , 1996, Molecular phylogenetics and evolution.

[135]  S. Pääbo,et al.  DNA damage and DNA sequence retrieval from ancient tissues. , 1996, Nucleic acids research.

[136]  Hong Yang,et al.  Phylogenetic resolution within the Elephantidae using fossil DNA sequence from the American mastodon (Mammut americanum) as an outgroup. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[137]  N. Vereshchagin,et al.  Mammoth DNA sequences , 1994, Nature.

[138]  E. Hagelberg,et al.  DNA from ancient mammoth bones , 1994, Nature.

[139]  T. Lindahl.  Instability and decay of the primary structure of DNA , 1993, Nature.

[140]  M. Braun,et al.  Phylogenetic relationships of the thylacine (Mammalia: Thylacinidae) among dasyuroid marsupials : evidence from cytochrome b DNA sequences , 1992, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[141]  S. Pääbo,et al.  DNA phylogeny of the extinct marsupial wolf , 1989, Nature.

[142]  S. Pääbo.  Ancient DNA: extraction, characterization, molecular cloning, and enzymatic amplification. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[143]  A. Wilson,et al.  DNA sequences from the quagga, an extinct member of the horse family , 1984, Nature.

[144]  W. Brown,et al.  Rapid evolution of animal mitochondrial DNA. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[145]  B. Shapiro,et al.  Ancient DNA , 2020, Definitions.

[146]  D. Penny,et al.  Tinamous and moa flock together: mitochondrial genome sequence analysis reveals independent losses of flight among ratites. , 2010, Systematic biology.

[147]  S. Ho,et al.  Ancient mitogenomics. , 2010, Mitochondrion.

[148]  Philip L. F. Johnson,et al.  Array-Based Sequence Capture Targeted Investigation of the Neandertal Genome , 2010 .

[149]  S. Pääbo,et al.  Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. , 2009, BioTechniques.

[150]  S. Schuster.  Next-generation sequencing transforms today's biology , 2008, Nature Methods.

[151]  D. Penny,et al.  Resolving the root of the avian mitogenomic tree by breaking up long branches. , 2007, Molecular phylogenetics and evolution.

[152]  C. Wiuf,et al.  Evaluating Neanderthal Genetics and Phylogeny , 2006, Journal of Molecular Evolution.

[153]  A. Wilson,et al.  Calibration of mitochondrial DNA evolution in geese , 2005, Journal of Molecular Evolution.

[154]  L. Agenbroad.  North American Proboscideans: Mammoths: The state of Knowledge, 2003 , 2005 .

[155]  M. Hofreiter,et al.  The Systematic Position of the Cave Bear from Potočka zijalka (Slovenia) , 2004 .