Evolutionary processes shaping genetic structure in Ethiopia and the Sudans

Lead Research Organisation: University College London
Department Name: UCL Genetics Institute

Abstract

Individuals sampled from across the world show great diversity in their DNA. However the primary features that lead to this diversity are poorly understood. For example, it is well-known that groups residing in close geographic proximity often have similar DNA patterns relative to groups residing further away, but what sorts of anthropological or topographical features best predict these similarities? Do rivers provide gateways for promoting interactions among different groups and thus lead to DNA exchange among these groups throughout history? Do natural features such as mountains provide a major barrier to such interactions, or is not sharing a language or religion a more important barrier? Have the important features that promote genetic diversity changed over time?

The Federal Democratic Republic of Ethiopian, the Republic of Sudan, and the Republic of South Sudan show great cultural diversity, with for example over 100 different languages spoken and over 100 different ethnic groups living within. The history of many of these peoples are poorly understood, with historical records often incomplete or contradictory. Recent studies have shown that the DNA of these groups are also highly diverse. This DNA provides a powerful means of resolving historical inaccuracies, and identifying the aforementioned features that promote intermixing among the different groups that have shaped the genetic landscape of this region for tens of thousands of years.

In this project, we will develop and apply new, state-of-the-art statistical methodology to a novel DNA collection consisting of samples from several hundred Ethiopian and Sudanese individuals. We will identify the features that have shaped the genetic diversity of this unique region of the world, identifying historical events where different ethnic groups within these regions exchanged DNA, as well as DNA contributions from sources outside the countries' borders. Some of this methodology has been successfully used recently to explore the history of the United Kingdom, a part of the world with considerably less cultural and genetic diversity (http://www.peopleofthebritishisles.org/). Elucidating the dynamics of how groups interact genetically will have great implications for understanding how gene flow persists among populations historically and today. Understanding the genetic structure of this diverse region will also help future researchers design sampling strategies for studies testing whether particular regions of the genome are associated with common phenotypes such as height or disease status.

This region of east Africa is also vital for studying human origins, housing the earliest known human fossil remains that confirm a history going back approximately 200,000 years. It is well-established that modern humans first arose in sub-Saharan Africa, and it is believed that Ethiopia and the Sudans were the gateway for the initial migrations of peoples out of sub-Saharan Africa when colonizing the rest of the world. By careful comparison of the DNA of the groups from this region with those outside of sub-Saharan Africa, we may be able to infer the routes taken by these early explorers and map out precisely how the world was colonized by migrating humans.

Technical Summary

Although it is well established that DNA differs substantially among different world-wide groups, the principle forces driving human genetic diversity are not well understood. One of the major outstanding questions in human evolution is whether present-day levels of diversity are primarily attributable to recent intermixing among populations (i.e. admixture) or ancient substructure. In addition, we still have only a limited understanding of the impact of factors that influence DNA exchange among populations, such as topography and geographic proximity, access to rivers, or other social factors such as shared language or religion.

With this project, we will genotype 2000 individuals spanning 95 different ethnic, occupational, or regional groups sampled from the Federal Democratic Republic of Ethiopia, the Republic of Sudan, and the Republic of South Sudan. Each Ethiopian and Sudanese sample has information on the donor's birthplace, first and second languages, cultural label, and religion for some samples, plus the equivalent information (excluding religion) for the donor's father, mother, paternal grandfather, and maternal grandmother. We also have cartographical and altitude information on numerous villages across these regions. We will apply novel statistical methodology to these samples to identify recent admixture events among these different groups, as well as DNA contributions from neighboring populations. We will then elucidate the anthropological and topographical features that most strongly determine which groups exchange DNA. We will infer the DNA of the ancestors of these present-day groups by subtracting out the signals of recent admixture we identify, and we will quantify the extent of genetic distinction among these ancient sources. By developing new statistical methods, we also aim to exploit the rich history contained in the DNA of this part of the world to infer details of human origins, including the early migration(s) out of Africa.

Planned Impact

Collaborator Endashaw Bekele is Professor at Addis Ababa University and Director of the Human Genetic Variation Center (HGVC) at the Ministry of Health in Ethiopia. The HGVC has a remit from the Ethiopian government to encourage the study of human genetic variation in Ethiopia by overseas researchers, with a view to developing local expertise in undertaking clinical trials that take account of sub-Saharan genetic diversity. For example, Bekele and collaborator Neil Bradman have collected blood and phenotype data from 300 Ethiopian samples, including 25 individuals from each of five distinct Ethiopian groups who are being whole genome sequenced (WGS) by collaborators Luca Pagani and Chris Tyler-Smith. This phenotype information includes height, weight, BMI, standard anthropometric data, blood pressure, spirometer, colorimeter, spirobank, bio-impedance readings, urine analysis, personal disease histories and lifestyle information, as well as sociological data for the subject and the subject's parents and grandparents as recorded in the larger collection described in this study. The proposed study will elucidate the genetic diversity among over 80 additional ethnic and regional groups from Ethiopia and the Sudans, thus defining sampling strategies for forthcoming similar phenotype collections. All samples and our results exploring genetic diversity will be made freely available to researchers upon publication of the first primary manuscript (anticipated at the end of year 1-2). The PI will also visit Addis Ababa University as a guest of Prof Bekele during years 1-3 of the project, explaining the primary results of our studies into the genetic landscape of Ethiopia and the Sudans and advising on sampling strategies for future phenotype collections.

