James Haile

Dr James Haile

Postdoctoral Research Assistant

Research Laboratory for Archaeology and the History of Art
Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY


Tel: +44 (0)1865 275116

Fax: +44 (0)1865 285220

E-mail: james.haile@arch.ox.ac.uk

I am an ERC-funded Postdoctoral Research Assistant with the Palaeo-BARN Research Group.

My principal research interests involve using highly degraded DNA to investigate human/animal/plant interactions in the past. For example, my work has included examining patterns of extinction and extirpation in Pleistocene megafauna such as mammoth, moa and horse, as well as investigating changes in arctic plant communities over millennia. I am now focussing my research on human/animal interactions in the Holocene, studying specifically the complex process of animal domestication in dogs, chickens and pigs.

Publications

2015

Pedersen, M., Overballe-Petersen, S., Ermini, L., Der Sarkissian, C., Haile, J., Hellstrom, M., Spens, J., Thomsen, P., Bohmann, K., Cappillini, E., Schnell, I., Wales, N.,
 Carøe, C., Campos, P., Torti, A., Lever, M., Schmidt, A., Gilbert, T., Hansen, A., Orlando, L., Willerslev, E. Review article: Ancient and modern environmental DNA Phil. Trans. R. Soc. B 2015 370 20130383;DOI: 10.1098/rstb.2013.0383 

2014

Willerslev, E.*, Davison, J.*, Moora, M.*, Zobel, M.*, Coissac, E.*, Edwards, M.*, Lorenzen, E.*, Madsen, M.*, Gussarova, G.*, Haile, J.*, Craine, J., Bergmann, G., Gielly, L., Epp, L., Boessenkool, S., Pearman, P., Cheddadi, R., Murray, D., Bråthen, K., Yoccoz, N., Binney, H., Cruaud, C., Wincker, P., Goslar, T., Alsos, I., Bellemain, E., Brysting, A., Elven, R., Sønstebø, J., Rasmussen, M., Andersen, K., Rønn, R., Mourier, T., Cooper, A., Möller, P., Froese, D., Zazula, G., Tikhonov, A., Savvinov, G., Gilbert, T., Kjær, K., Orlando, L., Brochmann, C., Taberlet, P. Fifty-five thousand years of arctic vegetation change and implications for the extinctions of northern megafauna. Nature 2014 doi:10.1038/ nature12921. *Joint First Author

Tridico, S., Rigby, P., Kirkbride, P., Haile, J., Bunce, M. Megafaunal split ends: Microscopical characterisation of hair structure and function in extinct woolly mammoth and woolly rhino. Quaternary Science Reviews 2014 83 68–75

Haouchar, D., Haile, J., McDowell, M, Murray, D., White, N., Allcock, R., Phillips, M., Prideaux, G., Bunce, M. Thorough assessment of DNA preservation from fossil bone and sediments excavated from a Quaternary cave deposit on Kangaroo Island, South Australia. Quaternary Science Reviews 2014 84(1) 56-64

2013

Coghlan, M., White, N., Murray, D., Houston, J., Rutherford, W., Bellgard, M., Haile, J., Bunce, M. Metabarcoding avian diets at airports: implications for birdstrike hazard management planning. Investigative Genetics 2013 4:27 

Murray, D., Haile, J., Dortch, J., White, N., Haouchar, D., Bellgard, M., Allcock, R., Prideaux, G., Bunce, M. Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages. Scientific Reports 2013 3 3371 doi:10.1038/srep03371 

Burgar, J., Murray, D., Craig, M., Haile, J., Houston, J., Stokes, V., Bunce, M. Who’s’ for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed. Molecular Ecology 2013 doi: 10.1111/mec.12531

Parducci, L., Matetovici, I., Fontana, S., Bennett, K., Suyama, Y., Haile, J., Kjær, K., Larsen, N., Drouzas, A., Willerslev, E. Molecular and pollen-based vegetation analysis in lake sediments from central Scandinavia. Molecular Ecology 2013 doi: 10.1111/mec.12298

2012

Bellemain, E., Davey, M., Kauserud, H., Epp, L., Boessenkool, S., Coissac, E., Geml, J., Edwards, M., Willerslev, E., Gussarova, G., Taberlet, P., Haile, J., Brochmann, C. Fungal palaeodiversity revealed using high-throughput metabarcoding of ancient DNA from arctic permafrost. Environmental Microbiology 2012 doi:10.1111/1462-2920.12020

