596 lines
52 KiB
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596 lines
52 KiB
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<document ID-DOI="10.1126/science.1147046" ID-GBIF-Dataset="ca98d9e2-c4c7-4471-86db-014365e4f385" ID-PMC="PMC2694913" ID-PubMed="18174420" ID-Zenodo-Dep="3746080" checkinTime="1586425715404" checkinUser="jeremy" docAuthor="Mike Buckley, Angela Walker, Simon Y. W. Ho, Yue Yang, Colin Smith, Peter Ashton, Jane Thomas Oates, Enrico Cappellini, Hannah Koon, Kirsty Penkman, Ben Elsworth, Dave Ashford, Caroline Solazzo, Phillip Andrews, John Strahler, Beth Shapiro, Peggy Ostrom, Hasand Gandhi, Webb Miller, Brian Raney, Maria Ines Zylber, M. Thomas P. Gilbert, Richard V. Prigodich, Michael Ryan, Kenneth F. Rijsdijk, Anwar Janoo & Matthew J. Collins" docDate="2008" docId="962587B2FFF8FF9EFF2A38EEF59DB87E" docLanguage="en" docName="Buckley_etal_2008ABBYY.pdf" docOrigin="Science 319" docStyle="DocumentStyle{}" docTitle="Tyrannosaurus rex" docType="treatment" docVersion="10" masterDocId="6A1CFFCAFFF9FF9CFFD33C52F33BB03D" masterDocTitle="Comment on “ Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry ”" masterLastPageNumber="33" masterPageNumber="33" pageNumber="33" updateTime="1668126658545" updateUser="ExternalLinkService">
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<mods:mods xmlns:mods="http://www.loc.gov/mods/v3">
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<mods:titleInfo>
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<mods:title>Comment on “ Protein Sequences from Mastodon and Tyrannosaurus rex Revealed by Mass Spectrometry ”</mods:title>
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</mods:titleInfo>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Mike Buckley</mods:namePart>
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<mods:affiliation>1 BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Angela Walker</mods:namePart>
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<mods:affiliation>Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109 - 0404, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Simon Y. W. Ho</mods:namePart>
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<mods:affiliation>Evolutionary Biology Group, Department of Zoology, University of Oxford, OX 1 3 PS, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Yue Yang</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Colin Smith</mods:namePart>
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<mods:affiliation>Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D- 04103, Leipzig, Germany</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Peter Ashton</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Jane Thomas Oates</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Enrico Cappellini</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Hannah Koon</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Kirsty Penkman</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Ben Elsworth</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Dave Ashford</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Caroline Solazzo</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Phillip Andrews</mods:namePart>
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<mods:affiliation>Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109 - 0404, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>John Strahler</mods:namePart>
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<mods:affiliation>Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109 - 0404, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Beth Shapiro</mods:namePart>
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<mods:affiliation>Department of Biology, Pennsylva- niaStateUniversity, UniversityPark, PA 16802, USA</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Peggy Ostrom</mods:namePart>
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<mods:affiliation>Department of Zoology, Michigan State University, East Lansing, MI 48824, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Hasand Gandhi</mods:namePart>
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<mods:affiliation>Department of Zoology, Michigan State University, East Lansing, MI 48824, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Webb Miller</mods:namePart>
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<mods:affiliation>Department of Biology, Pennsylva- niaStateUniversity, UniversityPark, PA 16802, USA</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Brian Raney</mods:namePart>
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<mods:affiliation>Center for Biomolecular Science and Engineering, University of California-Santa Cruz, CA 95064, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:role>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Maria Ines Zylber</mods:namePart>
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<mods:affiliation>Department of Parasitology, Kuvin Center, Hebrew University of Jerusalem, Israel.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>M. Thomas P. Gilbert</mods:namePart>
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<mods:affiliation>BiologicalInstitute, UniversityofCopenhagen, Univer- sitetsparken 15, 2100 Copenhagen, Denmark.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Richard V. Prigodich</mods:namePart>
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<mods:affiliation>Chemistry Department, Trinity College, 300 Summit Street, Hartford, CT 06106, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Michael Ryan</mods:namePart>
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<mods:affiliation>ClevelandMuseumofNaturalHistory, 1 Wade Oval Drive, University Circle, Cleveland, OH 44106, USA.</mods:affiliation>
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</mods:name>
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<mods:name type="personal">
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Kenneth F. Rijsdijk</mods:namePart>
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<mods:affiliation>National Museum of Natural History “ Naturalis, ” P. O. Box 9517, 2300 RA Leiden, Netherlands.</mods:affiliation>
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</mods:name>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Anwar Janoo</mods:namePart>
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<mods:affiliation>National Heritage Trust Fund Mauritius, Mauritius Institute, La Chausse'e Street Port Louis, Mauritius.</mods:affiliation>
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<mods:roleTerm>Author</mods:roleTerm>
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</mods:role>
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<mods:namePart>Matthew J. Collins</mods:namePart>
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<mods:affiliation>BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO 10 5 YW, UK</mods:affiliation>
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<mods:nameIdentifier type="email">mc80@york.ac.uk</mods:nameIdentifier>
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<mods:title>Science</mods:title>
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<mods:part>
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<mods:date>2008</mods:date>
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<mods:detail type="volume">