Dr. Bradman is Chairman of Henry Stewart Talks Ltd (http://hstalks.com/), which publishes The Biomedical and Life Sciences Collection of over 1,600 specially prepared online seminars by leading world experts. These seminars are provided for free to over 75 universities in sub-Saharan Africa, including 15 from Ethiopia. Subscribers to the collection includes most of the world's largest pharmaceutical companies as well as research institutes and universities in over 40 countries. We will provide at least one seminar describing our project's findings, anticipated for year 2-3 of the project.

The post-doc employed on this project will develop and apply state-of-the-art statistical techniques to a large-scale genetic data collection, as well as lead an international collaboration. Any new methodology developed during this project will be made freely available to academic researchers upon publication of methods. Visits to Addis Ababa University may lead to collaborations between UCL and Ethiopian PhD students, similar to UCL Prof Dallas Swallow's on-going co-supervision of Tamiru Oljira of Addis Ababa University on projects studying allelic heterogeneity in lactase persistence among Ethiopian groups (e.g. Ingram et al 2009, J Mol Evol 69:579-588).

Finally, understanding human history, including the genetic legacies of known population migrations, is of enormous interest to the wider public. The PI has participated in two public presentations of a similar study to the one proposed here that instead uses United Kingdom samples (POBI). This work featured in both The Royal Society Summer Exhibition 2012 (http://sse.royalsociety.org/2012/exhibits/genetic-maps/) and the Big Bang UK Young Scientists and Engineers Fair 2013 (http://www.thebigbangfair.co.uk/). We anticipate similar interest from the public and media from this project, from our initial publications describing the genetic structure of Ethiopia and the Sudans in years 1-2 of the project to our findings on ancient human demography anticipated for year 3.

Publications

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Broushaki F (2016) Early Neolithic genomes from the eastern Fertile Crescent. in Science (New York, N.Y.)

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Hofmanová Z (2016) Early farmers from across Europe directly descended from Neolithic Aegeans. in Proceedings of the National Academy of Sciences of the United States of America

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López S (2015) Human Dispersal Out of Africa: A Lasting Debate. in Evolutionary bioinformatics online

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Van Dorp L (2019) Genetic legacy of state centralization in the Kuba Kingdom of the Democratic Republic of the Congo in Proceedings of the National Academy of Sciences

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Veeramah KR (2018) Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria. in Proceedings of the National Academy of Sciences of the United States of America

 
Description Four key achievements of this BBSRC-funded work include:

(1) The first comprehensive understanding of the genetic structure of Ethiopia, and how this correlates with - and is in part driven by - geography, common language, ethnicity, religious affiliation and shared cultural practices (preprint available: 10.1101/756536). We have also dated when ancestors of Ethiopians intermixed with peoples related to west Africans and west Eurasians, with our inferred signals suggesting the genetic impact of the Kingdom of Axum and the migrations of Bantu-speaking peoples from thousands of years ago. We have released an interactive map that allows researchers and the public to see which Ethiopian ethnicities are most genetically similar (https://www.well.ox.ac.uk/~gav/work_in_progress/ethiopia/v5/), which will help inform sampling strategies for forthcoming genetic studies. In particular future researchers, from Ethiopia and elsewhere, can now identify how best to sample individuals using ethnic labels, geography and other factors, in a way that most efficiently captures the large amount of genetic diversity in the region. For example, this will enable better genetic matching of sick individuals and healthy controls, which is a major complication in studies that attempt to identify specific genetic variants that increase disease risk in order to develop targetable drugs.

(2) Curation of one of the most comprehensive collections of genome-wide genetic variation data in Africans, consisting of >650,000 markers from 2863 individuals, as well as 369 individuals from Eurasia, in total representing over 300 different populations. These data will be freely available to other researchers and be used by our research group and others to learn about (e.g.): (a) the ancestral history of other African countries, (b) the initial migrations of humans out-of-Africa and (c) genes that have allowed humans to adapt to changing environments.

(3) Dissemination of findings to academics and public members of Ethiopia, through 9 lectures and discussions across 8 Ethiopian cities during Feb-March 2017. We also freely distributed 500 pamphlets on our initial findings at that time, and we will next make an on-line lecture summarising our final conclusions that will be freely available to over 75 African researchers on Henry Stewart Talks (https://hstalks.com/). The dissemination of these findings (which we will continue through our collaborator Dr. Ayele Tarekegn at Addis Ababa University) will feed back to the communities that provided the data, allow our insights to be incorporated into future work involving Ethiopian researchers (perhaps through additional international collaborations) and in general promote scientific growth and education in Ethiopia. Feedback during our visit was very positive and demonstrated the strong interest in learning about the diverse ancestry of Ethiopia's many ethnicities.

