LeCHE  
Lactase persistence and the early Cultural History of Europe  
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TRINITY COLLEGE DUBLIN

SmurfitTrinity College Dublin is the top research University in the Republic of Ireland; it has a strong international reputation and has a substantial overseas student cohort. The Department of Genetics, Smurfit Institute is a leading biology department and was described in a recent review of the department’s international standing by Prof. Arnold Levine, Princeton, as “first rate” and able to “compete with any in the U.S., or elsewhere”. Entry to the Department of Genetics is the most competitive of any science course in Ireland. The department has a consistent record in attracting substantial research funding by competitive grant application (standing currently at several million euro per annum). The Bradley Lab is housed in the recently built Smurfit institute with excellent workspace and facilities. The research Group consists of three post-docs, five PhD students.

ESR5 Genetics of modern cattle
Prof. Dan Bradley
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Given that only a small fraction of genomic diversity may be addressed in any aDNA program, a key question for bovine aDNA is which Single Nucleotide Polymorphisms (SNPs) or sequences will give the maximally useful information when typed in early European remains? LeCHE is timely given the resources currently emerging from the bovine genome project. In particular, Bradley is a member of the consortium conducting the analysis of an emerging cattle ‘hapmap’ data set where population samples from 19 breeds have been genotyped for 33,000 SNPs. However, the breeds typed to date were chosen on economic rather than biogeographic or archaeogenetic criteria. Here we will type, using the existing and emerging bovine high-throughput SNP typing resources, a series of additional population samples chosen to inform the origins and dispersal of cattle; samples are already in place in TCD. We will identify panels of markers which are diagnostic for the major biogeographical divisions in European cattle - subsequent typing of these in ancient remains will inform on the time depth and origins of these divisions. Another output will be the identification of loci in genome regions which show a population genetic signature of selection. This will include genes linked to milk production and SNPs that are informative for dairy-associated biological change in cattle through time will be identified. This project will link with ESR6 , be guided by ER1 and ESR13 and report to ER2.

 
STAFF
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DanDr Dan Bradley is a senior lecturer. He has active research in: aDNA (2001, Nature); genetic diversity within and between genomes (2002, Science); Y-chromosome diversity and Irish human origins (Nature 2000); origins of livestock as discerned using genetic diversity (Nature Genetics, 2003; Nature Reviews Genetics, 2003; PNAS, 2001); development of detection methods for the presence of animal material in livestock feedstuffs; examination of selection around genes affected by the domestication process in livestock. He is a former member of a Wellcome Trust Panel in Bioarchaeology and jury for the European Young Scientists Competition. He supervised 9 students successfully. He has a total of 89 publications (62 in international scientific journals); he is primary or principal/corresponding author of 50 of these; and elicited ~2000 citations in total.

The ESRwill be working in a strongly supportive environment where other staff members contribute significantly to research project development. These staff members include experienced postdoctoral researchers in the Molecular Population Genetics laboratory where s/he will be primarily situated (Dr Emma Finlay, whole genome SNP analysis in cattle, mapping of production traits; Dr Ceiridwen Edwards, aDNA analysis; Dr Valeria Mattiangeli, detection of population genetic signatures of selection). Interaction with the wider community is facilitated by a weekly seminar series in molecular evolution which is conducted among four research groups of international standing (Drs Ken Wolfe, Mario Fares, Aoife McLysaght and Bradley) and a thesis committee comprising the supervisor and two of these staff members will be put in place.

 
FACILITIES
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The Smurfit institute houses labs with research facilities specialised for genetic research, including access to an Illumina Infinium genotyping platform. Importantly the facilities include a parallel dedicated aDNA facility on a separate floor from other molecular genetic activities which has a proven record of authenticated aDNA results.

 
REFERENCES
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1. Beja-Pereira A, et al., Gene-culture coevolution between cattle milk protein genes and human lactase genes. (2003) Nature Genetics 35:311-3

2. Troy CS, et al., Genetic evidence for Near Eastern origins of European cattle. (2001) Nature 2001 410:108-1091

3. Hanotte O, et al., African pastoralism: genetic imprints of origins and migrations. (2002) Science 296:366-369