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<mods:number>319</mods:number>
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<mods:start>33</mods:start>
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<mods:end>33</mods:end>
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<mods:classification>journal article</mods:classification>
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<mods:identifier type="DOI">10.1126/science.1147046</mods:identifier>
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<mods:identifier type="GBIF-Dataset">ca98d9e2-c4c7-4471-86db-014365e4f385</mods:identifier>
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<mods:identifier type="PMC">PMC2694913</mods:identifier>
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<mods:identifier type="PubMed">18174420</mods:identifier>
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<mods:identifier type="Zenodo-Dep">3746080</mods:identifier>
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<treatment ID-DOI="http://doi.org/10.5281/zenodo.3809411" ID-GBIF-Taxon="163540457" ID-Zenodo-Dep="3809411" LSID="urn:lsid:plazi:treatment:962587B2FFF8FF9EFF2A38EEF59DB87E" httpUri="http://treatment.plazi.org/id/962587B2FFF8FF9EFF2A38EEF59DB87E" lastPageId="2" pageId="1">
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<subSubSection lastPageId="2" pageId="1" type="nomenclature">
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<paragraph blockId="1.[150,2325,211,1418]" pageId="1">
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Early reports of DNA preservation in multimillion-year-old bones (i.e.,
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<emphasis box="[772,841,1256,1286]" italics="true" pageId="1">from</emphasis>
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dinosaurs) have been largely dismissed (
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<bibRefCitation author="E. Willerslev & A. Cooper" box="[167,183,1344,1376]" journalOrPublisher="Proc. R. Soc. London. B. Biol. Sci." pageId="1" pagination="3" part="272" refId="ref2378" refString="1. E. Willerslev, A. Cooper, Proc. R. Soc. London. B. Biol. Sci. 272, 3 (2005)." type="journal article" year="2005">1</bibRefCitation>
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,
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<bibRefCitation author="J. M. Asara & M. H. Schweitzer & L. M. Freimark & M. Phillips & L. C. Cantley" box="[194,213,1344,1376]" journalOrPublisher="Science" pageId="1" pagination="280" part="316" refId="ref2409" refString="2. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007)." type="journal article" year="2007">2</bibRefCitation>
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) (table S1), but reports of protein recovery are persistent [see (
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<bibRefCitation author="M. H. Schweitzer" box="[426,444,1389,1417]" journalOrPublisher="Palaeontologia Electronica" pageId="1" part="2" publicationUrl="http://palaeo-electronica.org/2002_2/r_and_p.pdf" refId="ref2447" refString="3. M. H. Schweitzer, Palaeontologia Electronica 5, editorial 2 (2003); http: // palaeo-electronica. org / 2002 _ 2 / r _ and _ p. pdf" type="journal volume" year="2003">3</bibRefCitation>
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) for review]. Most of these studies used secondary methods of detection, but Asara
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<emphasis box="[305,371,1476,1504]" italics="true" pageId="1">et al</emphasis>
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. (
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<bibRefCitation author="J. M. Asara & M. H. Schweitzer & L. M. Freimark & M. Phillips & L. C. Cantley" box="[405,423,1476,1504]" journalOrPublisher="Science" pageId="1" pagination="280" part="316" refId="ref2409" refString="2. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007)." type="journal article" year="2007">2</bibRefCitation>
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) recently reported the direct identification of protein sequences, arguably the gold standard for molecular palaeontology, from fossil bones of an extinct mastodon and
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<taxonomicName authority="Osborn, 1905" box="[150,422,1650,1678]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
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<emphasis box="[150,422,1650,1678]" italics="true" pageId="1">Tyrannosaurus rex</emphasis>
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</taxonomicName>
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. After initial optimism gen erated by reports of dinosaur DNA, there has been increasing awareness of the problems and pitfalls that bedevil analysis of ancient samples (
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<bibRefCitation author="E. Willerslev & A. Cooper" box="[161,179,1825,1853]" journalOrPublisher="Proc. R. Soc. London. B. Biol. Sci." pageId="1" pagination="3" part="272" refId="ref2378" refString="1. E. Willerslev, A. Cooper, Proc. R. Soc. London. B. Biol. Sci. 272, 3 (2005)." type="journal article" year="2005">1</bibRefCitation>
|
|||
|
|
), leading to a series of recommendations for future analysis (
|
|||
|
|
<bibRefCitation author="E. Willerslev & A. Cooper" box="[378,396,1868,1896]" journalOrPublisher="Proc. R. Soc. London. B. Biol. Sci." pageId="1" pagination="3" part="272" refId="ref2378" refString="1. E. Willerslev, A. Cooper, Proc. R. Soc. London. B. Biol. Sci. 272, 3 (2005)." type="journal article" year="2005">1</bibRefCitation>
|
|||
|
|
,
|
|||
|
|
<bibRefCitation author="M. T. P. Gilbert & H. - J. Bandelt & M. Hofreiter & I. Barnes" box="[415,432,1868,1896]" journalOrPublisher="Trends Ecol. Evol." pageId="1" pagination="541" part="20" refId="ref2483" refString="4. M. T. P. Gilbert, H. - J. Bandelt, M. Hofreiter, I. Barnes, Trends Ecol. Evol. 20, 541 (2005)." type="journal article" year="2005">4</bibRefCitation>
|
|||
|
|
). As yet, there are no equiv alent standards for fossil protein, so here we apply the recommended tests for DNA (
|
|||
|
|
<bibRefCitation author="M. T. P. Gilbert & H. - J. Bandelt & M. Hofreiter & I. Barnes" box="[723,741,1955,1983]" journalOrPublisher="Trends Ecol. Evol." pageId="1" pagination="541" part="20" refId="ref2483" refString="4. M. T. P. Gilbert, H. - J. Bandelt, M. Hofreiter, I. Barnes, Trends Ecol. Evol. 20, 541 (2005)." type="journal article" year="2005">4</bibRefCitation>
|
|||
|
|
) to the authentication of the reported mastodon and
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[892,976,1258,1286]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[892,915,1258,1286]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[930,976,1258,1286]" italics="true" pageId="1">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
protein sequences (
|
|||
|
|
<bibRefCitation author="J. M. Asara & M. H. Schweitzer & L. M. Freimark & M. Phillips & L. C. Cantley" box="[1283,1302,1258,1286]" journalOrPublisher="Science" pageId="1" pagination="280" part="316" refId="ref2409" refString="2. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007)." type="journal article" year="2007">2</bibRefCitation>
|
|||
|
|
) (
|
|||
|
|
<tableCitation box="[1334,1449,1257,1287]" pageId="1">
|
|||
|
|
<emphasis box="[1334,1421,1257,1287]" italics="true" pageId="1">Table</emphasis>
|
|||
|
|
1
|
|||
|
|
</tableCitation>
|
|||
|
|
).
