Who Do You Think You Are? Live 2013 Days 1 and 2

Who Do You Think You Are? Live, the large family history show held every year over three days at Olympia in London, is now firmly established as the most important event in the genealogical calendar in the UK. I have been to all the shows except for the very first one in 2007 and it has been interesting to see how WDYTYA has evolved over the years. One of the biggest changes has been the increase in the number of overseas visitors, and many of these overseas visitors have come to WDYTYA because of a growing interest in DNA testing. The DNA workshop, sponsored by Family Tree DNA, has been a regular feature of WDYTYA since 2009. A number of dedicated volunteer FTDNA project administrators in America have paid their own air fares and hotel accommodation to attend WDYTYA each year to help out on the Family Tree DNA stand and to educate the British public about DNA testing. ISOGG - the International Society of Genetic Genealogy - has had a presence at WDYTYA since 2010 thanks to the initiative of Brian Swann, the Regional Co-ordinator for England and Wales. The ISOGG stand is manned by volunteers from both England and America, and I have been involved with the ISOGG stand from the beginning.

This year we had a record number of DNA visitors from overseas. I was very pleased to be reunited again with my DNA friends from America: Emily Aulicino, Katherine Borges, Candy Campise, Linda Magellan, Derrell Oakley Teat, Craig Trout, George Valko and Cynthia Wells, all of whom very kindly gave up their free time to help to promote DNA testing by helping out on the ISOGG and FTDNA stands. This year I was delighted to make the acquaintance of five new DNA visitors from the US: Dick Kenyon, Charles Moore, Nora Probasco, Barbara Rae-Venter and Jennifer Zinck. I was particularly honoured to have the opportunity to get to know Charles Moore, who is held in high regard in the world of genetic genealogy. Charles is one of the content experts for the ISOGG Y-SNP tree and is renowned for his work on the haplogroup R1b-U106 project. U106 is the subclade to which my dad belongs, so Charles's work is of particular interest to me. Charles is a wizard with spreadsheets and has the ability to spot patterns in Y-STR markers in order to predict the most downstream subclade. Project members can then order individual SNPs à la carte from Family Tree DNA rather than ordering a more expensive Geno 2.0 test. ISOGG in England was represented by project administrators John and Ann Blair, Sue Curd, Maurice Gleeson and Brian Swann. Chris Pomery, Family Tree DNA's representative in England, was also attending the show and helping out on the FTDNA stand.

I managed to have a very quick chat with Gail Riddell from New Zealand, who runs the New Zealand DNA Project, and project administrator Susan Hedeen from America. I briefly said hello to Carolyn Dyess Bales, one of my friends in the US from the Guild of One-Name Studies, who was attending WDYTYA with her cousin Cammie Dyess Mercer. This was her first trip outside the US, and she had to buy a passport especially for the trip! Another Guild member, Elizabeth Kipp from Canada, was attending with her husband Ed, but in the rush I never managed to meet up with her.

DNA testing has been very much in the news in the last few weeks with the worldwide publicity generated by Richard III. Most conveniently the BBC put out a two-part documentary entitled Meet the Izzards on the Wednesday and Thursday before WDYTYA in which the comedian Eddie Izzard traced the migration of his ancestors out of Africa and into Europe. The combination of Richard III and Meet the Izzards generated a huge amount of interest in DNA testing at this year's WDYTYA and we were all rushed off our feet for the entire three days. Family Tree DNA brought more than double the usual number of kits and sold a record number of tests this year. Some of the tests were on sale at a special show price. The 12-marker Y-DNA test was on sale for just £30. The headline price helped to draw in lots of visitors to the stand but most people chose to opt instead for the 37-marker test at the special show price of £85, though I understand that quite a few 12-marker kits were sold on the Sunday. I would have liked to have taken some photos of the ISOGG and FTDNA stands with all the crowds but I was busy non-stop throughout the show and hardly had the chance to take any photos. I only had a break when I sat down to listen to some of the talks. The FTDNA stand had two large tables with five chairs arranged in front of the stand where people could sit down, place their orders and get swabbed. Those five chairs were occupied almost continuously throughout the three days. There were still people turning up to be tested after the show had officially ended each day. Nora Probasco and I were operating a triage system by talking to the people who were waiting and making sure they understood what the tests were all about and establishing whether or not they wished to place an order. This meant that by the time they got to sit down at the tables they were ready to be swabbed. At some times it got so busy that people had to be taken to the nearby cafe area to place their orders and get the swabbing done.

