mtDNA H1j6

My Mum recently upgraded her FTDNA mtDNA results to the Full Sequence and we are H1j6.
This appears to be a very rare group. I have submitted her data to the FTDNA H project and will be submitting to Gen Bank too.

I'm hoping that more H1j6's might share their maternal origins so that we can all find out more about this line. If you are reading this and you are H1j6 please leave a comment saying where your earliest direct maternal ancestress is from :) thank you!

Rare SNP finder update

As I can't seem to add an update under the table of rare SNPs, I'll have to post here.
I checked the African SNP over at SPSmart and sure enough it does seem to be only African. I say does seem because it is only recognised on the HapMap database which I think has very limited populations, whereas the other African SNPs I found were on databases that included a variety of populations from each continent.

It seems this SNP is only found in 7% of Africans and only in the Yoruba on the West Coast over at SPSmart. I checked the SNPs location and it seems to be at the end of the chromosome so this again makes me cautious as I have read that matches here can be very old ie ancient. That plus the limited populations means (I think) that I can't confirm this is definitely from the ancestor responsible for the larger segment. But given it is found in west coast populations and Caribbean's, then it does make sense. Nothing shows up on the admixture calculators so I will archive it as a maybe.

Rare SNP finder tool at Gedmatch

I'm just looking at this latest feature to find any rare SNPs and when I have time, I will look them up at SPSmart. A lot seem very common across world populations, but here are a few that may support recent findings. The Ashkenazi is interesting as this is in the same location as two overlapping Ashkenazi segments on Ancestry Finder.

rs7244226

18

42812004

aC

1.34887

KATNAL2

Romania

rs11680909

2

91398768

Ag

0.348383

Ashkenazi

rs2069806

5

131426616

Gt

0.279574

IL3

Lithuania Poland Slovakia

rs8004819

14

19333265

cT

1.41066

Bahamas Cameroon Haiti

Which African populations get these SNPs?

I decided to have a look where the two SNPs only found in African populations that my mother has, come from in Africa. Using the SPSmart browser, I was able to check against individual African populations, rather than just the continent as a whole.
For the first SNP rs11224346 T didn't show up in Mbuti Pygmies, Kenyan Bantu or Namibian San, they all got C/C just like 100% of Europeans and Asians. The following populations did get T (I think as C/T or T/T):
Senegal Mandeka 0.04%
South African Bantu 0.06%
Nigeria Yoruba 0.07%
Even within Africans it seems rare but I am amazed that two out of the three populations who do have T are on the West Coast. According to Wikipedia, between the 16th and 18th centuries, almost a third of the Mandeka were shipped to the US and they suggest a significant portion of African Americans are descended from the Mandeka. Similarly, Wikipedia states that out of the 45 distinct ethnic groups taken to the Americas during the slave trade, at number 8 are the Yoruba of southwestern Nigeria.
Having a look on the NCBI website only the Nigeria Yoruba get T/T.
Within the 227 Yoruba people from Nigeria that were tested 80% got C/C, 18% got C/T and 2% got T/T which gives you an idea of how rare it is!
Interestingly, 25% of African Americans from SW America get the C/T combination with the rest getting C/C.
The other SNP rs17130316 appears to be rare but common across Africa. The highest score is the South African Bantu at 31% getting an A (I think this includes A/G and A/A), followed by the Kenyan Bantu at 22%, Senegal Mandeka 18%, Nigeria Yoruba 16%, Namibia San 10% and Biaka Pygmy 4% (A is not found in Mbuti Pygmies).
According to NCBI, African Americans and the Nigerian Yoruba are the highest getting 0.02% and 0.03% A/A respectively.
Could this be something to do with having ancestry from the west coast of Africa?

Quick calculator update

I just had a look at the reduced size chromosome paintings at Gedmatch and for some reason the Dodecad k7b picks up the African segment (it's small, but there and the pale green of the Atlantic-Baltic doesn't help as it makes the yellow dificult to see) but the full size version doesn't show the segment?
Not sure why this has happened but I'm pleased that it does appear in at least one version of the k7b!
There's no point adding it here, but when I copied and pasted it against the Eurogenes k9 to check the location was correct, it was in the same location.
Yesterday I got in touch with Dr David K Faux about his African ancestry. He managed to use his family's DNA to verify an African ancestor who was born in 1680. I am thrilled to see that he also used the same methods as I did to verify that his segment was real.
His segment is 0.1% at speculative level. My mother's appears at standard level.
You can read his story here: www.davidkfaux.org and click on African ancestry: Wife of Sgt. Daniel Young.
I just wish I had a few more family members to test!
Many thanks to Dr Faux for all his help.