|
|||
|
|
</paragraph>
|
|||
|
|
<paragraph blockId="1.[150,2325,211,1418]" pageId="1">
|
|||
|
|
First, the likelihood of collagen survival needs to be considered. The extremely hierarchical structure of collagen results in unusual, catastrophic degradation (
|
|||
|
|
<bibRefCitation author="M. J. Collins & M. S. Riley & A. M. Child & G. Turner-Walker" box="[2001,2018,255,283]" journalOrPublisher="J. Archaeol. Sci." pageId="1" pagination="175" part="22" refId="ref2520" refString="5. M. J. Collins, M. S. Riley, A. M. Child, G. Turner-Walker, J. Archaeol. Sci. 22, 175 (1995)." type="journal article" year="1995">5</bibRefCitation>
|
|||
|
|
) as a consequence of fibril collapse. The rate of collagen degradation in bone is slow because the mineral “locks” the components of the matrix together, preventing helical expansion, which is a prerequisite of fibril collapse (
|
|||
|
|
<bibRefCitation author="C. A. Miles & M. Ghelashvili" box="[1770,1788,473,501]" journalOrPublisher="Biophys. J." pageId="1" pagination="3243" part="76" refId="ref2557" refString="6. C. A. Miles, M. Ghelashvili, Biophys. J. 76, 3243 (1999)." type="journal article" year="1999">6</bibRefCitation>
|
|||
|
|
). The packing that stabilizes collagen fibrils (
|
|||
|
|
<bibRefCitation author="C. A. Miles & M. Ghelashvili" box="[1736,1754,517,545]" journalOrPublisher="Biophys. J." pageId="1" pagination="3243" part="76" refId="ref2557" refString="6. C. A. Miles, M. Ghelashvili, Biophys. J. 76, 3243 (1999)." type="journal article" year="1999">6</bibRefCitation>
|
|||
|
|
) also increases the temperature sensitiv ity of degradation (
|
|||
|
|
<emphasis box="[1925,1961,550,578]" italics="true" pageId="1">Ea</emphasis>
|
|||
|
|
173 kJ mol -1) (
|
|||
|
|
<figureCitation box="[2215,2303,549,579]" captionStart="Fig. 1" captionText="Fig. 1. Plot of radiocarbon age versus estimated effective collagen degradation temperature for radiocarbon-dated bones from laboratory databases (principally Oxford and Groningen). The line represents the expected calendar age at which 1% of the original collagen remains following a zero-order reaction; almost no bone collagen survives beyond this predicted limit. (Inset) The 99% confidence intervals of amino acid compositions by first two principal component analyses (48% of total variance) for bones from NW Europe aged <11 ky (n= 324), 11 to 110 ky (n = 210), 110 to 130 ky (n= 26), and 130 to 700 ky (n = 31). Pliocene samples are not plotted, as their composition (n = 8) is highly variable and yields of amino acids are low. The orange line indicates a compositional trend observed when compact bone is heated for 32 days at 95°C, which reduces collagen to 1% of the initial concentration [each inflection represents a separate analysis; n = 32)]. The composition becomes more similar to mixed tissue samples (meat and bone meal; n = 32), principally due to the depletion of Gly. An amino acid profile for mammoth is consistent with collagen, unlike the associated sediment sample [data from (11)]. " pageId="1" targetBox="[150,1952,170,1276]" targetPageId="2">Fig. 1</figureCitation>
|
|||
|
|
). Collagen decomposition would be much faster in the
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1742,1829,648,676]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1742,1762,648,676]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1787,1829,648,676]" italics="true" pageId="1">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
buried in the then-megathermal (>20°C) (
|
|||
|
|
<bibRefCitation author="K. R. Johnson & D. J. Nichols & J. H. Hartman" box="[1785,1803,691,719]" journalOrPublisher="Geological Society of America Special Paper" pageId="1" pagination="503 - 510" part="361" refId="ref2580" refString="7. K. R. Johnson, D. J. Nichols, J. H. Hartman, The Hell Creek Formation and the Cretaceous-Tertiary Boundary in the Northern Great Plains: Geological Society of America Special Paper 361, 503 - 510 (2002)." title="The Hell Creek Formation and the Cretaceous-Tertiary Boundary in the Northern Great Plains" type="journal article" year="2002">7</bibRefCitation>
|
|||
|
|
) environment of the Hell Creek formation [collagen half-life (
|
|||
|
|
<emphasis box="[2055,2073,737,765]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
1/2) = ~ 2 thousand years (ky] than it would have been in the mastodon lying within the Doeden Gravel Beds (present-day mean temperature, 7.5°C; collagen T1/2 = 130 ky) (
|
|||
|
|
<figureCitation box="[1847,1930,910,940]" captionStart="Fig. 1" captionText="Fig. 1. Plot of radiocarbon age versus estimated effective collagen degradation temperature for radiocarbon-dated bones from laboratory databases (principally Oxford and Groningen). The line represents the expected calendar age at which 1% of the original collagen remains following a zero-order reaction; almost no bone collagen survives beyond this predicted limit. (Inset) The 99% confidence intervals of amino acid compositions by first two principal component analyses (48% of total variance) for bones from NW Europe aged <11 ky (n= 324), 11 to 110 ky (n = 210), 110 to 130 ky (n= 26), and 130 to 700 ky (n = 31). Pliocene samples are not plotted, as their composition (n = 8) is highly variable and yields of amino acids are low. The orange line indicates a compositional trend observed when compact bone is heated for 32 days at 95°C, which reduces collagen to 1% of the initial concentration [each inflection represents a separate analysis; n = 32)]. The composition becomes more similar to mixed tissue samples (meat and bone meal; n = 32), principally due to the depletion of Gly. An amino acid profile for mammoth is consistent with collagen, unlike the associated sediment sample [data from (11)]. " pageId="1" targetBox="[150,1952,170,1276]" targetPageId="2">Fig. 1</figureCitation>
|
|||
|
|
).
|
|||
|
|
</paragraph>
|
|||
|
|
<paragraph blockId="1.[150,2325,211,1418]" lastBlockId="2.[150,843,1779,2986]" lastPageId="2" pageId="1">
|
|||
|
|
This risk of contamination also needs to be evaluated. Collagen is an ideal molecular target for this assessment because the protein has a highly characteristic motif that is also sufficient ly variable to enable meaningful comparison between distant taxa if enough sequence is ob tained (
|
|||
|
|
<figureCitation box="[1750,1844,1213,1243]" captionStart="Fig" captionStartId="3.[150,207,2165,2197]" captionTargetBox="[338,2132,170,2134]" captionTargetPageId="3" captionText="Fig. 2. Phylogenetic networks of α1(I) sequences using Neighbor-Net analysis (A) with the most recent Asara et al. assignments (13) and (B) after our reinterpretation of the mass spectrometric data (12). T. rex does not group with bird/reptile using either set of sequence alignments. More sequence is required for a full, model-based phylogenetic analysis." figureDoi="http://doi.org/10.5281/zenodo.3746084" httpUri="https://zenodo.org/record/3746084/files/figure.png" pageId="1">Fig. 2</figureCitation>
|
|||
|
|
). Compared with ancient DNA amplification,
|
|||
|
|
<emphasis box="[1845,2047,1257,1287]" italics="true" pageId="1">contamination</emphasis>
|
|||
|
|
by collagen is
|
|||
|
|
<emphasis box="[2287,2325,1257,1287]" italics="true" pageId="1">in</emphasis>
|
|||
|
|
herently less likely. Furthermore, because the bones sampled in (
|
|||
|
|
<bibRefCitation author="J. M. Asara & M. H. Schweitzer & L. M. Freimark & M. Phillips & L. C. Cantley" box="[1930,1949,1345,1373]" journalOrPublisher="Science" pageId="1" pagination="280" part="316" refId="ref2409" refString="2. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007)." type="journal article" year="2007">2</bibRefCitation>
|
|||
|
|
) were excavated by the authors, obvious contamination sources such as animal glue (used in conservation) can be ex cluded. However, concentrating protein from the large amounts of bone used (2.5 g) may have heightened the risk of extraneous proteins entering the sample during extraction, although there have been no systematic studies of this phenomenon. Independent extraction and analy ses would have strengthened claims for the authenticity of the origin of the peptides (and potentially ameliorated the original problems of data interpretation) (
|
|||
|
|
<bibRefCitation author="M. T. P. Gilbert & H. - J. Bandelt & M. Hofreiter & I. Barnes" box="[444,462,2260,2288]" journalOrPublisher="Trends Ecol. Evol." pageId="2" pagination="541" part="20" refId="ref2483" refString="4. M. T. P. Gilbert, H. - J. Bandelt, M. Hofreiter, I. Barnes, Trends Ecol. Evol. 20, 541 (2005)." type="journal article" year="2005">4</bibRefCitation>
|
|||
|
|
).