(4) This work has also shed insights into the migrations of humanity's first farmers (DOI:10.1126/science.aaf7943) and into the genetic legacy of one of the world's oldest extant religions: Zoroastrianism (10.1016/j.ajhg.2017.07.013). Finally, we also wrote a review article on the current genetic and archaeological evidence on mysteries surrounding these initial migrations out-of-Africa (DOI: 10.4137/EBO.S33489), which these new data resources are uniquely placed to provide new insights on.
Exploitation Route (1) Our nine lecture Ethiopian tour, including a radio interview (105.3 Afro FM) and distribution (including to libraries) of 500 pamphlets intended for lay (English-speaking) audiences, have informed the academic and public sectors in Ethiopia about how DNA can be used to trace our ancestry, and the genetic inter-relatedness of Ethiopian ethnicities. Our detailed discussions with audience members following our lectures suggested we changed opinions and perceptions on how DNA evidence can contribute to aspects of Ethiopian history. We hope to continue this work through our collaborator Dr. Ayele Tarekegn at Addis Ababa University.

(2) Our publication (preprint: 10.1101/756536) and interactive webpage (https://www.well.ox.ac.uk/~gav/work_in_progress/ethiopia/v5/) will be used by other researchers to (A) design future genetic studies in Ethiopia and (B) assess genetic evidence for hypotheses (e.g. generated through linguistic and anthropological studies) about groups' origins.

(3) Our newly genotyped data collection, one of the most comprehensive in terms of African ethnic groups, have either been made freely available to academics through publications (10.1016/j.ajhg.2017.07.013, 10.1016/j.cell.2017.08.049, 10.1038/s41586-020-1929-1) or will be made available upon or before the first publications analysing these data (e.g. 10.1101/756536).

(4) our new analytical technique SOURCEFIND, developed in part through this work, has currently been requested 29 times since 2018
Sectors Education,Healthcare,Culture, Heritage, Museums and Collections,Pharmaceuticals and Medical Biotechnology

 
Description The post-doctoral researcher (Dr. Saioa Lopez) and I organized a visit to Ethiopia during February to March 2017 to disseminate key findings on our work to Ethiopian universities. This involved contacting hosts at each location, which we accomplished using the contacts of our collaborators involved in the original sample collection. We secured invitations to visit eight universities in Adama, Addis Ababa, Arsi, Axum, Gondar, Haramaya, Harar and Hawassa. Through £1000 of funding achieved by the PDRA through UCL's "Focus on the Positive" scheme, we also generated and printed 500 pamphlets that we distributed to researchers at each venue (https://blogs.ucl.ac.uk/focus-on-the-positive/2017/05/05/focusing-on-ethiopian-identity/). These pamphlets were well-received and highly popular. They were distributed to libraries and to communities involved in the original sample collections, giving us the opportunity to feed results back to the Ethiopian public that made this study possible. We also received an invitation to provide a public lecture at the Ethiopian Academy of the Sciences (EAS) from Non-voting Member and Secretary Professor Masresha Fetene. This EAS lecture was held at Addis Ababa University and attended by over 100 academics, high school students, politicians and other members of the public (http://eas-et.org/node/275). This was followed by a lengthy discussion on our findings, plus interviews with reporters for local television stations in Ethiopia. I met with several people after the talk who noted their views on Ethiopian genetic history had been changed and that in general they had a better understanding of what we can learn about history from genetics and what drives the genetic structure of Ethiopian peoples today. One key element our work showed was how different Ethiopian ethnic groups, including those that at times historically have been at war with one another, share common genetic origins. The discussions often focused on this common ancestry of groups, in addition to how genetics can be used to tease apart historical interactions. While not available at the time, we have now developed a freely-available interactive webpage (https://www.well.ox.ac.uk/~gav/work_in_progress/ethiopia/v5/) that illustrates the genetic structure of different ethnic groups, including showcasing which groups are most genetically similar. A key aim of this webpage is to facilitate sampling strategies for forthcoming genome-wide association studies (GWAS) that look for genetic associations with phenotypes using Ethiopian cohorts, as -- for such studies -- it is essential to control for ancestral differences in e.g. cases/controls (and sample accordingly to do so). For example, collaborator Prof Endashaw Bekele of Addis Ababa University is Director of the Human Genetic Variation Center (HGVC) at the Ministry of Health in Ethiopia. The HGVC has a remit from the Ethiopian government to encourage the study of human genetic variation in Ethiopia by overseas researchers, with a view to developing local expertise in undertaking clinical trials that take account of sub-Saharan genetic diversity. This webpage was designed to be useful for this purpose. Through our collaborators on this project, including Dr. Ayele Tarekegn at Addis Ababa University and Neil Bradman at Henry Stewart Talks, we will discuss how best to disseminate this webpage to academics of multiple disciplines in Ethiopia and beyond academia to members of the Ethiopian (and other) public. Eventually, we also plan for this webpage to include our inference about the ancestral history of each Ethiopian group, including detailed results on the intermixing of peoples in Ethiopia's history, which is of major public interest in Ethiopia (as revealed through our lectures) and elsewhere.
First Year Of Impact 2017
Sector Education,Culture, Heritage, Museums and Collections
Impact Types Cultural

 
Description ELIXIR-IIB short course Naples
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact I was asked to participate in a short course, designing and providing practicals and lectures on applying software I have developed throughout my time as a Sir Henry Dale Fellow and while working on my BBSRC grant. Individuals from this course (which consisted of post-doctoral research assistants and postgraduate students from multiple universities) have requested this software and are actively using it in their research into the genetic structure and ancestral history of world-wide populations.
URL https://elixir-iib-training.github.io/website/2018/04/21/PopGen-Napoli.html
 