Murray, D., Pearson, S., Fullagar, R., Chase, B., Houston, J., Atchison, J., White, N., Bellgard, M., Clarke, E., Macphail, M., Gilbert, T., Haile, J., Bunce, M. An Arid Zone Archive: ancient DNA preserved in herbivore middens as a source of palaeoecological data. Quaternary Science Reviews 2012 58 135-145

Haouchar, D., Haile, J., Bunce, M., Spencer, P. The identity of the Depuch Island Rock Wallaby revealed through Ancient DNA. Australian Mammalogy 2012 doi: 10.1071/AM11044 

Allentoft, M., Collins, M., Harker, D., Haile, J., Oskam, C., Hale, M., Campos, P., Samaniego, J., Gilbert, T., Willerslev, E., Zhang, G., Scofield, R., Holdaway, R., Bunce, M. The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils. Proc. R. Soc. B 2012 doi:10.1098/rspb.2012.1745

Oskam, C., Allentoft, M., Walter, R., Scofield, R., Haile, J., Holdaway, R., Bunce, M., Jacomb, C. Ancient DNA analyses of early archaeological sites in New Zealand reveals extreme exploitation of moa (Aves: Dinornithiformes) at all life stages. Quaternary Science Reviews 2012 52 41e48

Epp, L., Boessenkool, S., Bellemain, E., Haile, J. Esposito, A., Riaz, T., Erséus, C., Gusarov, V., Edwards, M., Johnsen, A., Stenøien, H., Hassel, K., Willerslev, E., Taberlet, P., Coissac, E., Christian, C. New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Molecular Ecology 2012 21 (8) pp. 2045-2050

Coghlan, M., Haile, J., Houston, H., Murray, D., White, N., Moolhuijzen, P., Bellgard, M., Bunce, M. Deep Sequencing of Plant and Animal DNA Contained Within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns. PLoS Genetics 2012 8(4): e1002657. doi:10.1371/journal.pgen.1002657

Yoccoz, N., Bråthen, K., Gielly, L., Haile, J., Edwards, M., Goslar, T., von Steding, H., Brysting, A., Coissac, E., Pompanon, F., Sønstebø, J., Miquel, C., Valentini, A., Bello, F., Chave, J., Thuiller, W., Wincker, P., Cruaud, C., Gavory, F., Rasmussen, M., Gilbert, T., Orlando, L., Brochmann, C., Willerslev, E., Taberlet, P. DNA in soil mirrors plant functional and structural diversity. Molecular Ecology 2012 doi: 10.1111/j.1365-294X.2012.05545.x

Parducci, L., Jørgensen, T., Tollefsrud, M., Elverland, E., Alm, T., Fontana, S., Bennett, K., Haile, J., Matetovici, I., Suyama, Y., Edwards, M., Andersen, K., Rasmussen, M., Boessenkool, S., Coissac, E., Brochmann, C., Taberlet, P., Houmark-Nielsen, M., Larsen, N., Orlando, L., Gilbert, T., Kjær, K., Alsos, I., Willerslev, E. Glacial Survival of Boreal Trees in Northern Scandinavia. Science 2012 335 6072 1083-1086. 

Boessenkool, S., Epp, L., Haile, J., Bellemain, E., Edwards, M., Coissac, E., Willerslev, E., Brochmann, C. Blocking human contaminant DNA during PCR allows amplification of rare mammal species from sedimentary ancient DNA. Molecular Ecology 201221 (8) pp. 1806-1815. 

Jørgensen, T., Haile, J., Möller, P., Andreev, A., Boessenkool, S., Rasmussen, M., Kienast, F., Coissac, E., Taberlet, P., Brochmann, C., Andersen, K., Orlando, L., Gilbert, T., Willerslev, E. A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long-term vegetational stability. Molecular Ecology 2012 21 (8) pp. 1989-2003

Andersen, K., Bird, K., Rasmussen, M., Haile, J., Breuning-Madsen, H., Kjær, K., Orlando, L., Gilbert, T., Willerslev, E. Metabarcoding of ‘Dirt’ DNA from Soil Reflects Vertebrate Biodiversity. Molecular Ecology 2012. DOI: 10.1111/j.1365-294X.2011.05261.x