|
|||
|
|
</paragraph>
|
|||
|
|
</subSubSection>
|
|||
|
|
<caption ID-Table-UUID="4AF3662CFFF8FF9DFCAF392FFBEBB5A0" box="[892,2256,1405,1437]" httpUri="http://table.plazi.org/id/4AF3662CFFF8FF9DFCAF392FFBEBB5A0" pageId="1" startId="1.[892,979,1405,1437]" targetBox="[892,2326,1483,2967]" targetIsTable="true" targetPageId="1">
|
|||
|
|
<paragraph blockId="1.[892,2256,1405,1437]" box="[892,2256,1405,1437]" pageId="1">
|
|||
|
|
<emphasis bold="true" box="[892,979,1405,1437]" pageId="1">Table</emphasis>
|
|||
|
|
1. Key questions to ask about ancient biomolecular investigations [adapted from (
|
|||
|
|
<bibRefCitation author="M. T. P. Gilbert & H. - J. Bandelt & M. Hofreiter & I. Barnes" box="[2206,2228,1405,1437]" journalOrPublisher="Trends Ecol. Evol." pageId="1" pagination="541" part="20" refId="ref2483" refString="4. M. T. P. Gilbert, H. - J. Bandelt, M. Hofreiter, I. Barnes, Trends Ecol. Evol. 20, 541 (2005)." type="journal article" year="2005">4</bibRefCitation>
|
|||
|
|
)].
|
|||
|
|
</paragraph>
|
|||
|
|
</caption>
|
|||
|
|
<paragraph pageId="1">
|
|||
|
|
<table box="[892,2326,1483,2967]" gridcols="4" gridrows="10" pageId="1">
|
|||
|
|
<tr box="[892,2326,1483,1515]" gridrow="0" pageId="1">
|
|||
|
|
<th box="[892,1366,1483,1515]" gridcol="0" gridrow="0" pageId="1">Test</th>
|
|||
|
|
<th box="[1438,1684,1483,1515]" gridcol="1" gridrow="0" pageId="1">Sample</th>
|
|||
|
|
<th box="[1756,1819,1483,1515]" gridcol="2" gridrow="0" pageId="1">Pass</th>
|
|||
|
|
<th box="[1891,2326,1483,1515]" gridcol="3" gridrow="0" pageId="1">Observation</th>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,1542,1703]" gridrow="1" pageId="1">
|
|||
|
|
<th box="[892,1366,1542,1703]" gridcol="0" gridrow="1" pageId="1">Do the age, environmental history, and preservation of the sample suggest collagen survival?</th>
|
|||
|
|
<td box="[1438,1684,1542,1703]" gridcol="1" gridrow="1" pageId="1">Mastodon, 300 to 600 ky old</td>
|
|||
|
|
<td box="[1756,1819,1542,1703]" gridcol="2" gridrow="1" pageId="1">Yes</td>
|
|||
|
|
<td box="[1891,2326,1542,1703]" gridcol="3" gridrow="1" pageId="1">
|
|||
|
|
Collagen
|
|||
|
|
<emphasis box="[2023,2036,1545,1575]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
1/2 at 7.5°
|
|||
|
|
<emphasis bold="true" box="[2163,2185,1545,1575]" italics="true" pageId="1">C</emphasis>
|
|||
|
|
= 130 ky
|
|||
|
|
</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,1716,1790]" gridrow="2" pageId="1" rowspan-0="1">
|
|||
|
|
<td box="[1438,1684,1716,1790]" gridcol="1" gridrow="2" pageId="1">
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1438,1518,1716,1746]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1438,1457,1716,1746]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1472,1518,1716,1746]" italics="true" pageId="1">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
, 65 million years old
|
|||
|
|
</td>
|
|||
|
|
<td box="[1756,1819,1716,1790]" gridcol="2" gridrow="2" pageId="1">No</td>
|
|||
|
|
<td box="[1891,2326,1716,1790]" gridcol="3" gridrow="2" pageId="1">
|
|||
|
|
Collagen
|
|||
|
|
<emphasis box="[2024,2037,1719,1749]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
1/2 at 20°
|
|||
|
|
<emphasis bold="true" box="[2155,2177,1719,1749]" italics="true" pageId="1">C</emphasis>
|
|||
|
|
= 2 ky
|
|||
|
|
</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,1804,2095]" gridrow="3" pageId="1">
|
|||
|
|
<th box="[892,1366,1804,2095]" gridcol="0" gridrow="3" pageId="1">Do the biomolecular and/or macromolecular preservation of the sample, the molecular target, the innate nature of the sample, and its handling history suggest that contamination is a risk?</th>
|
|||
|
|
<td box="[1438,1684,1804,2095]" gridcol="1" gridrow="3" pageId="1">Biomolecular preservation</td>
|
|||
|
|
<td box="[1756,1819,1804,2095]" gridcol="2" gridrow="3" pageId="1">?</td>
|
|||
|
|
<td box="[1891,2326,1804,2095]" gridcol="3" gridrow="3" pageId="1">
|
|||
|
|
Range of evidence presented (
|
|||
|
|
<bibRefCitation author="M. H. Schweitzer" box="[2083,2100,1847,1877]" journalOrPublisher="Science" pageId="1" pagination="277" part="316" refId="ref2629" refString="8. M. H. Schweitzer et al., Science 316, 277 (2007)." type="journal article" year="2007">8</bibRefCitation>
|
|||
|
|
) but no amino acid compositional data
|
|||
|
|
</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,2109,2313]" gridrow="4" pageId="1" rowspan-0="1">
|
|||
|
|
<td box="[1438,1684,2109,2313]" gridcol="1" gridrow="4" pageId="1">Macromolecular preservation</td>
|
|||
|
|
<td box="[1756,1819,2109,2313]" gridcol="2" gridrow="4" pageId="1">Yes</td>
|
|||
|
|
<td box="[1891,2326,2109,2313]" gridcol="3" gridrow="4" pageId="1">
