My research involves the use of molecular techniques to investigate evolutionary problems. I mainly use ancient DNA - DNA recovered from historical, archaeological and palaeontological materials - in these studies. The main focus at present is in a NERC-funded project, "The Genetics of Faunal Change in the Late Pleistocene Holarctic."

Biologists use evolutionary theory as a means to understand and explain the natural world. Two of the fundamental processes in evolution are extinction, where species die out, and speciation, where new species come into existence. It is particularly important to understand these processes at present, as climate and environment change seem to be having a major effect on the world's plants and animals. One way in which biologists try to understand how environmental changes affect living things is by studying past times and places where we know these changes occurred, and to try to deduce what effect they had on the native animals and plants.

One such place, where environmental change seems linked to both speciation and extinction is in the Holarctic, a region from Europe across Asia into North America, during the Late Pleistocene, a period between 100 to 10 thousand years ago. During this time, many large animal species died out, but some seem to have flourished. At the same time, we see a complex series of changes in climate, plants, sea-levels and glaciers, as well as the arrival of modern humans in these areas. It is the relationship between the histories of these large animals and the complexities of environmental change that I am interested in.

When studying animals, a common method is to examine their bones to see which species died, and use radiocarbon dating to see when. This suggests the time at which extinctions occurred, and we can see how this relates to environmental changes that we know about from other sources of information. Another method, phylogeography, looks at the DNA of modern animals, and explores similarities between different populations of a species. Very large DNA differences between populations suggest that they split from each other a long time ago, and are on the way to becoming different species.

However, these methods have some problems. For large animals, bones are often not very informative about fine-scale differences between populations. Modern DNA data is not clear if the changes are very complicated, and are not very easy to relate to a particular time-point, and a particular environmental cause. To avoid these problems, I use DNA contained in the bones of animals that died in the late Pleistocene Holarctic, so-called "ancient DNA".

The work focuses on two particular animals: the woolly mammoth, which went extinct at this time, and the red deer, a species which shows considerable DNA variation between populations, and which is still alive today. I use the DNA data as markers of different populations to track movements of the animals at different times. Changes in DNA diversity at different times can be compared to environmental and climate changes. Using new mathematical techniques, it is also now possible to estimate the change in the size of animal populations through time.

Hong H.A., Khaneja R., Tam N.M., Cazzato A., Tan S., Urdaci M., Brisson A., Gasbarrini A., Barnes I., Cutting S.M. (2008) Bacillus subtilis isolated from the human gastrointestinal tract. Research in Microbiology, [Epub ahead of print, doi:10.1016/j.resmic.2008.11.002] [PubMed]

Valdiosera, C.E., García-Garitagoitia J. L., Garcia, N., Doadrio, I., Thomas, M.G., Hänni, C., Arsuaga, J-L., Barnes, I., Hofreiter, M., Orlando, L. and Götherström, A. (2008) Surprising migration and population size dynamics in ancient Iberian brown bears (Ursus arctos) Proceedings of the National Academy of Science, USA 105, 5123-5128. [PubMed]

Thomas, M.G., Barnes, I., Weale, M.E., Jones, A., Forster, P., Bradman, N. and Pramstaller, P.P. (2008) New genetic evidence supports isolation and drift in the Ladin communities of the South Tyrolean Alps but not an ancient origin in the Middle East. European Journal of Human Genetics 16, 124–134. [PubMed]

Barnes, I., Shapiro, B., Lister, A., Kuznetsova, T., Sher, A., Guthrie, D. and Thomas, M. (2007) Genetic Structure and Extinction of the Woolly Mammoth, Mammuthus primigenius. Current Biology, 17, 1072-1075.[PubMed]

Barnett, R., Yamaguchi, N., Barnes, I. and Cooper, A. (2006) The origin, current diversity, and future conservation of the modern lion (Panthera leo) Proceedings of the Royal Society Series B, 273, 2119-2125.[PubMed]

Krause, J., Dear, P., Pollack, J., Slatkin, M., Spriggs, H., Barnes, I., Lister, A., Pääbo, S. and Hofreiter M. (2006). Multiplex amplification of the complete mitochondrial genome of a Pleistocene mammoth. Nature, 439, 724-727. [PubMed]

Barnes, I. and Thomas, M. (2006) Bacterial pathogen DNA in museum osteological collections. Proceedings of the Royal Society Series B, 273, 645-653.

Barnett, R., Yamaguchi, N., Barnes, I. and Cooper, A. (2006) Lost populations and preserving genetic diversity in the lion Panthera leo: implications for its ex-situ conservation. Conservation Genetics. DOI: 10.1007/s10592-005-9062-0.

Gilbert, T., Bandelt H.-J., Hofreiter, M. and Barnes, I. (2005) Assessing ancient DNA studies. Trends in Ecology and Evolution, 20, 541-544.

