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review of scientific and news articles on dna testing and popular genetics

Balkan DNA Studies Compare Former Yugoslav Populations

Monday, January 30, 2012

Serbs, Croats “have most similar DNA”

SKOPJE -- A six-year long DNA research of the Balkan peoples conducted by Skopje Forensics Medicine Institute has showed remarkable resemblance among them.

The analysis of the data has showed that residents of Macedonia have the most similar DNA with Bulgarians and Serbs, Croats with Bosnian and Serbian population while Kosovo Albanians have the fewest similarities with the others,” says Forensics Medicine Institute’s Dr Zlatko Jakovski.

The Macedonian scientists received samples and data from most of the Balkan countries, except from Greece, who refused to take part in the project. All the other countries sent DNA analyses of the victims who had died in their territory to Skopje.

“By using sophisticated computer technology we have compared the data from Macedonia, Serbia, Bosnia, Bulgaria, Croatia and Kosovo,” Jakovski explained.

The research has been published in the leading world forensics magazines and the results will be used in criminal investigations in cases when victims are from the Balkans.

Jakovski pointed out that the research represented a very useful scientific work and that it had nothing to do with daily politics.


Photo:  A Serb. 

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Basque DNA Studied in Festival Participants

Saturday, December 10, 2011

Geneticists seized the opportunity provided by an international Basque cultural event held in Idaho in 2010 to sample volunteers and study Basque DNA. The result was two studies, including "The Y-STR Genetic Diversity of an Idaho Basque population, published in Human Biology.

It was the first DNA study to document the spread of the Basque male chromosome overseas. The Basque people were renowned seafarers.

"The idea is to better understand health risks for Basque people, including an increased incidence of both Alzheimer's and Parkinson's diseases," said Josu Zubizarreta, a Boise State graduate who conducted research with the lead author, Greg Hampikian.

Mitochondrial DNA, which reflects a deeper history, was also studied.

Basques are credited with the invention of the rudder. They provided the crew and navigators for Magellan. Basque names are common on antique maps. The Bay of Biscayne is named for them, and many harbors, points and landfalls on the Atlantic Coast of North America are thought to come from the Basque language, which is known as an isolate and is unrelated to other European languages.

Sculpture of Basque sailor, Victorio Macho, Toledo. Travelpod.

Citation
Zubizarreta, Josu; Davis, Michael C.; and Hampikian, Greg (2011) "The Y-STR genetic diversity of an Idaho Basque population, with comparison to European Basques and US Caucasians," Human Biology: Vol. 83: Iss. 6, Article 2.
Available at: http://digitalcommons.wayne.edu/humbiol/vol83/iss6/2





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Gene Surfing and the French-Canadian Frontier

Sunday, November 27, 2011

Gene surfing is a process in population expansion whereby certain variations become prominent and dominant in a short time, appearing to skip the slow, steady, uniform accumulation of variegation and diversification. According to a study of the population structure and genealogies of Saguenay Lac-Saint-Jean in Quebec, this type of drastic change accompanied the immigrant wave front that spread over the area in the 17th century. "Deep Human Genealogies Reveal a Selective Advantage to Be on an Expanding Wave Front" in Science magazine describes the resulting demographics.

Abstract
Since their origin, human populations have colonized the whole planet, but the demographic processes governing range expansions are mostly unknown. We analyzed the genealogy of more than one million individuals resulting from a range expansion in Quebec between 1686 and 1960 and reconstructed the spatial dynamics of the expansion. We find that a majority of the present Saguenay Lac-Saint-Jean population can be traced back to ancestors having lived directly on or close to the wave front. Ancestors located on the front contributed significantly more to the current gene pool than those from the range core, likely due to a 20% larger effective fertility of women on the wave front. This fitness component is heritable on the wave front and not in the core, implying that this life-history trait evolves during range expansions.

So gene surfing in an expanding colonization phase can produce a genetic revolution whose effects will be felt for hundreds or thousands of years downstream in history.

We wonder if the same wave front demographics might explain some of the following population phenomena:

  • Large scale triumph of Norman male lineages following the conquest of England in 1066.
  • Selective expansion of Middle Eastern genes in Tennessee (including Cherokee families, Jewish male and female lines and Melungeons)
  • Relatedness among Jews and "Jewish diseases"
  • Diversity-within-uniformity of Polynesians
  • Population replacement of Old European (U, N) by Middle Eastern genes (T, J)  in Europe as a result of the Neolithic Agricultural Revolution

Many students of history are puzzled why old populations have the allele frequencies and heterozygosity clines they have. Genetic drift is only part of the answer. Gene surfing and selection in deep history are the rest of it.