Description EMBO short course Naples
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact I was asked to participate in a short course, designing and providing practicals and lectures on applying software I have developed throughout my time as a Sir Henry Dale Fellow and while working on my BBSRC grant. Individuals from this course (which consisted of university lecturers, post-doctoral research assistants and postgraduate students) have requested this software and are actively using it in their research into the genetic structure and ancestral history of world-wide populations.
URL http://meetings.embo.org/event/17-population-genomics
 
Description EMBO short course Procida
Geographic Reach Multiple continents/international 
Policy Influence Type Influenced training of practitioners or researchers
Impact I was again asked to participate in a short course, designing and providing practicals and lectures on applying software I have developed throughout my time as a Sir Henry Dale Fellow and while working on my BBSRC grant. Individuals from this course (which consisted of post-doctoral research assistants and postgraduate students from multiple universities, including from Latin America) have requested this software and are actively using it in their research into the genetic structure and ancestral history of world-wide populations.
URL https://meetings.embo.org/event/19-population-genomics
 
Description distribution of 500 pamphlets (about genetic structure and history of Ethiopian peoples) to academics and lay audiences in Ethiopia
Geographic Reach Africa 
Policy Influence Type Influenced training of practitioners or researchers
 
Description Bogue Fellowship for Saioa Lopez to have academic visit at Harvard Medical School (D.Reich's laboratory)
Amount £2,740 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 07/2016 
End 07/2016
 
Description University College London
Amount £1,000 (GBP)
Organisation University College London 
Sector Academic/University
Country United Kingdom
Start 11/2016 
End 11/2016
 
Title African genotypes 
Description We have currently genotyped over 3200 individuals from over 200 ethnic groups sampled across Africa, including 113 groups from Ethiopia and the Sudans, as part of the BBSRC grant. Specifically, these data were genotyped on the Affymetrix Human Origins chip, which allows them to be incorporated with over 200 additional world-wide groups genotyped on the same chip that are presently publicly available. 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? No  
Impact All samples genotyped as part of the BBSRC grant will be made publicly available to academic researchers upon our first publication related to analysing these data. Approximately 100 have already been made available through publications, and a further 1100 will be released upon (or before) publication of a paper currently under revision after a first round of positive review. The remaining samples should be released following publication within the coming months. 
 
Title SOURCEFIND 
Description As part of this project, I have developed a new tool, in R, called "Sourcefind" that can identify which groups share recent ancestry (e.g. due to admixture). This tool is very fast, easy-to-use and flexible relative to current approaches. It is presently being used by members of my research group. But one of my PhD students has incorporated it into software that will be released soon, to be freely available to academics. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? No  
Impact This new code was used to infer sources of ancestry in new data generated as part of this grant, for example for data from Ethiopian individuals. Results have been disseminated to academics and non-academics in Ethiopia via talks and with the distribution of two different pamphlets (500 copies total), one intended for lay audiences and one for genetics-based scientific audiences, and a manuscript on these results for publication in an academic journal is currently in preparation. 
 
Description Ethiopian researchers 
Organisation Addis Ababa University
Country Ethiopia 
Sector Academic/University 
PI Contribution During the period 27/2/17 to 11/3/17, the PDRA (Dr. Saioa Lopez) and I undertook a series of nine lectures at nine different venues across Ethiopia, as part of our BBSRC grant. This included talks at University of Gondar, Hawassa University, Arsi University, Adama Science and Technology University, Axum University, Haramaya University College of Health and Medicine, Haramaya University main campus (Harar), Addis Ababa University, and the Ethiopian Academy of Sciences (EAS). The latter EAS lecture was for a broad audience of over 100 people that included Ethiopian academics, politicians, university students, high school students and lay people. These lectures disseminated the early results from our analysis of the DNA of over 1,100 Ethiopian individuals representing over 70 ethnic and social groups. We met with Ethiopian academics from each of the above institutions. We also provided a radio interview to 105.3 Afro FM (http://www.afro105fm.com/i/index.php) in Ethiopia. I also recorded an interview following the EAS presentation, to be aired on local television. Also as part of this trip, Dr. Lopez and I wrote two versions of a pamphlet that summarized the key findings. One "simplified" version was 13 pages long and offered a simplified report of our findings appropriate for a very broad, lay audience without scientific training. The other "extended" version was 33 pages long and offered a more detailed report appropriate for a scientific (e.g. university) audience. The printing of this pamphlet was paid for using £1000 in funds won by Dr. Lopez from a "Focus on the Positive" program contest arranged through UCL, which allowed the printing of 400 "simplified" versions and 100 "extended" versions. These pamphlets were distributed to the audiences that attended our lectures, with some "extended" versions provided to our academic hosts to provide to campus libraries and to people (e.g. their students) with more technical backgrounds. We further left copies of the pamphlets at other venues, including airports and a library in Harar.
Collaborator Contribution Our tour of nine lectures across Ethiopian institutions were followed by debates and discussions that lasted from 30 minutes to 1 hour and 30 minutes per lecture. As these lectures were attended by Ethiopian academics with specialist knowledge in linguistics, history, anthropology and other fields, we were provided with invaluable feedback about (i) how to into interpret our genetic findings, (ii) how best to relay this information to the public in light of ethnic sensitivities within Ethiopia, and (iii) a list of specific hypotheses, involving relationships within and among different ethnic groups, to test using genetic evidence. Furthermore our contacts in the above universities enabled the above lectures to take place. In particular, Dr. Ayele Tarekegn, then of Henry Stewart Talks and currently a faculty member of the Department of Archaeology and Heritage Management at Addis Ababa University, accompanied us on our entire trip. Dr. Tarekegen acted as an interpreter for Amharic-to-English, a guide (with a degree in history), and an invaluable resource as someone who (i) did the vast majority of sample collection across Ethiopia and (ii) has recently translated a book recording the oral traditions of groups in the Southern Nations, Nationalities and People's Regions (SNNPR) that was initially printed (in Amharic) by the Council of Nationalities of the SNNPR. He also arranged our flight and car travel and hotel accommodation, in addition to arranging the final times and locations of each lecture.
Impact (1) the printing and distribution of 500 pamphlets "Exploring the genetics and ancestry of peoples in Ethiopia" relaying early results of our genetic findings on Ethiopian samples included in this project (2) a radio interview with 105.3 Afro FM (3) a recorded interview for local Ethiopian TV (4) our Ethiopian research has now resulted in a publication, with my former PDRA Lopez and Dr. Tarekegn as joint first authors, that is currently under review and available as a pre-print: doi.org/10.1101/756536
Start Year 2016
 