Max Blankfeld, Family Tree DNA's Vice President of Marketing and Operations, was on his own this year as Bennett Greenspan, the President and CEO of FTDNA, was unable to attend. Max was very grateful for the assistance from all the volunteer project administrators who helped out on the stand. It would have been impossible for FTDNA to attend the show without the help of all the many volunteers who so freely gave of their time.

I was presenting a talk in the DNA workshop at WDYTYA this year for the first time. The subject of my presentation was "DNA for beginners: the different tests". All the seats were taken for my talk on each of the three days and there were people standing four or five deep at the back of the workshop area trying to listen in.

I understand FTDNA had a surge in sales after my talk so I must have been doing something right! I had some very nice positive feedback from one of my Twitter followers Maggie who had attended my talk and then wrote up her experiences in a blog post. I was very pleased to learn that mine was the "most illuminating" of all the presentations she had attended. Most of the talks on Friday and Saturday were similarly packed out with people having to stand at the back, but Sunday was much quieter.

On Friday night the DNA project administrators got together for an enjoyable meal at Pizza Express.

On Saturday I arrived extra early, taking full advantage of my ISOGG exhibitor's pass which allowed me to get into Olympia before the doors opened to the public, to ensure that I got a ticket for Turi King's talk on Richard III. I was not disappointed. She gave a very interesting and entertaining talk. The original aim of the project was to locate the church of the Greyfriars. No one had ever expected to find Richard III and Richard Buckley, the lead archaeologist from the University of Leicester, had famously promised to eat his hat if Richard III were found. The team held him to his word but fortunately for him had a special hat-shaped cake made up specially for him to eat! Turi King explained the painstaking process of testing ancient DNA specimens. The samples have to be tested independently in two separate labs. She did some of the ancient DNA testing in the lab of Professor Michael Hofreiter at the University of York. She then replicated the tests in the lab of Patricia Balaresque at the Université Paul Sabatier in Toulouse. This of course meant a trip across the Channel and Turi described how she had to negotiate customs with Richard III's tooth, terrified that customs would want to open up the package for inspection, thus contaminating the sample and making the whole process worthless. The return journey was even more nail-biting as in order to extract the DNA the tooth had to be ground down into a fine white powder which was guaranteed to raise alarm bells with customs officers! Fortunately she got through customs unscathed, helped by official letters from the University of Leicester. The results of the ancient DNA analysis were only received on the weekend before the press conference. Turi described the moment that the results came through and she saw that there was a match. She went silent for a minute and then did a little dance around the lab!

The ancient DNA analysis will now continue. The next step will be to see if it is possible to extract some Y-chromosome DNA from the remains to compare against the Y-DNA samples obtained from living descendants of Henry Somerset, the 5th Duke of Beaufort, who should share the same Y-DNA signature as Richard III. Turi King is not able to release the details of the Y-chromosome haplogroup of the Beaufort lineage at present. The University has an agreement with Nature and it is planned to publish two papers back to back. Full details of the DNA analysis and the haplogroups will then be given. According to the terms of the agreement the papers have to be submitted to Nature within the next year, though they will of course still have to go through the usual peer-review process.

After Turi King's talk I rushed back to the DNA area to catch the presentation by Bruce Winney on the People of the British Isles Project. The project has now collected 4,300 samples from people in the British Isles with four grandparents born in the same rural county. The researchers have genotyped 2,800 of these samples across 600,000 SNP markers. Strong regional variations have been found with, for example, the people of Devon and Cornwall, forming distinct clusters.  The samples have also been compared with samples from Europe in order to identify the source of the structure seen in the UK.

A scientific paper is in preparation which will be submitted to Nature,  but it will still be a few more months before the paper is ready to be submitted. Once the paper has been published everyone will have the opportunity to examine the stunning maps that were shown to us at Olympia. Little progress seems to have been made on the analysis of the Y-chromosome and mitochondrial DNA data. I also asked about the X-chromosome data but no one has as yet considered analysing that data.