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Interbreeding with Neanderthals and Denisovans Conferred Immunity to Diseases, Aided Spread of Humans in Asia, Europe

Friday, July 01, 2011

According to a professor of immunology and microbiology at Stanford University, humans were able to survive, spread and expand their populations once they left Africa because of immunities to disease they acquired from Neanderthals and Denisovans, who had lived in Europe and Asia already for hundreds of thousands of years.

A review of the new research appears in the online science magazine Discover under the date of June 20, 2011. The professor's name is Peter Parham.

Crux of the matter, according to Royal Society report

  • Parham began by taking a close look at a family of genes called  human leukocyte antigens (HLAs), which play a central role in our body’s immune responses. We are able to react to a wide array of diseases because our HLA genes are highly variable, each containing dozens of  alleles (forms of genes).
  • Our ancestors in Africa, however, would have had a small number of HLA alleles because they likely traveled in small bands and had little contact with other groups. Moreover, their HLAs would have only protected them against African diseases.
  • When Parham compared the HLAs of modern humans with those of Neanderthals and Denisovans, he noticed some overlaps. In particular, he found that HLA-C*0702, an allele common in Europeans and Asians but nonexistent in Africans, was also present in the Neanderthal genome. Similarly, HLA-A*11, which is found in modern Asians but not in Africans, popped up in Denisovan DNA.
  • Overall, about 50 percent of HLA Class I alleles in Europeans seemed to come from Neanderthals, 70 to 80 percent in East Asians from Denisovans, and 90 to 95 percent in Papuans from Denisovans, Parham said at a recent Royal Society meeting.
The latest revelation about the true nature of Neanderthals shows how fast current scientific and popular thinking is moving on the subject. Two years ago it was still debated whether "humans" could interbreed with Neanderthals, or whether Neanderthals were even a human species. Denisovans were only discovered in the last year.

DNA Consultants introduced its Neanderthal Index, a measure of affinity with archaic populations of Europe and the Middle East, one year ago this month.

Dr. Donald Yates says he is planning a visit to Vindija cave near Varazdin in Croatia this month to see firsthand the world's most important site for the discovery of Neanderthal bones and lifeways, dating to about 30,000 years ago.

Human history changed drastically with the 1974 Neanderthal discoveries at Vindija Cave. Photo Tomislav Kranjcic.


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Emerging Prehistory of Ethnic Groups

Thursday, June 16, 2011
As Revealed by Autosomal Markers

No scientific work, to our knowledge, has ever hazarded a guess on what the mutation rate for autosomal CODIS-type markers might be. Is it like mitochondrial DNA, which has a molecular clock measured in the thousands or tens of thousands of years, or is it like STRs on the Y chromosome, with its much shorter timeframe? The question is important if you are trying to extrapolate the history of the human race from today's autosomal population statistics.

From what we can see, putting on diachronistic lenses, the mutation rates for the DYS values on what are commonly called CODIS markers or the DNA profile for individuals are very small. The values appear to have been set from the beginning of mankind and to have mutated little in the past 100,000 years.

If this is true -- and it cannot be a very big "if" or we would have more diversity between populations than what is known -- the oldest markers are Sub-Saharan African and the newest European. Statistical divides bear out this reading of the human genetic record, as shown now in our updated map included with the DNA Fingerprint Plus.

We will try to make some notes on the individual markers in future posts.

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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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Validation Notes on Jewish Markers

Saturday, May 07, 2011

This posting will review some of the material we have previously made available about the science behind our three Jewish markers in the autosomal 18 Marker Ethnic Panel. First, it may be worthwhile to recount the chronology of our testing innovations in this area.

2006 - DNA Consultants introduces the DNA Fingerprint Test, one of the first simple autosomal ancestry tests based on population databases

2009 -Donald N. Yates, Ph.D., principal investigator, makes the discoveries in July that lay the foundation for the DNA Fingerprint Plus, rolled out in early September. The enhanced product includes simple autosomal markers for Native American, European, Jewish, Asian and African ancestry, based upon their frequencies of occurrence in these ethnicities.

2010 - Several important studies on Jewish genetics appear; DNA Consultants introduces Jewish DNA Test

2011 - DNA Consultants releases version 2.0 of its autosomal population database atDNA, marking the addition of the population Melungeon (n=40).

One of the first of the Jewish markers to be blogged about was Jewish II, characteristic of Ashkenazi Jews. Theodor Herzl, the nineteenth-century Austro-Hungarian Zionist thinker-organizer who helped inspire the founding of the State of Israel, is an example of a famous Ashkenazi Jew. There was another post titled Jewish Marker II Statistical Notes.

A post on Jewish I soon followed, together with a discussion about its European connections. There has been an ongoing discussion on the Jewish Forum on DNA Communities.

Jewish III has been the slowest to emerge. Its Middle Eastern nature has been explored and expanded upon in several threads on DNA Communities.

