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Biography

Dan Bradley was brought up on a Northern Irish farm and after a degree in Genetics from Cambridge University and PhD in medical genetics from Trinity College Dublin he started to work on the genetics of each species present on that farm, including Irish humans, and has done for over 30 years. With his colleagues he has combined analysis of ancient and modern cattle to inform on the origins of these and other domesticates and pioneered the molecular genetic analysis of Irish populations. He holds a Personal Chair in Population Genetics in Trinity and was awarded the 2020 Royal Irish Academy Gold Medal in the Life Sciences

Research Tags

ADMIXTURE Ancient DNA analysis and origins of Irish mammals ANIMAL DOMESTICATION Archaeozoological genetics and the origins of cattle pastoralism BOVINE EVOLUTION BREED RELATIONSHIPS CATTLE CATTLE BOS-TAURUS CONTROL REGION Detection of recombination in mammalian mtDNA DNA-SEQUENCE DOMESTICATION EQUUS CABALLUS EUKARYOTIC GENOMES EUROPEAN CATTLE EUROPEAN POPULATIONS EVOLUTION FAMILY FARMED GENE GENETIC CONSERVATION GENETIC DIVERSITY GENETIC VARIATION HORSE HUMAN DNA INTROGRESSION LINKAGE ANALYSIS LINKAGE GROUP LOCALIZATION LOCI MAP MICROSATELLITE MITOCHONDRIAL MITOCHONDRIAL DNA MTDNA MUTATION MYOTONIC-DYSTROPHY GENE ORIGIN ORIGINS PIGS POLYMORPHISMS Population genetic signatures of selection in cattle and other domesticates Population genetics, selection, structure and origins in Irish human populations PREVALENCE RELEASE RYANODINE RECEPTOR GENE SARCOPLASMIC-RETICULUM SEQUENCE SHEEP Y chromosome diverisity and the genetic architecture of Irish surnames

Research Projects

Project Title

AncestralWeave: 1000 ancient genomes: gene-economy innovation in cattle, sheep and goat

From

December 2020

November 2025

Summary

The genetic threads of goat, cattle and sheep ancestry have been woven by human breeding, environmental pressures, hybridisation and the chance effects of genetic drift. The ancestral weaves of these key animals intertwine with human creativity in the most profoundly innovative episodes of the human past. Three broad episodes of particular import were: initial domestications circa 11 kya in Southwest Asia; the intensification circa 6 kya of use of those animal products which are harvested without killing such as wool, milk and traction; and the development of exceptionally productive landraces, later formalized into breeds, in recent millennia. However, each of these is loosely defined in time and space, the key traits are often osteologically invisible, and the vectors of causality in their virtuous cycles of gene-economy innovation are completely unknown. A combination of high coverage ancient whole genome data coupled with new analysis methods that allow efficient computation of genomewide locus genealogies will be used to untangle the threads of ancestry in sheep, cattle and goat across the whole genome in these transformative phases. Combining these with additional low coverage genomes generated from less preserved samples will generate a total set of 1,000 ancient animal genomes. These data will be unprecedented and will allow tracking of selection at trait genes, in order to detect human agency in breeding and, in collaboration with archaeologist partners, asking are there periods and places where threads of innovation coalesce. The project will also use ancient epigenetics to explore archaeological variation in gene activation patterns and will seek to understand the problematic build up of harmful mutations that threaten livestock today. With cognate disciplines, it will compare signals of animal mobility identifying distinct genetic strata correlating with archaeological horizons and affording the prospect of DNA-dating in future excavation.