Flook or real?

I decided last night to have a look on Gedmatch at their feature that lets you see who else matches you on a given chromosome in a given area. In this case I chose to look up the segment where the African is located. Two matches showed up so I then ran them through the Gedmatch chromosome painting feature specifically in this location.
Anyone who has read my blog previously will remember that when I did this with my mother's Szekely cousin, they both shared a peak of North Asian, so I thought I'd have a look with these two new matches to see if either of them shared any African in the same place.
The first one didn't. But the second one did! I have emailed the person to see if it is possible that they could have some minority African ancestry but from doing a quick name search it appears their family has roots in the deep south. I really hope they answer my email!

UPDATE: This match got in touch and sure enough they have ancestry from North Carolina, Georgia, Tennessee, Kansas, Kentucky and Alabama to name a few States. I read one source that said one ancestor owned many slaves. The match tells me they have a few unknowns and haven't been able to go back beyond 1798 in most cases and although they are not aware of any black ancestors, they do not rule them out.
Below is a screen shot of the location where they both share a small segment. The segment is small but packed with SNPs (over 2000). West African is shown in turquoise and the shared African appears across most calculators at Gedmatch.

Nearly missed this!

My mother has done many DNA tests to work out her unknown American ancestry. Luckily, some have been provided by leading geneticists for free as part of DNA projects using DNA data from the companies she did pay for.

There are currently two ways a woman can get clues about her father’s ancestry:

1. by matching segments of autosomal DNA which is DNA passed down from all ancestors.

2. by using an admixture prediction which breaks down the DNA and decides whether it is from different ethnic groups.

My mother has done 3 tests, 23andme, deCODEme and FamilyTreeDNA.

When several cousin matches appeared at 23andme from people who lived in Hungary (that is they shared actual segments of DNA with my mother), then I was amazed to discover that we had some ancestry from this region, in particular with the Szekely (pronounced “say kay”) people of Transylvania-3 cousins even managed to locate surnames and a town in common! Even the admixture predictions showed some Central/Eastern European, so I accepted this as my lot-my US Grandpa had some ancestry from Hungary.

However in December, 23andme, released arguably the best admixture prediction analysis available based on thousands of DNA samples from all over the world. It had been rigorously tested and the company published an article in a research journal as well as featuring in other scientific literature. If this couldn’t pick up specific ancestries then nothing would.

When I looked at my mother’s results, I was quite impressed-it predicted 59% of her is British/Irish-not bad for some at least half British! The rest is a mish mash of Northern and Southern European-the programme wasn’t quite sure, but this is common in people with ancestry from more than one region, especially Americans. It’s a bit like guessing the breed of dogs-pedigrees are easy but mongrels are harder!!

So that’s British/Irish, generic European (Hungarian would fit here, maybe some German? Dutch?), African. Wait, African?! Yep. Right there, a little pink segment of African amongst the sea of blue European on chromosome 11:

Odd. It must be a mistake, this “noise” you can sometimes get when the test has a hissy fit. So I dismissed it as that. But it kept bugging me. Mum had similar admix results done elsewhere-I never noticed African before but what if I missed it?

So I checked her results from Professor Doug McDonald at Illinois University who is responsible for creating numerous DNA programmes and studies. He gives you an ancestry prediction like the one above, where your chromosomes are “painted” based on where the programme thinks each part is from in the world.

He had always said Mum had some kind of Central European ancestry with British so I was content with that, it fitted with the Hungarian cousins. So I never bothered to look at the chromosome painting he also sent me. Perhaps I should have done before:

This is the same chromosome but red is European and guess what? Blue is African.

I looked at my mother's deCODEme browser. That lets you see what populations you match with on each chromosome. Sure enough in this location that too shows 28.90% of it as African.

So let’s check another test, Eurogenes. I now know where the segment is on the chromosome thanks to Doug’s analysis, so I can check the exact location on Eurogenes.

The images below show the same segment as above but as peaks rather than a block. Each colour represents a world population. Most of the colours below are different European populations. Here is that segment throughout all of the analyses provided by Eurogenes:

K9 African is turquoise.

k10 African is turquoise.

K12 African is turquoise.

K13 this shows West African in orange.

 Hunter gatherer analysis aims to show ancient admixture. Here African is show in purple which most closely matches the Bantu people.

