Friday, August 02, 2019

The Genetic History of France

The Genetic History of France

Aude SAINT PIERRE, Joanna Giemza, Mathilde Karakachoff, Isabel Alves, Philippe Amouyel, Jean-Francois Dartigues, Christophe Tzourio, Martial Monteil, Pilar Galan, Serge Hercberg, Richard Redon, Emmanuelle Genin, Christian Dina



doi: https://doi.org/10.1101/712497


Full paper and supplementary info at

https://www.biorxiv.org/content/10.1101/712497v2

This article is a preprint and has not been peer-reviewed


Abstract

The study of the genetic structure of different countries within Europe has provided significant insights into their demographic history and their actual stratification. Although France occupies a particular location at the end of the European peninsula and at the crossroads of migration routes, few population genetic studies have been conducted so far with genome-wide data. In this study, we analyzed SNP-chip genetic data from 2184 individuals born in France who were enrolled in two independent population cohorts.

Using FineStructure, six different genetic clusters of individuals were found that were very consistent between the two cohorts. These clusters match extremely well the geography and overlap with historical and linguistic divisions of France. By modeling the relationship between genetics and geography using EEMS software, we were able to detect gene flow barriers that are similar in the two cohorts and corresponds to major French rivers or mountains. Estimations of effective population sizes using IBDNe program also revealed very similar patterns in both cohorts with a rapid increase of effective population sizes over the last 150 generations similar to what was observed in other European countries. A marked bottleneck is also consistently seen in the two datasets starting in the fourteenth century when the Black Death raged in Europe.

In conclusion, by performing the first exhaustive study of the genetic structure of France, we fill a gap in the genetic studies in Europe that would be useful to medical geneticists but also historians and archeologists.

Saturday, June 15, 2019

Father's Day Sale Prices for Autosomal DNA tests

These prices are good to 17 June 2019:


In addition FTDNA has sales on Y DNA and mtDNA tests.



Sunday, May 05, 2019

Mother's Day autosomal DNA test prices:

Mother's Day autosomal test prices:




23andme. $99. Also a $30 discount on the Health & Ancestry package.

Ancestry. $59. Offer ends May 13.

Family Tree DNA. $79.

Living DNA, $79.

MyHeritage. $69. Sales ends May 13.

Irish DNA Atlas

The Irish DNA Atlas has been published to present the results of a study on DNA in Ireland.

From Nature:

Article | OPEN | Published: 08 December 2017

The Irish DNA Atlas: Revealing Fine-Scale Population Structure and History within Ireland

Edmund Gilbert, Seamus O’Reilly, Michael Merrigan, Darren McGettigan, Anne M. Molloy, Lawrence C. Brody, Walter Bodmer, Katarzyna Hutnik, Sean Ennis, Daniel J. Lawson, James F. Wilson & Gianpiero L. Cavalleri

Scientific Reports volume 7, Article number: 17199 (2017) | Download Citation


An Author Correction to this article was published on 03 May 2018

This article has been updated



Abstract

The extent of population structure within Ireland is largely unknown, as is the impact of historical migrations. Here we illustrate fine-scale genetic structure across Ireland that follows geographic boundaries and present evidence of admixture events into Ireland. Utilising the ‘Irish DNA Atlas’, a cohort (n = 194) of Irish individuals with four generations of ancestry linked to specific regions in Ireland, in combination with 2,039 individuals from the Peoples of the British Isles dataset, we show that the Irish population can be divided in 10 distinct geographically stratified genetic clusters; seven of ‘Gaelic’ Irish ancestry, and three of shared Irish-British ancestry. In addition we observe a major genetic barrier to the north of Ireland in Ulster. Using a reference of 6,760 European individuals and two ancient Irish genomes, we demonstrate high levels of North-West French-like and West Norwegian-like ancestry within Ireland. We show that that our ‘Gaelic’ Irish clusters present homogenous levels of ancient Irish ancestries. We additionally detect admixture events that provide evidence of Norse-Viking gene flow into Ireland, and reflect the Ulster Plantations. Our work informs both on Irish history, as well as the study of Mendelian and complex disease genetics involving populations of Irish ancestry.

See the article for discussion and maps.