Funding Agency

European Research Council

Programme

Advanced Grant

Representations

Details	Date
Member of a Wellcome Trust Panel responsible for the disbursement of research funds in Bioarchaeology
Appointed to Editorial Board of the international journal, Animal Genetics
Five times juror in the European Contest for Young Scientists
Member of the Royal Irish Academy Advisory Committee on Genetic Anthropology
Served as an expert consultant on genetic distance and biodiversity to the Food and Agriculture Organisation of the United Nations
Member, PHG Funded PI's and Researchers, All Researchers funded under Cycle 3 PRTLI - Programme for Human Genomics

Memberships

Membership of Professional Institutions, Associations, Societies

Details	Date From	Date To
Member of International Society of Animal Genetics
former President of Irish Society of Human Genetics

Publications and other Research Outputs

Cooke N.P., Murray M., Cassidy L.M., Mattiangeli V., Okazaki K., Kasai K., Gakuhari T., Bradley D.G., Nakagome S., Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan, iScience, 27, (110050), 2024, Journal Article, PUBLISHED DOI

Cooke N.P., Mattiangeli V., Cassidy L.M., Okazaki K., Kasai K., Bradley D.G., Gakuhari T., Nakagome S., Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands, Evolutionary Huma Sciences, 5, 2023, pe23-, Journal Article, PUBLISHED DOI

Cooke, N.P. and Mattiangeli, V. and Cassidy, L.M. and Okazaki, K. and Stokes, C.A. and Onbe, S. and Hatakeyama, S. and Machida, K. and Kasai, K. and Tomioka, N. and Matsumoto, A. and Ito, M. and Kojima, Y. and Bradley, D.G. and Gakuhari, T. and Nakagome, S., Ancient genomics reveals tripartite origins of Japanese populations, Science Advances, 7, (38), 2021, Notes: [cited By 46], Journal Article, PUBLISHED DOI

Verdugo, M.P. and Mullin, V.E. and Scheu, A. and Mattiangeli, V. and Daly, K.G. and Maisano Delser, P. and Hare, A.J. and Burger, J. and Collins, M.J. and Kehati, R. and Hesse, P. and Fulton, D. and Sauer, E.W. and Mohaseb, F.A. and Davoudi, H. and Khazaeli, R. and Lhuillier, J. and Rapin, C. and Ebrahimi, S. and Khasanov, M. and Vahidi, S.M.F. and MacHugh, D.E. and ErtuÄ rul, O. and Koukouli-Chrysanthaki, C. and Sampson, A. and Kazantzis, G. and Kontopoulos, I. and Bulatovic, J. and StojanoviÄ , I. and Mikdad, A. and Benecke, N. and LinstÃ€dter, J. and Sablin, M. and Bendrey, R. and Gourichon, L. and Arbuckle, B.S. and Mashkour, M. and Orton, D. and Horwitz, L.K. and Teasdale, M.D. and Bradley, D.G., Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent, Science (New York, N.Y.), 365, (6449), 2019, p173-176 , Notes: [cited By 0], Journal Article, PUBLISHED DOI

Ring, S.C. and Purfield, D.C. and Good, M. and Breslin, P. and Ryan, E. and Blom, A. and Evans, R.D. and Doherty, M.L. and Bradley, D.G. and Berry, D.P., Variance components for bovine tuberculosis infection and multi-breed genome-wide association analysis using imputed whole genome sequence data, PLoS ONE, 14, (2), 2019, Notes: [cited By 1], Journal Article, PUBLISHED TARA - Full Text DOI

