ERC FUNDED PROJECTS

"This project explores the concept of agricultural spread as analogous to enforced climate change and asks how cereals adapted to new environments when agriculture was introduced into Europe. Archaeologists have long recognized that the ecological pressures placed on crops would have had an impact on the spread and subsequent development of agriculture, but previously there has been no means of directly assessing the scale and nature of this impact. Recent work that I have directed has shown how such a study could be carried out, and the purpose of this project is to exploit these breakthroughs with the goal of assessing the influence of environmental adaptation on the spread of agriculture, its adoption as the primary subsistence strategy, and the subsequent establishment of farming in different parts of Europe. This will correct the current imbalance between our understanding of the human and environmental dimensions to the domestication of Europe. I will use methods from population genomics to identify loci within the barley and wheat genomes that have undergone selection since the beginning of cereal cultivation in Europe. I will then use ecological modelling to identify those loci whose patterns of selection are associated with ecogeographical variables and hence represent adaptations to local environmental conditions. I will assign dates to the periods when adaptations occurred by sequencing ancient DNA from archaeobotanical assemblages and by computer methods that enable the temporal order of adaptations to be deduced. I will then synthesise the information on environmental adaptations with dating evidence for the spread of agriculture in Europe, which reveals pauses that might be linked to environmental adaptation, with demographic data that indicate regions where Neolithic populations declined, possibly due to inadequate crop productivity, and with an archaeobotanical database showing changes in the prevalence of individual cereals in different regions."

2 492 964 €

Start date: 2014-02-01, End date: 2019-01-31

"Prostate cancer is the commonest solid cancer in men in the European Community. There is evidence for genetic predisposition to the development of prostate cancer and our group has found the largest number of such genetic variants described to date worldwide. The next challenge is to harness these discoveries to advance the clinical care of populations and prostate cancer patients to improve screening and target treatments. This proposal, BARCODE, aims to be ground-breaking in this area. BARCODE has two components (1) to profile a population in England using the current 77 genetic variant profile and compare screening outcomes with those from population based screening studies to determine if genetics can target screening more effectively in this disease by identifying prostate cancer that more often needs treatment and (2) genetically profiling men with prostate cancer in the uro-oncology clinic for a panel of genes which predict for worse outcome so that these men can be offered more intensive staging and treatment within clinical trials. This will use next generation sequencing technology using a barcoding system which we have developed to speed up throughput and reduce costs. The PI will spend 35% of her time on this project and she will not charge for her time spent on this grant as she is funded by The University of London UK. The research team at The Institute Of Cancer Research, London, UK is a multidisciplinary team which leads the field of genetic predisposition to prostate cancer and its clinical application and so is well placed to deliver on this research. This application will have a dramatic impact on other researchers as it is ground –breaking and state of the art in its application of genetic findings to public health and cancer care. It will therefore influence the work being undertaken in both these areas to integrate genetic profiling and gene panel analysis into population screening and cancer care respectively."

2 499 123 €

Start date: 2014-10-01, End date: 2019-09-30

The aim of the BEEHIVE project is to generate novel insight into HIV biology, evolution and epidemiology, leveraging next-generation high-throughput sequencing and bioinformatics to produce and analyse whole-genomes of viruses from approximately 3,000 European HIV-1 infected patients. These patients have known dates of infection spread over the last 25 years, good clinical follow up, and a wide range of clinical prognostic indicators and outcomes. The primary objective is to discover the viral genetic determinants of severity of infection and set-point viral load. This primary objective is high-risk & blue-skies: there is ample indirect evidence of polymorphisms that alter virulence, but they have never been identified, and it is not known how easy they are to discover. However, the project is also high-reward: it could lead to a substantial shift in the understanding of HIV disease. Technologically, the BEEHIVE project will deliver new approaches for undertaking whole genome association studies on RNA viruses, including delivering an innovative high-throughput bioinformatics pipeline for handling genetically diverse viral quasi-species data (with viral diversity both within and between infected patients). The project also includes secondary and tertiary objectives that address critical open questions in HIV epidemiology and evolution. The secondary objective is to use viral genetic sequences allied to mathematical epidemic models to better understand the resurgent European epidemic amongst high-risk groups, especially men who have sex with men. The aim will not just be to establish who is at risk of infection, which is known from conventional epidemiological approaches, but also to characterise the risk factors for onwards transmission of the virus. Tertiary objectives involve understanding the relationship between the genetic diversity within viral samples, indicative of on-going evolution or dual infections, to clinical outcomes.

2 499 739 €

Start date: 2014-04-01, End date: 2019-03-31

" Why do people convert to Islam? The contemporary relevance of this question is immediately apparent.""Becoming Muslim"" will transform our knowledge about Islamisation processes and contexts through archaeological research in Harar, Eastern Ethiopia, and examine this in comparison to other regions in sub-Saharan Africa via publication and a major conference. Assessing genuine belief is difficult, but the impact of trade, Saints, Sufis and Holy men, proselytisation, benefits gained from Arabic literacy and administration systems, enhanced power, prestige, warfare, and belonging to the larger Muslim community have all been suggested. Equally significant is the context of conversion. Why were certain sub-Saharan African cities key points for conversion to Islam, e.g. Gao and Timbuktu in the Western Sahel, and Harar in Ethiopia? Archaeological engagement with Islamisation processes and contexts of conversion in Africa is variable, and in parts of the continent research is static. This exciting 4-year project explores, for the first time, Islamic conversion and Islamisation through focusing on Harar, the most important living Islamic centre in the Horn of Africa, and its surrounding region. Islamic archaeology has been neglected in Ethiopia, and is wholly non-existent in Harar. Excavation at 5 key sites: 2 shrines, 2 abandoned settlements, 1 urban site, will permit evaluation of urban Islam, the veneration of saints, pilgrimage and shrine based practices, rural Islam, architecture and jihad, changes in lifeways, and early and comparative evidence for Islam and long-distance trade, through analysis of, e.g. architecture, epigraphy, burial orientation, imported artifacts, and faunal and botanical remains. Although it is fully acknowledged that conversion to Islam and Islamisation processes are not universal, my project is groundbreaking in developing and applying a transferable methodology for the archaeological explanation of ""Becoming Muslim"" in sub-Saharan Africa."

1 031 105 €

Start date: 2016-09-01, End date: 2021-08-31