Also, see, People of the British Isles: preliminary analysis of genotypes and surnames in a UK-control population

April 2019 update from Living DNA

Living DNA is a DNA ancestry service from England. Originally it specialized in providing a geographic breakdown of your DNA to locations in England, Wales, Scotland, and Northern Ireland. It has added Eire and is going to be adding Germany to its reports. A news update is available at this link,

https://livingdna.com/news/living-dna-april-2019-product-update




Wednesday, May 01, 2019

Genomic data and the GDPR

From the PHG Foundation:

The potential of technologies such as these, together with other digital technologies to fall outside existing regulatory frameworks has prompted radical reform of data protection law across Europe. Thus, in May 2018 the EU General Data Protection Regulation (GDPR) came into force across the continent and in the UK, further national legislation has been implemented through the UK’s Data Protection Act 2018. This legal framework governs of the use of personal data in healthcare and research, and it explicitly recognises the category of genetic data for the first time (it will continue to apply in the UK regardless of Brexit).

However many, including Secretary of State for Health and Social Care, Matt Hancock, are concerned that the rules governing the use of genetic data could hinder the legitimate use of data for healthcare and research.

http://www.phgfoundation.org/blog/how-does-the-gdpr-apply-to-genomic-data




Tuesday, January 01, 2019

Ancient nuclear genomes enable repatriation of Indigenous human remains

http://advances.sciencemag.org/content/4/12/eaau5064

Abstract

After European colonization, the ancestral remains of Indigenous people were often collected for scientific research or display in museum collections. For many decades, Indigenous people, including Native Americans and Aboriginal Australians, have fought for their return. However, many of these remains have no recorded provenance, making their repatriation very difficult or impossible. To determine whether DNA-based methods could resolve this important problem, we sequenced 10 nuclear genomes and 27 mitogenomes from ancient pre-European Aboriginal Australians (up to 1540 years before the present) of known provenance and compared them to 100 high-coverage contemporary Aboriginal Australian genomes, also of known provenance.

We report substantial ancient population structure showing strong genetic affinities between ancient and contemporary Aboriginal Australian individuals from the same geographic location. Our findings demonstrate the feasibility of successfully identifying the origins of unprovenanced ancestral remains using genomic methods.

Article continues http://advances.sciencemag.org/content/4/12/eaau5064

Tuesday, December 25, 2018

Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders

https://www.sciencedirect.com/science/article/pii/S0960982218314957

Pinotti, T., Bergström, A., Geppert, M., Bawn, M., Ohasi, D., Shi, W., Lacerda, D.R., Solli, A., Norstedt, J., Reed, K. and Dawtry, K., 2018.

Current Biology.


The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15–25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1, 2, 3, 4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation (“Beringian Standstill” [8, 9]) for 2..4–9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions.

  • First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America.
  • Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya.
  • Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya.
  • Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.

Friday, November 23, 2018

Black Friday DNA test deals

The following companies are offering reduced cost autosomal DNA tests. These tests can be used to reliably find immediate family and cousins out to 4th or 5th cousins. Less reliably, they can give you ethnic ancestry results.


  • MyHeritage DNA - $49 plus free shipping with coupon code Free18 (ends Nov 23)
  • 23andMe - $69 per kit, shipping extra, or $129 for the Ancestry + Health version (ends Nov 25)
  • AncestryDNA - $49 per kit, plus shipping (ends Nov 26)
  • Family Tree DNA - $39 per DNA test, shipping extra (ends Nov 26)
  • LivingDNA through Findmypast, $59 plus shipping (ends Nov 26)
  • LivingDNA direct - $69 per kit, plus shipping (no posted end date)

I have tested at all of these companies.

I recommend the following testing strategy:
Test at AncestryDNA and 23andMe and then upload the raw data to the others. This is the lowest cost strategy and gets your results into the largest commercial genetic genealogy databases.

An additional upload is to Gedmatch. This will allow people who have tested at only one company to match other people from different companies. Gedmatch has both free and fee services. The free services get you their matching service.

There is a new company Dante Labs, doing whole genome testing for $199.00 (L169.00) for Black Friday Week. This is a 30x coverage of your whole genome and can be used for learning about medical propensities. Not really useful for genealogy.

If you already have a test result, be sure to upload to MyHeritage and Living DNA before 1 December to avoid their new fee schedule.

If you are interested in graphical representation of your relative network, Rootsfinder is another company to join before 1 December.

NOTE: I do not earn any money from your using any of these links.