Description Naser Ansari Pour academic visit 
Organisation University of Tehran
Country Iran, Islamic Republic of 
Sector Academic/University 
PI Contribution During April-August 2016, we welcomed Dr. Naser Ansari Pour (University of Tehran) as a visiting academic at University College London. During this visit, we collaborated with him on analysis and interpretation of genetic data on Indian and African individuals that was acquired as part of our BBSRC grant.
Collaborator Contribution Dr. Ansari Pour (now at the Big Data Institute in Oxford) has provided expertise from his studies at UCL on Y chromosome and mitochondrial data from African individuals taken from the same UCL collection that we now have genome-wide genotype data for as part of our BBSRC grant. In particular he performed Y and mtDNA analyses on data we acquired through the BBSRC grant from India and the Democratic Republic of the Congo, which complimented our work using the nuclear genomes of the same individuals. He is currently also analysing new data on Ethiopians that we acquired through this BBSRC grant.
Impact Our work was published, with Dr. Ansari-Pour as co-author, in two publications: (1) 10.1016/j.ajhg.2017.07.013 (2) 10.1073/pnas.1811211115
Start Year 2016
 
Description Paleogenetics group Mainz 
Organisation Johannes Gutenberg University of Mainz
Country Germany 
Sector Academic/University 
PI Contribution We (in particular the PDRA Dr. Lopez) have analysed ancient DNA samples provided by Prof Joachim Burger's group at Johannes Gutenberg University (Mainz) using our in-house techniques, in order to shed light on early Neolithic communities in Europe and the Near East, as well as the population structure of Early Medieval Bavaria. This works constitutes a major aspect of a consortium including collaborators from the universities listed above.
Collaborator Contribution The partners have provided expertise and samples, in particular DNA from ancient human remains sampled from modern-day Germany, Iran, Turkey and Greece.
Impact We have three publications thus far directly resulting from this work (noted elsewhere): (1) 10.1073/pnas.1719880115 (2) 10.1126/science.aaf7943 (3) 10.1073/pnas.1523951113 This work has also generated press interest, due to the high interest with the public, e.g: http://www.npr.org/sections/thesalt/2016/07/15/485722228/where-did-agriculture-begin-oh-boy-its-complicated https://www.sciencenews.org/article/two-groups-spread-early-agriculture http://www.dailymail.co.uk/sciencetech/article-3690448/Does-farming-multiple-roots-DNA-reveals-communities-began-growing-crops-10-000-years-ago-spreading.html http://www.sciencemag.org/news/2016/07/worlds-first-farmers-were-surprisingly-diverse https://cosmosmagazine.com/biology/farming-invented-by-several-populations-at-once http://www.latimes.com/science/sciencenow/la-sci-sn-first-farmers-dna-20160714-snap-story.html http://www.bbc.co.uk/news/science-environment-36788165 https://www.sciencealert.com/mystery-strange-elongated-skulls-finally-solved-deformed-artificial-cranial-bavaria https://mysteriousuniverse.org/2018/03/mysterious-bavarian-elongated-skulls-are-not-from-bavaria/ https://news.nationalgeographic.com/2018/03/barbarian-huns-dna-germany-migration-antiquity-skull/ https://www.sciencemag.org/news/2018/03/strange-elongated-skulls-reveal-bulgarian-treaty-brides-ancient-germany https://www.newsweek.com/origin-mysteriously-elongated-skulls-medieval-women-revealed-dna-study-843512 https://www.independent.co.uk/news/world/europe/women-dark-ages-europe-pioneers-medieval-skulls-head-binding-a8253071.html
Start Year 2015
 