|
|||
|
|
Macromolecular preservation is not the equivalent of
|
|||
|
|
<emphasis bold="true" box="[1926,2104,2240,2270]" pageId="1">biomolecular</emphasis>
|
|||
|
|
preservation (
|
|||
|
|
<emphasis bold="true" box="[2117,2145,2283,2313]" pageId="1">
|
|||
|
|
<bibRefCitation author="N. S. Gupta & D. E. G. Briggs & R. D. Pancost" box="[2117,2134,2283,2313]" journalOrPublisher="J. Geol. Soc. London" pageId="1" pagination="897" part="163" refId="ref2648" refString="9. N. S. Gupta, D. E. G. Briggs, R. D. Pancost, J. Geol. Soc. London 163, 897 (2006)." type="journal article" year="2006">9</bibRefCitation>
|
|||
|
|
)
|
|||
|
|
</emphasis>
|
|||
|
|
</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,2327,2360]" gridrow="5" pageId="1" rowspan-0="1" rowspan-3="1">
|
|||
|
|
<td box="[1438,1684,2327,2360]" gridcol="1" gridrow="5" pageId="1">Molecular target</td>
|
|||
|
|
<td box="[1756,1819,2327,2360]" gridcol="2" gridrow="5" pageId="1">Yes</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,2371,2444]" gridrow="6" pageId="1" rowspan-0="1">
|
|||
|
|
<td box="[1438,1684,2371,2444]" gridcol="1" gridrow="6" pageId="1">Handling history</td>
|
|||
|
|
<td box="[1756,1819,2371,2444]" gridcol="2" gridrow="6" pageId="1">Yes?</td>
|
|||
|
|
<td box="[1891,2326,2371,2444]" gridcol="3" gridrow="6" pageId="1">
|
|||
|
|
Large (
|
|||
|
|
<emphasis bold="true" box="[1988,2032,2371,2401]" pageId="1">2.5</emphasis>
|
|||
|
|
g) samples increase risk
|
|||
|
|
<emphasis bold="true" box="[1952,1979,2414,2444]" pageId="1">of</emphasis>
|
|||
|
|
contamination?
|
|||
|
|
</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,2458,2662]" gridrow="7" pageId="1">
|
|||
|
|
<th box="[892,1366,2458,2662]" gridcol="0" gridrow="7" pageId="1">Do the data suggest that the sequence is authentic, rather than the result of damage and contamination?</th>
|
|||
|
|
<td box="[1438,1684,2458,2662]" gridcol="1" gridrow="7" pageId="1">
|
|||
|
|
Mastodon and
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1536,1611,2501,2531]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1536,1556,2501,2531]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1570,1611,2501,2531]" italics="true" pageId="1">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
</td>
|
|||
|
|
<td box="[1756,1819,2458,2662]" gridcol="2" gridrow="7" pageId="1">No</td>
|
|||
|
|
<td box="[1891,2326,2458,2662]" gridcol="3" gridrow="7" pageId="1">
|
|||
|
|
Errors in interpretation of spectra [see table
|
|||
|
|
<emphasis bold="true" box="[2220,2241,2501,2531]" pageId="1">S</emphasis>
|
|||
|
|
1 and (
|
|||
|
|
<bibRefCitation author="J. M. Asara" box="[2000,2035,2544,2574]" journalOrPublisher="Science" pageId="1" pagination="1324" part="317" refId="ref2832" refString="13. J. M. Asara et al., Science 317, 1324 (2007)." type="journal article" year="2007">13</bibRefCitation>
|
|||
|
|
)]? Damage-induced errors in sequence
|
|||
|
|
</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,2676,2836]" gridrow="8" pageId="1">
|
|||
|
|
<th box="[892,1366,2676,2836]" gridcol="0" gridrow="8" pageId="1">Do the results make sense, and are there enough data to make the study useful and/or to support the conclusions?</th>
|
|||
|
|
<td box="[1438,1684,2676,2836]" gridcol="1" gridrow="8" pageId="1">Mastodon</td>
|
|||
|
|
<td box="[1756,1819,2676,2836]" gridcol="2" gridrow="8" pageId="1">Yes</td>
|
|||
|
|
<td box="[1891,2326,2676,2836]" gridcol="3" gridrow="8" pageId="1">Weak affinity to mammals</td>
|
|||
|
|
</tr>
|
|||
|
|
<tr box="[892,2326,2849,2967]" gridrow="9" pageId="1" rowspan-0="1">
|
|||
|
|
<td box="[1438,1684,2849,2967]" gridcol="1" gridrow="9" pageId="1">
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1438,1513,2849,2879]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="1" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1438,1457,2849,2879]" italics="true" pageId="1">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1472,1513,2849,2879]" italics="true" pageId="1">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
</td>
|
|||
|
|
<td box="[1756,1819,2849,2967]" gridcol="2" gridrow="9" pageId="1">No</td>
|
|||
|
|
<td box="[1891,2326,2849,2967]" gridcol="3" gridrow="9" pageId="1">Affinity of α1(I) peptides to amphibians, not birds or reptiles</td>
|
|||
|
|
</tr>
|
|||
|
|
</table>
|
|||
|
|
</paragraph>
|
|||
|
|
<footnote pageId="1">
|
|||
|
|
<paragraph blockId="1.[150,842,2063,2865]" pageId="1">
|
|||
|
|
1BioArch, Departments of Biology, Archaeology, Chemistry and Technology Facility, University of York, Post Office Box 373, York YO10 5YW, UK. 2Department of Biological Chem istry, University of Michigan Medical School, Ann Arbor, MI 48109-0404, USA.
