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.
SourceAvailable from: Christina Warinner
Article: Ancient human microbiomes[Show abstract] [Hide abstract]
ABSTRACT: Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.Journal of Human Evolution 01/2015; 79. DOI:10.1016/j.jhevol.2014.10.016 · 3.87 Impact Factor
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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.PLoS ONE 09/2014; 9(9):e106651. DOI:10.1371/journal.pone.0106651 · 3.53 Impact Factor
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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.Progress in Physical Geography 12/2014; 38(6):807-817. DOI:10.1177/0309133314540690 · 3.89 Impact Factor