Tuesday 27 November 2012

Family Tree DNA Conference 2012 - citizen science comes of age

Each year in October or November Family Tree DNA host a conference in Houston, Texas, for their volunteer project administrators. The two-day programme includes a mixture of talks from FTDNA scientists, staff and project administrators. The conference is often the place where exciting new developments are announced. This year's conference, which took place from 10th to 11th November, was no exception. A number of the attendees were tweeting from the conference which enabled us to pick up most of the news as it happened. Twitter does not allow old tweets to be searched so you can no longer search for the #FTDNA2012 hashtag. You can, however, access the tweets from the accounts of the individual users: @ancestryjourney @Smitty327 @TrevorRix @khborges @CeCeLMoore @Genealem @RichardHillDNA @RobertaJEstes ‏@winincentive @Greenleafy and @spwells.

The big news from the conference was the announcement of the new Y-DNA haplogroup A00 in a joint presentation by Bonnie Schrack, Thomas Krahn and Michael Hammer which was unassumingly entitled "In Search of the Root: Discovery of a Highly Divergent Y-chromosome Lineage". The new haplogroup A00 is now the oldest and deepest-rooted branch of the human Y-DNA tree and is thought to date back about 338,000 years, making Y-Adam much older than mitochondrial Eve, who dates back around 200,000 years. Earlier studies had suggested that Y-chromosomal Adam, the common patrilineal ancestor of all males alive today, lived around 142,000 years ago. The new date for the root of the Y-tree now takes us back into uncharted territory because the earliest example of an anatomically modern human from the fossil record dates back only 196,000 years ago. However, the most astonishing aspect of this discovery is that it came about not because of the research of university scientists but from the hard work and dedication of an amateur genetic genealogist, Bonnie Schrack, who became involved in the world of DNA testing through her genealogical research and a simple desire to learn more about her roots. Bonnie is the volunteer project administrator of the haplogroup A project at Family Tree DNA, a job which she does in her spare time. Bonnie galvanised the support of her project members and the wider genetic genealogy community to arrange for some tests to be done on selected members of the haplogroup A project as part of FTDNA's Walk through the Y programme. Funding for the WTY tests was provided not from academic research grants but by members of the genetic genealogy community from around the world. Stan Pietrzak from Poland has been one of the project's most generous and enthusiastic supporters. Thomas Krahn, who heads up Family Tree DNA's Genomics Research Center in Houston, is in charge of the WTY programme. He and his wife Astrid were reportedly up all night doing the landmark WTY test, scoring more and more markers with a growing sense of disbelief before they finally realised what an amazing discovery had been made. Dr Michael Hammer, FTDNA's Chief Scientist, who has his own laboratory at the University of Arizona, then became involved when the momentous nature of the discovery was realised. In order to determine the placement of the new SNPs on the Y-tree Thomas went on to do WTY tests on samples from a chimp and a gorilla, and also analysed gorilla and chimp Y-STR markers. The person whose sample was used in the WTY project is a gentleman from South Carolina who is descended from a former slave. Little did he know when he agreed to take the test to help with his family history research that he would be making history! Further information on the new haplogroup A00 can be found in the following blog posts and websites:

The Y haplogroup A website, a new website from Bonnie Schrack which includes links to the slides from her talk at the conference as well as her speaking notes
The new root - haplogroup A00 by Roberta Estes
Your paternal line just got much longer by Dave Dowell
A00 on the Y haplogroup tree: a new view of African origins from a Y-chromosome perspective Thomas Krahn's very technical slides for his presentation at the FTDNA conference. This presentation includes links to the Ysearch IDs for the gorilla and chimp Y-STRs (25 markers) and the haplogroup A00 Y-STR signature (94 markers)
Walk through the Y project Thomas Krahn's WTY presentation from FTDNA 2012
A00 at FTDNA 2012: history in the making? A blog post from Dienekes Pontikos
Haplogroups A and the top of the modern human tree a diagram from Stan Pietrzak

A scientific paper is in preparation and will be published in the near future. These findings beg the question as to what other discoveries are waiting to be made. The world population is now over seven billion. Family Tree DNA have the world's largest Y-DNA database with almost 250,000 Y-DNA results from around the world, yet this represents just a tiny fraction of the total male population. I am sure there will be many more exciting discoveries to be made in the years to come as more people get their DNA tested.

