DNA Sequence of Extinct Ancient Cattle Uncovered
ScienceDaily (Mar. 1, 2010) — Researchers, based in Ireland and Britain, have found the complete mitochondrial DNA genome sequence of ancient wild cattle using a sample from a 6,700 year-old bone.
This aurochs bone sample was discovered in a Derbyshire cave. (Credit: Image courtesy of University of Oxford)
The researchers, from University College Dublin, Trinity College, Dublin, Oxford University and Sheffield and Leeds Universities, extracted the DNA using recently developed DNA sequencing technology. This new DNA sequencing method can extract vast amounts of genetic information very rapidly and was performed at the UCD Conway Institute of Biomolecular and Biomedical Research at University College Dublin.
The mitochondrial DNA genome sequence traces maternal inheritance but the researchers hope the next stage will be to assemble the full nuclear DNA genome of the aurochs. The researchers' success in determining the first mitochondrial genome sequence raises hopes of reopening the Ancient Biomolecules Centre at the University of Oxford. The centre was mothballed in 2005 but, to further develop this research project at Oxford, the team needs specially filtered laboratories to prevent ancient samples being contaminated by modern DNA.
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1 Smurfit Institute of Genetics, Trinity College, Dublin, Ireland,
2 Animal Genomics Laboratory, School of Agriculture, Food Science and Veterinary Medicine, College of Life Sciences, University College Dublin, Dublin, Ireland,
3 Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland,
4 Henry Wellcome Ancient Biomolecules Centre, Department of Zoology, Oxford University, Oxford, United Kingdom,
5 Department of Archaeology, University of Sheffield, Sheffield, United Kingdom,
6 Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
Abstract
Abstract
Background
The derivation of domestic cattle from the extinct wild aurochs (Bos primigenius) has been well-documented by archaeological and genetic studies. Genetic studies point towards the Neolithic Near East as the centre of origin for Bos taurus, with some lines of evidence suggesting possible, albeit rare, genetic contributions from locally domesticated wild aurochsen across Eurasia. Inferences from these investigations have been based largely on the analysis of partial mitochondrial DNA sequences generated from modern animals, with limited sequence data from ancient aurochsen samples. Recent developments in DNA sequencing technologies, however, are affording new opportunities for the examination of genetic material retrieved from extinct species, providing new insight into their evolutionary history. Here we present DNA sequence analysis of the first complete mitochondrial genome (16,338 base pairs) from an archaeologically-verified and exceptionally-well preserved aurochs bone sample.
Methodology
DNA extracts were generated from an aurochs humerus bone sample recovered from a cave site located in Derbyshire, England and radiocarbon-dated to 6,738±68 calibrated years before present. These extracts were prepared for both Sanger and next generation DNA sequencing technologies (Illumina Genome Analyzer). In total, 289.9 megabases (22.48%) of the post-filtered DNA sequences generated using the Illumina Genome Analyzer from this sample mapped with confidence to the bovine genome. A consensus B. primigenius mitochondrial genome sequence was constructed and was analysed alongside all available complete bovine mitochondrial genome sequences.
Conclusions
For all nucleotide positions where both Sanger and Illumina Genome Analyzer sequencing methods gave high-confidence calls, no discrepancies were observed. Sequence analysis reveals evidence of heteroplasmy in this sample and places this mitochondrial genome sequence securely within a previously identified aurochsen haplogroup (haplogroup P), thus providing novel insights into pre-domestic patterns of variation. The high proportion of authentic, endogenous aurochs DNA preserved in this sample bodes well for future efforts to determine the complete genome sequence of a wild ancestor of domestic cattle.
Citation: Edwards CJ, Magee DA, Park SDE, McGettigan PA, Lohan AJ, et al. (2010) A Complete Mitochondrial Genome Sequence from a Mesolithic Wild Aurochs (Bos primigenius). PLoS ONE 5(2): e9255. doi:10.1371/journal.pone.0009255
Editor: Michael Knapp, University of Otago, New Zealand
Received: October 1, 2009; Accepted: January 29, 2010; Published: February 17, 2010
Copyright: © 2010 Edwards et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: This work was supported by Principal Investigator Grants from Science Foundation Ireland (project numbers: SFI/01/F.1/B028; 08/IN.l/B2038) and a Research Stimulus Grant from the Department of Agriculture, Fisheries and Food (project number: RSF 06 406). B.J.L. is supported by a Science Foundation Ireland Research Professorship (grant number: 05/RP1/908/EC07). C.J.E. was supported by a Science Foundation Ireland Research Frontiers Programme (project number: 05/RF/MAT031). Science Foundation Ireland (SFI) website: http://www.sfi.ie. Department of Agriculture, Fisheries and Food (DAFF) website: http://www.agriculture.gov.ie/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Competing interests: The authors have declared that no competing interests exist.
* E-mail: david.machugh@ucd.ie
# These authors contributed equally to this work.
¤a Current address: Research Laboratory for Archaeology, Oxford University, Oxford, United Kingdom
¤b Current address: Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
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