|
|||
|
|
<emphasis box="[382,391,2213,2234]" italics="true" pageId="1">’</emphasis>
|
|||
|
|
Evolutionary Biology Group, Department of Zoology, University of Oxford, OX1 3PS, UK. 4Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany. 5Department of Zoology, Michigan State University, East Lansing, MI 48824, USA. 6Department of
|
|||
|
|
<emphasis box="[627,709,2377,2402]" italics="true" pageId="1">Biology</emphasis>
|
|||
|
|
, Pennsylva-
|
|||
|
|
<emphasis box="[152,380,2412,2437]" italics="true" pageId="1">niaStateUniversity</emphasis>
|
|||
|
|
,UniversityPark,
|
|||
|
|
<emphasis box="[576,616,2412,2437]" italics="true" pageId="1">PA</emphasis>
|
|||
|
|
16802,USA.7Center for Biomolecular
|
|||
|
|
<emphasis box="[367,448,2452,2477]" italics="true" pageId="1">Science</emphasis>
|
|||
|
|
and Engineering, University of California -Santa Cruz,
|
|||
|
|
<emphasis box="[412,443,2487,2512]" italics="true" pageId="1">CA</emphasis>
|
|||
|
|
95064, USA. 8Department of Par asitology, Kuvin Center, Hebrew University of Jerusalem, Israel. 9BiologicalInstitute, UniversityofCopenhagen, Univer- sitetsparken 15, 2100 Copenhagen, Denmark. 10Chemistry Department, Trinity
|
|||
|
|
<emphasis box="[377,462,2628,2653]" italics="true" pageId="1">College</emphasis>
|
|||
|
|
, 300 Summit Street, Hartford, CT 06106,USA.11
|
|||
|
|
<emphasis box="[323,757,2659,2684]" italics="true" pageId="1">ClevelandMuseumofNaturalHistory</emphasis>
|
|||
|
|
,1Wade Oval Drive, University Circle, Cleveland, OH 44106, USA. 12National Museum of Natural History “Naturalis,” P.O. Box 9517, 2300 RA Leiden, Netherlands. 13National Heritage Trust Fund Mauritius, Mauritius Institute, La Chausse'e Street Port
|
|||
|
|
<emphasis box="[208,266,2840,2865]" italics="true" pageId="1">Louis</emphasis>
|
|||
|
|
, Mauritius.
|
|||
|
|
</paragraph>
|
|||
|
|
</footnote>
|
|||
|
|
<footnote pageId="1">
|
|||
|
|
<paragraph blockId="1.[150,843,2888,2948]" pageId="1">*To whom correspondence should be addressed. E-mail: mc80@york.ac.uk</paragraph>
|
|||
|
|
</footnote>
|
|||
|
|
<caption ID-DOI="http://doi.org/10.5281/zenodo.3746082" ID-Zenodo-Dep="3746082" httpUri="https://zenodo.org/record/3746082/files/figure.png" pageId="2" startId="2.[150,207,1304,1336]" targetBox="[150,1952,170,1276]" targetPageId="2">
|
|||
|
|
<paragraph blockId="2.[150,1943,1304,1707]" pageId="2">
|
|||
|
|
<emphasis bold="true" box="[150,207,1304,1336]" italics="true" pageId="2">Fig</emphasis>
|
|||
|
|
. 1. Plot of radiocarbon age versus estimated effective collagen degradation temperature for radiocarbon-dated bones from laboratory databases (principally Oxford and Groningen). The line represents the
|
|||
|
|
<emphasis box="[1255,1378,1344,1376]" italics="true" pageId="2">expected</emphasis>
|
|||
|
|
calendar age at which 1% of the original collagen remains following a zero-order reaction; almost no bone collagen survives beyond this predicted limit. (
|
|||
|
|
<emphasis bold="true" box="[1718,1796,1384,1416]" pageId="2">Inset</emphasis>
|
|||
|
|
) The 99% confidence intervals of amino acid compositions by first two principal component analyses (48% of total variance) for bones from
|
|||
|
|
<emphasis box="[150,200,1467,1499]" italics="true" pageId="2">NW</emphasis>
|
|||
|
|
Europe aged <11 ky (
|
|||
|
|
<emphasis box="[498,518,1467,1499]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 324), 11 to 110 ky (
|
|||
|
|
<emphasis box="[820,839,1467,1499]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 210), 110 to 130 ky (
|
|||
|
|
<emphasis box="[1162,1182,1467,1499]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 26), and 130 to 700 ky (
|
|||
|
|
<emphasis box="[1543,1562,1467,1499]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 31). Pliocene samples are not plotted, as their composition (
|
|||
|
|
<emphasis box="[649,668,1509,1541]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 8) is highly variable and yields of amino acids are low. The orange line indicates a compositional trend observed when compact bone is heated for 32 days at
|
|||
|
|
<emphasis bold="true" box="[1231,1268,1551,1583]" pageId="2">95</emphasis>
|
|||
|
|
°C, which reduces collagen to 1% of the initial concentration [each inflection represents a separate analysis;
|
|||
|
|
<emphasis box="[1022,1041,1592,1624]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 32)]. The composition becomes more similar to mixed tissue samples (meat and bone meal;
|
|||
|
|
<emphasis box="[573,593,1634,1666]" italics="true" pageId="2">n</emphasis>
|
|||
|
|
= 32), principally due to the depletion of Gly. An amino acid profile for mammoth is consistent with collagen, unlike the associated sediment sample [data from (
|
|||
|
|
<bibRefCitation author="M. Schweitzer & C. L. Hill & J. M. Asara & W. S. Lane & S. H. Pincus" box="[994,1031,1675,1707]" journalOrPublisher="J. Mol. Evol." pageId="2" pagination="696" part="55" refId="ref2780" refString="11. M. Schweitzer, C. L. Hill, J. M. Asara, W. S. Lane, S. H. Pincus, J. Mol. Evol. 55, 696 (2002)." type="journal article" year="2002">11</bibRefCitation>
|
|||
|
|
)].