The other big news from the FTDNA conference was the announcement that FTDNA's parent company has undergone a major restructuring and is now known as GenebyGene with four separate divisions: Family Tree DNA for genetic genealogy; DNA Traits for health tests; DNADTC for research-use genetic tests; and DNAFindings for paternity testing. The research arm DNADTC is now offering complete genome sequencing, and they are the first commercial company to do so. The test costs $5495 with a minimum order of three tests. No data analysis is provided. The test is not targeted at the consumer market but, as the price of sequencing drops, it cannot be too long before complete genome sequencing becomes a reality at an affordable price for the genetic genealogist, though data processing, analysis and interpretation will be a challenge.

A number of conference attendees have blogged about their experiences. Each blogger brings a slightly different perspective and all the posts are well worth reading:

-  8th Annual Conference on Genetic Genealogy - Day 1 by Jennifer Zinck
-  8th Annual Conference on Genetic Genealogy - Day 2 by Jennifer Zinck
-  Family Tree DNA Conference: Nits and Grits by Roberta Estes
-  Family Tree DNA's 8th International Conference on Genetic Genealogy Day I by Emily Aulicinio
-  Family Tree DNA's 8th International Conference on Genetic Genealogy Day 2 by Emily Aulicinio
-  FTDNA 2012: Geno 2.0 and more by Judy Russell
-  Native American Focus Meeting by Roberta Estes
-  Photos from FTDNA 2012 from Trevor Rix
-  A visit to Family Tree DNA's state-of-the-art lab by CeCe Moore

I would like to thank everyone who tweeted and blogged from the conference. It made all the difference to those of who could not attend in person. If I've missed any links do let me know and I will update this blog post accordingly.

This post was originally written on 27th November 2012 but was embargoed for publication until 28th February 2013 when the paper on the new root of the Y-tree was published in the American Journal of Human Genetics: http://www.sciencedirect.com/science/article/pii/S0002929713000736

© 2012-2013 Debbie Kennett

Thursday 22 November 2012

First results from Geno 2.0

A few people have started to receive their first results for the new Geno 2.0 test from the Genographic Project. CeCe Moore has posted some screenshots on her blog showing results for the autosomal DNA component of the test. Dave Dowell has blogged about his mtDNA results and has published an example of a "heat map" for haplogroup H. We are still waiting to see the first Y-DNA results.

I have not ordered the Geno 2.0 test for myself as I have already taken the full mitochondrial sequence test with Family Tree DNA.  The ethnicity percentages from the autosomal part of the test will not yield any meaningful information and should only confirm that I am "British", which I already know from my family history research! As a female I do not have a Y-chromosome and I would, therefore, not be able to receive any Y-DNA results. However, if you are interested in your deep ancestry and wish to know your mtDNA and Y-DNA haplogroups then the Geno 2.0 test is a good choice. The Y-DNA and mtDNA results can also be transferred to Family Tree DNA where you can join the relevant haplogroup projects and order additional testing for genealogical purposes. The Geno 2.0 test will provide very detailed Y-DNA haplogroup assignments and has essentially replaced the old deep clade test offered by Family Tree DNA.

I contributed my mtDNA results from Family Tree DNA to the first phase of the Genographic Project. I am still able to log into my Genographic account to access my results. The website has been updated and I am now getting the same screenshot as the Geno 2.0 participants. However, I note that I have been downgraded to a simple haplogroup U rather than a U4, and I am no longer able to access any information on haplogroup U4. It may be that the new haplogroup pages have not yet gone live and my haplogroup will be adjusted when this has been done.

© 2012 Debbie Kennett

Sunday 18 November 2012

Extinct and endangered surnames

My new Surnames Handbook has received a very welcome mention in an article in today's Sunday Telegraph. However, there are a number of errors in the article which I would like to correct. The article gives the impression that the extinct and endangered surnames featured in the article are mentioned in the book, but in fact I don't cover the subject, though I do discuss the differing distribution patterns of many surnames.The survival of surnames is indeed a random process but some surnames have multiple origins and have a much better chance of surviving than a surname with a single origin.

Surnames were in fact in use in Ireland before they were introduced in England following the Norman Conquest. In Scotland the situation is more complicated but, as a result of English influence, some surnames were in use in Scotland after the Conquest, but surnames developed much later in the Gaelic-speaking areas in the Highlands. While there are some "seasonal" surnames which are from days of the week (Friday), festivals (Christmas) and months (February, May), the derivation is not always what it appears. Reaney and Wilson suggest, for example, that the surname May is derived from the Middle English word may meaning "young lad or girl" or that it might be a pet form of Matthew, from Mayheu or Mayhew.

