Native American Haplogroup C Update – Progress!!

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Haplogroup C-P39 is the Native American branch of Y DNA paternal haplogroup C.  It’s rare as chicken’s teeth.  Most Native American males fall into haplogroup Q, making our haplogroup C-P39 project participants quite unusual and unique.  So are the tools needed to identify branches on the Native American haplogroup C tree.

Last week, Family Tree DNA added a group of 9 SNPs found in haplogroup C to their product offering.  This was done without an announcement and without any fanfare – but it’s really important.  Without the ongoing support of Family Tree DNA, we wouldn’t have the Big Y test, nor the refining SNP tests that can be added to the Big Y in areas where the results are ambiguous.  Individuals who don’t want to purchase the Big Y can purchase these haplogroup defining SNPs individually as well.

The Native defining SNP for haplogroup C is P39.  People who test positive for C-P39 will then want to test Z30750 and Z30764.

  • Z30503
  • Z30601
  • FGC21495
  • Z30750
  • Z30764
  • PF3239
  • Z30729
  • FGC263
  • FGC31712

However, because haplogroup C-P39 is so rare – and to date – we have found several new SNPs in every man who has taken the Big Y test – and because those new, never before discovered SNPs are the bread crumbs that we need to follow to discover how our ancestors settled and dispersed across the Americas – we strong recommend the Big Y test at Family Tree DNA for all C-P39 men.  The Big Y test doesn’t just look at known SNP locations, it scans the entire Y chromosome for mutations.  Therefore, it’s both a genealogy and a research tool.

To that end, we very much want to fund this testing from the project coffers where necessary to advance our understanding.  Just to whet your appetite, we have participants now across Canada and also in the American Southwest.  We desperately want these men to take the Big Y test so we can get a much clearer picture of how they are related, and how many mutations they have individually – but don’t share – because that is how we estimate when they last shared a common ancestor.  In other words, the mutations build the branches of the tree.

This week, we’ve ordered another new C-P39 Big Y test.  If you are C-P39 – Native American haplogroup C – and have not yet taken the Big Y – please consider doing so.

If you are Native American and haplogroup C – please join the C-P39 and the American Indian projects.  You can do so from your home page at Family Tree DNA by clicking on the “Projects” tab at the upper left of your personal page, then on “join projects.”  You can search for the word “Indian” in the project list to find the American Indian project and scrolling down to the Y haplogroup projects and clicking on C will take you to the C-P39 link.

project join

If you can contribute to funding these Big Y tests, please do – even small amounts help.  The link to donate directly to the C-P39 project is: https://www.familytreedna.com/group-general-fund-contribution.aspx?g=Y-DNAC-P39

Each individual who takes the Big Y test is also encouraged to upgrade to 111 markers.  We need as much information as we can get.

Marie Rundquist and I are co-administrators of the C-P39 project, and she wrote the following verbiage in honor of the 5 year anniversary of the first discovery of what is now C-P39 in the Native Community.  We, as a community, have come a very long way in just 5 years!

It was in 2010, five years ago, when Keith Doucet first tested for the C P39 Y DNA (formerly C3b) Native American DNA type in the Amerindian Ancestry out of Acadia Family Tree DNA study — with numbers of Doucets (and Doucettes!) having the same, Native American, C P39 Y DNA result.  It’s amazing when you think of our journey and how much this research has benefitted our knowledge of our history in North America!

Who can ever forget Keith Doucet’s discovery? http://www.familyheritageresearchcommunity.org/doucet_dna.html

Or Emile Broome’s Y DNA discovery, also from 2010? http://www.familyheritageresearchcommunity.org/broome_dna.html

…and the subsequent discoveries of related Doucets and Doucettes and other project members from all regions of the US and Canada who tested in our project and whose results showed the same Native American C P39 Y DNA haplogroup type?

There is great similarity among the DNA test results for our C P39 Y DNA candidates despite differences in geographic locations and surnames, with testers from across the United States, including the American Southwest, the North East, the South, and Canada compared.  Initial Big Y DNA test results for project members have shown remarkable similarity as well.  Additional Big Y test results for tests underway and the availability of 9 new SNPs for our project members help us discover whether this trend is amplified by the additional tests or if we (the C P39 Y DNA project) can distinguish downstream uniqueness among our participants. The C P39 Y DNA test has received the generous support of its members, Family Tree DNA leadership and scientists, product managers, and volunteer administrators in establishing our superior C P39 Y DNA baseline and we are grateful for your support.

Visit the C P39 Y DNA project site to learn more. https://www.familytreedna.com/public/ydna_C-P39/

Thank you to our project members for your continued participation!  And thank you to Family Tree DNA for their ongoing dedication, research and support.  Collectively, we discover more of our history every day!

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Some Native Americans Had Oceanic Ancestors

This week has seen a flurry of new scientific and news articles.  What has been causing such a stir?  It appears that Australian or more accurately, Australo-Melanese DNA has been found in South America’s Native American population. In addition, it has also been found in Aleutian Islanders off the coast of Alaska.  In case you aren’t aware, that’s about 8,500 miles as the crow flies.  That’s one tired crow.  As the person paddles or walks along the shoreline, it’s even further, probably about 12,000 miles.

Aleutians to Brazil

Whatever the story, it was quite a journey and it certainly wasn’t all over flat land.

This isn’t the first inkling we’ve had.  Just a couple weeks ago, it was revealed that the Botocudo remains from Brazil were Polynesian and not admixed with either Native, European or African.  This admixture was first discovered via mitochondrial DNA, but full genome sequencing confirmed their ancestry and added the twist that they were not admixed – an extremely unexpected finding.  This is admittedly a bit confusing, because it implies that there were new Polynesian arrivals in the 1600s or 1700s.

Unlikely as it seems, it obviously happened, so we set that aside as relatively contemporary.

The findings in the papers just released are anything but contemporary.

The First Article

The first article in Science, “Genomic evidence for the Pleistocene and recent population history of Native Americans” by Raghaven et al published this week provides the following summary (bolding is mine):

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.

This article in EurekAlert and a second one here discuss the Science paper.

Raghaven 2015

Migration map from the Raghaven paper.

The paper included the gene flow and population migration map, above, along with dates.

The scientists sequenced the DNA of 31 living individuals from the Americas, Siberia and Oceana as follows:

Siberian:

  • Altai – 2
  • Buryat – 2
  • Ket – 2
  • Kiryak – 2
  • Sakha – 2
  • Siberian Yupik – 2

North American Native:

  • Tsimshian (number not stated, but by subtraction, it’s 1)

Southern North American, Central and South American Native:

  • Pima – 1
  • Huichol -1
  • Aymara – 1
  • Yakpa – 1

Oceana:

  • Papuan – 14

The researchers also state that they utilized 17 specimens from relict groups such as the Pericues from Mexico and Fuego-Patagonians from the southernmost tip of South America.  They also sequenced two pre-Columbian mummies from the Sierra Tarahumara in northern Mexico.  In total, 23 ancient samples from the Americas were utilized.

They then compared these results with a reference panel of 3053 individuals from 169 populations which included the ancient Saqqaq Greenland individual at 400 years of age as well as the Anzick child from Montana from about 12,500 years ago and the Mal’ta child from Siberia at 24,000 years of age.

Not surprisingly, all of the contemporary samples with the exception of the Tsimshian genome showed recent western Eurasian admixture.

As expected, the results confirm that the Yupik and Koryak are the closest Eurasian population to the Americas.  They indicate that there is a “clean split” between the Native American population and the Koryak about 20,000 years ago.

They found that “Athabascans and Anzick-1, but not the Greenlandis Inuit and Saqqaq belong to the same initial migration wave that gave rise to present-day Amerindians from southern North America and Central and South America, and that this migration likely followed a coastal route, given our current understanding of the glacial geological and paleoenvironmental parameters of the Late Pleistocene.”

Evidence of gene flow between the two groups was also found, meaning between the Athabascans and the Inuit.  Additionally, they found evidence of post-split gene flow between Siberians and Native Americans which seems to have stopped about 12,000 years ago, which meshes with the time that the Beringia land bridge was flooded by rising seas, cutting off land access between the two land masses.

They state that the results support all Native migration from Siberia, contradicting claims of an early migration from Europe.

The researchers then studied the Karitiana people of South America and determined that the two groups, Athabascans and Karitiana diverged about 13,000 years ago, probably not in current day Alaska, but in lower North America.  This makes sense, because the Clovis Anzick child, found in Montana, most closely matches people in South America.

By the Clovis period of about 12,500 years ago, the Native American population had already split into two branches, the northern and southern, with the northern including Athabascan and other groups such as the Chippewa, Cree and Ojibwa.  The Southern group included people from southern North America and Central and South America.

Interestingly, while admixture with the Inuit was found with the Athabascan, Inuit admixture was not found among the Cree, Ojibwa and Chippewa.  The researchers suggest that this may be why the southern branch, such as the Karitiana are genetically closer to the northern Amerindians located further east than to northwest coast Amerindians and Athabascans.

Finally, we get to the Australian part.  The researchers when trying to sort through the “who is closer to whom” puzzle found unexpected results.  They found that some Native American populations including Aleutian Islanders, Surui (Brazil) and Athabascans are closer to Australo-Melanesians compared to other Native Americans, such as Ojibwa, Cree and Algonquian and South American Purepecha (Mexico), Arhuaco (Colombia) and Wayuu (Colombia, Venezuela).  In fact, the Surui are one of the closest populations to East Asians and Australo-Melanese, the latter including Papuans, non-Papuan Melanesians, Solomon Islanders and hunter-gatherers such as Aeta. The researchers acknowledge these are weak trends, but they are nonetheless consistently present.

Dr. David Reich, from Harvard, a co-author of another paper, also published this past week, says that 2% of the DNA of Amazonians is from Oceana.  If that is consistent, it speaks to a founder population in isolation, such that the 2% just keeps getting passed around in the isolated population, never being diluted by outside DNA.  I would suggest that is not a weak signal.

The researchers suggest that the variance in the strength of this Oceanic signal suggests that the introduction of the Australo-Melanese occurred after the initial peopling of the Americas.  The ancient samples cluster with the Native American groups and do not show the Oceanic markers and show no evidence of gene flow from Oceana.

The researchers also included cranial morphology analysis, which I am omitting since cranial morphology seems to have led researchers astray in the past, specifically in the case of Kennewick man.

One of the reasons cranial morphology is such a hotly debated topic is because of the very high degree of cranial variance found in early skeletal remains.  One of the theories evolving from the cranial differences involving the populating of the Americans has been that the Australo-Melanese were part of a separate and earlier migration that gave rise to the earliest Americans who were then later replaced by the Asian ancestors of current day Native Americans.  If this were the case, then the now-extinct Fuego-Patagonains samples from the location furthest south on the South American land mass should have included DNA from Oceana, but it didn’t.

The Second Article

A second article published this week, titled “’Ghost population’ hints at long lost migration to the Americas” by Ellen Callaway discusses similar findings, presented in a draft letter to Nature titled “Genetic evidence for two founding populations of the Americas” by Skoglund et al.  This second group discovers the same artifact Australo-Melanesian DNA in Native American populations but suggests that it may be from the original migration and settlement event or that there may have been two distinct founding populations that settled at the same time or that there were two founding events.

