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  • Elephants/*genetics  (2)
  • Phylogeny  (2)
  • American Association for the Advancement of Science (AAAS)  (4)
  • American Geophysical Union
  • American Physical Society (APS)
  • Annual Reviews
Collection
Keywords
Publisher
  • American Association for the Advancement of Science (AAAS)  (4)
  • American Geophysical Union
  • American Physical Society (APS)
  • Annual Reviews
  • Nature Publishing Group (NPG)  (4)
Years
  • 1
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    Whole-genome shotgun sequencing of mitochondria from ancient hair shafts (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-29
    Description: Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was 〉50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gilbert, M Thomas P -- Tomsho, Lynn P -- Rendulic, Snjezana -- Packard, Michael -- Drautz, Daniela I -- Sher, Andrei -- Tikhonov, Alexei -- Dalen, Love -- Kuznetsova, Tatyana -- Kosintsev, Pavel -- Campos, Paula F -- Higham, Thomas -- Collins, Matthew J -- Wilson, Andrew S -- Shidlovskiy, Fyodor -- Buigues, Bernard -- Ericson, Per G P -- Germonpre, Mietje -- Gotherstrom, Anders -- Iacumin, Paola -- Nikolaev, Vladimir -- Nowak-Kemp, Malgosia -- Willerslev, Eske -- Knight, James R -- Irzyk, Gerard P -- Perbost, Clotilde S -- Fredrikson, Karin M -- Harkins, Timothy T -- Sheridan, Sharon -- Miller, Webb -- Schuster, Stephan C -- HG002238/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Sep 28;317(5846):1927-30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Ancient Genetics, University of Copenhagen, Universitetsparken 15, DK-2100 Copenhagen, Denmark.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17901335" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bone and Bones/chemistry ; DNA Damage ; DNA, Mitochondrial/chemistry/genetics/*history ; Elephants/*genetics ; Genes, Mitochondrial ; *Genome ; *Hair/chemistry/ultrastructure ; History, Ancient ; Mitochondria/*genetics ; Molecular Sequence Data ; Preservation, Biological ; *Sequence Analysis, DNA ; Siberia ; Temperature
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Comment on "Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry" (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-01-05
    Description: We used authentication tests developed for ancient DNA to evaluate claims by Asara et al. (Reports, 13 April 2007, p. 280) of collagen peptide sequences recovered from mastodon and Tyrannosaurus rex fossils. Although the mastodon samples pass these tests, absence of amino acid composition data, lack of evidence for peptide deamidation, and association of alpha1(I) collagen sequences with amphibians rather than birds suggest that T. rex does not.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694913/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2694913/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckley, Mike -- Walker, Angela -- Ho, Simon Y W -- Yang, Yue -- Smith, Colin -- Ashton, Peter -- Oates, Jane Thomas -- Cappellini, Enrico -- Koon, Hannah -- Penkman, Kirsty -- Elsworth, Ben -- Ashford, Dave -- Solazzo, Caroline -- Andrews, Phillip -- Strahler, John -- Shapiro, Beth -- Ostrom, Peggy -- Gandhi, Hasand -- Miller, Webb -- Raney, Brian -- Zylber, Maria Ines -- Gilbert, M Thomas P -- Prigodich, Richard V -- Ryan, Michael -- Rijsdijk, Kenneth F -- Janoo, Anwar -- Collins, Matthew J -- 076905/Wellcome Trust/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2008 Jan 4;319(5859):33; author reply 33. doi: 10.1126/science.1147046.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18174420" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Bone and Bones/*chemistry ; Collagen/*chemistry ; *Dinosaurs ; *Elephants ; *Fossils ; Mass Spectrometry ; Phylogeny
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Metagenomics to paleogenomics: large-scale sequencing of mammoth DNA (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-12-22
    Description: We sequenced 28 million base pairs of DNA in a metagenomics approach, using a woolly mammoth (Mammuthus primigenius) sample from Siberia. As a result of exceptional sample preservation and the use of a recently developed emulsion polymerase chain reaction and pyrosequencing technique, 13 million base pairs (45.4%) of the sequencing reads were identified as mammoth DNA. Sequence identity between our data and African elephant (Loxodonta africana) was 98.55%, consistent with a paleontologically based divergence date of 5 to 6 million years. 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.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Poinar, Hendrik N -- Schwarz, Carsten -- Qi, Ji -- Shapiro, Beth -- Macphee, Ross D E -- Buigues, Bernard -- Tikhonov, Alexei -- Huson, Daniel H -- Tomsho, Lynn P -- Auch, Alexander -- Rampp, Markus -- Miller, Webb -- Schuster, Stephan C -- HG02238/HG/NHGRI NIH HHS/ -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2006 Jan 20;311(5759):392-4. Epub 2005 Dec 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉McMaster Ancient DNA Center, McMaster University, 1280 Main Street West, Hamilton ON, L8S 4L9 Canada. poinarh@mcmaster.ca〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16368896" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Base Composition ; Computational Biology ; Cytochromes b/genetics ; DNA, Mitochondrial/genetics ; Dogs/genetics ; Elephants/*genetics ; *Fossils ; Gene Library ; Genome ; *Genomics ; Humans ; Mandible/*chemistry ; *Paleontology ; Polymerase Chain Reaction ; Sequence Alignment ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Siberia
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 4
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    Molecular and genomic data identify the closest living relative of primates (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-11-03
    Description: A full understanding of primate morphological and genomic evolution requires the identification of their closest living relative. In order to resolve the ancestral relationships among primates and their closest relatives, we searched multispecies genome alignments for phylogenetically informative rare genomic changes within the superordinal group Euarchonta, which includes the orders Primates, Dermoptera (colugos), and Scandentia (treeshrews). We also constructed phylogenetic trees from 14 kilobases of nuclear genes for representatives from most major primate lineages, both extant colugos, and multiple treeshrews, including the pentail treeshrew, Ptilocercus lowii, the only living member of the family Ptilocercidae. A relaxed molecular clock analysis including Ptilocercus suggests that treeshrews arose approximately 63 million years ago. Our data show that colugos are the closest living relatives of primates and indicate that their divergence occurred in the Cretaceous.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janecka, Jan E -- Miller, Webb -- Pringle, Thomas H -- Wiens, Frank -- Zitzmann, Annette -- Helgen, Kristofer M -- Springer, Mark S -- Murphy, William J -- HG02238/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 2;318(5851):792-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77843, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17975064" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; *Biological Evolution ; Dna ; Evolution, Molecular ; Fossils ; Genome ; Humans ; Mammals/classification/genetics ; Molecular Sequence Data ; Phylogeny ; Primates/classification/*genetics ; Scandentia/classification/genetics ; Sequence Alignment
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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