On Saturday I was briefly able to say hello to my friend Princess Maria Sviatopolk-Mirski though she unfortunately arrived at the stand during one of our busiest spells. I was also very pleased to have the opportunity to meet Andrew Millard, a friend from the Guild of One-Name Studies. I had a brief chat with Andy Grierson from Sheffield University, one of the citizen scientists who published an important paper on the phylogeny of haplogroup R1b1a2 based on detailed analysis of public datasets such as the 1000 Genomes Project. He is now working on another interesting collaborative project which will no doubt be the subject of a new paper in due course.

On Saturday night I attended the dinner at Pizza Express organised by the Association of Professional Genealogists. It was good to catch up again with Rosemary Morgan. I was finally able to meet Kirsty Wilkinson who I had known for some time on Twitter but had never actually met face to face. I also briefly chatted with Bruce Durie who I had met over twenty years ago in another life at a pharmaceutical conference in Montreux in Switzerland. By an extraordinary twist of fate we now both share the same publisher in the form of the History Press. Then it was time for the long train ride home and a few snatched hours of sleep before another long day at Olympia on Sunday.

See also
- Who Do You Think You Are? Live Day 3: Alistair Moffat on how DNA is rewriting British history
- Who Do You Think You Are? Live Day 3 Part 2: The new ancient root of the Y-tree

© 2013 Debbie Kennett

ASHG abstracts

The annual meeting of the American Society of Human Genetics will take place from 6 - 10 November in San Francisco. The posters can be searched online from the ASHG meeting website. The following three abstracts will be of particular interest to the genetic genealogy community.

The GenoChip: a new tool for genetic anthropology
S. Wells, E. Greenspan, S. Staats, T. Krahn, C. Tyler-Smith, Y. Xue, S. Tofanelli, P. Francalacci, F. Cucca, L. Pagani, L. Jin, H. Li, T. G. Schurr, J. B. Gaieski, C. Melendez, M. G. Vilar, A. C. Owings, R. Gomez, R. Fujita, F. Santos, D. Comas, O. Balanovsky, E. Balanovska, P. Zalloua, H. Soodyall, R. Pitchappan, G. Arun Kumar, M. F. Hammer, B. Greenspan, E. Elhaik

 Background: The Genographic Project is an international effort aimed at charting human history using genetic data. The project is non-profit and non-medical, and through the sale of its public participation kits it supports cultural preservation efforts in indigenous and traditional communities. To extend our knowledge of the human journey, interbreeding with ancient hominins, and modern human demographic history, we designed a genotyping chip optimized for genetic anthropology research. Methods: Our goal was to design, produce, and validate a SNP array dedicated to genetic anthropology. The GenoChip is an Illumina HD iSelect genotyping bead array with over 130,000 highly informative autosomal and X-chromosomal SNPs ascertained from over 450 worldwide populations, ~13,000 Y-chromosomal SNPs, and ~3,000 mtDNA SNPs. To determine the extent of gene flow from archaic hominins to modern humans, we included over 25,000 SNPs from candidate regions of interbreeding between extinct hominins (Neanderthal and Denisovan) and modern humans. To avoid any inadvertent medical testing we filtered out all SNPs that have known or suspected health or functional associations. We validated the chip by genotyping over 1,000 samples from 1000 Genomes, Family Tree DNA, and Genographic Project populations. Results: The concordance between the GenoChip and the 1000 Genomes data was over 99.5%. The GenoChip has a SNP density of approximately (1/100,000) bases over 92% of the human genome and is highly compatible with Illumina and Affymetrix commercial platforms. The ~10,000 novel Y SNPs included on the chip have greatly refined our understanding of the Y-chromosome phylogenetic tree. By including Y and mtDNA SNPs on an unprecedented scale, the GenoChip is able to delineate extremely detailed human migratory paths. The autosomal and X-chromosomal markers included on the GenoChip have revealed novel patterns of ancestry that shed a detailed new light on human history. Interbreeding analysis with extinct hominids confirmed some previous reports and allowed us to describe the modern geographical distribution of these markers in detail. Conclusions: The GenoChip is the first genotyping chip completely dedicated to genetic anthropology with no known medically relevant markers. We anticipate that the large-scale application of the GenoChip using the Genographic Project’s diverse sample collection will provide new insights into genetic anthropology and human history.
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People of the British Isles: An analysis of the genetic contributions of European populations to a UK control population
S. Leslie, B. Winney, G. Hellenthal, S. Myers, P. Donnelly, W. Bodmer