In the Fall of 2010, our project administrator tabulated results for more than 450 people who had ordered a Jewish Ancestry Test through our partner Jewish Voice. It was found that 99.97% showed at least one Jewish marker, that is, had some Jewish ancestry.  Some had all three markers while others had a combination of the three in some way.  The informal study indicated 74% of Jewish Ancestry Test takers had Jewish I, 30% had Jewish II and 82% Jewish III.



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Two New Autosomal DNA Population Studies: England, Ireland and Rural Europe

Thursday, April 14, 2011

Two reports in the European Journal of Human Genetics underline how specific autosomal DNA can be in revealing the geographical structure among populations. One uses genome-wide data from the Illumina Human Hap300 project to predict the village of origin of a person's four grandparents given European origins. The other used genotyping from 3,367 individuals from seven different European, mostly British Isles populations to lay bare the detailed population structure and linkage disequilibrium patterns of Ireland, England, Scotland and Wales.

Both studies have Colm O'Duschlaine of Trinity College, Dublin as their lead author and highlight how genotyping with autosomal DNA dominates genetics today (and DNA testing), eclipsing in many respects the older style of tests known as sex-linked haplotyping or lineage analysis, which focused on the male Y chromosome and female mitochondrial lines only.

Colm O'Duschlaine et al., "Genes Predict Village of Origin in Rural Europe," Eur. J of Hum. Genet. (2010) 18, 1269-1270. Abstract.

Colm O'Duschlaine et al., "Population Structure and Genome-Wide Patterns of Variation in Ireland and Britain," Eur. J of Hum. Genet. (2010) 18, 1248-1254. Abstract.


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Pre-historic Arabia Crossroads for Early Humans (and Neanderthal Hybrids?)

Saturday, February 05, 2011
The Southern Route “Out of Africa”: Evidence for an Early Expansion of Modern Humans into Arabia

Science 28 January 2011: Vol. 331 no. 6016 pp. 453-456 DOI: 10.1126/science.1199113

By Simon J. Armitage, Sabah A. Jasim, Anthony E. Marks, Adrian G. Parker, Vitaly I. Usik, and Hans-Peter Uerpmann

Abstract

The timing of the dispersal of anatomically modern humans (AMH) out of Africa is a fundamental question in human evolutionary studies. Existing data suggest a rapid coastal exodus via the Indian Ocean rim around 60,000 years ago. We present evidence from Jebel Faya, United Arab Emirates, demonstrating human presence in eastern Arabia during the last interglacial. The tool kit found at Jebel Faya has affinities to the late Middle Stone Age in northeast Africa, indicating that technological innovation was not necessary to facilitate migration into Arabia. Instead, we propose that low eustatic sea level and increased rainfall during the transition between marine isotope stages 6 and 5 allowed humans to populate Arabia. This evidence implies that AMH may have been present in South Asia before the Toba eruption (1).

First paragraph.
The deserts of the Arabian Peninsula have been thought to represent a major obstacle for human dispersal out of Africa. AMH were present in East Africa by about 200 thousand years ago (ka) (2). It is likely that the first migration of AMH out of Africa occurred immediately before or during the last interglacial [marine isotope stage (MIS) 5e] (3). During MIS 6, the Afro-Asiatic arid belt was hyperarid, restricting movements of human populations out of Africa. Finds from Qafzeh and Skhul in the Near East, dated between 119 ± 18 and 81 ± 13 thousand years ago (ka) (4, 5), suggest that AMH first migrated along the “Nile Corridor” and into the Levant. 



The location of Jebel Faya, United Arab Emirates, along with key sites mentioned in the text. The dashed line represents the –120-m paleoshoreline, indicating the maximum exposure of land during marine lowstands. Science.

Did Modern Humans Travel Out of Africa Via Arabia?

By Andrew Lawler

Science 28 January 2011: 387. [DOI:10.1126/science.331.6016.387]


JEBEL FAYA, UNITED ARAB EMIRATES—The barren desert and hills here seem wholly inhospitable, with sparse rain and sandy soil supporting only a few nomadic Bedouin. But things were different 125,000 years ago, when the desert was savanna, with plentiful water and game, and under the protection of a rock overhang, a group of hominids whiled away their time making stone tools. A Germanled team argues on page 453 that these tools were made by modern humans who may have crossed directly from Africa as part of a migration spreading across Europe, Asia, and Australia. Although most researchers agree that our species came out of Africa in one or more waves (see p. 392), those dates are more than 50,000 years earlier than most believe our ancestors left the continent.