Lister, A., Edwards, C., Nock D., Bunce, M., van Pijlen, I., Bradley, D., Thomas, M. and Barnes I. (2005) Phylogenetic position of the 'giant deer', Megaloceros giganteus. Nature, 438, 850-853.[PubMed]

Barnett, R., Barnes, I., Phillips, M., Martin, L.D., van Bree, P. and Cooper, A. (2005) Evolution of the extinct sabertooth and American cheetah. Current Biology, 15, 589-590. [PubMed]

Gilbert, M.*, Barnes, I.*, Collins, M., Smith, C., Eklund, J., Goudsmit, J., Poinar, H., Cooper A. (2005) The long-term survival of ancient DNA in Egypt. American Journal of Physical Anthropology, 128, 110-114. (* Joint first authors). [PubMed]

Bunce, M., Szulkin, M, Lerner, H.R.L., Barnes, I., Shapiro, B., Cooper, A. and Holdaway, R. (2005) Ancient DNA provides new insights into the evolutionary history of New Zealand's extinct giant eagle. Public Library of Science: Biology, 3. [PubMed]

Shapiro, B., Drummond, A., Rambaut, A., Wilson, M., Matheus, P., Sher, A., Pybus, O., Gilbert, M., Barnes, I., Binladen, J., Willerslev, E., Hansen, A., Baryshnikov, G., Burns, J., Davidov, S., Driver, J., Froese, D., Harington, R., Keddie, G., Kosintsev, P., Kuntz, M., Martin, L., Stephenson, R., Storer, J., Tedford, R., Zimov, S. and Cooper, A. (2004) Rise and fall of the Beringian Steppe Bison. Science, 306, 1561-1565.[PubMed]

Gilbert, M., Hansen, A., Willerslev, E., Rudbeck, L., Barnes, I., Lynnerup, N., Cooper, A. (2003) Characterization of genetic miscoding lesions caused by postmortem damage. American Journal of Human Genetics, 72, 48-61.[PubMed]

Gilbert, M., Willerslev, E., Hansen, A., Barnes, I., Rudbeck, L., Lynnerup, N., Cooper, A. (2003) Distribution patterns of postmortem damage in human mitochondrial DNA. American Journal of Human Genetics, 72, 32-47.[PubMed]

Willerslev E., Hansen A.J., Rønn R., Brand T.B., Barnes I., Wiuf C., Gilichinsky D., Mitchell D., and Cooper, A. (2003) Long-term persistence of bacterial DNA. Current Biology, 14, R9-R10.

Barnes, I., Matheus, P., Shapiro, B., Jensen, D., Cooper, A. (2002) Dynamics of Pleistocene Population Extinctions in Beringian Brown Bears. Science 295, 2267-2270.[PubMed]

Barnes, I. and Thomas, M. (2002) Ancient DNA in The Oxford Encyclopedia of Evolution, M. Pagel (editor-in-chief).

Willerslev, E., Mourier, T., Hansen, A., Christensen, B., Barnes, I., Salzberg S. (2002) Contamination in the draft of the human genome masquerades as lateral gene transfer. DNA Sequence, 13, 75-6.

Spigleman, M.*, Barnes, I.*, Holton, J., Vaira, D. and Thomas, M. (2001) Long-term DNA Survival in Ethanol-Preserved Archival Material. Annals of the Royal College of Surgeons, 83, 283-4. *Joint authorship.[PubMed]

Poinar, H., Kuch, M., Sobolik, K., Barnes, I., Stankiewicz, A., Kuder, T., Spaulding, W., Bryant, V., Cooper, A., Pääbo S. (2001) A Molecular Analysis of Dietary Diversity for Three Archaic Native Americans. Proceedings of the National Academy of Science, USA, 98, 4317-4322.[PubMed]

Barnes, I., Spigelman, M., Holton, J. Vaira, D. and Thomas, M. (2000). An Assessment of the Long-Term Preservation of the DNA of a Bacterial Pathogen in Ethanol-Preserved Archival Material. Journal of Pathology, 192, 554-559.[PubMed]

Barnes, I., Dobney, K. and Young, J.P.W. (2000). DNA-based Identification of Goose species from Two Archaeological Sites in Lincolnshire. Journal of Archaeological Science, 27, 91-100.

Chatterjee, H., Barnes, I. and Thomas, M. (1998). Hylobatid Systematics: An analysis based on morphological and molecular data. American Journal of Physical Anthropology, 28, 105.

Barnes, I., Dobney K. and Young J.P.W. (1998). The Molecular Palaeoecology of Wildfowl. Ancient Biomolecules, 1: 251.

Barnes, I., Dobney, K. and Young, J.P.W. (1998). The Molecular Palaeoecology of Geese: Identification of Archaeological Goose Remains using Ancient DNA Analysis. International Journal of Osteoarchaeology, 8, 218-223.

Tuross, N., Barnes, I. and Potts, R. (1996). Protein Identification of Blood Residues on Experimental Stone Tools. Journal of Archaeological Science, 23, 289-296.

My Erdös number is also 4.