EurekAlert discusses the article as well.

It’s good to have confirmation and agreement between the two labs who happened across these results independently that the Australo-Melanesian DNA is present in some Native populations today.

Their interpretations and theories about how this Oceanic DNA arrived in some of the Native populations vary a bit, but if you read the details, it’s really not quite as different as it first appears from the headlines.  Neither group claims to know for sure, and both discuss possibilities.

Questions remain.  For example, if the founding group was small, why, then, don’t all of the Native people and populations have at least some Oceanic markers?  The Anzick Child from 12,500 years ago does not.  He is most closely related to the tribes in South America, where the Oceanic markers appear with the highest frequencies.

In the Harvard study, the scientists fully genome sequenced 63 individuals without discernable evidence of European or African ancestors in 21 Native American populations, restricting their study to individuals from Central and South America that have the strongest evidence of being entirely derived from a homogenous First American ancestral population.

Their results show that the two Amazonian groups, Surui and Karitians are closest to the “Australasian populations, the Onge from the Andaman Island in the Bay of Bengal (a so-called ‘Negrito’ group), New Guineans, Papuans and indigenous Australians.”  Within those groups, the Australasian populations are the only outliers – meaning no Africans, Europeans or East Asian DNA found in the Native American people.

When repeating these tests, utilizing blood instead of saliva, a third group was shown to also carry these Oceanic markers – the Xavante, a population from the Brazilian plateau that speaks a language of the Ge group that is different from the Tupi language group spoke by the Karitians and Surui.

Skoglund 2015-2

The closest populations that these Native people matched in Oceana, shown above on the map from the draft Skoglund letter, were, in order, New Guineans, Papuans and Andamanese.  The researchers further state that populations from west of the Andes or north of the Panama isthmus show no significant evidence of an affinity to the Onge from the Andaman Islands with the exception of the Cabecar (Costa Rica).

That’s a very surprising finding, given that one would expect more admixture on the west, which is the side of the continent where the migration occurred.

The researchers then compared the results with other individuals, such as Mal’ta child who is known to have contributed DNA to the Native people today, and found no correlation with Oceanic DNA.  Therefore, they surmised that the Oceanic admixture cannot be explained by a previously known admixture event.

They propose that a mystery population they have labeled as “Population Y” (after Ypykuera which means ancestor in the Tupi language family) contributed the Australasian lineage to the First Americans and that is was already mixed into the lineage by the time it arrived in Brazil.

According to their work, Population Y may itself have been admixed, and the 2% of Oceanic DNA found in the Brazilian Natives may be an artifact of between 2 and 85% of the DNA of the Surui, Karitiana and Xavante that may have come from Population Y.  They mention that this result is striking in that the majority of the craniums that are more Oceanic in Nature than Asiatic, as would be expected from people who migrated from Siberia, are found in Brazil.

They conclude that the variance in the presence or absence of DNA in Native people and remains, and the differing percentages argue for more than one migration event and that “the genetic ancestry of Native Americans from Central and South America cannot be due to a single pulse of migration south of the Late Pleistocene ice sheets from a homogenous source population, and instead must reflect at least two streams of migration or alternatively a long drawn out period of gene flow from a structured Beringian or Northeast Asian source.”

Perhaps even more interesting is the following statement:

“The arrival of population Y ancestry in the Americas must in any scenario have been ancient: while Population Y shows a distant genetic affinity to Andamanese, Australian and New Guinean populations, it is not particularly closely related to any of them, suggesting that the source of population Y in Eurasia no longer exists.”

They further state they find no admixture indication that would suggest that Population Y arrived in the last few thousand years.

So, it appears that perhaps the Neanderthals and Denisovans were not the only people who were our ancestors, but no longer exist as a separate people, only as an admixed part of us today.  We are their legacy.

The Take Away

When I did the Anzick extractions, we had hints that something of this sort might have been occurring.  For example, I found surprising instances of haplogroup M, which is neither European, African nor Native American, so far as we know today.  This may have been a foreshadowing of this Oceanic admixture.  It may also be a mitochondrial artifact.  Time will tell.  Perhaps haplogroup M will turn out to be Native by virtue of being Oceanic and admixed thousands of years ago.  There is still a great deal to learn.  Regardless of how these haplogroups and Oceanic DNA arrived in Brazil in South America and in the Aleutian Islands off of Alaska, one thing is for sure, it did.

We know that the Oceanic DNA found in the Brazilian people studied for these articles is not contemporary and is ancient.  This means that it is not related to the Oceanic DNA found in the Botocudo people, who, by the way, also sport mitochondrial haplogroups that are within the range of Native people, meaning haplogroup B, but have not been found in other Native people.  Specifically, haplogroups B4a1a1 and B4a1a1a.  Additionally, there are other B4a1a, B4a1b and B4a1b1 results found in the Anzick extract which could also be Oceanic.  You can see all of the potential and confirmed Native American mitochondrial DNA results in my article “Native American Mitochondrial Haplogroups” that I update regularly.

We don’t know how or when the Botocudo arrived, but the when has been narrowed to the 1600s or 1700s.  We don’t know how or when the Oceanic DNA in the Brazilian people arrived either, but the when was ancient.  This means that Oceanic DNA has arrived in South America at least twice and is found among the Native peoples both times.

We know that some Native groups have some Oceanic admixture, and others seem to have none, in particular the Northern split group that became the Cree, Ojibwa, Algonquian, and Chippewa.

We know that the Brazilian Native groups are most closely related to Oceanic groups, but that the first paper also found Oceanic admixture in the Aleutian Islands.  The second paper focused on the Central and South American tribes.

We know that the eastern American tribes, specifically the Algonquian tribes are closely related to the South Americans, but they don’t share the Oceanic DNA and neither do the mid-continent tribes like the Cree, Ojibwa and Chippewa.  The only Paleolithic skeleton that has been sequenced, Anzick, from 12,500 years ago in Montana also does not carry the Oceanic signature.

In my opinion, the disparity between who does and does not carry the Oceanic signature suggests that the source of the Oceanic DNA in the Native population could not have been a member of the first party to exit out of Beringia and settle in what is now the Americas.  Given that this had to be a small party, all of the individuals would have been thoroughly admixed with each other’s ancestral DNA within just a couple of generations.  It would have been impossible for one ancestor’s DNA to only be found in some people.  To me, this argues for one of two scenarios.

First, a second immigration wave that joined the first wave but did not admix with some groups that might have already split off from the original group such as the Anzick/Montana group.

Second, multiple Oceanic immigration events.  We still have to consider the possibility that there were multiple events that introduced Oceanic DNA into the Native population.  In other words, perhaps the Aleutian Islands Oceanic DNA is not from the same migration event as the Brazilian DNA which we know is not from the same event as the Botocudo.  I would very much like to see the Oceanic DNA appear in a migration path of people, not just in one place and then the other.  We need to connect the dots.

What this new information does is to rule out the possibility that there truly was only one wave of migration – one group of people who settled the Americas at one time.  More likely, at least until the land bridge submerged, is that there were multiple small groups that exited Beringia over the 8,000 or so years it was inhabitable.  Maybe one of those groups included people from Oceana.  Someplace, sometime, as unlikely as it seems, it happened.

The amazing thing is that it’s more than 10,000 miles from Australia to the Aleutian Islands, directly across the Pacific.  Early adventurers would have likely followed a coastal route to be sustainable, which would have been significantly longer.  The fact that they survived and sent their DNA on a long adventure from Australia to Alaska to South America – and it’s still present today is absolutely amazing.

Australia to Aleutians

We know we still have a lot to learn and this is the tip of a very exciting iceberg.  As more contemporary and ancient Native people have their full genomes sequenced, we’ll learn more answers.  The answer is in the DNA.  We just have to sequence enough of it and learn how to understand the message being delivered.

DNA Testing Strategy for Adoptees and People with Uncertain Parentage

Adoptees aren’t the only people who don’t know who their parents are.  There are many people who don’t know the identity of one of their two parents…and it’s not always the father.  Just this week, I had someone who needed to determine which of two sisters was her mother.  Still, the “who’s your Daddy” crowd, aside from adoptees, is by far the largest.

The DNA testing strategy for both of these groups of people is the same, with slight modifications for male or female. Let’s take a look.

Males have three kinds of DNA that can be tested and then compared to other participants’ results.  The tests for these three kinds of DNA provide different kinds of information which is useful in different ways.  For example, Y DNA testing may give you a surname, if you’re a male, but the other two types of tests can’t do that, at least not directly.

Females only have two of those kinds of DNA that can be tested.  Females don’t have a Y chromosome, which is what makes males male genetically.

adopted pedigree

If you look at this pedigree chart, you can see that the Y chromosome, in blue, is passed from the father to the son, but not to daughters.  It’s passed intact, meaning there is no admixture from the mother, who doesn’t have a Y chromosome, because she is female.  The Y chromosome is what makes males male.

The second type of DNA testing is mitochondrial, represented by the red circles.  It is passed from the mother to all of her children, of both genders, intact – meaning her mitochondrial DNA is not admixed with the mtDNA of the father.  Woman pass their mtDNA on to their children, men don’t.

Therefore when you test either the Y or the mtDNA, you get a direct line view right down that branch of the family tree – and only that direct line on that branch of the tree.  Since there is no admixture from spouses in any generation, you will match someone exactly or closely (allowing for an occasional mutation or two) from generations ago.  Now, that’s the good and the bad news – and where genealogical sleuthing comes into play.

On the chart above, the third kind of DNA testing, autosomal DNA, tests your DNA from all of your ancestors, meaning all of those boxes with no color, not just the blue and red ones, but it does include the blue and red ancestors too.  However, autosomal DNA (unlike Y and mtDNA) is diluted by half in each generation, because you get half of your autosomal DNA from each parent, so only half of the parents DNA gets passed on to each child.

Let’s look at how these three kinds of DNA can help you identify your family members.

Y DNA

Since the Y DNA typically follows the paternal surname, it can be extremely helpful for males who are searching for their genetic surname.  For example, if your biological father’s surname is Estes, assuming he is not himself adopted or the product of a nonpaternal event (NPE) which I like to refer to as undocumented adoptions, his DNA will match that of the Estes ancestral line.  So, if you’re a male, an extremely important test will be the Y DNA test from Family Tree DNA, the only testing company to offer this test.

Let’s say that you have no idea who your bio-father is, but when your results come back you see a preponderance of Estes men whom you match, as well as your highest and closest matches being Estes.

By highest, I mean on the highest panel you tested – in this case 111 markers.  And by closest, I mean with the smallest genetic distance, or number of mutations difference.  On the chart below, this person matches only Estes males at 111 markers, and one with only 1 mutation difference (Genetic Distance.)  Please noted that I’ve redacted first names.

Hint for Mr. Hilbert, below – there is a really good chance that you’re genetically Estes on the direct paternal side – that blue line.