2011

Murray, D., Bunce, M., Cannell, B., Oliver, R., Houston, J., White, N., Barrero, R., Bellgard, M., Haile, J. DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches. PLoS ONE 2011 6(10): e25776. doi:10.1371/ journal.pone.0025776

White, N., Dawson, R., Hodder, M., Tridico, S., Mawson, P., Haile, J., Bunce, M. Application of STR markers in wildlife forensic casework involving Australian black-cockatoos (Calyptorhynchus spp.). Forensic Science International: Genetics (2011), doi:10.1016/ j.fsigen.2011.10.003

Jørgensen, T., Kjær, K., Haile, J., Rasmussen, M., Boessenkool, S., Andersen, K., Coissac, E., Taberlet, P., Orlando, L., Gilbert, T., Willerslev, E. Islands in the Ice: Detecting past vegetation on Greenlandic Nunataks using historical records and sedimentary DNA meta-barcoding. Molecular Ecology 2011 21 (8) pp. 1980-1988

Lorenzen, E., Nogués-Bravo, D., Orlando, L., Weinstock, J., Binladen, J., Marske, K., Ugan, A., Borregaard, M., Gilbert, T., Nielsen, R., Ho, S., Goebel, T., Graf, K., Byers, D., Stenderup, J., Rasmussen, M., Campos, P., Leonard, J., Koepfli, K., Froese, D., Zazula, G., Stafford, T., Aaris-Sørensen, K., Batra, P., Haywood, A., Valdes, P., Boeskorov, G., Burns, J., Davydov, S., Haile, J., Jenkins, D., Kosintsev, P., Kuznetsova, T., Lai, X., Martin, L., McDonald, H., Mol, D., Meldgaard, M., Munch, K., Stephan, E., Sablin, M., Sommer, R., Sipko, T., Scott, E., Suchard, M., Tikhonov, A., Willerslev, R., Wayne, R., Cooper, A., Hofreiter, M., Sher, A., Shapiro, B., Rahbek, C., Willerslev, E. Individualistic species responses to climate and humans determine Late Quaternary megafaunal extinction and survival. Nature 2011. 479, 359–364

Bjørk, A., Björck, S., Cronholm, A., Haile, J., Ljung, K., Porter, C. Possible Late Pleistocene volcanic activity on Nightingale Island, South Atlantic Ocean, based on geoelectrical resistivity measurements, sediment corings and 14C dating. GFF 2011

Oskam, C., Jacomb, C., Allentoft, M., Walter, R., Scofield, R., Haile, J., Holdaway, R., Bunce, M. Molecular and morphological analyses of avian eggshell excavated from a late thirteenth century earth oven. Journal of Archaeological Science 2011 doi:10.1016/ j.jas.2011.05.00

Coghlan, M., White, N., Parkinson, L., Haile, J., Spencer, P., Bunce, M. Egg forensics: An appraisal of DNA sequencing to assist in species identification of illegally smuggled eggs. Forensic Science International: Genetics 2011 DOI:10.1016/j.fsigen.2011.06.006

2010

Kuzmina, S., Sher, A.V., Edwards, M.E., Haile, J. Yan, E.V., Kotov, A.V. Willerslev, E. The Late Pleistocene environment of the eastern West Beringia based on the principal section at the Main River, Chukotka. Quaternary Science Reviews 2010  doi: 10.1016/ j.quascirev.2010.03.01

Arnold, L., Roberts, R., MacPhee, R., Haile, J., Brock, F., Möller, P., Froese, D., Tikhonov, A., Chivas, A., Willerslev, E. Paper II - Dirt, dates and DNA: OSL and radiocarbon chronologies of perennially-frozen sediments in Siberia, and their implications for sedimentary ancient DNA studies. Boreas 2010 doi: 10.1111/j.1502-3885.2010.00181.x

Sønstebø, J., Gielly, L., Brysting, A. K., Elven, R., Edwards, M., Haile, J., Willerslev, E., Bråthen K. A., Yoccoz, N., Coissac, E., Rioux, D., Sannier, J., Taberlet, P, Brochmann, C.Using Next-Generation Sequencing for Molecular Reconstruction of Past Arctic Vegetation and Climate. Molecular Ecology Resources 2010 10 1009–1018

