Palaeoproteomics of bird bones for taxonomic classification

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

Palaeoproteomics of bird bones for taxonomic classification. / Horn, Ivo R.; Kenens, Yvo; Palmblad, N. Magnus; Van Der Plas-Duivesteijn, Suzanne J.; Langeveld, Bram W.; Meijer, Hanneke J.M.; Dalebout, Hans; Marissen, Rob J.; Fischer, Anja; Vincent Florens, F. B.; Niemann, Jonas; Rijsdijk, Kenneth F.; Schulp, Anne S.; Laros, Jeroen F.J.; Gravendeel, Barbara.

In: Zoological Journal of the Linnean Society, Vol. 186, No. 3, 2019, p. 650-665.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

Horn, IR, Kenens, Y, Palmblad, NM, Van Der Plas-Duivesteijn, SJ, Langeveld, BW, Meijer, HJM, Dalebout, H, Marissen, RJ, Fischer, A, Vincent Florens, FB, Niemann, J, Rijsdijk, KF, Schulp, AS, Laros, JFJ & Gravendeel, B 2019, 'Palaeoproteomics of bird bones for taxonomic classification', Zoological Journal of the Linnean Society, vol. 186, no. 3, pp. 650-665. https://doi.org/10.1093/zoolinnean/zlz012

APA

Horn, I. R., Kenens, Y., Palmblad, N. M., Van Der Plas-Duivesteijn, S. J., Langeveld, B. W., Meijer, H. J. M., Dalebout, H., Marissen, R. J., Fischer, A., Vincent Florens, F. B., Niemann, J., Rijsdijk, K. F., Schulp, A. S., Laros, J. F. J., & Gravendeel, B. (2019). Palaeoproteomics of bird bones for taxonomic classification. Zoological Journal of the Linnean Society, 186(3), 650-665. https://doi.org/10.1093/zoolinnean/zlz012

Vancouver

Horn IR, Kenens Y, Palmblad NM, Van Der Plas-Duivesteijn SJ, Langeveld BW, Meijer HJM et al. Palaeoproteomics of bird bones for taxonomic classification. Zoological Journal of the Linnean Society. 2019;186(3):650-665. https://doi.org/10.1093/zoolinnean/zlz012

Author

Horn, Ivo R. ; Kenens, Yvo ; Palmblad, N. Magnus ; Van Der Plas-Duivesteijn, Suzanne J. ; Langeveld, Bram W. ; Meijer, Hanneke J.M. ; Dalebout, Hans ; Marissen, Rob J. ; Fischer, Anja ; Vincent Florens, F. B. ; Niemann, Jonas ; Rijsdijk, Kenneth F. ; Schulp, Anne S. ; Laros, Jeroen F.J. ; Gravendeel, Barbara. / Palaeoproteomics of bird bones for taxonomic classification. In: Zoological Journal of the Linnean Society. 2019 ; Vol. 186, No. 3. pp. 650-665.

Bibtex

@article{674959df7a7f46b7a0f51aeef1b14417,
title = "Palaeoproteomics of bird bones for taxonomic classification",
abstract = "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.",
keywords = "ancient proteins, bird taxonomy, dodo, extant birds, great auk, palaeoproteomics, phylogeny",
author = "Horn, {Ivo R.} and Yvo Kenens and Palmblad, {N. Magnus} and {Van Der Plas-Duivesteijn}, {Suzanne J.} and Langeveld, {Bram W.} and Meijer, {Hanneke J.M.} and Hans Dalebout and Marissen, {Rob J.} and Anja Fischer and {Vincent Florens}, {F. B.} and Jonas Niemann and Rijsdijk, {Kenneth F.} and Schulp, {Anne S.} and Laros, {Jeroen F.J.} and Barbara Gravendeel",
year = "2019",
doi = "10.1093/zoolinnean/zlz012",
language = "English",
volume = "186",
pages = "650--665",
journal = "Zoological Journal of the Linnean Society ",
issn = "0024-4082",
publisher = "Oxford Academic",
number = "3",

}

RIS

TY - JOUR

T1 - Palaeoproteomics of bird bones for taxonomic classification

AU - Horn, Ivo R.

AU - Kenens, Yvo

AU - Palmblad, N. Magnus

AU - Van Der Plas-Duivesteijn, Suzanne J.

AU - Langeveld, Bram W.

AU - Meijer, Hanneke J.M.

AU - Dalebout, Hans

AU - Marissen, Rob J.

AU - Fischer, Anja

AU - Vincent Florens, F. B.

AU - Niemann, Jonas

AU - Rijsdijk, Kenneth F.

AU - Schulp, Anne S.

AU - Laros, Jeroen F.J.

AU - Gravendeel, Barbara

PY - 2019

Y1 - 2019

N2 - 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.

AB - 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.

KW - ancient proteins

KW - bird taxonomy

KW - dodo

KW - extant birds

KW - great auk

KW - palaeoproteomics

KW - phylogeny

U2 - 10.1093/zoolinnean/zlz012

DO - 10.1093/zoolinnean/zlz012

M3 - Journal article

AN - SCOPUS:85083789607

VL - 186

SP - 650

EP - 665

JO - Zoological Journal of the Linnean Society

JF - Zoological Journal of the Linnean Society

SN - 0024-4082

IS - 3

ER -

ID: 241594299