Description Paleogenetics group Mainz 
Organisation Stony Brook University
Country United States 
Sector Academic/University 
PI Contribution We (in particular the PDRA Dr. Lopez) have analysed ancient DNA samples provided by Prof Joachim Burger's group at Johannes Gutenberg University (Mainz) using our in-house techniques, in order to shed light on early Neolithic communities in Europe and the Near East, as well as the population structure of Early Medieval Bavaria. This works constitutes a major aspect of a consortium including collaborators from the universities listed above.
Collaborator Contribution The partners have provided expertise and samples, in particular DNA from ancient human remains sampled from modern-day Germany, Iran, Turkey and Greece.
Impact We have three publications thus far directly resulting from this work (noted elsewhere): (1) 10.1073/pnas.1719880115 (2) 10.1126/science.aaf7943 (3) 10.1073/pnas.1523951113 This work has also generated press interest, due to the high interest with the public, e.g: http://www.npr.org/sections/thesalt/2016/07/15/485722228/where-did-agriculture-begin-oh-boy-its-complicated https://www.sciencenews.org/article/two-groups-spread-early-agriculture http://www.dailymail.co.uk/sciencetech/article-3690448/Does-farming-multiple-roots-DNA-reveals-communities-began-growing-crops-10-000-years-ago-spreading.html http://www.sciencemag.org/news/2016/07/worlds-first-farmers-were-surprisingly-diverse https://cosmosmagazine.com/biology/farming-invented-by-several-populations-at-once http://www.latimes.com/science/sciencenow/la-sci-sn-first-farmers-dna-20160714-snap-story.html http://www.bbc.co.uk/news/science-environment-36788165 https://www.sciencealert.com/mystery-strange-elongated-skulls-finally-solved-deformed-artificial-cranial-bavaria https://mysteriousuniverse.org/2018/03/mysterious-bavarian-elongated-skulls-are-not-from-bavaria/ https://news.nationalgeographic.com/2018/03/barbarian-huns-dna-germany-migration-antiquity-skull/ https://www.sciencemag.org/news/2018/03/strange-elongated-skulls-reveal-bulgarian-treaty-brides-ancient-germany https://www.newsweek.com/origin-mysteriously-elongated-skulls-medieval-women-revealed-dna-study-843512 https://www.independent.co.uk/news/world/europe/women-dark-ages-europe-pioneers-medieval-skulls-head-binding-a8253071.html
Start Year 2015
 
Description Paleogenetics group Mainz 
Organisation University of Fribourg
Department Department of Biology
Country Switzerland 
Sector Academic/University 
PI Contribution We (in particular the PDRA Dr. Lopez) have analysed ancient DNA samples provided by Prof Joachim Burger's group at Johannes Gutenberg University (Mainz) using our in-house techniques, in order to shed light on early Neolithic communities in Europe and the Near East, as well as the population structure of Early Medieval Bavaria. This works constitutes a major aspect of a consortium including collaborators from the universities listed above.
Collaborator Contribution The partners have provided expertise and samples, in particular DNA from ancient human remains sampled from modern-day Germany, Iran, Turkey and Greece.
Impact We have three publications thus far directly resulting from this work (noted elsewhere): (1) 10.1073/pnas.1719880115 (2) 10.1126/science.aaf7943 (3) 10.1073/pnas.1523951113 This work has also generated press interest, due to the high interest with the public, e.g: http://www.npr.org/sections/thesalt/2016/07/15/485722228/where-did-agriculture-begin-oh-boy-its-complicated https://www.sciencenews.org/article/two-groups-spread-early-agriculture http://www.dailymail.co.uk/sciencetech/article-3690448/Does-farming-multiple-roots-DNA-reveals-communities-began-growing-crops-10-000-years-ago-spreading.html http://www.sciencemag.org/news/2016/07/worlds-first-farmers-were-surprisingly-diverse https://cosmosmagazine.com/biology/farming-invented-by-several-populations-at-once http://www.latimes.com/science/sciencenow/la-sci-sn-first-farmers-dna-20160714-snap-story.html http://www.bbc.co.uk/news/science-environment-36788165 https://www.sciencealert.com/mystery-strange-elongated-skulls-finally-solved-deformed-artificial-cranial-bavaria https://mysteriousuniverse.org/2018/03/mysterious-bavarian-elongated-skulls-are-not-from-bavaria/ https://news.nationalgeographic.com/2018/03/barbarian-huns-dna-germany-migration-antiquity-skull/ https://www.sciencemag.org/news/2018/03/strange-elongated-skulls-reveal-bulgarian-treaty-brides-ancient-germany https://www.newsweek.com/origin-mysteriously-elongated-skulls-medieval-women-revealed-dna-study-843512 https://www.independent.co.uk/news/world/europe/women-dark-ages-europe-pioneers-medieval-skulls-head-binding-a8253071.html
Start Year 2015
 
