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

Abstract

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.

Ancient human microbiomes

“…Human DNA within coprolites (presumably from shed epithelial cells of the gastrointestinal tract) may make up as much as 50% of the total DNA in well-preserved samples (Bon et al, 2012). Host biomolecules have been used to validate the coprolite species of origin (Wood et al, 2008; Bon et al, 2012), and to identify and date the presence of humans at early Paleoindian sites where few cultural artifacts are present (Gilbert et al, 2008). Steroidal hormones like estrogen, testosterone, progesterone, and estradiol have been detected in coprolites using radioimmunoassay procedures (Sobolik et al, 1996; Rhode, 2003).…”

“…Ancient feces preserve dietary macrofossils, such as undigested or indigestible plant, animal, and fish remains (Callen and Martin, 1969; Fry, 1985; Holden, 1991), microfossils, such as pollen and phytoliths (Reinhard and Bryant, 1992), and dietary DNA molecules (Poinar et al, 1998, 2001; Wood et al, 2008; Bon et al, 2012). Likewise, dental calculus entraps plant microfossils and environmental debris, including plant phytoliths (Fox et al, 1994, 1996), starches (Boyadjian et al, 2007; Henry and Piperno, 2008; Piperno and Dillehay, 2008; Hardy et al, 2009, 2012; Henry et al, 2011), and fibers (Blatt et al, 2011), providing evidence for the consumption of starchy soft plant foods that otherwise rarely preserve in the archaeological record, including tubers, rhizomes, squashes, and legumes (Piperno and Dillehay, 2008; Mickleburgh and Pagán-Jiménez, 2012).…”

Calcium phosphate preservation of faecal bacterial negative moulds in hyaena coprolites

“…A variety of inclusions may be found inside coprolites, such as pollen, spores, phytoliths and other microfossils that provide information about the environment in which the producing animal lived. In addition, they also offer valuable insights into past ecosystems (Carrión et al 2000(Carrión et al , 2001(Carrión et al , 2007Scott et al 2003;Prasad et al 2005;Yll et al 2006;Farlow et al 2010;Fernández-Jalvo et al 2010;Bon et al 2012).…”

Recent methodological advances in Quaternary palaeoecological proxies

“…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.…”