title: Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.
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.
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Jesse
authors.initials: J
authors.lastname: Dabney
authors.forename: Michael
authors.initials: M
authors.lastname: Knapp
authors.forename: Isabelle
authors.initials: I
authors.lastname: Glocke
authors.forename: Marie-Theres
authors.initials: MT
authors.lastname: Gansauge
authors.forename: Antje
authors.initials: A
authors.lastname: Weihmann
authors.forename: Birgit
authors.initials: B
authors.lastname: Nickel
authors.forename: Cristina
authors.initials: C
authors.lastname: Valdiosera
authors.forename: Nuria
authors.initials: N
authors.lastname: García
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
authors.forename: Juan-Luis
authors.initials: JL
authors.lastname: Arsuaga
authors.forename: Matthias
authors.initials: M
authors.lastname: Meyer
mesh_terms: D000818:Animals; D001483:Base Sequence; D059552:Caves; D004247:DNA / Q000235:genetics* / Q000302:isolation & purification; D054629:Genome, Mitochondrial / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D013997:Time Factors; D001503:Ursidae / Q000235:genetics*
chemical_list: D004247:DNA
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