Description Paleogenetics group Mainz 
Organisation University of Geneva
Department Department of Anthropology and Sociology of Development (ANSO)
Country Switzerland 
Sector Academic/University 
PI Contribution We (in particular the PDRA Dr. Lopez) have analysed ancient DNA samples provided by Prof Joachim Burger's group at Johannes Gutenberg University (Mainz) using our in-house techniques, in order to shed light on early Neolithic communities in Europe and the Near East, as well as the population structure of Early Medieval Bavaria. This works constitutes a major aspect of a consortium including collaborators from the universities listed above.
Collaborator Contribution The partners have provided expertise and samples, in particular DNA from ancient human remains sampled from modern-day Germany, Iran, Turkey and Greece.
Impact We have three publications thus far directly resulting from this work (noted elsewhere): (1) 10.1073/pnas.1719880115 (2) 10.1126/science.aaf7943 (3) 10.1073/pnas.1523951113 This work has also generated press interest, due to the high interest with the public, e.g: http://www.npr.org/sections/thesalt/2016/07/15/485722228/where-did-agriculture-begin-oh-boy-its-complicated https://www.sciencenews.org/article/two-groups-spread-early-agriculture http://www.dailymail.co.uk/sciencetech/article-3690448/Does-farming-multiple-roots-DNA-reveals-communities-began-growing-crops-10-000-years-ago-spreading.html http://www.sciencemag.org/news/2016/07/worlds-first-farmers-were-surprisingly-diverse https://cosmosmagazine.com/biology/farming-invented-by-several-populations-at-once http://www.latimes.com/science/sciencenow/la-sci-sn-first-farmers-dna-20160714-snap-story.html http://www.bbc.co.uk/news/science-environment-36788165 https://www.sciencealert.com/mystery-strange-elongated-skulls-finally-solved-deformed-artificial-cranial-bavaria https://mysteriousuniverse.org/2018/03/mysterious-bavarian-elongated-skulls-are-not-from-bavaria/ https://news.nationalgeographic.com/2018/03/barbarian-huns-dna-germany-migration-antiquity-skull/ https://www.sciencemag.org/news/2018/03/strange-elongated-skulls-reveal-bulgarian-treaty-brides-ancient-germany https://www.newsweek.com/origin-mysteriously-elongated-skulls-medieval-women-revealed-dna-study-843512 https://www.independent.co.uk/news/world/europe/women-dark-ages-europe-pioneers-medieval-skulls-head-binding-a8253071.html
Start Year 2015
 
Description Reich lab 
Organisation Harvard University
Department Harvard Medical School
Country United States 
Sector Academic/University 
PI Contribution As part of this BBSRC grant, we have currently curated a dataset of over 2000 individuals, primarily sampled from Africa, as outlined in the grant proposal. These data will be used in our group and the Reich group for studies on evolutionary history, with a focus on groups from Africa, before being made freely available to other academics. For example, we are currently collaborating to compare the DNA of our modern day samples to that from ancient human remains from Africa in the Reich lab.
Collaborator Contribution Our collaboration with Dr. Reich enabled a discount on his Affymetrix Human Origins chip when genotyping the samples we collected as part of this BBSRC grant, as well as the ability to incorporate these samples into a larger collection he has accumulated on the same chip. Relative to other genotyping centers we contacted prior to sending off our samples, this gave us a savings of up to £33,348 on our ~£120,000 purchase. This resource will be made freely available to academics upon publication of our first manuscript, making a major contribution to available human genome-wide DNA resources, for which African groups are under-represented. In addition, Dr. Reich's group performed quality control on our samples. They have incorporated a subset of our samples into their analyses of ancient DNA, which have resulted in high profile publications listed below.
Impact The genetic variation information for ~100 of our samples genotyped on the Affymetrix Human Origins chip (as part of the BBSRC grant), have been released following publication in the first two papers listed below. We will be releasing remaining samples through forthcoming publications -- in particular this includes for >1100 samples that will be released upon (or before) our publication that is currently under review: doi.org/10.1101/756536. These data are all on the same chip of an earlier dataset from the Reich lab consisting of over 200 world wide groups, as well as additional forthcoming samples collected by David Reich's laboratory and collaborators. publications: (1) 10.1016/j.cell.2017.08.049 (2) 10.1038/s41586-020-1929-1 (3) doi.org/10.1101/756536
Start Year 2014
 
Description economists in Harvard 
Organisation Harvard University
Country United States 
Sector Academic/University 
PI Contribution My former PDRA (Saioa Lopez), PhD student (Lucy van Dorp) and I contributed extensively to this project, applying our methods to analyse 690 individuals sampled from 27 different ethnic groups from the Kasai Central Province of the Democratic Republic of the Congo (DRC). In doing so, we described the genetic impact of the formation of the eminent precolonial Kuba Kingdom in the DRC in the 17th century.
Collaborator Contribution The partners provided genetic data they had sampled from the DRC over several visits, as well as information about ethnicity and origins of the individuals, to be used for this collaboration. Given genotyping costs ~85 per sample, I estimate the value (as an in-kind contribution) of 690 such samples to be ~58,650 USD. They also provided their expertise on these samples, with lead investigator Dr. Nathan Nunn (Harvard) sharing co-last authorship with me on our publication.
Impact This work has resulted in a publication: doi: 10.1073/pnas.1811211115 and international press interest: https://www.bbc.co.uk/sounds/play/m00021r4 https://www.deutschlandfunk.de/das-koenigreich-der-kuba-was-genetik-ueber-afrikanische.676.de.html?dram:article_id=440734
Start Year 2014
 
