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  • 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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    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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  • 3
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    Intraspecific phylogenetic analysis of Siberian woolly mammoths using complete mitochondrial genomes (2008)
    National Academy of Sciences
    Details
    Publication Date: 2008-06-09
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 4
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    X-ray computed tomography of two mammoth calf mummies (2014)
    Paleontological Society
    Details
    Publication Date: 2014-07-11
    Description: A bstract Two female woolly mammoth neonates from permafrost in the Siberian Arctic are the most complete mammoth specimens known. Lyuba, found on the Yamal Peninsula, and Khroma, from northernmost Yakutia, died at ages of approximately one and two months, respectively. Both specimens were CT-scanned, yielding detailed information on the stage of development of their dentition and skeleton and insight into conditions associated with death. Both mammoths died after aspirating mud. Khroma's body was frozen soon after death, leaving her tissues in excellent condition, whereas Lyuba's body underwent postmortem changes that resulted in authigenic formation of nodules of the mineral vivianite associated with her cranium and within diaphyses of long bones. CT data provide the only comprehensive approach to mapping vivianite distribution. Three-dimensional modeling and measurement of segmented long bones permits comparison between these individuals and with previously recovered specimens. CT scans of long bones and foot bones show developmental features such as density gradients that reveal ossification centers. The braincase of Khroma was segmented to show the approximate morphology of the brain; its volume is slightly less (~2,300 cm 3 ) than that of neonate elephants (~2,500 cm 3 ). Lyuba's premaxillae are more gracile than those of Khroma, possibly a result of temporal and/or geographic variation but probably also reflective of their age difference. Segmentation of CT data and 3-D modeling software were used to produce models of teeth that were too complex for traditional molding and casting techniques.
    Print ISSN: 0022-3360
    Electronic ISSN: 1937-2337
    Topics: Geosciences
    Published by Paleontological Society
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