In the book I did discuss the difficulties in trying to establish how many surnames there actually are. There are no precise figures available for England and Wales, and it is almost impossible to say how many surnames there actually are in the world. The General Register Office does of course keep records of all births, deaths and marriages in England and Wales, but their records are not available in a database format that can be searched to produce comparative statistics for surnames. Recent electoral registers are not available for public inspection, though it is possible to search an edited version on websites such as 192.com.

The information on the extinct surnames that were used in the Telegraph article was provided by some of my fellow members of the Guild of One-Name Studies. As the Telegraph only provided very brief details of these surnames I have taken this opportunity to provide further information and I've added a few more names to the list which arrived too late to be included in the article. If you know of any more extinct or endangered surnames do let me know.

Guild member Andrew Millard is studying the surname Bodimeade. He tells me that some of the variant spellings of his surname have now died out.  The last bearer of the surname Bodiman died in 1820, and the last member of a family which consistently spelled their name Bodymead died out in 1901. You can read more about Andrew's study on his Guild profile page.

Guild member Phil Hand is studying the surnames Boyell, Boyall and Boyall. Boyell is a variant spelling of Boyall and first appeared in the records in about 1810. There are only about 45 people born with the Boyell variant spelling, all of whom are descendants of a Richard Boyell who had the 'a' of his surname crossed out on his 1814 marriage entry and an 'e' written above it. The name is now held by a single lady in England, though there are also a couple of Boyells in the USA. The Boyells in the US appear to be Boyles who have changed the spelling of their surname quite recently. The surname Boyall is centred around Lincolnshire and Rutland.

The surname Bythewood has been investigated by Guild member Ros Dunning though she has not as yet registered the surname with the Guild. The surname became extinct in Britain in the middle of the nineteenth century but a single Bythewood emigrated to the United States.  Ros tells me that "he had so many children both legitimate and illegitimate (by slaves) that he managed to keep them going in the States!" The surname Bythewood does not appear in any surname dictionaries but is most probably not an occupational surname as the reporter supposed but was probably a topographical surname which would originally have been written as "By the wood".

The surname DOOGOOD, which is being studied by Guild member John Hill, is on the brink of extinction in the UK though it is alive and well in Australia. There are no more than seven people with the surname in England and Wales and, as far as John knows, none in Scotland or Northern Ireland. John's research indicates that the living male Doogoods have either not married or had no male children so there appears to be little chance of the surname continuing in use.

It is probably a nickname which probably arose independently in several locations. Prior to about 1800 there were Doogoods in various counties including Hampshire, Norfolk, Lincolnshire, Somerset, Herefordshire and Worcestershire as well as in London. There were also a few in Scotland. John's research has shown that all the other branches died out. All the living Doogoods can be traced back to the parishes of Leigh and Bransford in Worcestershire in the mid 1500s. They remained in this area until about 1800. Further information about the Doogood surname can be found on John's Guild profile page.

Guild member Michael Simpkin is studying the surname Earthridge which appears to be extinct in the UK, though it's possible that it might still be found in North America and in the Republic of Ireland. Having studied the surname for some time Michael has come to the conclusion that it is probably a rare variant of a group of surnames of which Etheridge is the most common.

The surname Foothead is being studied by Guild member Carol Gilbert. The surname is now extinct in the UK but still lives on in Australia and New Zealand. Carol's great grandfather Edward James Foothead was at one time the only male of the name in the world. He emigrated to New Zealand in 1874 where he had ten children, all but one of whom were boys. Most had children of their own so there are a few more now than there were though still not many.  You can read more about Carol's research into the Foothead surname on her profile page on the Guild's website.

Guild member Pamela Bishop is studying the surname Hudgill. This name is on the verge of extinction and there is currently just one living male left in the whole world with this surname. Hudgill is a variant of the name Hudgell which, in contrast, has continued to thrive. Further information on the Hudgill surname can be found on Pamela's one-name study website.

Guild member James Mackman is studying his own surname Mackman. During the course of his research he has also studied the surname Mackmain. He tells me:
The name Mackmain seems to have died out. At one time we thought it was related to Mackman but we've never found a connection. On the off-chance that there was a connection I have spent many hours checking Mackmain references. Altogether I have about 70 Mackmains. The last one (Norman Langford Mackmain) died in 1964. There are no Mackmains in any phone book I've come across anywhere in the world. There are no references to living Mackmains on Google.
James has been able to trace his own Mackman name back to a James Makeman who was christened on 10 January 1747/8 and is the common ancestor of 411 of the 477 living Mackmans he has traced. Fifty-three Mackmans are descended from four different ancestors whose surname changed to Mackman for various reasons. The ancestors of the remaining 13 Mackmans have yet to be identified. The origin of the common ancestor's surname is not known.