Frantz, L.A.F. and Haile, J. and Lin, A.T. and Scheu, A. and GeÃ¶rg, C. and Benecke, N. and Alexander, M. and Linderholm, A. and Mullin, V.E. and Daly, K.G. and Battista, V.M. and Price, M. and Gron, K.J. and Alexandri, P. and Arbogast, R.-M. and Arbuckle, B. and BÇ lÇ Å escu, A. and Barnett, R. and Bartosiewicz, L. and Baryshnikov, G. and Bonsall, C. and BoriÄ , D. and BoroneanÅ£, A. and BulatoviÄ , J. and Ã akirlar, C. and Carretero, J.-M. and Chapman, J. and Church, M. and Crooijmans, R. and De Cupere, B. and Detry, C. and Dimitrijevic, V. and DumitraÅ cu, V. and Du Plessis, L. and Edwards, C.J. and Erek, C.M. and Erim-Ã-zdoÇ§an, A. and Ervynck, A. and Fulgione, D. and Gligor, M. and GÃ¶therstrÃ¶m, A. and Gourichon, L. and Groenen, M.A.M. and Helmer, D. and Hongo, H. and Horwitz, L.K. and Irving-Pease, E.K. and Lebrasseur, O. and Lesur, J. and Malone, C. and Manaseryan, N. and Marciniak, A. and Martlew, H. and Mashkour, M. and Matthews, R. and Matuzeviciute, G.M. and Maziar, S. and Meijaard, E. and McGovern, T. and Megens, H.-J. and Miller, R. and Mohaseb, A.F. and Orschiedt, J. and Orton, D. and Papathanasiou, A. and Pearson, M.P. and Pinhasi, R. and RadmanoviÄ , D. and Ricaut, F.-X. and Richards, M. and Sabin, R. and Sarti, L. and Schier, W. and Sheikhi, S. and Stephan, E. and Stewart, J.R. and Stoddart, S. and Tagliacozzo, A. and TasiÄ , N. and Trantalidou, K. and Tresset, A. and Valdiosera, C. and Van Den Hurk, Y. and Van Poucke, S. and Vigne, J.-D. and Yanevich, A. and Zeeb-Lanz, A. and Triantafyllidis, A. and Gilbert, M.T.P. and Schibler, J. and Rowley-Conwy, P. and Zeder, M. and Peters, J. and Cucchi, T. and Bradley, D.G. and Dobney, K. and Burger, J. and Evin, A. and Girdland-Flink, L. and Larson, G., Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe, Proceedings of the National Academy of Sciences of the United States of America, 116, (35), 2019, p17231-17238 , Notes: [cited By 2], Journal Article, PUBLISHED TARA - Full Text DOI

Chen, N. and Cai, Y. and Chen, Q. and Li, R. and Wang, K. and Huang, Y. and Hu, S. and Huang, S. and Zhang, H. and Zheng, Z. and Song, W. and Ma, Z. and Ma, Y. and Dang, R. and Zhang, Z. and Xu, L. and Jia, Y. and Liu, S. and Yue, X. and Deng, W. and Zhang, X. and Sun, Z. and Lan, X. and Han, J. and Chen, H. and Bradley, D.G. and Jiang, Y. and Lei, C., Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia, Nature Communications, 9, (1), 2018, Notes: [cited By 4], Journal Article, PUBLISHED TARA - Full Text DOI

Daly, K.G. and Delser, P.M. and Mullin, V.E. and Scheu, A. and Mattiangeli, V. and Teasdale, M.D. and Hare, A.J. and Burger, J. and Verdugo, M.P. and Collins, M.J. and Kehati, R. and Erek, C.M. and Bar-Oz, G. and Pompanon, F. and Cumer, T. and Ã akÄ±rlar, C. and Mohaseb, A.F. and Decruyenaere, D. and Davoudi, H. and Ã evik, Ã-. and Rollefson, G. and Vigne, J.-D. and Khazaeli, R. and Fathi, H. and Doost, S.B. and Sorkhani, R.R. and Vahdati, A.A. and Sauer, E.W. and Kharanaghi, H.A. and Maziar, S. and Gasparian, B. and Pinhasi, R. and Martin, L. and Orton, D. and Arbuckle, B.S. and Benecke, N. and Manica, A. and Horwitz, L.K. and Mashkour, M. and Bradley, D.G., Ancient goat genomes reveal mosaic domestication in the Fertile Crescent, Science, 361, (6397), 2018, p85-88 , Notes: [cited By 3], Journal Article, PUBLISHED DOI

