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
    • "Coprolites, scats or dung can provide valuable data in relation the palaeoenvironment, palaeobiology and palaeoeconomy, since fossil faeces trap pollen, beetles or parasites, and biomarkers (Carrión et al., 2001; Bon et al., 2012; Marinova et al., 2013; Taru and Backwell, 2013; Argant, 2014; Gil-Romera et al., 2014). However, to date, only hyenid coprolites have been analysed macro and microscopically (Horwitz and Goldberg, 1989; Fernández Rodríguez et al., 1995; Larkin et al., 2000). "
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    ABSTRACT: Three morphotypes of fossil fecal material (coprolites) have been identified from the Upper Pleistocene site of Cova del Coll Verdaguer (NE Iberian Peninsula). Coprolites are commonly found in Pleistocene records and also in places in which human and carnivore activities co-occurred. However, coprolite identification is typically limited to hyenids, the most readily recognizable fossilized feces, owing to their distinctive shape and good preservation, although non-hyena carnivore coprolites are also likely to be present in these assemblages. Several criteria for a multi-scale integrative analysis are proposed here for discriminating different morphotypes. Hence, this analysis provides an opportunity to assess the involvement of several carnivores in bone accumulations, to identify carnivores not specifically represented by skeletal remains and to evaluate interactions between humans and the carnivore guild, especially medium and small carnivores.
    No preview · Article · Dec 2015 · Palaeogeography Palaeoclimatology Palaeoecology
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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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    ABSTRACT: This progress report reviews and assesses recent developments in the analysis and interpretation of palaeoecological proxies that have led to important advances in our understanding of past Quaternary environments that emerge as crucial elements of more robust and reliable predictions of future climates and their ecological implications. Recently discovered archives, or technological advances associated with the biological proxies they contain, are leading to higher resolution and more detailed reconstructions of environments in a wide range of geographical circumstances. There are also important emerging palaeoecological methodologies that enable scientists to reconstruct past environments in greater detail and to apply chronologies that are more precise and accurate. Given these developments, a variety of applications, some of which are more obviously aimed at resolving practical problems in, for example, conservation science and even archaeology, are explored.
    Full-text · Article · Dec 2014 · Progress in Physical Geography
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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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    ABSTRACT: Most evidence of climate change impacts on food webs comes from modern studies and little is known about how ancient food webs have responded to climate changes in the past. Here, we integrate fossil evidence from 71 fossil sites, body-size relationships and actualism to reconstruct food webs for six large mammal communities that inhabited the Iberian Peninsula at different times during the Quaternary. We quantify the long-term dynamics of these food webs and study how their structure changed across the Quaternary, a period for which fossil data and climate changes are well known. Extinction, immigration and turnover rates were correlated with climate changes in the last 850 kyr. Yet, we find differences in the dynamics and structural properties of Pleistocene versus Holocene mammal communities that are not associated with glacial-interglacial cycles. Although all Quaternary mammal food webs were highly nested and robust to secondary extinctions, general food web properties changed in the Holocene. These results highlight the ability of communities to re-organize with the arrival of phylogenetically similar species without major structural changes, and the impact of climate change and super-generalist species (humans) on Iberian Holocene mammal communities.
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