Description BBC radio interview on Kuba Kingdom (Lucy van Dorp) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact My former PhD student, Dr. Lucy van Dorp, gave an interview on BBC Inside Science to discuss the results of our study (for which former PDRA Saioa Lopez participated) on the genetic impact of the 17th century Kuba Kingdom in the Democratic Republic of the Congo. The interviewer (Adam Rutherford) remarked this was his favorite paper of 2019 thus far, and the positive impact of migration on fostering fruitful political dynasties was discussed.
Year(s) Of Engagement Activity 2019
URL https://www.bbc.co.uk/sounds/play/m00021r4
 
Description Deutschlandfunk radio interview on Kuba Kingdom (Lucy van Dorp) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact My former PhD student, Dr. Lucy van Dorp, gave an interview on Deutschlandfunk, a German public broadcasting radio station, to discuss the results of our study (for which former PDRA Saioa Lopez participated) on the genetic impact of the 17th century Kuba Kingdom in the Democratic Republic of the Congo. The interview is in German, so it's difficult for me to understand its impact (there doesn't seem to be a user comments board for the associated article online).
Year(s) Of Engagement Activity 2019
URL https://www.deutschlandfunk.de/das-koenigreich-der-kuba-was-genetik-ueber-afrikanische.676.de.html?d...
 
Description Ethiopian Academy of Sciences 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Through contacts involved with this BBSRC-funded project, I arranged to give a seminar at the Ethiopian Academy of Sciences (EAS), through invitation by Non-voting Member and Secretary, Professor Masresha Fetene. This seminar was chaired by Professor Endashaw Bekele of Addis Ababa University and took place on March 9, 2017. The presentation was attended by over 100 academics, non-academics, high school students, politicians and other Ethiopian individuals. After a one-hour presentation relaying key results from this BBSRC-funded project (specifically on "Exploring the genetics and ancestry of different groups in Ethiopia"), Prof Bekele and I had ~1 hour of discussion and question answering with audience members. This was followed by interviews with reporters for local television stations in Ethiopia. As part of this presentation, we handed out ~50 pamphlets the postdoctoral research assistant Dr. Lopez and I had written. These pamphlets are intended for a broad lay audience and outline the key results discussed in the talk. I met with several people after the talk who noted their views on Ethiopian genetic history had been changed and that in general they had a better understanding of what we can learn about history from genetics and what drives the genetic structure of Ethiopian peoples today.
Year(s) Of Engagement Activity 2017
URL http://eas-et.org/node/275
 
Description Focus on the Positive 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The postdoctoral research assistant on the project, Dr. Saioa Lopez, presenting preliminary findings about the genetic history of groups in Ethiopia at a lecture to the general public in east London. This talk was organized by "Focus on the Positive" at UCL, and resulted in audience members voting on who would receive £1000 or £2000 in funding for a particular activity. Dr. Lopez was awarded £1000, to be spent on printing pamphlets that relay the preliminary findings of our analysis of DNA of Ethiopian peoples to a lay (English-speaking) audience. In the end, we printed 500 copies of these pamphlets and distributed them to academics, high school students, participants who contributed DNA, other members of the public, and libraries across Ethiopia during February 26 - March 11, 2017.
Year(s) Of Engagement Activity 2016
URL https://www.ucl.ac.uk/public-engagement/creating-change/projects/focus-on-the-positive
 
Description UNESCO conference -- Great migrations 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact I was invited to a conference on "Great Migrations in Ancient Asia Minor: Circulation, Exchange and Social Transformation" that was held in UNESCO Headquarters in Paris, France, on 29-30 November 2016. This conference was part of the framework of the International Decade for the Rapprochement of Cultures (2013-2022) and formed part of the achievement of this framework's Action Plan. I gave a talk to an audience consisting of the general public and experts on Asia Minor from other fields (archaeology, linguistics, history), with my topic about what we have learned from the history of modern-day populations in Asia Minor based on studying their DNA. This was followed by a panel discussion, with questions from academics and audience members. The presentations have recently been compiled into a book for publishing, with the organizer of this conference noting that this would mark an important "tool for Global Citizenship Education (GCED) also - in particular during the World Humanities Conference (WHC) to be held in Liege, Belgium from 6 to 12 August 2017." This talk included analyses conducted by my postdoctoral research assistant (Dr. Saioa Lopez) using data developed through this project.
Year(s) Of Engagement Activity 2016
URL http://en.unesco.org/events/international-conference-great-migrations-ancient-asia-minor-circulation...
 
Description radio interview with 105.3 Afro FM (Ethiopia) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact The postdoctoral research assistant (PDRA) Saioa Lopez and I were invited to give a radio interview with 105.3 Afro FM, an Ethiopian radio station. The topic of this interview was a discussion of key findings from our analysis of the DNA from over 1,100 Ethiopian individuals representing over 70 different ethnic and social groups, funded by this BBSRC grant. We answered the interviewer's questions and discussed the main findings of our study to date, and in general discussed the information we have learned about human history (and in particular Ethiopian history) using DNA.
Year(s) Of Engagement Activity 2017
URL http://www.afro105fm.com/i/index.php