Palaeoproteomics of bird bones for taxonomic classification

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  • Ivo R Horn
    University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
  • Yvo Kenens
    University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
  • N Magnus Palmblad
    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
  • Suzanne J van der Plas-Duivesteijn
    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
  • Bram W Langeveld
    Natural History Museum Rotterdam, Museumpark, Rotterdam, The Netherlands
  • Hanneke J M Meijer
    Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
  • Hans Dalebout
    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
  • Rob J Marissen
    Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
  • Anja Fischer
    University of Amsterdam, Faculty of Humanities, Amsterdam, The Netherlands
  • F B Vincent Florens
    Tropical Island Biodiversity, Ecology and Conservation Pole of Research, University of Mauritius, Réduit, Mauritius
  • Jonas Niemann
    Natural History Museum of Denmark, Copenhagen, Denmark
  • Kenneth F Rijsdijk
    BIOMAC group, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Faculty of Natural Sciences, Science Park, Amsterdam, The Netherlands
  • Anne S Schulp
    Naturalis Biodiversity Center, Endless Forms Group, Darwinweg, CR Leiden, The Netherlands
  • Jeroen F J Laros
    Leiden Genome Technology Center, Leiden, The Netherlands
  • Barbara Gravendeel
    University of Applied Sciences Leiden, Faculty of Science and Technology, Zernikedreef, CK, Leiden, The Netherlands
  • non-UU output of UU-AW members

書誌事項

公開日
2019-04-16
権利情報
  • http://creativecommons.org/licenses/by-nc/4.0/
DOI
  • 10.1093/zoolinnean/zlz012
公開者
Oxford University Press (OUP)

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説明

We used proteomic profiling to taxonomically classify extinct, alongside extant bird species using mass spectrometry on ancient bone-derived collagen chains COL1A1 and COL1A2. Proteins of Holocene and Late Pleistocene-aged bones from dodo (Raphus cucullatus) and great auk (Pinguinus impennis), as well as bones from chicken (Gallus gallus), rock dove (Columba livia), zebra finch (Taeniopygia guttata) and peregrine falcon (Falco peregrinus), of various ages ranging from the present to 1455 years old were analysed. HCl and guandine-HCL-based protein extractions from fresh bone materials yielded up to 60% coverage of collagens COL1A1 and COL1A2, and extractions from ancient materials yielded up to 46% coverage of collagens COL1A1 and COL1A2. Data were retrieved from multiple peptide sequences obtained from different specimens and multiple extractions. Upon alignment, and in line with the latest evolutionary insights, protein data obtained from great auk grouped with data from a recently sequenced razorbill (Alca torda) genome. Similarly, protein data obtained from bones of dodo and modern rock dove grouped in a single clade. Lastly, protein data obtained from chicken bones, both from ancient and fresh materials, grouped as a separate, basal clade. Our proteomic analyses enabled taxonomic classification of all ancient bones, thereby complementing phylogenetics based on DNA.

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