There is much interest in fine scale population structure in the UK, as a signature of historical migration events and because of the effect population structure may have on disease association studies. Population structure appears to have a minor impact on the current generation of genome-wide association studies, but will probably be important for the next generation of studies seeking associations to rare variants. Furthermore there is great interest in understanding where the British people came from. Thus far genetic studies have been limited to a small number of markers or to samples not collected to specifically address these questions. A natural method for understanding population structure is to control and document carefully the provenance of samples. We describe the collection of a cohort of rural UK samples (The People of the British Isles), aimed at providing a well-characterised UK control population. This will be a resource for research community as well as providing fine-scale genetic information on the history of the British. Using a novel clustering algorithm, approximately 2000 samples were clustered purely as a function of genetic similarity, without reference to their known sampling locations. When each individual is plotted on a UK map, there is a striking association between inferred clusters and geography, reflecting to a major extent the known history of the British peoples. A similar analysis is performed on samples from different parts of Europe. Using the European samples as ‘source populations’ we apply a novel algorithm to determine the proportion of the genomes within each of the derived British clusters that are most closely related to each of the source populations. Thus we can observe the relative contribution (under our model) of each of these European populations to the genomes of samples in different regions of Britain. Our results strikingly reflect much of the known historical and archaeological record while raising some important questions and perhaps answering others. We believe this is the first detailed analysis of very fine-scale genetic structure and its origin in a population of very similar humans. This has been achieved through both a careful sampling strategy and an approach to analysis that accounts for linkage disequilibrium.
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Inferring Y Chromosome Phylogeny by Sequencing Diverse Populations
G. D. Poznik, P. A. Underhill, B. M. Henn, M. C. Yee, E. Sliwerska, G. M. Euskirchen, L. Quintana-Murci, E. Patin, M. Snyder, J. M. Kidd, C. D. Bustamante

The male-specific region of the Y chromosome (MSY) harbors the longest stretch of non-recombining DNA in the human genome and is therefore a unique tool that enables the tracking of migrations and inference of demographic history. We have sequenced 69 male samples from nine globally diverse populations, including three African hunter-gatherer groups. Due to inefficient selection, a relatively high mutation rate, and a small effective population size, the Y chromosome is particularly subject to drift. It has accumulated large expanses of highly repetitive sequence, which pose considerable challenge within a short read sequencing paradigm. To overcome this hurdle, we have built an informatics pipeline to reliably call Y chromosome alleles from moderate coverage short read shotgun sequence data. First, we defined a callability mask, learned from the mapping quality and depth of coverage patterns in the data, and then we tuned base-pair level quality control thresholds. Based on 13,000 provisional SNP calls, we inferred a tree of the 69 sequenced Y chromosomes. Using this tree, we then called individual genotypes for each SNP with a custom-built, phylogeny-aware, EM algorithm. With these high quality calls in hand, samples were assigned haplogroup labels using standard YCC nomenclature; 29 distinct named haplogroups were represented. We find that the maximum likelihood tree we construct recapitulates the extant Y chromosome phylogeny, thus confirming the fruits of decades of work based on ascertained SNPs. Further, we resolve a major long-standing polytomy by identifying a variant for which one haplogroup retains the ancestral allele, whereas its brother clades share the derived allele, thus indicating common ancestry and uniting the latter two branches. This finding has been confirmed by genotyping a larger panel. Finally, we estimate the MSY rate of mutation recurrence and the time to the most recent common ancestor of the sampled chromosomes.
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People of the British Isles Project

I had the opportunity yesterday to attend the Royal Society’s Summer Science Exhibition. My main interest in attending was to find out more about the People of the British Isles Project, who had been invited to take a stand at the exhibition to present their work. The exhibition was packed out all day and there seemed to be a constant crowd of people around the People of the British Isles exhibit as can be seen from the photos below.