Murton, J.; Edwards, M. E.; Murton, D.; Bateman, M.; Haile, J. Age and origin of ice-rich Yedoma silts at Duvanny Yar, northeast Siberia: a record of Beringian environmental change since the last interglacial.  American Geophysical Union 2010 AGUFMPP13A1484M

Haile, J., Larson, G., Owens, K., Dobney, K., Shapiro, B., Ancient DNA typing of archaeological pig remains corroborates historical records. Journal of Archaeological Sciences. 2010 37 (1) 174-177

Oskam, C., Haile, J., McLay, E., Rigby, P., Allentoft, M., Olsen, M., Bengtsson, C., Miller, G., Schwenninger, J-L., Jacomb, C., Walter, R., Baynes, A., Dortch, J., Parker-Pearson, M., Gilbert, T., Holdaway, R., Willerslev, E., Bunce, M. 2010 Fossil avian eggshell preserves ancient DNA. Proceedings of the Royal Society B 277 1991-2000 

2009

Haile, J., MacPhee, R., Roberts, R., Arnold, L., Brook, B., Nielsen, R., Gilbert, M., Brock, F., Munch, K., Chivas, A., Tikhonov, A., Willerslev, E. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. PNAS. 2009 106: 52 22363-22368

Shepherd, L., Cooper, J., Haile, J., Scofield, P., Tennyson, A., Worthy, T. 2009 Selection of a neotype for Apteryx mantelli Bartlett, 1852, with support of genetic data. The Bulletin of
 the British Ornithologists’ Club 129 p.195

Bunce, M., Worthy, T. H., Phillips, M. J., Holdaway, R. N., Willerslev, E., Haile, J. Shapiro, B., Scofield, R. P., Drummond, A., Kamp, P. J. J. and Cooper, A. The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. PNAS. 2009 106: 49 20646-20651

Rijsdijk, K. Hume, J., Bunnik, F., Florens, F., Baider, C., Shapiro, B., van der Plicht, J., Janoo, A., Griffiths, O., van den Hoek Ostende, L., Cremer, H., Vernimmen, T., De Louw, P., Bholah, A., Saumtally, S., Porch, N., Haile, J., Buckley, M., Collins, M., Gittenberger, E. 2009 Mid-Holocene vertebrate bone Concentration-Lagerstätte on oceanic island Mauritius provides a window into the ecosystem of the dodo (Raphus cucullatus). Quaternary Science Reviews. 28 (1-2) 14-24

Thomsen, P., Elias, S., Gilbert, M., Haile, J., Munch, K., Kuzmina, S., Froese, D., Sher, A., Holdaway, R., Willerslev, E. Non-Destructive Sampling of Ancient Insect DNA PLoS ONE. 2009; 4(4): e504 

2008

Ho, S., Saarma, U., Barnett, R., Haile, J., Shapiro, B. The Effect of Inappropriate Calibration: Three Case Studies in Molecular Ecology. PLoS ONE. 2008; 3(2): e1615

2007

Haile, J., Holdaway, R., Oliver, K., Bunce, M., Gilbert, M., Nielsen, R., Munch, K., Ho, S., Willerslev, E. Ancient DNA Chronology within Sediment Deposits: Are Paleobiological Reconstructions Possible and is DNA Leaching a Factor? Mol. Biol. Evol. 2007 24(4):982-989

Willerslev, E., Cappellini, E., Boomsma, W., Nielsen, R., Hebsgaard, M., Brand, T., Hofreiter, M., Bunce, M., Poinar, H., Dahl-Jensen, D., Johnsen, S., Steffensen, J. P., Bennike, O., Funder, S., Schwenninger, J-L., Nathan, R., Armitage, S., Barker, J., Sharp, M., Penkman, K., Haile, J., Taberlet, P., Gilbert, M., Casoli, A., Campani, E. & Collins, M. Ancient Biomolecules from Deep Ice Cores Reveal a Forested Southern Greenland. Science 2007 317, 111-114

2006

Binladen, J., Wiuf, C., Gilbert, M., Bunce, M., Barnett, R., Larson, G., Greenwood, A., Haile, J., Ho, S., Hansen, A., Willerslev, E. Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes. Genetics, 2006 172, 733-741

 

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