Estes match ex

The next step will be to see which Estes line you match the most closely and begin to work from there genealogically.  In this case, that would be the first match with only one difference.  Does your match have a tree online?  In this case, they do – as noted by the pedigree chart icon.  Contact this person.  Where did their ancestors live?  Where did their descendants move to?  Where were you born?  How do the dots connect?

The good news is, looking at their DNA results, you can see that your closest match has also tested autosomally, indicated by the FF icon, so you can check to see if you also match them on the Family Finder test utilizing the Advanced Matching Tool.  That will help determine how close or distantly related you are to the tester themselves.  This gives you an idea how far back in their tree you would have to look for a common ancestor.

Another benefit is that your haplogroup identifies your deep ancestral clan, for lack of a better word.  In other words, you’ll know if your paternal ancestor was European, Asian, Native American or African – and that can be a hugely important piece of information.  Contrary to what seems intuitive, the ethnicity of your paternal (or any) ancestor is not always what seems evident by looking in the mirror today.

Y DNA – What to order:  From Family Tree DNA, the 111 marker Y DNA test.  This is for males only.  Family Tree DNA is the only testing company to provide this testing.  Can you order fewer markers, like 37 or 67?  Yes, but it won’t provide you with as much information or resolution as ordering 111 markers.  You can upgrade later, but you’ll curse yourself for that second wait.

FTDNA Y

Mitochondrial DNA

Males and females both can test for mitochondrial DNA.  Matches point to a common ancestor directly up the matrilineal side of your family – your mother, her mother, her mother – those red circles on the chart.  These matches are more difficult to work with genealogically, because the surnames change in every generation.  Occasionally, you’ll see a common “most distant ancestor” between mitochondrial DNA matches.

Your mitochondrial DNA is compared at three levels, but the most accurate and detailed is the full sequence level which tests all 16,569 locations on your mitochondria.  The series of mutations that you have forms a genetic signature, which is then compared to others.  The people you match the most closely at the full sequence level are the people with whom you are most likely to be genealogically related to a relevant timeframe.

You also receive your haplogroup designation with mitochondrial DNA testing which will place you within an ethnic group, and may also provide more assistance in terms of where your ancestors may have come from.  For example, if your haplogroup is European and you match only people from Norway….that’s a really big hint.

Using the Advanced Matching Tool, you can also compare your results to mitochondrial matches who have taken the autosomal Family Finder test to see if you happen to match on both tests.  Again, that’s not a guarantee you’re a close relative on the mitochondrial side, but it’s a darned good hint and a place to begin your research.

Mitochondrial DNA – What to Order:  From Family Tree DNA, the mitochondrial full sequence test.  This is for males and females both.  Family Tree DNA is the only company that provides this testing.

FTDNA mtDNA

Autosomal DNA

Y and mitochondrial DNA tests one line, and only one line – and shoots like a laser beam right down that line, telling you about the recent and deep history of that particular lineage.  In other words, those tests are deep and not wide.  They can tell you nothing about any of your other ancestors – the ones with no color on the pedigree chart diagram – because you don’t inherit either Y or mtDNA from those ancestors.

Autosomal DNA, on the other hand tends to be wide but not deep.  By this I mean that autosomal DNA shows you matches to ancestors on all of your lines – but only detects relationships back a few generations.  Since each child in each generation received half of their DNA from each parent – in essence, the DNA of each ancestor is cut in half (roughly) in each generation.  Therefore, you carry 50% of the DNA of your parents, approximately 25% of each grandparent, 12.5% of the DNA of each great-grandparent, and so forth.  By the time you’re back to the 4th great-grandparents, you carry only about 1% of the DNA or each of your 64 direct ancestors in that generation.

What this means is that the DNA testing can locate common segments between you and your genetic cousins that are the same, and if you share the same ancestors,  you can prove that this DNA in fact comes from a specific ancestor.  The more closely you are related, the more DNA you will share.

Another benefit that autosomal testing provides is an ethnicity prediction.  Are these predictions 100% accurate?  Absolutely not!  Are they generally good in terms of identifying the four major ethnic groups; African, European, Asian and Native American?  Yes, so long at the DNA amounts you carry of those groups aren’t tiny.  So you’ll learn your major ethnicity groups.  You never know, there may be a surprise waiting for you.

FTDNA myOrigins

The three vendors who provide autosomal DNA testing and matching all provide ethnicity estimates as well, and they aren’t going to agree 100%.  That’s the good news and often makes things even more interesting.  The screen shot below is the same person at Ancestry as the person above at Family Tree DNA.

Ancestry ethnicity

If you’re very lucky, you’ll test and find an immediate close match – maybe even a parent, sibling or half-sibling.  It does happen, but don’t count on it.  I don’t want you to be disappointed when it doesn’t happen.  Just remember, after you test, your DNA is fishing for you 24X7, every single hour of every single day.

If you’re lucky, you may find a close relative, like an uncle or first cousin.  You share a common grandparent with a first cousin, and that’s pretty easy to narrow down.  Here’s an example of matching from Family Tree DNA.

FTDNA close match

If you’re less lucky, you’ll match distantly with many people, but by using their trees, you’ll be able to find common ancestors and then work your way forward, based on how closely you match these individuals, to the current.

Is that a sometimes long process?  Yes.  Can it be done?  Absolutely.

If you are one of the “lottery winner” lucky ones, you’ll have a close match and you won’t need to do the in-depth genealogy sleuthing.  If you are aren’t quite as lucky, there are people and resources to help you, along with educational resources.  www.dnaadoption.com provides tools and education to teach you how to utilize autosomal DNA tools and results.

Of course, you won’t know how lucky or unlucky you are unless you test.  Your answer, or pieces of your answer, may be waiting for you.

Unlike Y and mtDNA testing, Family Tree DNA is not the only company to provide autosomal of testing, although they do provide autosomal DNA testing through their Family Finder test.

There are two additional companies that provide this type of testing as well, 23andMe and Ancestry.com.  You should absolutely test with all three companies, or make sure your results are in all three data bases.  That way you are fishing in all of the available ponds directly.

If you have to choose between testing companies and only utilize one, it would be a very difficult choice.  All three have pros and cons.  I wrote about that here.  The only thing I would add to what I had to say in the comparison article is that Family Tree DNA is the only one of the three that is not trying to obtain your consent to sell your DNA out the back door to other entities.  They don’t sell your DNA, period.  You don’t have to grant that consent to either Ancestry or 23andMe, but be careful not to click on anything you don’t fully understand.

Family Tree DNA accepts transfers of autosomal data into their data base from Ancestry.  They also accept transfers from 23andMe if you tested before December of 2013 when 23andMe reduced the number of locations they test on their V4 chip

Autosomal DNA:  What to Order

Ancestry.com’s DNA product at http://www.ancestry.com – they only have one and it’s an autosomal DNA test

23andMe’s DNA product at http://www.23andMe.com – they only have one and it’s an autosomal DNA test

Family Tree DNA – either transfer your data from Ancestry or 23andMe (if you tested before December 2013), or order the Family Finder test. My personal preference is to simply test at Family Tree DNA to eliminate any possibility of a file transfer issue.

FTDNA FF

Third Party Autosomal Tools

The last part of your testing strategy will be to utilize various third party tools to help you find matches, evaluate and analyze results.

GedMatch

At GedMatch, the first thing you’ll need to do is to download your raw autosomal data file from either Ancestry or Family Tree DNA and upload the file to www.gedmatch.com.  You can also download your results from 23andMe, but I prefer to utilize the files from either of the other two vendors, given a choice, because they cover about 200,000 additional DNA locations that 23andMe does not.

Ancestry.com provides you with no tools to do comparisons between your DNA and your matches.  In other words, no chromosome browser or even information like how much DNA you share.  I wrote about that extensively in this article, and I don’t want to belabor the point here, other than to say that GedMatch levels the playing field and allows you to eliminate any of the artificial barriers put in place by the vendors.  Jim Bartlett just wrote a great article about the various reasons why you’d want to upload your data to Gedmatch.

GedMatch provides you with many tools to show to whom you are related, and how.  Used in conjunction with pedigree charts, it is an invaluable tool.  Now, if we could just convince everyone to upload their files.  Obviously, not everyone does, so you’ll still need to work with your matches individually at each of the vendors and at GedMatch.

GedMatch is funded by donations or an inexpensive monthly subscription for the more advanced tools.

DNAGEDCOM.com

Another donation based site is http://www.dnagedcom.com which offers you a wide range of analytical tools to assist with making sense of your matches and their trees.  DNAGEDCOM works closely with the adoption community and focuses on the types of solutions they need to solve their unique types of genealogy puzzles.  While everyone else is starting in the present and working their way back, adoptees are starting with the older generations and piecing them together to come forward to present.  Their tools aren’t just for adoptees though.  Tools such as the Autosomal DNA Segment Analyzer are great for anyone.  Visit the site and take a look.

Third Party Y and Mitochondrial Tools – YSearch and MitoSearch

Both www.ysearch.org and www.mitosearch.org are free data bases maintained separately from Family Tree DNA, but as a courtesy by Family Tree DNA.  Ysearch shows only a maximum of 100 markers for Y DNA and Mitosearch doesn’t show the coding region of the mitochondrial DNA, but they do allow users to provide their actual marker values for direct comparison, in addition to other tools.

Furthermore, some people who tested at other firms, when other companies were doing Y and mtDNA testing, have entered their results here, so you may match with people who aren’t matches at Family Tree DNA.  Those other data bases no longer exist, so Ysearch or Mitosearch is the only place you have a prayer of matching anyone who tested elsewhere.

You can also adjust the match threshold so that you can see more distant matches than at Family Tree DNA.  You can download your results to Ysearch and Mitosearch from the bottom of your Family Tree DNA matches page.

Mitosearch upload

Answer the questions at Mito or Ysearch, and then click “Save Information.”  When you receive the “500” message that an error has occurred at the end of the process, simply close the window.  Your data has been added to the data base and you can obtain your ID number by simply going back to your match page at Family Tree DNA and clicking on the “Upload to Ysearch” or Mitosearch link again on the bottom of your matches page.  At that point, your Y or mitosearch ID will be displayed.  Just click on “Search for Genetic Matches” to continue matching.

Get Going!

Now that you have a plan, place your orders and in another 6 to 8 weeks, you’ll either solve the quandry or at least begin to answer your questions.  Twenty years ago you couldn’t have begun to unravel your parentage using DNA.  Now, it’s commonplace.  Your adventure starts today.

Oh, and congratulations, you’ve just become a DNA detective!

I wish you success on your journey – answers, cousins, siblings and most importantly, your genetic family.  Hopefully, one day it will be you writing to me telling me how wonderful it was to meet your genetic family for the first time, and what an amazing experience it was to look across the dinner table and see someone who looks like you.

Yamnaya, Light Skinned, Brown Eyed….Ancestors???

Late last fall, I reported that scientists had discovered a European ghost population.  This group of people then referred to as the ANE, Ancient Northern Europeans, was a previously unknown population from the north that had mixed into the known European populations, the Hunter-Gatherers and the farmers from the Middle East, the Neolithic.

That discovery came as a result of the full genome sequencing of a few ancient specimens, including one from the Altai.

