Y assignment BY-1551. Probably wrong again.

This is my latest assignment from Family Tree DNA:

screenshot-from-2016-12-14-11-23-20

BY-1551. This was an assignment from the National Geographic Geno 2.0+ data set. If you look at Big Tree ( go to link. Search for BY1551. click on it) and also the BY-1551 test at YSeq, they both say the normal base at this location is Cytosine.  But the raw data for my DNA says this base is Cytosine and yet also a mutation. This is an error in the assignment of the data.

 

Y assignment R-FGC11678. Probably wrong.

This is my latest assignment.

r-fgc11678-assignment

Very hard to believe a haplogroup where I am U106-, Z381-, and Z156-. This SNP is a Nat Geo 2.0 Next Gen SNP and the raw assignment is Cytosine. I need to know if X-> C is the actual mutation folks look  for. This could easily be another random mutation on our part.

Update: the U106 spreadsheet of Raymond Wing shows that this change should be G -> A, not a cytosine. So this is another natural mutation, not a diagnostic marker.

Update 2 6/25/2017: for the folks in the L21 Yahoo groups hitting this page repeatedly, thank you. I didn’t realize that my issue was more common than realized. The issue is pretty simple. Nat Geo Geno 2.0 transfers have a data issue in that any point mutation at a site is classed as a “true”, even though the odds of it being the mutation ‘on the books’ is one in three. These classifications wreak havoc with ftDNA terminal haplotype software (crufty stuff, not smart enough to double check the mutation) and so if you do not eventually do a Big Y, your life will become dominated by ftDNA mistakes that you will have to check manually. 

Phasing DNA. Pros and Cons.

I had my dad get an Autosomal test at ftDNA (whatever their merits or demerits, Family Tree DNA keeps your DNA sample for 25 years, so you can update testing anytime you want), and I have transferred that test to Gedmatch. His kit number is posted on Wikitree ( which is another genealogical resource you might find useful). But to repeat them here, Ysearch kit is MMB63. His autosomal kit on gedmatch is T141705. Anyone who has a gedmatch login can do ‘one to many’ comparisons with his gedmatch kit.

That said, with my Dad’s kit there, I can phase my own DNA kits, splitting them into a maternal and paternal side. Using these, I can now tell whether a DNA match is matching from the maternal side or paternal side. So, when trying to dig up dimly understood ancestors, this is quite valuable.

On the other hand, the admixture of my maternal side is a bit fanciful..

maternal-gedmatch-admixture-analysis-01

And the answer is, no I don’t believe it. The sanest of the admixtures so far seems to be 50% Scots/Irish/British, 30% Scandinavian, and 20% Southern Europe. That’s what I tend to believe, as of the moment.

And yes, they do warn you that phased data and admixture are not the best of ideas. Compare with my admixtures in previous posts.

R-S7123 haplotype.

That’s what Family Tree DNA now says. It’s a subtree of P312, perhaps the largest branch of R1b..

r-s7123

familytreeDNA hasn’t said they completed the M343 backbone testing, but the results look as if they have.

I’m looking to see if anyone else matches this, and so far, no hits.

Update 9/27/2016: working on the assumption that ftDNA has tested P311, P312, L21, Z2542 (DF13 alike), and L513, then L21 on down are all negative, and we get this positive S7123 test, derived from the Nat Geo array. It’s kind of a tree busting result.

Update 2 — Mystery Solved.

From this link, we note that the normal S7123 mutation is an Adenine to Guanine replacement. Raw data from my Nat Geo data set shows I have a Cytosine there.

s7123-is-cytosine

So, it’s not a diagnostic S7123 change, but a random mutation that popped into the picture and causes some noise. There is a DF27 test upcoming, one ftDNA ordered and I didn’t pay for. Much appreciative of that. We’ll see what that brings. Perhaps a DF27+ and another test. At this point, it’s fair to say I’m not S7123 but P312 and need to wait a bit more.

 

 

gedmatch admixture testing.

Gedmatch allows you to test autosomal data against a variety of autosomal testing tools. The value of this is to see how different reference populations , and different DNA tools, affect the outcome. Some sets of reference populations give very different results when tested.

This is a result using the Eurogenes program and their most popular population model.

eurogenes_01

This is the result when I use the Harappa World model. This is a population set that favors people of African, Middle Eastern, and South Asian ancestry.

harappa_world_01

Note that if my father were Lebanese and my mother came from the Sudan, this would have been a far better model to pick. I’ve noted in my reading that Americans of African descent often prefer the Harappa World model to the others in the gedmatch set.

The point is, depending on where you come from, the commercial admixtures may or may not best represent what your genetics are. In particular, we’ve already noted there are marked differences in how someone with Micronesian bloodlines is handled by the major commercial services versus Nat Geo’s Genographic Project.

So you’re mostly Micronesian and want to know how Asian and European you are?

My wife is half Chamorro and half Japanese, so on her side of the family they generally have two questions. Is the paternal ancestor European or Chamorro, and how much European blood do they have? On top of that, a sane admixture result (how much Japanese, how much Chamorro, how much European) was desired, so that reasonable guesses could be made as to how far back the European blood was introduced.