I did manage to have a brief chat with some of the scientists who are working on the project, including Bruce Winney and Simon Leslie, to find out what progress has been made since June when I attended the Ancient Britons conference in Cardiff where the genetic map of Britain was presented for the first time. The People of the British Isles Project has now taken DNA samples from 4,371 volunteers. To participate in the project volunteers must live in a rural area and all four of their grandparents must have been born in the same county.  The DNA of 2,031 of the volunteers has now been sampled extensively using modern chip-based sequencing technology, which is the same methodology used for the 23andMe test and Family Tree DNA's Family Finder test. The People of the British Project has looked at 600,000 different markers known as SNPs (single-nucleotide polymorphisms) for their analysis. Although the chip contains both Y-chromosome (Y-DNA) SNPs and mtDNA (mitochondrial DNA) SNPs, they have so far only analysed the autosomal SNPs. Autosomal DNA is shuffled up and recombined with each new generation and provides a picture of the genetic make up of all our ancestors, whereas Y-DNA and mtDNA only tell us about our direct paternal and maternal lines respectively.

The researchers analysed the DNA using a technique known as linkage disequilibrium. They are essentially looking for motifs or patterns within the DNA which are specific to whole populations or sub-populations. The DNA data was analysed using a computer program called Fine Structure, which places the results in clusters based on their genetic similarity. This process requires an astonishing amount of computer power and it apparently took a week to run all the UK samples through the program. Once the clustering had been completed, the researchers added the geographical data to the samples and plotted the co-ordinates on a map using an average derived from the birth place of each individual's four grandparents. The resultant genetic map of the British population that was on display at the exhibition can be seen on the Royal Society's website. The colours shown on the map represent distinct genetic clusters. This was essentially the same map that we saw at the Ancient Britons conference. It can be seen that certain parts of the British Isles, such as Devon and Cornwall, are genetically quite distinct, whereas others, such as the whole of the south-east of England, are a homogenous mass. In some places distinctions have even been found within regions. In Orkney, for example,  the people of Westray were distinct from those on the Mainland. There is a particularly large cluster in Anglesey but this is apparently because samples were taken at an agricultural fair on the island and the researchers were inundated with people wishing to take part in the project!

The researchers have compared the results of the British samples with a collection of European samples. They have access to genetic data from 6,300 people in Europe. The samples were taken from projects such as the International Multiple Sclerosis Genetics Consortium and other data which is included in the Wellcome Trust Case Control Consortium 2. These samples were originally collected for medical studies and the researchers do not know the place of birth of the four grandparents or have any other ancestral information from the participants. However, they do know the name of the hospital or centre where the samples were taken which has enabled them to provide some geographical context. It was found, perhaps not surprisingly, that people in the south-west of England in particular were genetically quite similar to the people of north-western France. In the north people showed greater similarity with Scandinavian populations. I was understandably not allowed to photograph the European maps in close-up but a view of the display is shown below where you can just about distinguish the different-coloured clusters in Europe.

A paper will be submitted for publication in the next month, probably to Nature. All the maps on display at the exhibition will be included in the paper, and additional maps will also be included showing the different levels of clustering analysis. Some of the genomes from the project (some from Cornwall and for one other county) have apparently been uploaded to the 1000 Genomes Project. The raw data from the project will not be published with the forthcoming paper but will eventually be submitted to the Wellcome Trust Case Control Consortium. Researchers wishing to use the data will have to submit an application to be granted access. The data will be made available to population geneticists and not just medical researchers.

Although Y-DNA and mtDNA SNPs are included on the chip used by the project, the researchers have not yet started analysing these data. I was told that Professor Mark Jobling at the University of Leicester will probably be doing the Y-DNA analysis. A D.Phil. is also due to join the project in the autumn to help with this work. The project is also hoping to do some ancient DNA analysis as a comparison, but nothing has as yet been planned. The project still has two more years to run, and there will no doubt be other interesting papers published in the next few years.

© Debbie Kennett 2012