Recently, several papers have been published as a result of ongoing sequencing efforts of another 200 or so ancient specimens.  As a result, scientists now believe that this ghost population has been identified as the Yamnaya and that they began a mass migration in different directions, including Europe, about 5,000 years ago.  Along with their light skin and brown eyes, they brought along with them their gene(s) for lactose tolerance.  So, if you have European heritage and are lactose tolerant, then maybe you can thank your Yamnaya ancestors.

1.Haak et al. http://doi.org/z9d (2015) from Feb. 18, 2015 “Steppe migration rekindles debate on language origin” by Ellen Callaway

1.Haak et al. http://doi.org/z9d (2015) from Feb. 18, 2015 “Steppe migration rekindles debate on language origin” by Ellen Callaway

For those of us who avidly follow these types of discoveries, this is not only amazing, it’s wonderful news.  It helps to continue to explain how and why some haplogroups are found in the Native American population and in the Northern European population as well.  For example, haplogroup Q is found in both places – not exact duplicates, but certainly close enough for us to know they were at one time related.  It also explains how people from Germany, for example, are showing small percentages of Native American ancestry.  Their common ancestors were indeed from central Asia, thousands of years ago, and we can still see vestiges of that population today in both groups of people.

So, if the Yamnaya people are the ghost people, the ANE, who are they?

The Yamna culture was primarily nomadic and was found in Russia in the Ural Region, the Pontic Steppe, dating to the 36th-23rd century BC.  It is also known as the Pit Grave Culture, the Ochre Grave Culture and feeds into the Corded Ware Culture.

"Corded Ware culture" by User:Dbachmann - Own work based based on Image:Europe 34 62 -12 54 blank map.png. Licensed under CC BY-SA 3.0 via Wikimedia Commons - https://commons.wikimedia.org/wiki/File:Corded_Ware_culture.png#/media/File:Corded_Ware_culture.png

“Corded Ware culture” by User:Dbachmann – Own work based based on Image:Europe 34 62 -12 54 blank map.png. Licensed under CC BY-SA 3.0 via Wikimedia Commons – https://commons.wikimedia.org/wiki/File:Corded_Ware_culture.png#/media/File:Corded_Ware_culture.png

Characteristics for the culture are burials in kurgans (tumuli) in pit graves with the dead body placed in a supine position with bent knees. The bodies were covered in ochre. Multiple graves have been found in these kurgans, often as later insertions.  The first known cart burial is also found in a kurgan grave.  A kurgan often appears as a hill, example shown below, and have been found in locations throughout eastern and northern Europe..

Hallstatt-era tumulus in the Sulm valley necropolis in Austria, photo by Hermann A. M. Mucke.

Hallstatt-era tumulus in the Sulm valley necropolis in Austria, photo by Hermann A. M. Mucke.

Additionally, some scientists believe that the Yamna culture was responsible for the introduction of PIE, Proto-Indo-European-Language, the now defunct mother-tongue of European languages.  Others think it’s way too soon to tell, and that suggestion is jumping the gun a bit.

Why might these recent discoveries be important to many genetic genealogists?  Primarily, because Y haplogroup R has been identified in ancient Russian remains dating from 2700-3400 BCE.  Haplogroup R and subgroups had not been found in the ancient European remains sequenced as of last fall.  In addition, subgroups of mitochondrial haplogroups U, W, H, T and W have been identified as well.

Keep in mind that we are still dealing with less than 300 skeletal remains that have been fully sequenced.  This trend may hold, or a new discovery may well cause the thought pattern to be “reconfigured” slightly or significantly.  Regardless, it’s exciting to be part of the learning and discovery process.

Oh yes, and before I forget to mention it…it seems that your Neanderthal ancestors may not be as far back in your tree as you thought.  They have now found 40,000 year old skeletal remains that suggest that person’s great-great-grandfather was in fact, full Neanderthal.  That’s significantly later than previously thought, by 10,000 or 20,000 years, and in Europe, not the Near East…and who knows what is just waiting to be found.  The new field of ancient DNA is literally bursting open as we watch.

I’ve accumulated several recent articles and some abstracts so that you can read about these interesting developments, in summary, and not have to do a lot of searching.  Enjoy!

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Modern Europe was formed by milk-drinking Russians: Mass migration brought new genetic makeup to continent 5,000 years ago
http://www.dailymail.co.uk/news/article-3119310/How-white-Europeans-arrived-5-000-years-ago-Mass-migration-southern-Russia-brought-new-technology-dairy-farming-continent.html

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DNA Deciphers Roots of Modern Europeans
http://www.nytimes.com/2015/06/16/science/dna-deciphers-roots-of-modern-europeans.html?smid=fb-nytimes&smtyp=cur&_r=1

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Science – Nomadic Herders Left a Strong Genetic Mark on Europeans and Asians
http://news.sciencemag.org/archaeology/2015/06/nomadic-herders-left-strong-genetic-mark-europeans-and-asians

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Nature – DNA Data Explosion Light Up the Bronze Age
http://www.nature.com/news/dna-data-explosion-lights-up-the-bronze-age-1.17723

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From the European Nucleotide Archive.  http://www.ebi.ac.uk/ena/data/view/PRJEB9021

Investigation of Bronze Age in Eurasia by sequencing from 101 ancient human remains. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native American

Description

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

Abstract

The Bronze Age (BA) of Eurasia (c. 3,000-1,000 years BC, 3-1 ka BC) was a period of major cultural changes. Earlier hunter-gathering and farming cultures in Europe and Asia were replaced by cultures associated with completely new perceptions and technologies inspired by early urban civilization. It remains debated if these cultural shifts simply represented the circulation of ideas or resulted from large-scale human migrations, potentially also facilitating the spread of Indo-European languages and certain phenotypic traits. To investigate this and the role of BA in the formation of Eurasian genetic structure, we used new methodological improvements to sequence low coverage genomes from 101 ancient humans (19 > 1X average depth) covering 3 ka BC to 600 AD from across Eurasia. We show that around 3 ka BC, Central and Northern Europe and Central Asia receive genetic input through people related to the Yamnaya Culture from the Pontic-Caspian Steppe, resulting in the formation of the Corded Ware Culture in Europe and the Afanasievo Culture in Central Asia. A thousand years later, genetic input from North-Central Europe into Central Asia gives rise to the Sintashta and Andronovo Cultures. During the late BA and Iron Age, the European-derived populations in Asia are gradually replaced by multi-ethnic cultures, of which some relate to contemporary Asian groups, while others share recent ancestry with Native Americans. Our findings are consistent with the hypothesised spread of Indo-European languages during early BA and reveal that major parts of the demographic structure of present-day Eurasian populations were shaped during this period. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency during the BA, contrary to lactose tolerance, indicating a more recent onset of positive selection in the latter than previously believed.

The findings echo those of a team that sequenced 69 ancient Europeans3. Both groups speculate that the Yamnaya migration was at least partly responsible for the spread of the Indo-European languages into Western Europe.

The report on the 69 ancient remains sequenced is below.

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Steppe migration rekindles debate on language origin
http://www.nature.com/news/steppe-migration-rekindles-debate-on-language-origin-1.16935

The Harvard team collected DNA from 69 human remains dating back 8,000 years and cataloged the genetic variations at almost 400,000 different points. The Copenhagen team collected DNA from 101 skeletons dating back about 3,400 years and sequenced the entire genomes.

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Population genetics of Bronze Age Eurasia
http://www.nature.com/nature/journal/v522/n7555/full/nature14507.html

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Dienekes Anthropology Blog
http://dienekes.blogspot.com/2014/06/ancient-dna-from-bronze-age-altai.html

Forensic Science International: Genetics Received 2 January 2014; received in revised form 21 May 2014; accepted 25 May 2014. published online 04 June 2014.

The Altai Mountains have been a long term boundary zone between the Eurasian Steppe populations and South and East Asian populations. Mitochondrial DNA analyses revealed that the ancient Altaians studied carried both Western (H, U, T) and Eastern (A, C, D) Eurasian lineages. In the same way, the patrilineal gene pool revealed the presence of different haplogroups (Q1a2a1-L54, R1a1a1b2-Z93 and C), probably marking different origins for the male paternal lineages.

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Dienekes Anthropology Blog
http://dienekes.blogspot.com/2013/06/mtdna-from-late-bronze-age-west-siberia.html

Includes mitochondrial haplogroups C, U2e, T, U5a, T1, A10.

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Population Genetics copper and Bronze Age populations of Eastern Steppe, thesis by Sandra Wilde
http://ubm.opus.hbz-nrw.de/volltexte/2015/3975/ (in German)

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Eurogenes blog discusses
http://eurogenes.blogspot.com/2015/03/population-genetics-of-copper-and.html

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Polish Genes Blog
http://polishgenes.blogspot.com/2015/05/r1a1a-from-early-bronze-age-warrior.html

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Early European May Have Had Neanderthal Great-Great-Greandparent
http://www.nature.com/news/early-european-may-have-had-neanderthal-great-great-grandparent-1.17534

40,000 year old Romanian skeleton with 5 – 11% Neanderthal, including large parts of some chromosomes – as close as a great-grandparent.  Previously thought that interbreeding was in the Middle East and 10,000 or 20,000 years earlier.

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How is this all happening?

The Scientist Magazine has a great overview in the June 1, 2015 edition, in “What’s Old is New Again.”
http://www.the-scientist.com/?articles.view/articleNo/43069/title/What-s-Old-Is-New-Again/

Are You Native? – Native American Haplogroup Origins and Ancestral Origins

At Family Tree DNA, having Haplogroup Origins and Ancestral Origins indicating Native American ancestry does not necessarily mean you are Native American or have Native American heritage.

This is a very pervasive myth that needs to be dispelled – although it’s easy to see how people draw that erroneous conclusion.  Let’s look at why – and how to draw a correct conclusion.

The good news is that more and more people are DNA testing.  The bad news is that errors in the system are tending to become more problematic, or said another way, GIGO – Garbage in, Garbage Out.

I want to address this problem in particular having to do with Native American ancestry – or the perception thereof.

At Family Tree DNA, everyone who tests their Y DNA or their mitochondrial DNA have both Haplogroup Origins and Ancestral Origins tabs as two of your 7 information tabs detailing your results.

haplogroup and ancestral orgins tab

The goals of these two pages are to provide the testers with locations around the world where their haplogroup is found, and locations where their matches’ ancestors are found – according to their matches.

Did a little neon danger sign start flashing?  It should have.

Haplogroup Origins

Haplogroup Origins provides testers with information about the origins of other individuals who match your haplogroup both exactly and nearly.  This data base uses the location information from both the Family Tree DNA participant data base and other academic or private databases.

haplogroup origins 2

Ancestral Origins

Ancestral Origins is comprised primarily of the results of the “most distant ancestor” country of your matches at Family Tree DNA.  This tab is designed to provide you a view into the locations where your closest matches are found at each of the testing levels.  After all, that’s where your ancestors are most likely to be from, as well.

ancestral origins 2

Most of the time this works really well, providing valuable information to testers, assuming two things:

1. Participants who are entering the information for their “most distant ancestor” understand that in the case of the Y line DNA – this is the most distant direct MALE ancestor who carries that paternal surname. Not his wife or someone else in that line.

