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.





Gedmatch is great!

I really can't praise the work of the volunteers at Gedmatch enough, they do a superb job. If you have done a DNA test via 23andme or FamilytreeDNA Family Finder and you are interested in finding more clues about your ancestry do upload your data to Gedmatch. It is anonymous and you are identified via an ID number and your emal should you wish to submit it (this allows potential cousins at Gedmatch to contact you).

Once you have uploaded your data to Gedmatch it is safely stored and you merely enter your ID number whenever you wish to check anything, so no messy uploading of your raw data files everytime!

They have recently added some "admixture calculators" which you can run your data through. These predict how much of your DNA comes from certain regions of the world. It's all based on statistics and I don't know how they do it, but it's interesting! It is through these calculators that I have been able to see that my mother has some Eastern European ancestry based on her higher scores compared to people who are 100% British. And really to use these calculators and make any sense of them, you need to compare your scores to people of a similar ethnic origin to you, right down to similar regions of a country if you can.
You can easily compare your results by posting them on the forums at 23andme and FTDNA-search for Gedmatch in each and you will find a multitude of threads about it!

One handy thing about Gedmatch is it allows you to reduce the "safe" threshold of 7cM (Centimorgans, a unit of measurement of DNA) and 700 SNPs (the little bits that make up segments of DNA).
23andme and FTDNA use thresholds around this number to make sure that the matches you get to other people are real and not just "noise." But many people have been successful at finding connections to people below this safety net cut off. It must be used with caution though. It has been suggested by some that anything between 5cM and 7cM has a 50/50 chance of being from a shared ancestor within a genealogical timeframe. It is possible that segment this small could be ancient throwbacks representative of an ethnic group rather than a specific family from the ethnic group. It could also be the computer that works it all out having a bit of a moment and joining to little fragments of DNA together (eg a tiny bit from your Mum and a tiny bit from your Dad) to make a bigger one which it thinks is worthy of a mention. 23andme and FTDNA do allow you to experiment below the 7cM threshold (see Ancestry Finder at 23andme or play around with the chromosome browser at FTDNA) and 23andme advise anything near to 5cM be taken with a pinch of salt.

So why would you want to use Gedmatch to go below this threshold? Perhaps I am missing out, but I do ignore anything below 6cM, however I decided to compare my mother's 5th cousin of Szekely descent and this cousins Granddaughter using 3cM! Shock horror, I don't know what came over me, I blame my recent root canal.

Sure enough they shared little segments with my Mum, some were the same others different. So I focussed on the segments that they shared in common with each other and my Mum (this would infer that the Grandmother had passed them to the Granddaughter). One segment in particular was on chromosome 18 both roughly 3.7cM and 648 SNPs.
I had been intrigued by a mystery Gedmatch user that was clearly related to both of them, so I decided to compare them to my mother too. Sure enough, they matched in this location too. I emailled the person in chrage of looking after the family Gedmatch accounts and it turns out the mystery match is the Grandmother's son!
So there is a small segment that has been passed from mother to son to daughter that is also shared by my mother via a shared ancestor in the past! Or at least that is how it appears, I have to take it with a pinch of salt but it seems plausible to me!

Gedmatch also ran a rare SNP feature which has since been removed and will have it's own website, which allows you to see what rare SNPs you have which may suggest a connection to a region.
Whilst it was still available I was able to compare my mother to the Grandmother and the Granddaughter to see if they all shared any rare SNPs. They did, one. Origin of the SNP was listed as Spain, Poland or Hungary! As they both have Hungarian ancestry I was quite impressed! It doesn't prove any recent connections using this method, but it was nice to have it supported by people we knew had ancestry from Hungary.

So if you have data, get uploading! If you find new cousins or find something out about your ancestry via Gedmatch, please consider making a donation to support their hard work!
http://www.gedmatch.com/

Gedmatch matches to Eastern Europe

Just a quick tally of Gedmatch matches over 700 cM and 700 SNPs:
7.1cM Ukraine
7.4cM Hungary
7.4cM Russia (Samara/Kazan region)
7.7cM Russia
8.4cM Hungary/Romania (Szekely cousin)
9.2cM Lithuania/Latvia (5th cousin)
9.5cM Lithuania
Addition using FTDNA kit:
7.3cM Hungary/Romania (Szekely cousin Granddaughter)

Latest Gedmatch Eurogenes chromosome comparison results.

I compared the K12 and the Hunter-Gatherer vs Farmer calculators with the Szekely cousin who has shown "peaks" in common in my previous post.
This time there is still something in that location that is shared in common but it appears a lot smaller. Not sure about the Pygmy gatherer, but African was picked up on one of the other comparisons too. Volga-Ural makes more sense.

Hungarian match number 6!

Yes via Gedmatch, we now have Hungarian match number 6. They don't think they have any Szekely ancestry, but I don't see why we can't have regular Hungarian ancestry too!
All their matches are either Jewish or Eastern European, there aren't any UK matches. I say this because it is always nice to affirm as much as possible the fact that the match is not possibly on our UK side!