Extinct species identification from Upper Pleistocene bone fragments not identifiable from their osteomorphological studies by proteomics analysis

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Abstract The ancient preserved molecules offer the opportunity to gain a better knowledge on the biological past. In recent years, bones proteomics has become an attractive method to study the animal biological origin, extinct species and species evolution as an alternative to DNA analysis which is limited by DNA amplification present in ancient samples and its contamination. However, the development of a proteomic workflow remains a challenge. The analysis of fossils must consume a low quantity of material to avoid damaging the samples. Another difficulty is the absence of genomic data for most of the extinct species. In this study, a proteomic methodology was applied to mammalian bones of 130,000 years old from the earlier Upper Pleistocene site of Scladina Cave (Belgium). Starting from 5 milligram samples, our results show a large majority of detected peptides matching collagen I alpha 1 and alpha 2 proteins with a sequence coverage up to 60%. Using sequence homology with modern sequences, a biological classification was successfully achieved and the associated taxonomic ranks to each bone were identified consistently with the information gained from osteomorphological studies and palaeoenvironmental and palaeodietary data. Among the taxa identified are the Felidae family, Bovinae subfamily, Elephantidae family and the Ursus genus. Amino acid substitutions on the collagens were identified providing new information on extinct species sequences and also helping in taxonomy-based clustering. Considering samples with no osteomorphological information, such as two bone retouchers, proteomics successfully identified the bovidae and ursidae families providing new information to the paleontologists on these objects. Combining osteomorphology studies and amino acid variations identified by proteomics, one retoucher was identified to be potentially from the Ursus spelaeus species.

Authors 8

1. Fabrice Bray corresponding

   Centre National de la Recherche Scientifique · Université de Lille · Miniaturisation pour la Synthèse, l'Analyse et la Protéomique

   Affiliation as printed

   Univ. Lille, CNRS, USR 3290 - MSAP - Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, F-59000 Lille, France

   Univ. Lille, CNRS, USR 3290 - MSAP - Minituristion pour l Synthèse, l'Anlyse et l Protéomique, F-59000 Lille, Frnce

2. Stéphanie Flament

   Centre National de la Recherche Scientifique · Université de Lille · Miniaturisation pour la Synthèse, l'Analyse et la Protéomique

   Affiliation as printed

   Univ. Lille, CNRS, USR 3290 - MSAP - Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, F-59000 Lille, France

   Univ. Lille, CNRS, USR 3290 - MSAP - Minituristion pour l Synthèse, l'Anlyse et l Protéomique, F-59000 Lille, Frnce

3. Grégory Abrams Aachen Faculty of Archaeology, Leiden University Faulty of Arhaeology

   Leiden University · Scladina

   Affiliation as printed

   Faculty of Archaeology, Leiden University, Van Steenis Building, Einsteinweg 2, 2333 CC Leiden, The Netherlands

   Scladina Cave Archaeological Centre, Rue Fond des Vaux 339d, 5300, Sclayn, Belgium

   Faulty of Arhaeology, Leiden University, Van Steenis Building, Einsteinweg 2, 2333 CC Leiden, The Netherlands

4. Dominique Bonjean

   University of Liège · Scladina

   Affiliation as printed

   Department of Prehistory, University of Liège, Place du XX Août 7, 4000, Liège, Belgium

   Scladina Cave Archaeological Centre, Rue Fond des Vaux 339d, 5300, Sclayn, Belgium

   Department of Prehistory, University of Liège, Place u XX Août 7, 4000, Liège, Belgium

5. Kévin Di Modica

   Scladina

   Affiliation as printed

   Scladina Cave Archaeological Centre, Rue Fond des Vaux 339d, 5300, Sclayn, Belgium

6. Christian H. Rolando

   Centre National de la Recherche Scientifique · Université de Lille · Miniaturisation pour la Synthèse, l'Analyse et la Protéomique

   Affiliation as printed

   Shrieking Sixties, 1-3 Allée Lavoisier, 59650 Villeneuve-d’Ascq, France

   Univ. Lille, CNRS, USR 3290 - MSAP - Miniaturisation pour la Synthèse, l’Analyse et la Protéomique, F-59000 Lille, France

   Shriking Sixtis, 1-3 Allé Lavoisir, 59650 Villnuv-d'Ascq, Franc

   Univ. Lille, CNRS, USR 3290 - MSAP - Minituristion pour l Synthèse, l'Anlyse et l Protéomique, F-59000 Lille, Frnce

7. Caroline Tokarski

   Université de Bordeaux · Bordeaux Proteome

   Affiliation as printed

   University of Bordeaux, Proteome Platform, 146 rue Leo Saignat, F-33076 Bordeaux, France

   University o Bordeaux, Proteome Platorm, 146 rue Leo Saignat, F-33076 Bordeaux, France

8. Patrick Auguste

   Centre National de la Recherche Scientifique · Université de Lille · Unité Évolution, Écologie et Paléontologie

   Affiliation as printed

   Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paléo, Unité Evolution, Ecologie et Paléontologie, F-59000 Lille, France

   Univ. Lille, CNRS, UMR 8198 - Evo-Eco-Paléo, Unité Evolution, Ecoloie et Paléontoloie, F-59000 Lille, France