The audacious claim by Simon Armitage of Royal Holloway, University of London, and colleagues is sparking interest and controversy. “This is really quite spectacular,” says archaeologist Michael Petraglia of the University of Oxford in the United Kingdom, who has previously argued that Homo sapiens left Africa before the massive eruption of an Indonesian volcano 74,000 years ago, a catastrophe thought to have left much of Asia unlivable for early humans (Science, 5 March 2010, p. 1187). “It breaks the back of the current consensus view.” But others, such as archaeologist Paul Mellars of the University of Cambridge in the United Kingdom, say that although the discovery is important and well dated, the conclusions are flawed. “I'm totally unpersuaded,” he says. “There's not a scrap of evidence here that these were made by modern humans, nor that they came from Africa.”

The debate centers on a collection of stone tools found here at Jebel Faya, a long limestone mountain an hour's drive from the bustling urban center of Sharjah and 55 kilometers from the Persian Gulf. A rock shelter indents the mountain's end, a few meters above a desolate plain where only camels graze today. The overhang is modest, but it has sheltered humans for millennia, say excavators Hans-Peter and Margarethe Uerpmann of the University of Tübingen in Germany. They began digging here in 2003, uncovering artifacts from the Iron, Bronze, and Neolithic periods before hitting material from the Middle Paleolithic era, roughly 300,000 to 30,000 years ago. Using single-grain optically stimulated luminescence, which measures how much time has passed since materials were last exposed to light, the team dated the oldest set of artifacts, including stone hand axes, blades, and scrapers, to about 125,000 years ago.

Arabia and its fierce deserts have long been seen more as obstacles than conduits to human migration, and most archaeology here has focused on historical times. Recent studies, however, show wetter periods such as one that began around 130,000 years ago. And a spate of findings in the past 25 years show that hominins were in the region during the Middle Paleolithic. Early H. sapiens skulls and tools from Skhul and Qafzeh caves in Israel are now dated to 100,000 to 130,000 years ago, for example.

Co-author Anthony Marks of Southern Methodist University in Dallas, Texas, says the combination of artifacts from Jebel Faya, such as two-sided blades and small hand axes, is remarkably similar to assemblages made during this period in East Africa, when our own species was the only known hominin on that continent. Other hominins, such as the Neandertals who populated Europe and north Asia, did not use this combination of tools and were not likely to have been in Arabia, he says. That makes the African origin likely “by process of elimination.”

Marks says the tools don't resemble those from Israel or the Aterian tools from the same era in North Africa (Science, 7 January, p. 20). He suggests that H. sapiens may have left Africa in different waves, with the Arabian tools representing a migration launched from East Africa.

Petraglia agrees that it's likely that H. sapiens made the tools and that they came from Africa. “This is out of the habitat range of Neandertals,” he notes. “So they make a really strong and plausible argument.” The team believes that these early modern humans may have even pushed on across the Persian Gulf, perhaps to India, Indonesia, and eventually Australia. Petraglia claims evidence of early H. sapiens in India both before and after the Indonesian eruption, though others dispute that assertion.

Mellars, in contrast, sees no evidence that the Jebel Faya artifacts are of an East African style. He says one of the bifacials is stout rather than narrow like those common in Africa and adds that the authors have not ruled out Neandertals and even H. erectus as the toolmakers. “Everything hinges on whether that material is explicitly African—and I don't see that.”

Other researchers are enthusiastic about the Jebel Faya discovery but cautious about the conclusions. Archaeologist Mark Beech, a visiting fellow at the University of York in the United Kingdom who has worked extensively in the United Arab Emirates, praises the paper but adds: “One site does not confirm the out-of-Africa-via-Arabia hypothesis.”

Hans-Peter Uerpmann agrees, saying that fossil bones are needed “before we can be absolutely sure” that the tools were made by H. sapiens. Other researchers are hot on the trail: Petraglia leaves this month to continue work in Saudi Arabia, and other archaeologists plan to comb Arabian caves and sands for signs that our ancestors passed this way.


We've been saying as much all along.

See our blog post on Prehistoric Arabia.




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Royal and Imperial Haplogroups

Monday, January 10, 2011

A blogger on Eupedia's genetics forum has deduced the haplogroups of many European kings and queens from living descendants who have been tested. It has long been known that mtDNA haplogroup H dominated the lines of Europe's aristocracies, while Y chromosomal R1b was the most common male lineage. Prince Phillip exhibits the stereotypical genes in this regard. More interesting than the royal personages listed are those that haven't yet made the list, like Elizabeth I or Charlemagne. It would be interesting to know what the mitochondrial DNA was of Elizabeth's mother Anne Boleyn or what Charlemagne's male lineage was.

One fascinating observation of the blogger is, "All kings of France supposedly belonged to haplogroup G2a3 (Y-DNA)." G2a makes up 5 to 10% of Mediterranean Europe but is rare in Northern Europe. It is believed to have originated with metalworking peoples from the Caucasus or Anatolia who accompanied the R1b-dominant Indo-Europeans on their conquest of Europe in the 3rd millennium BCE.

See "Geographic Spread and Ethnic Origins of European Haplogroups - Eupedia."

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