|
|||
|
|
</paragraph>
|
|||
|
|
</caption>
|
|||
|
|
<subSubSection pageId="2" type="discussion">
|
|||
|
|
<paragraph blockId="2.[150,843,1779,2986]" lastBlockId="2.[892,1584,1779,2986]" pageId="2">
|
|||
|
|
The remarkable soft-tissue preservation of the investigated
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[396,480,2347,2375]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[396,416,2347,2375]" italics="true" pageId="2">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[438,480,2347,2375]" italics="true" pageId="2">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
specimen (
|
|||
|
|
<materialsCitation ID-GBIF-Occurrence="2597491794" box="[659,831,2346,2376]" collectionCode="MOR" pageId="2" specimenCode="MOR 1125">MOR 1125</materialsCitation>
|
|||
|
|
) has been documented (
|
|||
|
|
<bibRefCitation author="M. H. Schweitzer" box="[484,502,2391,2419]" journalOrPublisher="Science" pageId="2" pagination="277" part="316" refId="ref2629" refString="8. M. H. Schweitzer et al., Science 316, 277 (2007)." type="journal article" year="2007">8</bibRefCitation>
|
|||
|
|
). However, microscop ic preservation does not equate with molecular preservation (
|
|||
|
|
<bibRefCitation author="N. S. Gupta & D. E. G. Briggs & R. D. Pancost" box="[341,359,2478,2506]" journalOrPublisher="J. Geol. Soc. London" pageId="2" pagination="897" part="163" refId="ref2648" refString="9. N. S. Gupta, D. E. G. Briggs, R. D. Pancost, J. Geol. Soc. London 163, 897 (2006)." type="journal article" year="2006">9</bibRefCitation>
|
|||
|
|
). Immunohistochemistry provides support for collagen preservation, but Asara
|
|||
|
|
<emphasis box="[772,833,2521,2549]" italics="true" pageId="2">et al</emphasis>
|
|||
|
|
. (
|
|||
|
|
<bibRefCitation author="J. M. Asara & M. H. Schweitzer & L. M. Freimark & M. Phillips & L. C. Cantley" box="[161,179,2565,2593]" journalOrPublisher="Science" pageId="2" pagination="280" part="316" refId="ref2409" refString="2. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007)." type="journal article" year="2007">2</bibRefCitation>
|
|||
|
|
) presented no data regarding inhibition assays with collagen from different species or cross reactivity with likely contaminants [e.g., fungi (
|
|||
|
|
<bibRefCitation author="P. Sepulveda" box="[161,197,2696,2724]" journalOrPublisher="Infect. Immun" pageId="2" pagination="2173" part="63" refId="ref2684" refString="10. P. Sepulveda et al., Infect. Immun. 63, 2173 (1995)." type="journal article" year="1995">10</bibRefCitation>
|
|||
|
|
)]. Curiously, no amino acid compositional analysis was conducted [see (
|
|||
|
|
<bibRefCitation author="M. Schweitzer & C. L. Hill & J. M. Asara & W. S. Lane & S. H. Pincus" box="[627,661,2740,2768]" journalOrPublisher="J. Mol. Evol." pageId="2" pagination="696" part="55" refId="ref2780" refString="11. M. Schweitzer, C. L. Hill, J. M. Asara, W. S. Lane, S. H. Pincus, J. Mol. Evol. 55, 696 (2002)." type="journal article" year="2002">11</bibRefCitation>
|
|||
|
|
)], although immonium
|
|||
|
|
<emphasis box="[316,375,2782,2812]" italics="true" pageId="2">ions</emphasis>
|
|||
|
|
were identified by time-of-flight secondary ion mass spectrometry. In our experi ence, collagen-like amino acid profiles have been obtained in all bones from which we could obtain collagen sequence (Fig. 1, inset). Regarding the proof of sequence authenticity, the spectra reported by Asara
|
|||
|
|
<emphasis box="[1364,1435,1824,1852]" italics="true" pageId="2">et al</emphasis>
|
|||
|
|
. (12) are inconsistent with some of the sequence assign ments (
|
|||
|
|
<bibRefCitation author="J. M. Asara" box="[1007,1042,1911,1939]" journalOrPublisher="Science" pageId="2" pagination="1324" part="317" refId="ref2832" refString="13. J. M. Asara et al., Science 317, 1324 (2007)." type="journal article" year="2007">13</bibRefCitation>
|
|||
|
|
) (table S1). A common diagenetic modification, deamidation, not considered in (
|
|||
|
|
<bibRefCitation author="J. M. Asara & M. H. Schweitzer & L. M. Freimark & M. Phillips & L. C. Cantley" box="[1545,1563,1955,1983]" journalOrPublisher="Science" pageId="2" pagination="280" part="316" refId="ref2409" refString="2. J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, L. C. Cantley, Science 316, 280 (2007)." type="journal article" year="2007">2</bibRefCitation>
|
|||
|
|
), may shed light on authenticity. The facile succinimide-mediated deamidation (
|
|||
|
|
<bibRefCitation author="N. E. Robinson" box="[1403,1438,2042,2070]" journalOrPublisher="J. Pept. Res" pageId="2" pagination="426" part="63" refId="ref2851" refString="14. N. E. Robinson et al., J. Pept. Res. 63, 426 (2004)." type="journal article" year="2004">14</bibRefCitation>
|
|||
|
|
) of aspar agine occurred at N229G and N1156G in ostrich peptides (Ost 4 and Ost5) (see table S1 for nomenclature), presumably during sample prep aration. Direct hydrolytic deamidation is slower (
|
|||
|
|
<bibRefCitation author="N. E. Robinson" box="[903,940,2260,2288]" journalOrPublisher="J. Pept. Res" pageId="2" pagination="426" part="63" refId="ref2851" refString="14. N. E. Robinson et al., J. Pept. Res. 63, 426 (2004)." type="journal article" year="2004">14</bibRefCitation>
|
|||
|
|
), and an expectation of elevated levels of such products is reasonable for old samples. We agree with the most recent interpretation (
|
|||
|
|
<bibRefCitation author="J. M. Asara" box="[1496,1532,2347,2375]" journalOrPublisher="Science" pageId="2" pagination="1324" part="317" refId="ref2832" refString="13. J. M. Asara et al., Science 317, 1324 (2007)." type="journal article" year="2007">13</bibRefCitation>
|
|||
|
|
) of the spectrum illustrated in
|
|||
|
|
<figureCitation box="[1319,1441,2390,2420]" captionStart="Fig" captionStartId="3.[150,207,2165,2197]" captionTargetBox="[338,2132,170,2134]" captionTargetPageId="3" captionText="Fig. 2. Phylogenetic networks of α1(I) sequences using Neighbor-Net analysis (A) with the most recent Asara et al. assignments (13) and (B) after our reinterpretation of the mass spectrometric data (12). T. rex does not group with bird/reptile using either set of sequence alignments. More sequence is required for a full, model-based phylogenetic analysis." figureDoi="http://doi.org/10.5281/zenodo.3746084" httpUri="https://zenodo.org/record/3746084/files/figure.png" pageId="2">Fig. 2B</figureCitation>
|
|||
|
|
as a1(I) G362SEGPEGVR370, the deamidated (Q^F.!67) form of the sequence found in most mammals (12). By way of contrast, none of the three glutamine residues in the reported
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1379,1455,2565,2593]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1379,1399,2565,2593]" italics="true" pageId="2">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1413,1455,2565,2593]" italics="true" pageId="2">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
peptides are deamidated (table S1). Only time will tell if Q^E is a useful marker for authentically old collagen, but from the evidence presented, the
|
|||
|
|
<emphasis box="[892,1583,2739,2769]" italics="true" pageId="2">mastodon sequence looks more diagenetically</emphasis>
|
|||
|
|
<emphasis box="[893,1156,2782,2812]" italics="true" pageId="2">
|
|||
|
|
altered than
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1067,1147,2783,2811]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1067,1088,2783,2811]" italics="true" pageId="2">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1103,1147,2783,2811]" italics="true" pageId="2">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
.