Sometimes, people enter the name of the person in that line, in general, who lived to be the oldest – but that’s not what this field is requesting – the most distant – meaning further back in that direct line.

For mitochondrial DNA, this is the most distant FEMALE in your mother’s mother’s mother’s mother’s direct line – directly on up that maternal tree until you run out of mothers who have been identified. I can’t tell you how many male names I see listed as the “most distant ancestor” when I do DNA reports for people – and I know immediately that information is incorrect – along with their associated geographic locations.

mtdna matches

In this mitochondrial example, the third match shows a male Indian Chief.  The first problem is that this is a mitochondrial DNA test, so the mitochondrial DNA could not have descended from a male.  If you don’t understand how Y and mitochondrial DNA descends from ancestors, click here.

Secondly, there is no known genealogical descent from this chief – but that really doesn’t matter because the mtDNA cannot descend from a male and the batter is out with the first problem, before you ever get to the second issue.  However, if you are someone who is “looking for” Native American ancestry, this information is very welcome and even seems to be confirming – but it isn’t.  It’s a red herring.

Unfortunately, this may now have perpetuated itself in some fashion, because look at the first and last lines of this next entry – again – another male chief.  The second entry with a name is another male too, Domenico.  Hmmm….maybe information entered by other participants isn’t always reliable and shouldn’t be taken at face value….

mtdna matches 2

2. This approach works well if people enter only known, verified, proven information, not speculation. Herein lies the problem with Native American heritage. Let’s say that the family oral history says that my mother’s mother’s line is Native American. I decide to DNA test, so for the “Most Distant Ancestor” location I select “United States – Native American.”

united states selection

The DNA test comes back and shows heritage other than Native, but that previous information that I entered is never changed in the system.  Now, we have a non-Native haplogroup showing as a Native American result.

Unfortunately, I see this on an increasingly frequent basis – Native American “location” associated with non-Native haplogroups.

non native hap

This scenario has been occurring for some time now.  Family Tree DNA at one point attempted to help this situation by implementing a system in which you can select “United States” meaning you are brick walled here, and “United States Native American” which means your most distant ancestor in that line is Native American.

Native American Haplogroups

There are a very limited number of major haplogroups that include Native American results.  For mitochondrial DNA, they are A, B, C, D, X and possibly M.  I maintain a research list of the subgroups which are Native.  Each of these base haplogroups also have subgroups which are European and/or Asian.  The same holds true for Native American Y haplogroups Q and C.

In the Haplogroup Origins and Ancestral Origins, there are many examples where Non-Native haplogroups are assigned as Native American, such as haplogroup H1a below.  Haplogroup H is European..

non native hap 2

A big hint as to an incorrect “Native” designation is when most or many of the other exact haplogroups, especially full sequence haplogroups, are not Native.  As Bennett Greenspan says, haplogroups and ethnicity are “guilt by genetic association.”  You aren’t going to find the same subhaplogroup in Czechoslovakia, Serbia or England and as a Native American too.

non native hap 3

Haplogroup J is European.

non native hap 4

Haplogroup K is European, and so is U2e1, below.

non native hap 5

Unfortunately, what is happening is that someone tests and see that out of several matches, one is Native American.  People don’t even notice the rest of their matches, they only see the Native match, like the example above.  They then decide that they too must be Native, because they have a Native match, so they change their own “most distant ancestor” location to reflect Native heritage.  This happens most often when someone is brick walled in the US.

non native hap 6

Another issue is that people see haplogroup X and realize that haplogroup X is one of the 5 mitochondrial haplogroups, A, B, C, D and X. that define Native American DNA.  However, those haplogroups have many subgroups and only a few of those subgroups are Native American.  Many are Asian or European.  Regardless, participants see the main haplogroup designation of X and assume that means their ancestor was Native.  They then enter Native American.

In the example above, haplogroup X1c has never been found in a Native American individual or population, although we are still actively looking.  Haplogroup X2a is a Native American subgroup.

In some cases, we are finding new subgroups of known Native haplogroups that are Native.  I recently wrote about this for haplogroup A4 where different subgroups are Asian, Jewish, Native and European.  This is, however, within an already known base haplogroup that includes a Native American subgroup – haplogroup A4.

When testers see these “Native American” results under Haplogroup and Ancestral Origins, they become very encouraged and excited.  Unfortunately, there is no way to verify which of your matches entered “Native American,” nor why, unless you have only a few matches and you can contact all of them.

When someone has tested at the full sequence level, remember that their results will show on these pages in the HVR1 section, the HVR2 section and the full sequence section.  So while it may look like there are three Native American results, there is only one, listed once in all three locations where it “counts.”  In the example below, there are two V3a1 full sequence matches that claim Native American.  Those were the chiefs shown above.  There are those two, plus one more HVR1+HVR2 individuals who has entered Native American as well.  However, if the match total was one for the HVR1, HVR2 and coding regions, that would mean there is one person who tested and matched in all 3 categories, not that 3 people tested.  In other words, you don’t add the match totals together.

non native hap 7

What Does A Native Match Look Like?

Of course, not all matches that indicate Native heritage are incorrect.  It’s a matter of looking at all of the available evidence and finding that guilt by genetic association.

In this first confirmed Native example, we see that the haplogroup is a known Native haplogroup, and all of the matches from outside the US are from areas known to have a preponderance of Native Americans in their population.  For example, about 80% of the people from Mexico carry Native American mitochondrial DNA.

Native 1

In this second example, we see Native American indicated, plus Mexico and Canada, which it typical.  In addition we see Spain.  Just like some people assume Native American, some people from Mexico, Central and South America presume that their ancestors are from Spain, so I always take these with a grain of salt.  Japan is a legitimate location for haplogroup B as well, especially given that this result is listed at the HVR1 level. If this individual tested at the HVR2 or full sequence level, they might be assigned to a different subgroup, and therefore would no longer be considered a match.

native 2

It’s not just what is present that’s important, but what is absent as well.  There is no long list of full sequence matches to people whose ancestors come from European countries like the U2 example above.  Spain is understandable, given the history of the settlement of the Americas, and that can be overlooked or considered and set aside.  Japan makes sense too.  But a European haplogroup combined with a long list of primarily European high level matches with only one or two “Native” matches is impossible to justify away.

What Does Native American Mean?

This discussion begs the question of what Native American means.

It’s certainly possible for someone with a European or African haplogroup to descend from someone who was a proven member of the a tribe.  How is that possible?  Adoption, slavery and kidnapping.  All three were very prevalent practices in the Native culture.

For example, Mary Jemison is a very well-known frontierswoman adopted by the Seneca with many descendants today.  Was she Native?  Yes, she was adopted by the tribe.  Is her DNA Native?  No.  Were her ancestors Native?  No, they were European.  So, are her descendants Native, through her?  She married a Native man, so her descendants are clearly Native through him.  Whether you consider her descendants Native through her depends on how you define Native.  I think the answer would be both yes and no, and both should be a part of the history of Mary Jemison and her descendants.

If a European or African women was kidnapped, enslaved or adopted into the tribe, and bore children, her children were full tribal members.  Of course, today her descendants might have be unaware of her European or African roots, prior to her tribal membership.  Her mtDNA would, of course, come back as European or African, not Native.

This is a case where the culture of the tribe involved may overshadow the DNA in terms of definition of “Indian.”  However, genetically, that ancestor’s roots are still in either Europe or African, not in the Americas.

How Do We Know Which Haplogroups Are Native?

One of the problems we have today is that because there are so many people who carry the oral history of grandmother being “Cherokee,” it has become common to “self-assign” oneself as Native.  That’s all fine and good, until one begins to “self-assign” those haplogroups as Native as well – by virtue of that “Native” assignment in the Family Tree DNA data base.  That’s a horse of a different color.

Because having a Native American ancestor has become so popular, there are now entities who collect “self-assigned” Native descendants and ancestors and, if you match one of those “self-assigned” Native descendants and their haplogroups, voila, you too are magically Native.

I can tell you, being an administrator for the American Indian, Cherokee, Tuscarora, Lumbee and other Native American DNA projects – that list of “self-assigned” Native haplogroups would include every European and African haplogroup in existence – so we would one and all be Native – using that yardstick for comparison.  How about that!

Bottom line – no matter how unhappy it makes people – that’s just not true.

A great deal of research has been undertaken over the past two decades into Native American genetic heritage – and continues today.  The reason I started my Native American Mitochondrial DNA Haplogroup list is because it’s difficult to track and keep track of legitimate developments.  Any time someone tells me they have “heard” that haplogroup H, for example, is Native, I ask them for a credible source.  I’ve yet to see one.

How do we determine whether a haplogroup is Native, or not?

The litmus paper test is whether or not the haplogroup has been found in pre-contact burials.  If yes, then it can be considered that the ancestor was living on this continent prior to European contact.  Native people arrived from Asia, across Beringia into what is now Alaska, and then scattered over thousands of years across all of North and South America.  We see subgroups of these same haplogroups across this entire space.

In some locations, the Native people are much less admixed than, for example, the tribes that came into the earliest and closest contact Europeans.  These tribes were decimated and many are now extinct.  I wrote about this in my paper titled, “Where Have All the Indians Gone.”

The tribes that are less admixed are probably the best barometers of Native heritage today.

We are hoping for new discoveries every day, but for today, we must rely on the information we have that is known and proven.

Interpreting Results Today

Native American haplogroup results today are subsets of Y DNA haplogroups Q and C.  If you find a haplogroup O result that might potentially be Native, PLEASE let me know.  This is also a possibility, but as yet unproven.

Mitochondrial Native American haplogroups include subgroups of A, B, C, D, X and possibly M.

If anyone tells you otherwise, personally or indirectly via Haplogroup or Ancestral Origins – keep in mind that extraordinary claims require extraordinary proof and data is only as good as its source.  Look at all of the information – what is present, what is absent, the testing level and what kind of documentation your matches have to share.

Finding your haplogroup listed as Native American in the Haplogroup or Ancestral Origins doesn’t make you Native American any more than it would make you an elephant if someone else listed “purple elephant.”

purple elephant

The only things that make you Native American are either a confirmed Native haplogroup subgroup, preferably with proven Native matches, or a confirmed genealogical paper trail.  Best of all scenarios is a combination of a Native haplogroup, matches that suggest or confirm your tribe and a proven paper trail.  That combination removes all doubt.

Evidence

Of the various kinds of evidence, some can stand alone, and some cannot.

Evidence Type Evidence Results Comments
DNA Y or mitochondrial Confirmed Native American subgroup – can stand alone sometimes With deep level testing, this can be enough to prove Native ancestry.  For Y  this generally means advanced SNP testing or matching to other proven Native participants.  For mitochondrial DNA, it means full sequence testing.
Proven paper trail Proven Native tribal membership, but does not prove ancestral origins Needs DNA evidence to prove whether the tribal member was admixed.
Matches to Haplogroup or Ancestral Origins If Native is indicated, need to evaluate the rest of the information. Level of testing, haplogroup, locations of most distant ancestors of other matches need to be evaluated, plus any paper trail evidence.
Autosomal DNA matches To people with Native ancestry Unless you can prove a common ancestor through triangulation, those individuals with Native ancestry could be related to you through any ancestor.  Matches to several people with Native ancestry does not indicate or suggest that you have Native ancestry.
Native DNA ethnicity through autosomal testing Native American results You can generally rely on these results, especially if they are over 5%.  Unless you have reason to believe that other regions could be providing some interfering results, this is probably a legitimate indication of Native heritage.  Locations that sometimes give Native results are Asia and eastern European countries that absorbed Asian invaders, such as the Slavic countries and Germany.  I wrote about this here.