Oal or Oall
Guild member Donald Grant is studying the surname Scoon, but has supplied information about another surname Oal or Oall which he has also researched. This surname appears in Caithness in the late 18th century as an Anglicisation of the Scots dialect name Auld. For some reason, most of the line(s) in which this happened gradually reverted to the Auld spelling, so the name (but not the lines) died out by 1910. Some later Auld death certificates indicate that the name was "formerly Oal".

Pauncefoot is a surname which appears in my own family tree.  I am descended from the Pauncefoots of Compton Pauncefoot in Somerset on my father's side of the family. My most recent Pauncefoot ancestor is Anne Pauncefoot, the daughter of Sir Walter Pauncefoot, lord of the manor of Compton Pauncefoot, and Tomasine Baumpfield. Anne was born on 4th July 1485, and we have a delightful proof of age document for Anne in which many of the local villagers turned out to testify to the date of her birth.2 Anne married John Whiting or Whyting, lord of the manor of Woode in the parish of Kentisbeare in Devon. The research on the early Pauncefoot tree has been done by my distant cousin the author Fay Sampson.

The earliest occurrence of the name is in the Domesday Book of 1086 where a Bernhard Pauncevolt was recorded as holding several manors in Hampshire. In early records the name appears with a variety of different spellings such as Pancefot, Pauncefot, Pauncefort, Pantesfort and Pauncheout. The Paunce element of the surname is derived from panche (Middle English), pance (Old French) or panche (Old Norman French) meaning "stomach". Volt is an Old French word for face, but also means "vaulted" or "arched". It is therefore suggested that the name refers to a man with an "arched and rounded belly". Alternatively the name may derive from the place name of Ponsford in Devon.3

The most recent reference to the surname that I can find dates from 1939 when a Miriam Pauncefoot was listed in the UK Electoral Register living at 3 Heythorp Street in Putney, London. The FreeBMD website has a single reference to the surname - the death of Emma Pauncefoot at the age of 67 in Hackney, London, in 1892.

Although the surname is now extinct the name is preserved as a manorial affix in the Somerset village of Compton Pauncefoot. There is a stone in the church in memory of my ancestor Anne Whiting née Pauncefoot, which also includes the coats of arms of both the Whiting and Pauncefoot families.

De Rippe
Ann McDonald has registered the surname Corner with the Guild but it is the De Rippe surname in her family tree which has become extinct. The last person with the name died in the 1890s. Ann has provided the following information on the surname:
The first records I can find of the De Rippe family (also spelt D'Rippe plus about 27 other deviant spellings!) are in Wakerley, Northamptonshire in the late 17th century.  I haven't been able to find any record of them in the Huguenot registers I've looked at but there is a family with a similar name, generally Darripe or D'Arippe, in Portarlington, Ireland who did come from France.  I can't establish a link between the two families but Abraham and Isaac are names common to both (a red herring?)  The name Derippe is still current in France.

The De Rippes were mostly farmers or bakers and in the mid-18th century some of them moved to London establishing successful businesses as bakers and merchants.  My heroine is Elizabeth who separated from her husband, a tea dealer in the City of London, in the late 18th century through Doctors' Commons, set up as a tea merchant on her own account, and was far more successful than her erstwhile husband.  A famous descendant of the family with a De Rippe grandmother was Edward Aveling, a Socialist with a Congregationalist minister father, who lived for sometime with Karl Marx's daughter Eleanor.  Eleanor committed suicide after Edward married another woman. The last person with the name was Charlotte who died in Epsom, Surrey in 1895 aged 94.

There are any number of us scattered throughout the world descended through the female line and De Rippe still appears as a middle name in some families to this day.  I've been able to tie pretty well every occurrence of the name as a surname or middle name in England, the USA and Australia to the one extended family.
Rowbree is a variant of the surname Rowberry which is being studied by Guild member Polly Rubery. Polly tells me that there are now just two living people with the surname Rowbree, neither of whom are likely to carry it forward. You can read more about the Rowberry surrname and its variants on Polly's website, where she also provides detailed information on the origin of the surname.

Guild member Gillian Stevens is doing a one-name study of the surname Blofeld, but has also been researching other surnames in her family tree including the rare surname Tillcott. She tells me:
My 3 x great grandmother was Jane Tillcott 1782-1842 which I believe to be an at risk surname.

In 1841 there were 2 Tillcotts in the census, the brother and sister in law of the above Jane. These 2 had died by 1851 and there are no other Tillcott in this census. The only other census transcriptions in the census were 1871 via Ancestry where the Tillcott should have been Tallbott and via findmypast where a 15 year old servant was indexed as Tillcott (not sure what her name should be).

