Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments
Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and pr...
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ftunisfloridatam:oai:digitalcommons.usf.edu:kip_articles-1905 2023-05-15T17:57:37+02:00 Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments Dabney, Jesse Knapp, Michael Glocke, Isabelle Gansauge, Maie-Theres Weihmann, Antje Nickel, Birgit Valdiosera, Cristina Garcí, Nuria Pääbo, Svante Arsuaga, Juan-Luis Meyer, Matthias 2013-01-01T08:00:00Z https://digitalcommons.usf.edu/kip_articles/906 https://doi.org/10.1073/pnas.1314445110 unknown Digital Commons @ University of South Florida https://digitalcommons.usf.edu/kip_articles/906 https://doi.org/10.1073/pnas.1314445110 KIP Articles text 2013 ftunisfloridatam https://doi.org/10.1073/pnas.1314445110 2022-10-27T17:50:42Z Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. Trace amounts of DNA can occasionally survive the decomposition of organic matter for long periods of time after the death of an organism. However, the retrieval of these ancient DNA molecules is severely impeded by their small size. DNA fragmentation is at least partly driven by depurination (1, 2), a continually occurring process. It is thus predicted that the degree of DNA fragmentation increases with sample age. This correlation has, in fact, been established in a recent study that analyzed samples of different ages from the same archeological sites (3), but the correlation vanishes in comparisons across different sites (4). The important role of environmental conditions, especially temperature, in DNA preservation is well recognized and reflected—for example, in the concept of thermal age (5). Unsurprisingly, permafrost environments have yielded the oldest credible records of DNA survival, including short stretches o Text permafrost Digital Commons University of South Florida (USF) Proceedings of the National Academy of Sciences 110 39 15758 15763 |
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Although an inverse relationship is expected in ancient DNA samples between the number of surviving DNA fragments and their length, ancient DNA sequencing libraries are strikingly deficient in molecules shorter than 40 bp. We find that a loss of short molecules can occur during DNA extraction and present an improved silica-based extraction protocol that enables their efficient retrieval. In combination with single-stranded DNA library preparation, this method enabled us to reconstruct the mitochondrial genome sequence from a Middle Pleistocene cave bear (Ursus deningeri) bone excavated at Sima de los Huesos in the Sierra de Atapuerca, Spain. Phylogenetic reconstructions indicate that the U. deningeri sequence forms an early diverging sister lineage to all Western European Late Pleistocene cave bears. Our results prove that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. Moreover, the techniques presented enable the retrieval of phylogenetically informative sequences from samples in which virtually all DNA is diminished to fragments shorter than 50 bp. Trace amounts of DNA can occasionally survive the decomposition of organic matter for long periods of time after the death of an organism. However, the retrieval of these ancient DNA molecules is severely impeded by their small size. DNA fragmentation is at least partly driven by depurination (1, 2), a continually occurring process. It is thus predicted that the degree of DNA fragmentation increases with sample age. This correlation has, in fact, been established in a recent study that analyzed samples of different ages from the same archeological sites (3), but the correlation vanishes in comparisons across different sites (4). The important role of environmental conditions, especially temperature, in DNA preservation is well recognized and reflected—for example, in the concept of thermal age (5). Unsurprisingly, permafrost environments have yielded the oldest credible records of DNA survival, including short stretches o |
format |
Text |
author |
Dabney, Jesse Knapp, Michael Glocke, Isabelle Gansauge, Maie-Theres Weihmann, Antje Nickel, Birgit Valdiosera, Cristina Garcí, Nuria Pääbo, Svante Arsuaga, Juan-Luis Meyer, Matthias |
spellingShingle |
Dabney, Jesse Knapp, Michael Glocke, Isabelle Gansauge, Maie-Theres Weihmann, Antje Nickel, Birgit Valdiosera, Cristina Garcí, Nuria Pääbo, Svante Arsuaga, Juan-Luis Meyer, Matthias Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments |
author_facet |
Dabney, Jesse Knapp, Michael Glocke, Isabelle Gansauge, Maie-Theres Weihmann, Antje Nickel, Birgit Valdiosera, Cristina Garcí, Nuria Pääbo, Svante Arsuaga, Juan-Luis Meyer, Matthias |
author_sort |
Dabney, Jesse |
title |
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments |
title_short |
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments |
title_full |
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments |
title_fullStr |
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments |
title_full_unstemmed |
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments |
title_sort |
complete mitochondrial genome sequence of a middle pleistocene cave bear reconstructed from ultrashort dna fragments |
publisher |
Digital Commons @ University of South Florida |
publishDate |
2013 |
url |
https://digitalcommons.usf.edu/kip_articles/906 https://doi.org/10.1073/pnas.1314445110 |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
KIP Articles |
op_relation |
https://digitalcommons.usf.edu/kip_articles/906 https://doi.org/10.1073/pnas.1314445110 |
op_doi |
https://doi.org/10.1073/pnas.1314445110 |
container_title |
Proceedings of the National Academy of Sciences |
container_volume |
110 |
container_issue |
39 |
container_start_page |
15758 |
op_container_end_page |
15763 |
_version_ |
1766166096751099904 |