If you don’t test, you can’t play.  If you think you have Native American ancestry, you can take the Y DNA test (at least to 37 markers) if you are a male, the full sequence test if you are testing mitochondrial DNA, or Family Finder to match family members from all ancestral lines and discover if you show any Native American in your ethnicity estimate provided in myOrigins.  Men can take all 3 tests and women can take the mitochondrial DNA and Family Finder tests.  Family Tree DNA is the only testing company providing this comprehensive level of testing.

Haplogroup A4 Unpeeled – European, Jewish, Asian and Native American

Mitochondrial DNA provides us with a unique periscope back in time to view our most distant ancestors, and the path that they took through time and place to become us, here, today.  Because mitochondrial DNA is passed from generation to generation through an all-female line, un-admixed with the DNA from the father, the mitochondrial DNA we carry today is essentially the same as that carried by our ancestors hundreds or even thousands of years ago, with the exception of an occasional mutation.

Y and mito

You can see in the pedigree chart above that the red mitochondrial DNA is passed directly down the matrilineal line.  Women contribute their mitochondrial DNA to all of their children, of both genders, but only the females pass it on.

Because this DNA is preserved in descendants, relatively unchanged, for thousands of years, we can equate haplogroups, or clans, to specific regions of the world where that particular haplogroup was born by virtue of a specific mutation.  All descendants carry that mutation from that time forward, so they are members of that new haplogroup.

For example, here we see the migration path of haplogroup A, after being born in the Middle East, spreading across Eurasia into the Americas, courtesy of Family Tree DNA.

Hap A map crop

This pie chart indicates the frequency level at which haplogroup A is found in the Americas as compared to haplogroups B, C, D and X.

Hap A distribution

However, not all of haplogroup A arrived in the Americas.  Some subgroups are found along the path in Asia, and some made their way into Europe.  There are currently 48 sub-haplogroups of haplogroup A defined, with most of them being found in Asia.  Every new haplogroup and sub-haplogroup is defined by a new mutation that occurs in that line.  I wrote about how this works recently in the article, Haplogroups and The Three Brothers.

In the Americas, Native American mitochondrial haplogroups are identified by being subgroups of haplogroup A, B, C, D and X, as shown in the chart below.

beringia map

In the paper, Beringian Standstill and Spread of Native American Founders, by Tamm et al (2007), haplogroup A2 was the only haplogroup A subgroup identified as being Native American.

As of that time, no other sub-haplogroups of A had been found in either confirmed Native American people or burials.

In June, 2013, I realized that a subgroup of mitochondrial haplogroup A4 might, indeed, be Native American.

The haplogroup A4 project was formed as a research project with Marie Rundquist as a co-administrator and we proceeded to recruit people to join who either were haplogroup A4 or a derivative at Family Tree DNA, or had tested at Ancestry.com and appeared to be haplogroup A4 based on a specific mutation at location 16249 in the HVR1 region.  As it turns out, location 16249 is a haplogroup defining marker for haplogroup A4a1.

There weren’t many of these Ancestry people – maybe 20 in total at that time.  Ancestry has since discontinued their mitochondrial and Y DNA testing and has destroyed the data base, so it’s a good thing I checked when I did.  That resource is gone today.

Family Tree DNA has always been extremely supportive of scientific studies, whether through traditional academic channels or via citizen science, and they were kind enough to subsidize our testing efforts by offering reduced prices for mitochondrial testing to project members.  I want to thank them for their support.

Other haplogroup administrators have also been supportive.  I contacted the haplogroup A administrator and she was kind enough to send e-mails to her project members who were qualified to join the A4 project.  Supportive collaboration is critically important.

I wrote an article about the possibility that A4 might be Native, and through that article, raised money to enable people to test at Family Tree DNA or upgrade to the full sequence test.  Full sequence testing is critical to obtaining a full haplogroup designation.  Many of these people were only, at that time, defined by HVR1 or HVR1+HVR2 testing as haplogroup A.  Haplogroup A is, indeed, a Native American haplogroup, but it’s also an Asian haplogroup and we see it in Europe from time to time as well.  The only way to tell the difference between these groups is through full sequence testing.  Haplogroup A was born in Asia, about 30,000 years ago and has many subgroups.

What Do We Know About Haplogroup A4?

Haplogroup A4 has been identified as a subgroup of the parent haplogroup A and is the parent haplogroup of A2.  In essence, haplogroup A gave birth (through a mutation) to subgroup A4 who gave birth through a mutation to subgroup A2.

To date, before this research, all confirmed Native American haplogroups were subgroups of haplogroup A2.

In the Kumar et al 2011 paper, Schematic representation of mtDNA phylogenetic tree of Native American haplogroups A2 and B2 and immediate Siberian-Asian sister clades (A2a, A2b, A4a, A4b and A4c), no A4 was reported in the Americas, although A4 is clearly shown as the parent haplogroup of A2, which is found in the Americas.

On the graph below, from the paper, you can see the color coded “tabs” to the right of the haplogroup A designations that indicate where this haplogroup is found.  As you can see, A4 and subgroups is found only in Siberia and Asia, not in the Americas, which is indicated by yellow.

Hap A and B genesis

Schematic representation of mtDNA phylogenetic tree of Native American haplogroups A2 and B2 and immediate Siberian-Asian sister clades (A2a, A2b, A4a, A4b and A4c). Coalescent age calculated in thousand years (ky) as per the slow mutation rate of Mishmar et al. [58] and as per calibrated mutation rate of Soares et al. [59] are indicated in blue and red color respectively. The founder age wherever calculated are italicized. The geographical locations of the samples are identified with colors. For more details see complete phylogenetic reconstruction in additional file 2 (panels A-B) and additional file 3. Kumar et al. BMC Evolutionary Biology 2011 11:293 doi:10.1186/1471-2148-11-293

I then checked both GenBank and www.mtdnacommunity.org for haplogroup A4 submissions.  Ian Logan’s checker program makes it easy to check submissions by haplogroup.

MtDNACommunity reflected one A4 submission from Mexico and from the United States, which does not necessarily mean that the United States submission is indigenous – simply that is where the submission originated.  The balance of the submissions are from either academic papers or from Asia.

During this process, I utilized PhyloTree, Build 15, shown below, as my reference tree.  Build 16 was introduced as of February 2014.  It renames the A4 haplogroups.  In order to avoid confusion, I am utilizing the Build 15 nomenclature.  These are the haplogroup names currently in use by the vendors and utilized in academic papers.

Hap A tree

I am also utilizing the CRS version, not the RSRS version of mutations.  Again, these are the mutations referenced by academic papers and the version generally used among genealogists.

Family Tree DNA provides an easy reference chart of which mutations are haplogroup defining.  For haplogroup A4, we find the following progression.

A4 T16362C
A4a G1442A
A4a1 G9713A, T16249C
A4a1a T4928C

This means that everyone who falls in haplogroup A4 carries this specific mutation at location 16362.  The original value at that location was a T and in haplogroup A, that T has mutated to a C.  This defines haplogroup A4.  So, if you don’t have this mutation, you definitely aren’t in haplogroup A4.  Everyone in haplogroup A4 carries this mutation (unless you’ve had a back mutation, a very rare occurrence.)

This is actually a wonderful turn of events, because it means that the defining mutation for A4 is in the HVR1 region, which further means that regardless of how the haplogroup A individual is classified, I can tell with a quick glance if they are A4 or not.

In addition, subgroups are defined by other mutations as well, shown above.  For example, haplogroup A4a carries the A4 mutation of T16362C plus the additional mutation of G1442A that defines subclade A4a.

Full sequence testing showed that there was actually quite a variety of subhaplogroups in the project participants.

What Did We Find?

In the haplogroup A4 project, we now have 55 participants who fell into 11 different haplogroups when full sequence tested.

A4 project distribution crop

I have removed all haplogroup A2 individuals from further discussion, as we already know A2 is Native.  We have established a haplogroup A2 project for them, as well.

A4b

We found two haplogroup A4b individuals.  The most distant known ancestor of one is found in Tennessee, but the most distant ancestor of the other is found in England.  These two individuals have 19 HVR1 matches, of which many are to other A4b individuals.  There is no evidence of Native American ancestry in this group.

A4-A200G

This unusual haplogroup name indicates that this is a subgroup of haplogroup A4, defined by a mutation at location 200 that has changed from A to G.  The new subgroup is waiting to be named.  So eventually A4-A200G will be replaced with something like A4z, just as an example.

This individual is from Asia, so this haplogroup is not Native.

A10

One individual, upon full sequence testing, was found to carry haplogroup A10, which is not a subgroup of A4.  This is quite interesting, because the most distant ancestor is Catherine Pillard, originally believe to be one of the “Kings Daughters,” meaning French.  This article explains the situation and the question at hand.

All five of her full sequence matches are either to other descendants of Catherine Pillard, or designated as French Canadian.

One of this woman’s ten HVR2 matches shows her ancestor, Annenghton Annenghto, as born at the Ossosane Mission, Huronia, La Rochelle, Ontario, Canada and died in 1657 in Canada.  If this is correct and can be confirmed, haplogroup A10 could be Native, not French.  Her daughter, Marie Catherine Platt has a baptismal record dated March 30, 1651, was also born at the mission, and is believe to be Huron.

This article more fully explains the research and documents relevant to Catherine Pillard’s ancestry.

Based on these several articles, it seems that an assumption had originally been made that because the individual fell into haplogroup A, and haplogroup A was Asian and Native, that this individual would be Native as well.

This determination was made in 2007, based on only the HVR1 and HVR2 regions of the mitochondrial DNA, and on the fact that the DNA results fell within haplogroup A, as documented here.  The HVR1 and HVR2 regions do not include the haplogroup defining mutations for haplogroup A10, so until full sequence testing became available, this sequence could not be defined as A10.  The conclusion that haplogroup A equated to Native American was not a scientific certainty, only one of multiple possibilities, and may have been premature.

I contacted several French-Canadian scholars regarding the documents for Catherine Pillard and there is no consensus as to whether she was Native or European, based on the available documentation.  In fact, there are two very distinct and very different opinions.  There is also a possibility that there are two women whose records are confused or intermixed.

So it seems that both Catherine Pillard’s DNA and supporting documents are ambiguous at this point in time.

One of the ways we determine mitochondrial ethnicity in situations like this is “guilt by genetic association,” to quote Bennett Greenspan.  In other words, if you have exactly the same DNA and mutations as several other people, and they and their ancestors are proven to live in Scotland, or Paris, or Greece, you’re not Native American.  This works the other way too, as we’ll see in Kit 11 of the haplogroup A4 outliers group.

