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Surprises in English and Irish DNA

Sunday, May 22, 2011

Over a year ago, there appeared one of the few studies of autosomal DNA in Ireland and Britain. If you have English/Welsh, Irish, northern Irish, Highlands Scottish, Lowlands Scottish or Swedish matches, you will want to read this post. Here is the original article and abstract.

Eur J Hum Genet. 2010 Nov;18(11):1248-54. Epub 2010 Jun 23.

Population structure and genome-wide patterns of variation in Ireland and Britain.

Abstract

Located off the northwestern coast of the European mainland, Britain and Ireland were among the last regions of Europe to be colonized by modern humans after the last glacial maximum. Further, the geographical location of Britain, and in particular of Ireland, is such that the impact of historical migration has been minimal. Genetic diversity studies applying the Y chromosome and mitochondrial systems have indicated reduced diversity and an increased population structure across Britain and Ireland relative to the European mainland. Such characteristics would have implications for genetic mapping studies of complex disease. We set out to further our understanding of the genetic architecture of the region from the perspective of (i) population structure, (ii) linkage disequilibrium (LD), (iii) homozygosity and (iv) haplotype diversity (HD). Analysis was conducted on 3654 individuals from Ireland, Britain (with regional sampling in Scotland), Bulgaria, Portugal, Sweden and the Utah HapMap collection. Our results indicate a subtle but clear genetic structure across Britain and Ireland, although levels of structure were reduced in comparison with average cross-European structure. We observed slightly elevated levels of LD and homozygosity in the Irish population compared with neighbouring European populations. We also report on a cline of HD across Europe with greatest levels in southern populations and lowest levels in Ireland and Scotland. These results are consistent with our understanding of the population history of Europe and promote Ireland and Scotland as relatively homogenous resources for genetic mapping of rare variants.

Though the focus was on genome-wide association studies (GWAS) and linkage disequilibrium, or medical aspects of DNA, this study was groundbreaking in using supercomputing and has enormous implications for the history of the British Isles. It used data from over 3,000 individuals from seven populations:

1. Ireland/Dublin

2. Scotland/Aberdeen

3. Bulgaria

4. Portugal

5. Sweden

6. South/Southeast England

7. Utah

Data came from several sources:  the International Schizophrenia Consortium, Wellcome Trust Cast Control Consortium 1958 Birth Control Data set, Utah European ancestry population (CEU) and HapMap project.

The study aimed to describe, statistically, four measures of the Irish and English populations: 

1. Population structure

2. Linkage disequilibrium, with consequences for the study of common Irish and English genetic disorders

3. ROH, or runs of homozygosity, essentially a reflection of inbreeding and the remoteness of a population

4. Haplotype diversity (based on SNPs in atDNA)

The main conclusion was that Irish/English formed a separate and unique population since the Ice Age very different from either Bulgarian (SE Europe) or Portuguese (SW Europe), with great affinities to Sweden or Scandinavian populations (p. 1250). For instance, "the breakdown and patterning of LD [linkage disequilibrium] ... is virtually indistinguishable among the Irish, Scottish, southern English, Swedish..." (p. 1250).

"Diversity across Britain and Ireland is reduced in comparison with mainland European populations, with Scotland and Ireland having lower levels than southern England (p. 1251)."

The study postulates that Irish and English proneness to genetic disease came about as a result of population stasis or unchanging conditions. The agricultural revolution swept in a lot of additions to the gene pool in most of Europe, including Southeast England, but in areas like Ireland, Scotland and Sweden the same population stayed on the land with little increase, in fact with a negative effect during the Norse migrations of the 10th century and the Irish Potato Famine. The study mentions a "kinship effect" apparent in Irish and Scottish clan histories (p. 1254).

The surprising suggestion is that there will now be a groundswell of research into "Irish" and "Scottish" and "English" diseases comparable to Jewish diseases.

A related study is:

A. Auton, K. Bryc, A. Boyko, K. Lohmueller, J. Novembre, A. Reynolds, A. Indap, M. H. Wright, J. Degenhardt, R. Gutenkunst, K. S. King, M. R. Nelson and C. D. Bustamante, Global distribution of genomic diversity underscores rich complex history of continental human populations, Genome Research, February 2009. Abstract.

Comments

Stephanie Hayward commented on 27-May-2011 09:15 AM

I am reading the book "When Scotland was Jewish" and am also doing research on the mythical Milesians. Was wondering if this mythical Irish group had ever come up in your discussions. It is said they were descended from Jewish line and I started making
a connection by what is outlined in your book. By the way, the book is great! Stephanie

Teresa Panther-Yates commented on 08-Jun-2011 03:12 PM

How interesting! The Milesians are thought to be one of the mythical populations that started Ireland. They are thought to be Middle-Eastern and from Spain, but this population is not in the book and has not come up. Thank you for this adding this observation.
Teresa P. Yates


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Hunter Gatherer DNA from the Don

Saturday, January 09, 2010
The successful extraction of ancient DNA has been a rare accomplishment in genetic circles until recently. In the journal Current Biology, a German-Russian team details how it was possible to avoid the common pitfalls of contamination with modern human DNA in the instance of a 30,000 year-old hunter gatherer's grave in Russia. Svante Paabo, from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and colleagues used the latest DNA sequencing techniques to study genetic information from human remains unearthed in 1954 at Kostenki, Russia. According to a report by the BBC, the hunter gatherer's mitochondrial DNA type was U2. Haplogroup U is seen as a predecessor dominant type among Europeans before the arrival of agriculture and Middle Eastern culture about five to seven thousand years ago. It is hoped the new expertise will help unlock the secrets of other examples of ancient DNA.

Title and authors of the article:  A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia, by Johannes Krause, Adrian W. Briggs, Martin Kircher, Tomislav Maricic, Nicolas Zwyns, Anatoli Derevianko and Svante Pääbo 

Summary The recovery of DNA sequences from early modern humans (EMHs) could shed light on their interactions with archaic groups such as Neandertals and their relationships to current human populations. However, such experiments are highly problematic because present-day human DNA frequently contaminates bones. For example, in a recent study of mitochondrial (mt) DNA from Neolithic European skeletons, sequence variants were only taken as authentic if they were absent or rare in the present population, whereas others had to be discounted as possible contamination. This limits analysis to EMH individuals carrying rare sequences and thus yields a biased view of the ancient gene pool. Other approaches of identifying contaminating DNA, such as genotyping all individuals who have come into contact with a sample, restrict analyses to specimens where this is possible and do not exclude all possible sources of contamination. By studying mtDNA in Neandertal remains, where contamination and endogenous DNA can be distinguished by sequence, we show that fragmentation patterns and nucleotide misincorporations can be used to gauge authenticity of ancient DNA sequences. We use these features to determine a complete mtDNA sequence from a ∼30,000-year-old EMH from the Kostenki 14 site 

Kostenki 14 (Vladimir Gorodnianskiy)
Reconstruction of the hunter gatherer.  Courtesy BBC News.
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FOX News Showcases DNA Consultants

Thursday, December 03, 2009
Dr. Yates was interviewed by WBRC reporter Jeh Jeh Pruitt of FOX News Alabama at the company offices in Phoenix on October 22. The report was broadcast on affiliate stations in late November. Watch it on MyFoxAlabama.com.


Comments

M. Moore commented on 15-Dec-2009 01:44 PM

I hope there are many more interviews with DNA Consultants. Kudos and Cheers!


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