Coprolites as a source of information on the genome and diet of the cave hyena

iBiTec-S/SBiGeM, CEA Saclay, 91191 Gif-sur-Yvette cedex, France.
Proceedings of the Royal Society B: Biological Sciences (Impact Factor: 5.05). 03/2012; 279(1739):2825-30. DOI: 10.1098/rspb.2012.0358
Source: PubMed


We performed high-throughput sequencing of DNA from fossilized faeces to evaluate this material as a source of information on the genome and diet of Pleistocene carnivores. We analysed coprolites derived from the extinct cave hyena (Crocuta crocuta spelaea), and sequenced 90 million DNA fragments from two specimens. The DNA reads enabled a reconstruction of the cave hyena mitochondrial genome with up to a 158-fold coverage. This genome, and those sequenced from extant spotted (Crocuta crocuta) and striped (Hyaena hyaena) hyena specimens, allows for the establishment of a robust phylogeny that supports a close relationship between the cave and the spotted hyena. We also demonstrate that high-throughput sequencing yields data for cave hyena multi-copy and single-copy nuclear genes, and that about 50 per cent of the coprolite DNA can be ascribed to this species. Analysing the data for additional species to indicate the cave hyena diet, we retrieved abundant sequences for the red deer (Cervus elaphus), and characterized its mitochondrial genome with up to a 3.8-fold coverage. In conclusion, we have demonstrated the presence of abundant ancient DNA in the coprolites surveyed. Shotgun sequencing of this material yielded a wealth of DNA sequences for a Pleistocene carnivore and allowed unbiased identification of diet.

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Available from: Céline Bon, May 27, 2014
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    • "Hyaena coprolites are of interest to archaeologists in particular because they are most frequently preserved in the context of caves which provide the occupational localities for ancient people. Bon et al. (2012) explore how refinements in methodology, including the use of DNA sequencing techniques, provide robust palaeodiet evidence – and thereby enhanced palaeoenvironmental reconstruction – in this case for a cave site in France. But when the fossilized dung material reveals evidence of human remains, this seems to evoke an almost macabre fascination. "
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    • "Species eaten by Pleistocene carnivores are classically identified from indirect clues, such as cut marks, teeth marks or stone tools marks in the fossil bones [27]. There are methods to distinguish carnivorous vs. herbivorous species [28], [29], and to identify ancient species diet requirements using stable isotopes [21] and DNA from coprolites [30]. Here, food web links were designated following three criteria: (i) spatio-temporal co-occurrence as shown by fossil record data (Tables S1, S2 in File S1), (ii) body-size relationships (Table S3 in File S1), and (iii) actualism (applying current species diet to infer past trophic links). "
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    • "7) excavated a partially-articulated limb of C. antiquitatis at Kent's Cavern (England) that had been heavily chewed by hyaenas. Analysis of hyaena coprolites at Coumère Cave (Ariège, France) showed (as well as Crocuta DNA) a prevalence of C. elaphus DNA, indicating red deer as a major prey item for these animals (Bon et al., 2012). Lister (2001) deduced from the predominance of juveniles among woolly mammoth remains at Kent's Cavern (Devon, UK) that the hyaenas were hunting or scavenging this species but were limited in the size of individuals that they could hunt or drag (even as dismembered pieces of carcasses) back to the cave. "
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