Looking at other resources, MtDNA Community shows two references to A10, one submitted from Family Tree DNA and one from the below referenced article.

Haplogroup A10 has one reference in Mitogenomic Diversity in Tatars from the Volga-Ural Region of Russia by Malyarchuk et al, (201 Molecular Biological Evolution) but has since been reassigned as haplogroup A8, as follows:

However, some of the singular haplotypes appear to be informative for further development of mtDNA classification. Sample 23_Tm could be assigned to A10 according to nomenclature suggested by van Oven and Kayser (2009). However, phylogenetic analysis of complete mtDNAs (fig. 1) reveals that this sample belongs to haplogroup A8, which is defined now by transition at np 64 and consists of two related groups of lineages—A8a, with control region motif 146-16242 (previously defined as A8 by Derenko et al. [2007]), and A8b, with motif 16227C-16230 (supplementary table S3, Supplementary Material online). Analysis of HVS I and II sequences in populations indicates that transition at np 64 appears to be a reliable marker of haplogroup A8 (supplementary table S3, Supplementary Material online). The only exception, the probable back mutations at nps 64 and 146, has been described in Koryak haplotype EU482363 by Volodko et al. (2008). Therefore, parallel transitions at np 64 define not only Native American clusters of haplogroup A2, that is, its node A2c’d’e’f’g’h’i’j’k’n’p (Achilli et al. 2008; van Oven and Kayser 2009), but also northern Eurasian haplogroup A8. Both A8 and subhaplogroups are spread at relatively low frequencies in populations of central and western Siberia and in the Volga-Ural region. A8a is present even in Transylvania at frequency of 1.1% among Romanians, thus indicating that the presence of such mtDNA lineages in Europe may be mostly a consequence of medieval migrations of nomadic tribes from Siberia and the Volga-Ural region to Central Europe (Malyarchuk et al. 2006; Malyarchuk, Derenko, et al. 2008).

On Phylotree build 15, A10 is defined as T5393C, C7468T, C9948A, C10094T A16227c, T16311C! and the submissions are noted as the Malyarchuk 2010b paper noting it as “A8b”and a Family Tree DNA submission.

At this point, haplogroup A10 is indeterminate and could be either Native or European.  We won’t know until we have confirmed test results combined with confirmed genealogy or location for another A10 individual.

A4

Haplogroup A4 itself is not the haplogroup I originally suspected was Native.  When this project first began, we had few A4s, and I suspected that they would become A4a1 when full sequence tested.  I expected A4a1 would be Native American.

Subsequent testing has shown that haplogroup A4 very clearly falls into major subgroups, as defined by different mutations.

A4 European

The European A4 group is comprised of three participants.  Of those three, two are matches to each other and the third is quite distant with no matches.  I suspect that we are dealing with two different European sub-haplogroups of A4.

Two project participants, one from Romania and one from Poland match each other and both match one additional individual from Hungary who is not a project member.  This group is eastern European.

The Romanian and Polish kits that match each other both carry mutations at locations 16182C, 16183C, 16189C, 150T, 204C, 3213G, 3801C and 14025C.  The third person that they match, who is not a project member, from Hungary, matches one of those kits exactly, so that gives us three kits carrying this same series of mutations.  These mutations do not match any other individuals carrying haplogroup A4.  This group appears to be Jewish, as all three of the participants are of the Jewish faith.

This leaves the third project participant from Poland who does not have any matches today, within or outside of the project.  This participant is clearly a different subclade of A4.  They match none of the defining markers of the group above. They do have unique mutations at locations not found in other A4 participants within the project.

This provides us with the following European haplogroup A4 results:

  • Eastern European –Jewish – 2 participants plus one exact full sequence match outside of project
  • Eastern European – does not match group above, has no matches today, five unique mutations including 4 in the coding region.

A4 Chinese

This A4 participant is from China.

This sequence is actually very interesting because of its relative age.  This individual has 109 matches at the HVR1 level.  This means, of course, that they are exact matches.  They match many people in varying locations such as people with Spanish surnames, participants from Michigan, Mexico and Asia which include people with extended haplogroups of A, A4 and A4-A200G haplogroup designations.

At first this appears confusing, until you realize two things.  First, the participant doesn’t continue those matches at the HVR2 level and second, this means that all of those people still carry the Haplogroup “A4 signature” HVR1 mitochondrial DNA, exactly.

This means that those matches stretch back in time thousands of years, until before the divergence of Native Americans and Asians, so at least 12,000 years, if not longer.  People who have incurred mutations in the HVR1 region don’t match, but those who have not, and today, there are only 109 in the Family Tree DNA data base, still match each other – reaching back to their common Asian ancestor many millennia ago.

This individual has developed two mutations in the HVR2 region at locations 156G and 159G.  The participant also does not carry the haplogroup A defining mutation at location 263G which means either that 263G actually defines a subgroup, or this participant has had a back mutation to the original state at this location.  This individual did not test at the full sequence level.

A4 Americas

This leaves a total of 14 haplogroup A4 individuals within the project.

In order to show a comparison, I have removed all private mutations where none of this group matches each other.  I have also removed the haplogroup defining mutations as well as 16519C and all insertions and deletions since those areas are considered to be unstable.  In other words, what I’m looking for are groups of mutations where this group matches each other and no one else.  These are very likely sub-haplogroup defining mutations.

In addition to all private mutations, deleted columns include: 16223, 16332, 16290, 16319, 16362, 16519, 73, 152, 235, 263, 309.1, 309.2, 315.1, 522, 523, 663, 750, 1438, 1736, 2706, 4248, 4769, 4824, 7028, 8794, 8860, 11719, 12705, 14766, 15326.

I then rearranged the remaining columns and color coded groups.  You can click on the chart to enlarge.

A4 mutations

Note: na means not available, indicating that the participant did not test at that level.  An x in the cell indicates that the mutation indicated in that column was present.

The purple and apricot groupings show different clusters of matches.  The light purple is the largest group, and within that group, we find both a dark purple group and an apricot group.  However, not everyone fits within the groups.

A4 – Virginia

The first thing that is immediately evident is that the first kit, Kit 1, is not a member of this purple grouping.  This person has three full sequence matches outside of the project, one whose ancestor was born in Texas.  This individual has three unique full sequence mutations.  This grouping may be Native, but lacks proof.

Additional genealogical research might establish a confirmed Native American connection. If Kit 1 is Native, this line diverged from this larger A4 group long ago, before any of these purple or apricot mutations developed.

This participant’s ancestor traces to Virginia.  Regardless of whether this haplotype is Native or not, it is most likely a sub-haplogroup of A4.

A4 – Colombia

The next least likely match is Kit 2.  This individual shares two of the common HVR2 markers, 146 and 153, but did not test at the full sequence level.  Given what I’m seeing here, I suspect that 146 might be a sub-haplogroup defining mutation for this light purple group.  In addition, 8027 and 12007 might be as well.  That includes everyone (who has tested at the relevant levels) except for Kit 1 and Kit 11.

Haplogroup A4 from Colombia is most likely Native.  Few people are in the public data bases are from Colombia.  One would expect several mutations to have occurred as groups migrated.  At the HVR1 level, this individual has 18 matches, most of which have Spanish surnames.  This participant has no HVR2 matches.

A4 – California Group

The next group is the apricot group which I’ve nicknamed the California group.  Both of these participants, Kit 3 and Kit 4, find their ancestors in either southern California or Baja California, into Mexico.  Finding these haplogroups among the Mexican, Central and South American populations is an indicator of Native heritage, as between 85% and 90% of Mexicans carry Native American matrilineal lineage.

These participants also match a third individual who is not a project member whose ancestor is also found in Baja California.  This group’s defining mutations are likely 16209C, 5054T, 7604A, 7861C and 12513G.  Fortunately, these will be relatively easy to discern due to the HVR1 mutation at 16209.

A4 – Puerto Rico Group

The dark purple group, Kits 5-9, is the Puerto Rican group even though it includes one kit from Mexico and one from Cuba.  The Mexican kit, Kit 5, in teal, is only a partial match.  Kits 6-9 match each other plus several additional people not in the project whose most distant ancestors are found in Puerto Rico as well.  This group has several defining markers including 16083T, 16256T, 214G, 2836T, 6632C and possibly 16126C, although Kit 5 carries 16126C while Kit 9 does not.

The Puerto Rico DNA project has another 18 individuals classified as haplogroup A or A4 and they all carry 16083T, 16256T and those who have taken the HVR2 test (10) carry 214G as well.  Only one carries 16126C, so that would not be a defining mutation for this major group, but could be for a subgroup of the Puerto Rico group.

Given the history of Puerto Rico, this is probably a signature of the Taino or Carib people.

In 2003, 27 Taino DNA sequences were obtained from pre-Columbian remains and reported in this paper by Laluezo-Fox et al.  This was very early in DNA processing, especially of remains, and they were found to carry only haplogroups C and D.  These remains were not from the islands, but were from the La Caleta site in the Dominican Republic.

The Taino today are considered to be culturally extinct due to disease, enslavement and harsh treatment by the Spanish, but they maintained their presence into the 20th century and were a significant factor in the population of the West Indies, including Puerto Rico.  Their descendants would be expected to be found within the population today.  The Taino were the primary tribe found on Puerto Rico and were an Arawak indigenous people who arrived from South America.  The Taino were in conflict with the Caribs from the southern Lesser Antilles.

Carib women were sometimes taken as captives by the Taino.  The Caribs originated in South American near the Orinoco River and settled on the islands around 1200AD, after the Taino were already settled in the region.

It’s therefore possible that haplogroup A4 is a Carib signature.  In 2001, Martinez-Cruzaco et al published a paper titled Mitochondrial DNA analysis reveals substantial Native American ancestry in Puerto Rico in which they found that haplogroup A was absent in the Taino by testing the Yanomama whose territory was close to the Taino.  If this is the case, then haplogroup A must have arisen and admixed from another native culture, or, conversely, the Yanomama tested were an incomplete sampling or simply not adequately representative as a proxy for the Taino.  However, if haplogroup A4 is not found in the Taino, the most likely candidate would be the Caribs, assuming that the Martinez-Cruzaco paper conclusions are accurate, or the even older Ortoiroid, Saladoid culture or Arawak tribe who are believed to have assimilated with or were actually another name for the Taino.

A4 – Mexican/Puerto Rican Mutation 16126 Group

This group, Kits 5-8, is defined by mutation 16126C.  It’s quite interesting, because it includes Kit 5 that does not match the rest of the Puerto Rican markers.  Only some Puerto Rican samples carry 16126C.  Kits 5-8 in this the A4 project do carry this mutation, but 18 of the haplogroup A kits in the Puerto Rican project which do carry the dark purple signature mutations do not carry this mutation.  This mutation may be a later mutation in some of the people who settled on Puerto Rico and some of which remained on the mainland.  The most distant ancestor of Kit 5 is from Tangancícuaro de Arista, Michoacan de Ocampo, shown below.

Tangancícuaro de Arista, Michoacan de Ocampo

Kit 5 has five full sequence matches, all of which carry Spanish surnames.

