Dataset Information

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.

SUBMITTER: Dabney J

PROVIDER: S-EPMC3785785 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature

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

Dabney Jesse J Knapp Michael M Glocke Isabelle I Gansauge Marie-Theres MT Weihmann Antje A Nickel Birgit B Valdiosera Cristina C García Nuria N Pääbo Svante S Arsuaga Juan-Luis JL Meyer Matthias M

Proceedings of the National Academy of Sciences of the United States of America 20130909 39

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 mitoch ...[more]

PMID: 24019490

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Project description:Excavations at the Longtan Cave, Hexian, Anhui Province of Eastern China, have yielded several hominin fossils including crania, mandibular fragments, and teeth currently dated to 412 ± 25 ka. While previous studies have focused on the cranial remains, there are no detailed analyses of the dental evidence. In this study, we provide metric and morphological descriptions and comparisons of ten teeth recovered from Hexian, including microcomputed tomography analyses. Our results indicate that the Hexian teeth are metrically and morphologically primitive and overlap with H. ergaster and East Asian Early and mid-Middle Pleistocene hominins in their large dimensions and occlusal complexities. However, the Hexian teeth differ from H. ergaster in features such as conspicuous vertical grooves on the labial/buccal surfaces of the central incisor and the upper premolar, the crown outline shapes of upper and lower molars and the numbers, shapes, and divergences of the roots. Despite their close geological ages, the Hexian teeth are also more primitive than Zhoukoudian specimens, and resemble Sangiran Early Pleistocene teeth. In addition, no typical Neanderthal features have been identified in the Hexian sample. Our study highlights the metrical and morphological primitive status of the Hexian sample in comparison to contemporaneous or even earlier populations of Asia. Based on this finding, we suggest that the primitive-derived gradients of the Asian hominins cannot be satisfactorily fitted along a chronological sequence, suggesting complex evolutionary scenarios with the coexistence and/or survival of different lineages in Eurasia. Hexian could represent the persistence in time of a H. erectus group that would have retained primitive features that were lost in other Asian populations such as Zhoukoudian or Panxian Dadong. Our study expands the metrical and morphological variations known for the East Asian hominins before the mid-Middle Pleistocene and warns about the possibility that the Asian hominin variability may have been taxonomically oversimplified.

Dataset Information

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

Publications

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

Similar Datasets

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