Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

2013/09/09 by Jesse Dabney, Michael Knapp, Isabelle Glocke +8 · 38 citations
Biochemistry, Genetics and Molecular Biology · Social Sciences · Arts and Humanities · #Forensic and Genetic Research #Pleistocene-Era Hominins and Archaeology #Forensic Anthropology and Bioarchaeology Studies #Ancient DNA #Mitochondrial DNA #Pleistocene #Cave #Paleontology #DNA sequencing #Sequence (biology) #Biology #Sima #DNA #Phylogenetic tree #Evolutionary biology #Genome #Lineage (genetic) #Archaeology #Genetics #Geography #Gene #Ecology

paper · doi:10.1073/pnas.1314445110

openalex publication_date 2013/09/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

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.

Citations

• Comparison and Optimization of Ancient DNA Extraction
• Genetic history of an archaic hominin group from Denisova Cave in Siberia
• The first hominin of Europe
• New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing
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• Mitochondrial genomes reveal an explosive radiation of extinct and extant bears near the Miocene-Pliocene boundary

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