With regard to civil registration.There are 8 marriages from 1918 to 1948 all in the Hackney Registration District but I do not know where this "family" came from. There is one birth in 1930 of a Jean Tillcott belonging to one of the Hackney marriages. There are 3 deaths in Warwickshire 1837-1850 all relations of my Jane (her father and the two mentioned above) plus 8 London deaths including 3 from Hackney during the 20th century (I assume persons from the 8 Hackney marriages).

From Family Search there appears to be a small number in Canada and Ohio US. Similarly Google produces an extremely small number of the surname.
Gillian's Tillcots trace back to Northamptonshire but the origins of the surname are not known. The name does not appear in any surname dictionaries.

Alan Wellbelove registered his surname and the variant spellings Welbelove, Welbeloved, Wellbeloved and Wellbeluff with the Guild of One-Name Studies in 2008. His one-name study is small with fewer than 400 name-bearers in England and Wales in 2002, and probably no more than 600 in total worldwide. These were the only spellings of the surname to survive into the twentieth century. Alan has provided the following information:

- Wellbeluff became extinct worldwide in 1986 with the death of the last name-bearer.
- Welbeloved became extinct in England & Wales in 2004, but still survives mainly in New Zealand and Australia.
- Welbelove numbers were estimated at 21 in 2002 and the name is rarely found outside of the UK, so it is in most danger of extinction.
- Wellbelove is the most common variant with an estimated 273 in England & Wales in 2002.
- Wellbeloved is found especially in South Africa and the USA. There were only 88 in England and Wales in 2002.

Since the nineteenth century the surname has occasionally been abbreviated to Welby/Wellby/Wellbye as a nickname and sometimes an alias. There is no single explanation for the use as an alias, but it has occurred not only in England, but also with different families in Scotland, South Africa and the USA. Alan is exploring these links with Guild member Daniel Welby who is studying the surname Welby with variants Welbee, Welbey, Wellbie, Welbye, Wellby and Wellbye. Further information on the surname Wellbelove and its variants can be found on Alan's Guild profile page. Further details on the Welby one-name study can be found on Daniel's Welby profile page.

1. Reaney, PH, and Wilson RM. A Dictionary of English Surnames. 3rd edition. Oxford University Press, reprinted 2005, p304.
2. Proof of Age. Inquisition 1502. Chancery Series II. VII 15 (57). Typed transcript from the Moget collection at the West Country Studies Library in Exeter, Devon.
3. Reaney, PH, and Wilson RM. A Dictionary of English Surnames. 3rd edition. Oxford University Press, reprinted 2005, p342.

© Debbie Kennett 2012

Monday 12 November 2012

Family Tree DNA winter sale 2012

Family Tree DNA's winter sale has now started. The sale prices apply until midnight on 31st December (Houston time). The tests on sale include:

- Y-DNA 37 markers $119 (£75)  (usual price $169 = £106)
- Y-DNA 67 markers $199  (£125)  (usual price $268 = £169)
- Family Finder $199 (£125) (usual price $289 = £188)
- Full Mitochondrial Sequence $199 (£125) (usual price $299 = £188)

For prices in other currencies use a currency converter such as the XE Universal Currency Converter.

Special combination packages are also available. A full list of FTDNA products can be found here.

If you are thinking of ordering a Y-DNA test make sure you order your test through the relevant surname project so that your results can be compared with other people with your surname. By testing through a surname project you will also benefit from the assistance of a volunteer project administrator. If there is no project for your surname you can order a test through a geographical project. You can find a list of all the geographical projects for the British Isles here. There are also many other geographical projects, including projects for most European countries. You can find a full list of projects here. If you have documented ancestry from Devon I would be very pleased to welcome you to my Devon DNA Project. When you have received your test results and you know your Y-DNA and/or mtDNA haplogroup you can join the relevant haplogroup project. You can find a full list of Y-DNA haplogroup projects in the ISOGG Wiki. There is also a list of mtDNA haplogroup projects.

If you have already ordered a DNA test through Family Tree DNA and wish to order a new test, the special sale prices also apply. There are also reductions for upgrading Y-DNA and mtDNA tests. Click on Order an Upgrade on your personal page to check out the special offers. If you are upgrading a Y-DNA test I recommend upgrading to 37 or 67 markers. If you are upgrading a mitochondrial DNA test it is worthwhile upgrading to the full mitochondrial sequence at the current sale price.

Sunday 4 November 2012

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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