A4 Outliers

This leaves only kits 10-14.  These kits don’t match each other but do fall, at least on some markers, within the light purple group.

Kit 12 is from Costa Rica and has no matches at the HVR1 level because of a mutation at location 16086C, but has not tested at the HVR2 or full sequence levels.   They might fit into a group easily with additional testing.

Kit 13 is from Mexico and has only two HVR1 matches who have not tested at a higher level.  This kit, like Kit 5, does not carry mutation 16111T which could indicate an early split from the main group or a back mutation.

Kit 10 is from Mexico, has 17 HVR1 matches, some of which indicate that their ancestors are from Texas and Mexico.  Kit 10 has no HVR2 or full sequence matches.

Kit 11 is from Honduras and interestingly, has 158 HVR1 matches to a wide variety of people including those from Costa Rica, Mexico, South Carolina, Oklahoma, a descendant of a Crow Tribal member, North Dakota, Guatemaula, the Cree/Chippewa, a descendant of an Arikawa and one person who indicated their oldest ancestor is from Aragon, in Spain.  This means that all of these people carry the light purple group defining 16111T mutation.

Kit 14 is from Honduras and has only two matches at the HVR1 level, one which is from El Salvador.  Both of the matches have only tested to the HVR1 level.  Kit 14 does carry the 16111T mutation as well as most of the other light purple mutations, but is missing mutation 164C which is present in the entire rest of the light purple group.  This could signify a back mutation.  In addition, Kit 14 matches on marker 16189T with kit 6 from Puerto Rico and on 16311C with Kit 1 from Virginia, but with no other participants on these markers.

These people and their matches and mutations could well represent additional subgroups of haplogroup A4

A4a1

This leaves us with the A4a1 subgroup, which is where I started 18 months ago.

The haplogroup A4a1 group is very interesting, albeit not for the reasons I initially anticipated.  Again, the same columns were deleted as noted in A4, above, leaving only columns (mutations) unique to this group.  As with the other subgroups, these are likely sub-haplogroup defining mutations.

A4a1 mutations

Note:  na means not available, indicating that the participant did not test at that level

A4a1 Mexico

Kit 15, the pink individual did not take the HVR2 or full sequence test, but does not match any other participants at the HVR1 level.  This person’s maternal line is from Mexico.  Kit 15 could be Native and with additional testing could be a different subclade.

A4a1 European Group

The three yellow rows are positively confirmed from Europe.  Kits 1 and 2 do not match each other nor any other participants.

Kit 3 however, matches Kits 4-14.

Kits 3-14, all match each other at the HVR1 level.  One individual has not taken the HVR2 test and one has not taken the full sequence test, but otherwise, they also all match at the HVR2 and full sequence level.  Note that Kit 3 is also in the confirmed European group based on two sets of census documentation.

Within the group of participants comprising kits 3-14, several have oral history and some have circumstantial evidence suggesting Native ancestry, but not one has any documented proof, either in terms of their own ancestors being proven Native, their ancestor’s family members being proven Native, or the people they match being proven as Native.

Kit 3 states that their ancestor was born in England in 1838.  I verified that the 1880 census for New York City confirms that birth location of their ancestor.  The daughter’s mother’s birthplace is also noted to be England in the 1900 census.

Therefore, based on the fact that Kit 3 is proven to be English, according to the census, and this kit matches the rest of the group, Kits 4-14, at the HVR1, HVR2 and full sequence levels, it is very unlikely that this group is Native.

Kit 15, who does not match this group, but who has not tested above the HVR1 level, is the only likely exception and may be Native.  Full sequence testing would likely suggest a different or expanded subgroup of haplogroup A4a1.

Further documentation could add substantially to this information, but at this point, none has been forthcoming.

In Summary – The Layers of Haplogroup A4

Full sequence testing was absolutely essential in sorting through the various participant results.  As demonstrated, the full sequence results were not always what was expected.

When full sequence tested, one participant was determined to be Haplogroup A10, which is not a subgroup of A4.  Haplogroup A10 is indeterminate and could be Native but could also be European.  Additional A10 results will hopefully be forthcoming in the future which will resolve this question.

None of the haplogroup A4a1 participants provide any direct evidence of Native ancestry, with the possible exception of one A4a1 kit whose matrilineal ancestors are from Mexico and who has not tested at a higher level.  Three A4a1 participants have confirmed European ancestry and one of those participants matches most of the others.  A4a1, with possibly one exception, appears to be European.  The A4a1 participant whose ancestors are from Mexico does not match any of the other participants and could eventually be classified as a subhaplogroup.

Haplogroup A4 itself appears to be divided into multiple subgroups, several of which may eventually form new sub-haplogroups based on their clusters of mutations.

There is clearly a European and a Chinese A4 grouping.  The European group is broken into two subgroups, one of which is Jewish.

In the Americas, there are several A4 subgroups, including:

  • Virginia – indeterminate whether Native
  • Colombia – likely Native
  • California – likely Native
  • Puerto Rico (2 groups) – very likely Native

There are also 5 outliers who don’t match others within the group, hailing from:

  • Costa Rica – likely Native
  • Mexico (2) – likely Native
  • Honduras – matching several confirmed Native people in multiple tribes at the HVR1 level
  • Honduras – likely Native

A4 grid v2

Note: Undet, short for undetermined, means that the results could be Native or European but available evidence has not been able to differentiate between those alternatives today.

*A4 needs to be further divided into additional haplogroup subgroups.

Dedication

Obviously, a study of this complexity couldn’t be done without the many resources I’ve mentioned and probably some that I’ve forgotten.  I thank everyone who contributed and continues to contribute.  I also want to thank the people who contributed to the funding for participant testing.  We could not have done this without your contributions in combination with the discounts offered by Family Tree DNA.

However, the most important resource is the participants and their willingness to share – their DNA, their research and their family stories.  During this project, two of our participants have passed away.  I would like to take this opportunity to dedicate this research to them, and I hope they know that their DNA keeps on giving.  This is their legacy.

Acknowledgements

I would like to thank Ian Logan for his assistance with haplogroup designation, Family Tree DNA for testing support and discounts, my project co-administrator, Marie Rundquist, Bennett Greenspan, Dr. Michelle Fiedler and Dr. David Pike for paper review.

Haplogroups and The Three Brothers

3 brothers group

Do you remember when you first started working with genealogy and you encountered your first “three brothers” story?

For those of you who don’t have one, it goes like this:

There were three brothers who came to <fill in the location.>  They had an argument about <a woman, religion, where to settle, other> and they all three went in different directions, never to see each other or speak again.

Well, of course, that might have happened and it probably did from time to time, but not nearly as often as the story would have you believe.

In my case, I had several “three brother” stories and even a “seven brother” story.  Even as a novice genealogist, I began to get suspicious when I heard the third or fourth story and they all seemed eerily similar.  Too similar.  Too convenient.

Enter the age of DNA testing.  Many of the three brothers stories seem to stem from three men with the same surname found in different or sometimes not-so-distant locations whose ancestries could not be tied nearly together, so surely someone said, “well they must have been three brothers who went different ways” and from that the “three brothers “ myth was born, to take on an entire life of its own.

But then, there are the stories that are real.  In some cases, the DNA testing does prove that those men descended from a common ancestor.  Of course, we can’t ever prove that they were brothers by their descendants DNA testing today.  We can only prove that they weren’t, if their Y DNA doesn’t match.

Recently, someone asked me a very basic DNA question, and the answer that came to mind was, “well, there were three brothers, you see…..”

The question was: “How can one haplogroup have descendants on different continents?

For example, how can a specific haplogroup include people who are Asian, European and Native American.

Let’s take a look at how that works.  It’s a lot like a pedigree chart.  In fact, it’s exactly the same.

There isn’t a haplogroup Z Y-DNA haplogroup, so let’s use that as a hypothetical example.  This example is equally applicable to mitochondrial DNA as well.

3 brothers

In our example, haplogroup Z was born a very long time ago, let’s say 30,000 or 40,000 years ago in Eurasia – we don’t know where and it doesn’t matter.

Haplogroup Z had two sons, and each one had a mutation different from the father, haplogroup Z, so the sons were named haplogroups Z1 and Z2.  One liked the hill to the west and one liked the river to the east, so they settled in opposite directions from their father.

Over time, the families and descendants of these two sons expanded until they had to move to new ground in order to have enough game to hunt.

Haplogroup Z1’s descendants had had two mutations as well.  One group, Z1a, went to Siberia and one group, Z1b went to China – or what is today China.

On the other hand, haplogroup Z2’s descendants also had two mutations that set their lines apart from each other.  One of these, Z2c went to what is now Europe and one, Z2d, went north to Scandinavia.

You can see as you look on out to the fourth generation that haplogroup Z1a, in Siberia had two sons with mutations.  Z1a1 went to Russia and Z1a2 crossed into Beringia, following game, and eventually would settle in North America.

Z1a2 then had two sons as well, both with mutations.  One of those, Z1a2a, traveled across the north and today his descendants are found primarily in eastern Canada and the US.

Now here’s the important part.  Z1a2a is known ONLY as Native American, because that mutation happened here, in the New World, and is not found in either Europe or Asia.  Z1a2b is also only Native American, found primarily in South America because that son followed the western coastline instead of traveling east cross country.

On the other hand, haplogroup Z1a2 might be found in BOTH Asia and the New World if it was born in Siberia but then migrated to the New World.  Some carriers might be found in both places, so if found in the New World, it likely indicates Native American, and yet it is also found in Siberia.  It is not found in other parts of the world though.

You can see that while the base haplogroup Z is today found worldwide, as defined by its subgroups, the subgroups themselves tend to be localized to specific regions.  You can also begin to see why determining locations of the birth of haplogroups is so difficult.  Europe is one big melting pot, and so is the UK, the US, Canada, Australia and New Zealand.

We, as the genetic genealogy community, are still trying to sort through this, which is why you see new haplogroup subgroup designations on nearly a daily basis.  The Y tree changes almost hourly (thanks to advanced tests like the Big Y at Family Tree DNA) and the mitochondrial tree has had many additions in the past months and years, with more yet to come shortly as a result of ongoing research.

In the mitochondrial DNA world, haplogroups are still named in the pedigree type fashion.  For example, I’m J1c2f.  However, in the Y tree, the names became so unwieldy, some up to about 20 characters long, that the pedigree type name has been replaced by the defining mutation (SNP) for that haplogroup.  So, R1b1a2, the most common male haplogroup in Europe, is now referred to as R-M269.  Not as easy to tell the pedigree by looking, but much more meaningful, especially as branches are added and rearranged.  The SNP name assigned to the branch will never change, no matter where the branch is moved on the tree as more discoveries are made.

If a DNA participant only tests to the most basic of levels, they are only going to receive a rather basic haplogroup designation.  Let’s say, in our example, Z or Z1 or Z2.  Clearly, additional testing would be in order to figure out whether that individual is Native American or from Scandinavia.  And yes, we have exactly this situation in many of the Native American haplogroups – because all the Native American base haplogroups for Y DNA: C and Q, and for mitochondrial DNA: A, B, C, D, X and possibly M, were founded and born in Asia, thousands of years ago.

And yes, it seems they all had three siblings…..