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Comparing extraction method efficiency for high-throughput palaeoproteomic bone species identification

Publication . Mylopotamitaki, Dorothea; Harking, Florian S.; Taurozzi, Alberto J.; Fagernäs, Zandra; Godinho, Ricardo Miguel; Smith, Geoff M.; Weiss, Marcel; Schüler, Tim; McPherron, Shannon P.; Meller, Harald; Cascalheira, João; Bicho, Nuno; Olsen, Jesper V.; Hublin, Jean-Jacques; Welker, Frido

High-throughput proteomic analysis of archaeological skeletal remains provides information about past fauna community compositions and species dispersals in time and space. Archaeological skeletal remains are a finite resource, however, and therefore it becomes relevant to optimize methods of skeletal proteome extraction. Ancient proteins in bone specimens can be highly degraded and consequently, extraction methods for well-preserved or modern bone might be unsuitable for the processing of highly degraded skeletal proteomes. In this study, we compared six proteomic extraction methods on Late Pleistocene remains with variable levels of proteome preservation. We tested the accuracy of species identification, protein sequence coverage, deamidation, and the number of post-translational modifications per method. We find striking differences in obtained proteome complexity and sequence coverage, highlighting that simple acid-insoluble proteome extraction methods perform better in highly degraded contexts. For well-preserved specimens, the approach using EDTA demineralization and protease-mix proteolysis yielded a higher number of identified peptides. The protocols presented here allowed protein extraction from ancient bone with a minimum number of working steps and equipment and yielded protein extracts within three working days. We expect further development along this route to benefit large-scale screening applications of relevance to archaeological and human evolution research.

2023Journal article

Open Access

Peninsular southern Europe refugia during the Middle Palaeolithic: an introduction

Publication . Bicho, Nuno; Carvalho, Milena

Neanderthals faced great environmental and climatic instability during the Pleistocene, which may have influenced their lithic technology, subsistence patterns, mobility, behaviour and survival. Modern research assessing the effect of climate and environment on the Middle Palaeolithic and transition to the Upper Palaeolithic has often turned to southern Europe, specifically peninsular southern Europe (Iberia, Italy and the Balkans). These are regions typically regarded as refugia during periods of unfavourable climatic conditions, inspiring hundreds of palaeoenvironmental studies at Neanderthal sites and hypotheses on late Neanderthal survival in locations with relative ameliorated conditions. Here, we present the topic of the special issue focusing on peninsular southern Europe refugia during the Middle Palaeolithic covering the three main peninsulas. Its 16 contributions discuss relevant data on peninsular southern Europe as possible refugia during periods of unfavourable climate during the Middle Palaeolithic and transition to Upper Palaeolithic.

2022-01Journal article

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