New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains
Despite being plagued by heavily degraded DNA in palaeontological remains, most studies addressing the state of DNA degradation have been limited to types of damage which do not pose a hindrance to Taq polymerase during PCR. Application of serial qPCR to the two fractions obtained during extraction...
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2009
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fthighwire:oai:open-archive.highwire.org:nar:37/10/3215 2023-05-15T17:57:04+02:00 New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains Schwarz, Carsten Debruyne, Regis Kuch, Melanie McNally, Elizabeth Schwarcz, Henry Aubrey, Andrew D. Bada, Jeffrey Poinar, Hendrik 2009-06-01 00:00:00.0 text/html http://nar.oxfordjournals.org/cgi/content/short/37/10/3215 https://doi.org/10.1093/nar/gkp159 en eng Oxford University Press http://nar.oxfordjournals.org/cgi/content/short/37/10/3215 http://dx.doi.org/10.1093/nar/gkp159 Copyright (C) 2009, Oxford University Press Molecular Biology TEXT 2009 fthighwire https://doi.org/10.1093/nar/gkp159 2015-02-28T19:56:19Z Despite being plagued by heavily degraded DNA in palaeontological remains, most studies addressing the state of DNA degradation have been limited to types of damage which do not pose a hindrance to Taq polymerase during PCR. Application of serial qPCR to the two fractions obtained during extraction (demineralization and protein digest) from six permafrost mammoth bones and one partially degraded modern elephant bone has enabled further insight into the changes which endogenous DNA is subjected to during diagenesis. We show here that both fractions exhibit individual qualities in terms of the prevailing type of DNA (i.e. mitochondrial versus nuclear DNA) as well as the extent of damage, and in addition observed a highly variable ratio of mitochondrial to nuclear DNA among the six mammoth samples. While there is evidence suggesting that mitochondrial DNA is better preserved than nuclear DNA in ancient permafrost samples, we find the initial DNA concentration in the bone tissue to be as relevant for the total accessible mitochondrial DNA as the extent of DNA degradation post-mortem. We also evaluate the general applicability of indirect measures of preservation such as amino-acid racemization, bone crystallinity index and thermal age to these exceptionally well-preserved samples. Text permafrost HighWire Press (Stanford University) Nucleic Acids Research 37 10 3215 3229 |
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HighWire Press (Stanford University) |
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English |
topic |
Molecular Biology |
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Molecular Biology Schwarz, Carsten Debruyne, Regis Kuch, Melanie McNally, Elizabeth Schwarcz, Henry Aubrey, Andrew D. Bada, Jeffrey Poinar, Hendrik New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains |
topic_facet |
Molecular Biology |
description |
Despite being plagued by heavily degraded DNA in palaeontological remains, most studies addressing the state of DNA degradation have been limited to types of damage which do not pose a hindrance to Taq polymerase during PCR. Application of serial qPCR to the two fractions obtained during extraction (demineralization and protein digest) from six permafrost mammoth bones and one partially degraded modern elephant bone has enabled further insight into the changes which endogenous DNA is subjected to during diagenesis. We show here that both fractions exhibit individual qualities in terms of the prevailing type of DNA (i.e. mitochondrial versus nuclear DNA) as well as the extent of damage, and in addition observed a highly variable ratio of mitochondrial to nuclear DNA among the six mammoth samples. While there is evidence suggesting that mitochondrial DNA is better preserved than nuclear DNA in ancient permafrost samples, we find the initial DNA concentration in the bone tissue to be as relevant for the total accessible mitochondrial DNA as the extent of DNA degradation post-mortem. We also evaluate the general applicability of indirect measures of preservation such as amino-acid racemization, bone crystallinity index and thermal age to these exceptionally well-preserved samples. |
format |
Text |
author |
Schwarz, Carsten Debruyne, Regis Kuch, Melanie McNally, Elizabeth Schwarcz, Henry Aubrey, Andrew D. Bada, Jeffrey Poinar, Hendrik |
author_facet |
Schwarz, Carsten Debruyne, Regis Kuch, Melanie McNally, Elizabeth Schwarcz, Henry Aubrey, Andrew D. Bada, Jeffrey Poinar, Hendrik |
author_sort |
Schwarz, Carsten |
title |
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains |
title_short |
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains |
title_full |
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains |
title_fullStr |
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains |
title_full_unstemmed |
New insights from old bones: DNA preservation and degradation in permafrost preserved mammoth remains |
title_sort |
new insights from old bones: dna preservation and degradation in permafrost preserved mammoth remains |
publisher |
Oxford University Press |
publishDate |
2009 |
url |
http://nar.oxfordjournals.org/cgi/content/short/37/10/3215 https://doi.org/10.1093/nar/gkp159 |
genre |
permafrost |
genre_facet |
permafrost |
op_relation |
http://nar.oxfordjournals.org/cgi/content/short/37/10/3215 http://dx.doi.org/10.1093/nar/gkp159 |
op_rights |
Copyright (C) 2009, Oxford University Press |
op_doi |
https://doi.org/10.1093/nar/gkp159 |
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Nucleic Acids Research |
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37 |
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10 |
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3215 |
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3229 |
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1766165427246858240 |