Schroeder, H. and Sikora, M. and Gopalakrishnan, S. and Cassidy, L.M. and Delser, P.M. and Velasco, M.S. and Schraiber, J.G. and Rasmussen, S. and Homburger, J.R. and Ã vila-Arcos, M.C. and Allentoft, M.E. and VÃctor Moreno-Mayar, J. and Renaud, G. and GÃ³mez-Carballa, A. and Laffoon, J.E. and Hopkins, R.J.A. and Higham, T.F.G. and Carr, R.S. and Schaffer, W.C. and Day, J.S. and Hoogland, M. and Salas, A. and Bustamante, C.D. and Nielsen, R. and Bradley, D.G. and Hofman, C.L. and Willerslev, E., Origins and genetic legacies of the Caribbean Taino, Proceedings of the National Academy of Sciences of the United States of America, 115, (10), 2018, p2341-2346 , Notes: [cited By 3], Journal Article, PUBLISHED TARA - Full Text DOI

Byrne RP, Martiniano R, Cassidy LM, Carrigan M, Hellenthal G, Hardiman O, Bradley DG, McLaughlin RL, Insular Celtic population structure and genomic footprints of migration, PLOS Genetics, 14, 2018, pe1007152 , Journal Article, PUBLISHED TARA - Full Text DOI

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Oxen, Grolier Encyclopedia New Book of Knowledge, 2003, [Bradley DG ], Item in dictionary or encyclopaedia, etc, PUBLISHED

Bradley DG and Hill EW, Whats in a surname, Archaeology Ireland , 14, 2000, p22 - 23, Journal Article, PUBLISHED

Designing life: the role of inheritance in, editor(s)M. Jumker-Kenny , Designing life? Genetics, procreation and ethics, Aldershot, Ashgate Publishing Ltd, 1999, [Bradley DG], Book Chapter, PUBLISHED

Loftus R.T., D.E. MacHugh, P. Cunningham and D.G. Bradley, Animal domestication [letter], Science, 283, 1999, p329-30 , Journal Article, PUBLISHED

Loftus RT, D.G. Bradley, D.E. MacHugh, C.S. Troy, C.N. Meghen and E.P. Cunningham , Molecular genetics and the evolution of domesticated cattle, 8th World Conference on Animal Production, 1, 1998, pp144 - 145, Conference Paper, PUBLISHED

Meghen, C. N., Scott, C. S., Bradley, D. G., MacHugh, D. E., Loftus, R. T. and Cunningham, E. P. , DNA based traceability for the meat industry, 8th World Conference on Animal Production, 1998, pp774 - 775, Conference Paper, PUBLISHED

Bradley, DG and O'Sullivan, M., Tracing our ancient ancestors., Archaeology Ireland , 39, 1997, p18 - 20, Journal Article, PUBLISHED

McHugh, D. E., Loftus, R. T., Troy, C. S. and Bradley, D. G. , DNA Analysis and the origins and history of domesticated cattle, Archaeology of Southwest Asia (ASWA) conference, Budapest, 1996, Conference Paper, PUBLISHED

Bradley, D. G., Loftus, R. T., MacHugh, D. E. and Cunningham, P., The Molecular Evolution of Domestic cattle, Symposium on Mediterranean Animal Germplasm and Future Human Challenges, Salerno, 1996, Conference Paper, PUBLISHED

Cunningham, E. P., Loftus, R. T., MacHugh, D. E., Bradley, D. G., Molecular evolution of African, European and Asian Cattle, 21, 5th World Congress on Genetics Applied to Livestock Production, 1994, pp86 - 89, Conference Paper, PUBLISHED

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Awards and Honours

Award	Date
TCD Fellowship	2000
CGIAR award for outstanding scientific article	2003
Member of the Royal Irish Academy	2009
Royal Irish Academy Gold Medal in the Life Sciences	2020

Research Interests

Description Of Research Interests

I have active research in: ancient genomic analysis of western European humans, particularly Irish archaeological remains; ancient genomes of cattle sheep and goat.

Trinity College Dublin, The University of Dublin

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Professor Daniel Bradley