We ran into the issue first with Ancestry DNA. They had her mostly Asian, and a hodge podge of other assignments. Dissatisfaction with the admixture results from Ancestry led us to export the data from Ancestry and put a copy of this data up on gedmatch. Testing different Admixtures with the gedmatch tools made it clear that without a reference population of Southeast Asians/Oceania, then any real attempts to separate these two was not going to work. Ancestry DNA evidently has a Polynesian reference but not really a true Austronesian reference, which really is needed for any people populated by the Austronesian expansion.

Nat Geo Genographic was pretty excellent. They have a Southeast Asia/Oceania reference population, and it has my wife with about 53% Asian, 36% Oceania, and 9% European.

Upon transferring that data to Family Tree DNA, that separation has been lost. She’s now 80+% Asian, 9% European, and 1% Native American.

So, in short:

Ancestry – probably OK if you’re Polynesian. If you’re Melanesian, Micronesian, Filipino, Vietnamese, from New Guinea, Ceylon, or Madagascar, probably not.

Net Geo Genographic – the best of the three, with a sane reference population

Family Tree DNA – in terms of admixture percentages, not worth it if you’re descended from Austronesian people.

Note: my wife, in various gedmatch tests, often turns up substantial percentages of Siberian blood. The Siberians are the population from which Native Americans came, so the 1% Native American says that there are still traces of genes found in Native American populations.

Intro to the project

Ok, my family are the Myers from Texas, and a specific branch of the Myers from Texas.  My parents were born in Granbury, Texas, in Hood County Texas. On my father’s side, we have been told from time immemorial that we’re descended from Germans, if you go back far enough. But is that true?

Traditional genealogy was the hobby of my Dad’s brother Tom, recently deceased. He could take us back to Charles Myers, born 1789 in Somerset, PA, and died 1857 in Missouri. Beyond that? I recall a comment on the Internet that Charles was a veteran of the War of 1812 and that is dad was Jacob Myers, a Revolutionary War veteran, from Philadelphia. Poking around various trees on Ancestry, I find that Jacob Myers is called Jacob Myers II on some, with a father named Jacob Myers. His birth is given as 1720, sometimes in England, sometimes not. My Dad’s brother was not sure that Jacob and Jacob II were real (see comment below).

 

So, are there ways we can trace back to Germany? The above is where traditional genealogy has gotten us. My father, some six years ago, was given as a birthday present a Y-DNA test from Family Tree DNA. It was a STR (Y-67) test, which if I understand correctly, is a check of hypervariable regions of the Y chromosome and thus useful for finding relations anywhere from 5 to 30+ generations back. Using this, my Dad found a relative named Ross, whose parental line gets lost in North Carolina in the 18th century.  Given how close they are on the 67 test, Ross and my Dad have a common ancestor perhaps 12 generations back, or less (88% by the 8th generation). But that isn’t the leap to get the family to Germany.

These days I’m more interested in defining the Myers haplogroup. I did the Nat Geo Geno 2.0+ test. but for Europeans it has holes. The biggest of these is the lack of the P312 SNP, which is a major European branch. So I’m waiting on more testing at the moment. We are P310 positive, according to Nat Geo.

Anyway, this is enough to introduce you to the problem.  I’ll have more specifics for later.

  • The Jacob Myers comment probably needs elaboration. The Jacob Myers that gets pointed to is a real person, but how that person, born in Maryland and supposedly in Philadelphia for some time, gets out to Somerset PA (closer to Pittsburgh, really) to father Charles is really the trick. Sometimes the ancient genealogies contain a lot of wishful thinking, like mothers that give birth at 3 years of age (yes, I’ve seen that too in various records).

Some useful links

This article may be edited over time. It will contain live links and anything I regard useful when starting.

Two summary articles about genetic testing companies.These largely touch on autosomal testing. Autosomal testing is good for about 5-6 generations. After that there are losses. Getting back to the 10th generation, it’s estimated that only 10% of the 1024 predecessors actually contribute autosomal DNA. A number of companies offer autosomal testing.

DNA Explained’s take.

Legal Genealogist’s take

Y-DNA and mtDNA testing go back further. When looking for relatives, DNA techniques examine hypervariable regions and look for matches. The depth of matching is much greater, perhaps 500 years. The search for haplotypes or haplogroups is a much deeper look into the past, and can go back thousands of years.

Mitochondrial DNA is small, a bit more than 16,000 base pairs. The Y chromosome (which, incidentally, is dying on a evolutionary time scale) has over 50 million base pairs.

Y-DNA tests. STR versus SNP. STR tests are hypervariable tests, SNPs are used to determine haplotype.

DNA Explained

Tribal Joyce. This one gives more information about how to compare STR data.

STR probabilities for idiots. Works up to Y67.

STR probabilities for a Y111 comparison.

The R1b problem, by Origin Hunters.

Eupedia on health effects of haplogroup K.

Charles Myers (b 1789) links.

Family Newsletter

Gedmatch.com 101 for folks using it for the first time.

More genealogical links:

Bob’s Genealogy Filing Cabinet can make a lot of colonial era norms a lot simpler, such as how they used Junior and Senior.

18th century German naming customs.

1897 Guam census

German Name Frequencies Online