|
|||
|
|
</emphasis>
|
|||
|
|
</paragraph>
|
|||
|
|
<paragraph blockId="2.[892,1584,1779,2986]" lastBlockId="2.[1985,2326,167,1287]" pageId="2">
|
|||
|
|
The unusual, fragmented nature of the re ported
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[997,1081,2870,2898]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[997,1017,2870,2898]" italics="true" pageId="2">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[1039,1081,2870,2898]" italics="true" pageId="2">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
sequence does not make it ame nable to standard, model-based phylogenetic analysis. Instead, we examined the phylogenetic signal of the a1(I)
|
|||
|
|
<emphasis box="[2261,2324,167,197]" italics="true" pageId="2">frag</emphasis>
|
|||
|
|
ments of mastodon and
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1985,2069,255,283]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[1985,2004,255,283]" italics="true" pageId="2">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[2030,2069,255,283]" italics="true" pageId="2">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
using Neighbor- Net analysis and uncor rected genetic distances. Using the sequences reported in (
|
|||
|
|
<bibRefCitation author="J. M. Asara" box="[2191,2226,430,458]" journalOrPublisher="Science" pageId="2" pagination="1324" part="317" refId="ref2832" refString="13. J. M. Asara et al., Science 317, 1324 (2007)." type="journal article" year="2007">13</bibRefCitation>
|
|||
|
|
), both the
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[2047,2135,473,501]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
|||
|
|
<emphasis box="[2047,2068,473,501]" italics="true" pageId="2">T</emphasis>
|
|||
|
|
.
|
|||
|
|
<emphasis box="[2091,2135,473,501]" italics="true" pageId="2">rex</emphasis>
|
|||
|
|
</taxonomicName>
|
|||
|
|
and masto don signal display an affinity with amphibians (
|
|||
|
|
<figureCitation box="[1995,2118,603,633]" captionStart="Fig" captionStartId="3.[150,207,2165,2197]" captionTargetBox="[338,2132,170,2134]" captionTargetPageId="3" captionText="Fig. 2. Phylogenetic networks of α1(I) sequences using Neighbor-Net analysis (A) with the most recent Asara et al. assignments (13) and (B) after our reinterpretation of the mass spectrometric data (12). T. rex does not group with bird/reptile using either set of sequence alignments. More sequence is required for a full, model-based phylogenetic analysis." figureDoi="http://doi.org/10.5281/zenodo.3746084" httpUri="https://zenodo.org/record/3746084/files/figure.png" pageId="2">Fig. 2A</figureCitation>
|
|||
|
|
). Our reinter pretation of the spectra (12) changes the affinity of mastodon but not of
|
|||
|
|
<taxonomicName authority="Osborn, 1905" box="[1985,2084,778,806]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
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<emphasis box="[1985,2009,778,806]" italics="true" pageId="2">T</emphasis>
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.
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<emphasis box="[2036,2084,778,806]" italics="true" pageId="2">rex</emphasis>
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</taxonomicName>
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(
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<figureCitation box="[2119,2254,777,807]" captionStart="Fig" captionStartId="3.[150,207,2165,2197]" captionTargetBox="[338,2132,170,2134]" captionTargetPageId="3" captionText="Fig. 2. Phylogenetic networks of α1(I) sequences using Neighbor-Net analysis (A) with the most recent Asara et al. assignments (13) and (B) after our reinterpretation of the mass spectrometric data (12). T. rex does not group with bird/reptile using either set of sequence alignments. More sequence is required for a full, model-based phylogenetic analysis." figureDoi="http://doi.org/10.5281/zenodo.3746084" httpUri="https://zenodo.org/record/3746084/files/figure.png" pageId="2">Fig. 2B</figureCitation>
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). In addition to the a1(I) peptides used in the Neighbor-Net analysis, Asara
|
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<emphasis box="[2093,2171,953,981]" italics="true" pageId="2">et al</emphasis>
|
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. reported two other peptides from
|
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<taxonomicName authority="Osborn, 1905" box="[1985,2063,1040,1068]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
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<emphasis box="[1985,2004,1040,1068]" italics="true" pageId="2">T</emphasis>
|
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.
|
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<emphasis box="[2022,2063,1040,1068]" italics="true" pageId="2">rex</emphasis>
|
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</taxonomicName>
|
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(
|
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<bibRefCitation author="J. M. Asara" box="[2087,2123,1040,1068]" journalOrPublisher="Science" pageId="2" pagination="1324" part="317" refId="ref2832" refString="13. J. M. Asara et al., Science 317, 1324 (2007)." type="journal article" year="2007">13</bibRefCitation>
|
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); we question the interpretation of the a1(
|
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<emphasis bold="true" box="[2029,2057,1126,1156]" pageId="2">II</emphasis>
|
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) spectra (identical to frog) but not the a2(I) spectra (identical to chicken).
|
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</paragraph>
|
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<paragraph blockId="2.[1985,2326,1300,1766]" lastBlockId="2.[1633,2325,1780,2985]" pageId="2">
|
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We require more data to be convinced of the authenticity of the
|
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<taxonomicName authority="Osborn, 1905" box="[2246,2321,1388,1416]" class="Reptilia" family="Tyrannosauridae" genus="Tyrannosaurus" higherTaxonomySource="GBIF" kingdom="Animalia" order="Dinosauria" pageId="2" phylum="Chordata" rank="species" species="rex">
|
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|
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<emphasis box="[2246,2265,1388,1416]" italics="true" pageId="2">T</emphasis>
|
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|
|
.
|
|||
|
|
<emphasis box="[2282,2321,1388,1416]" italics="true" pageId="2">rex</emphasis>
|
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|
|
</taxonomicName>
|
|||
|
|
collagen sequences re ported by Asara
|
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|
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<emphasis box="[2246,2271,1476,1504]" italics="true" pageId="2">et</emphasis>
|
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|
al. Nevertheless, the hand ful of spectra reported for the temperate Pleisto cene mastodon fail nei ther phylogenetic nor diagenetic tests, thus highlighting the potential of protein mass spec trometry to bridge the present gulf in our un derstanding between the fate of archaeological and fossil proteins. To avoid past mistakes of ancient DNA research (
|
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|
|
<bibRefCitation author="E. Willerslev & A. Cooper" box="[1983,2002,1955,1983]" journalOrPublisher="Proc. R. Soc. London. B. Biol. Sci." pageId="2" pagination="3" part="272" refId="ref2378" refString="1. E. Willerslev, A. Cooper, Proc. R. Soc. London. B. Biol. Sci. 272, 3 (2005)." type="journal article" year="2005">1</bibRefCitation>
|
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), we recommend that future fossil protein claims be considered in light of tests for authenticity such as those presented here.
|
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</paragraph>
|
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</subSubSection>
|
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</treatment>
|
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</document>
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