Now let’s try the Dodecad Ancestry project:

World 9. The African is shown in brown.

K12b. The African is shown in light purple.

V3. The African is shown in yellow which represents the Yoruba, Mandenka and Bantu peoples and blue which is East African.

All show African in differing amounts due to the nature of the analysis, but it is still there. And as these are showing input from both parents, they do show a mix of populations not just African. If they did I would be worried-it's highly unlikely both parents would have African ancestry and 23andme and Doug only show the African as coming from one parent.

 I wrote to Professor McDonald and the project coordinator at Eurogenes for their advice. “If it appears on my test and at 23andme, then it’s most certainly real” said Professor McDonald. Goodness. “Well it certainly seems likely, but there is one way to double check” said David at Eurogenes, “look up the SNPs in that location and see if there are any only found in African people”. Good grief, that sounds painful.

 An SNP is a tiny fragment that makes up a segment. You can imagine how small that must be! So he provides me with the Stanford University DNA SNP checker and off I went. It was horrendous-so many SNPs!! Each SNP had a little pie chart showing how frequently it occurred in world populations. Now each SNP is made from both parents giving you a letter. It could be A, T, G or C and each SNP has its own combination pairs eg AA, AG or GG. All of Mum’s seemed to be common throughout the world and my eyes were going square. This wasn’t showing me anything!

Just as I was about to give up I put in one more SNP. Here is what I found:

SNP combinations	Parent 1.	Parent 2.	World populations that have this SNP.
	G	G	Found in 99% of the world including Africans and 100% of Europeans and Asians.
	A	G	Found in Africans and African Americans.
	A	A	Found only in Africans.
Mum	A	G	So one parent contributed G and the other the African A.

  And another:

SNP combinations	Parent 1.	Parent 2.	World populations that have this SNP.
	C	C	Found in 98% of the world including Africans and 100% of Europeans and Asians.
	T	C	Found in Africans and African Americans.
	T	T	Found only in Africans.
Mum	T	C	So one parent contributed C and the other the African T.

So these rare SNPs have been inherited down the generations from an African. There could be more but my eyes and sanity need preserving.

“Well then this is a case for actual African ancestry, probably from an African American ancestor,” said David.

 Now anyone that knows me knows that I am very skeptical. So was I convinced? Of course not! Not because I didn't believe David or Doug, but because there had to be a catch! DNA is very good at being noisy, that is you need to explore every avenue before you can be completely sure of what it is telling you sometimes.

So one last opinion was needed and I turned to the International Society of Genetic Genealogists (ISOGG) of which I am now a member. I told them everything I had found. I was fortunate enough to get a response from Cece Moore, who offers consultations and advice and is frequently consulted by DNA testing companies, genealogists and the press: http://www.yourgeneticgenealogist.com/ 

If she couldn't help then noone could! She said:"Under the circumstances, I think you can feel very confident that it is real.
Small single African and Native segments in Ancestry Composition appear to be
very accurate, unlike some of the older admixture tools.
Kudos on your persistent and thorough research in this regard.
Your next step should be to try to find anyone who matches her on this segment
to see if you can determine its origin."

So there you go!

Given 23andme say their results reflect ancestry within the last 500 years; I worked it out and reckon this ancestor was probably born around 1650-1700, just as the American colonies were taking on slavery. In 1670, there were 5,000 designated slaves in the British Colonies. By 1700 in Virginia, there were more Africans than Europeans.

Reading about Africans in America during this period, as you can imagine, many British men found their Anglicised African female slaves very attractive and it was even made legal that a British man could do what he wished with his female slaves. It was a sign of status if you produced a mixed race child with your slave. And of course these children would then be sold on.

However, not all mixed relations were like this. Often white father’s would free their mixed race children and during the early 17^th century, it is recorded that black indentured servants regularly socialised and had sexual relationships with white indentured servants; it is recorded that interracial relationships frequently occurred amicably, but by 1700 it was seen as a disgrace. It is thought that around 30% of today's white Americans  (that's roughly 66 million people) have an average of 2.3% African ancestry, with 0.9% of them having an African direct female line. That's quite a large number! Of course I will probably never know the person or the circumstances but I am pleased I have found them.

Often people say why bother? Well because it is a fascinating glimpse at the lives of people who ultimately made you. I am amazed! I could have so easily dismissed this! It just goes to show you need to explore all avenues when doing genealogy, either on paper or by DNA!

I would like to say a big thank you to all professionals involved in providing me with help and advice.