10 Things to Do With Your DNAPrint, renamed AncestrybyDNA, Test

birdcage

Please note, AncestrybyDNA is NOT the same as the AncestryDNA test sold by Ancestry.com.  Both CeCe Moore and David Dowell have written about this in their respective blogs.

Back in 2002 (no, that is not a typo,) a new product called DNAPrint was introduced by a company then called DNAPrint Genomics.  It provided you, in percentages, your percentages of 4 ethnic groups: Indo-European, East-Asian, Native American and African.  Family Tree DNA remarketed this test for just over a year but ceased when they realized there were issues.

It was the first of its kind of test ever to be offered commercially, and version 2.0 utilized a whopping 71 ancestrally informative markers, according to the user’s guide delivered with the product.  The next version of the test, 2.5, titled AncestrybyDNA included 175 markers, and a third version, which I don’t believe was ever released, was to include just over 300 markers.

In 2002, this was a baby step in a brand new world.  We, as a community, were thrilled to be able to obtain this type of information.  And of course, we believed it was accurate, or relatively so.  However, the questions and ensuing debate started almost immediately and became very heated.

The company’s representatives indicated that East-Asian and Native American could be combined for those without a “Chinese grandpa” and that would have given me a whopping 25% Native American.  Even then, before pedigree analysis, I thought this was a little high.  My East Asian was shown as 15%, Native American at 10% and Indo-European at 75%.  For reference, my real Native results are probably in the 1-3% range.  Keep in mind that we were all babes in the woods, kind of stumbling around, learning, in 2002 and 2003.

Interestingly enough, I found the answer recently, quite by accident, to one of the burning questions about Native American ancestry that was asked repeatedly of Tony Frudakis during that timeframe, then a corporate officer of DNAPrint, and left unanswered.  In Carolyn Abraham’s book, The Juggler’s Children, which is a wonderful read, on page 55, the answer to the forever-hanging question was answered:

“When I finally reached Frudakis, that’s how he explained the confusion over our Native ancestry result – semantics.  The Florida company had pegged its markers as being Native American to appeal to the American market, he told me.  But it was accurate to consider them Central Asian markers, he said, that had been carried to different regions by those who migrated from that part of the globe long ago – into the Americas, into East Asia, South Asia and even southern Europe – finding their way into today’s Greeks, Italians and Turks.  ‘We may do ourselves a favour and change the name of this ancestry [component] in the test,’ he said, since apparently I wasn’t the only one baffled by it.”

So, now we know, straight from the horses mouth, via Carolyn.

Of course, since that time, many advances have occurred in this field.  Today, Family Tree DNA, 23andMe, Ancestry.com and the Genographic Project utilize chip based technology and utilize over half a million markers to achieve ethnicity predictions.  If DNAPrint, renamed AncestybyDNA was the first baby step, today we are teenagers – trying to refine our identity.  Today’s tests, although not totally accurate, are, by far, more accurate than this first baby step.  Give us another dozen years in this industry, and they’ll be spot on!

For 2003, when I ordered mine, DNAPrint was an adventure – it was exciting – it was a first step – and we learned a lot.  Unfortunately, DNAPrint under the name AncestrybyDNA is still being sold today, currently owned by the DNA Diagnostics Center.  If you are even thinking about ordering this product, take a look first at the Yelp reviews and the Better Business Bureau complaints.

I don’t regret spending the money in 2003.  Spending money on this outdated test today would be another story entirely – a total waste.  The results are entirely irrelevant today in light of the newer and more refined technology.  Unfortunately, seldom a week goes by that I don’t receive an e-mail from someone who bought this test and are quite confused and unhappy.  The test has been marketed and remarketed by a number of companies over the years.

So, here are some suggestions about what might be appropriate to do with your DNAPrint or AncestybyDNA results if you don’t want to just throw them away:

  1. Line the bottom of the birdcage.
  2. Use to light the BBQ grill or camp fire.
  3. Use under boots in the hallway in the winter.
  4. Shred, then use as confetti.
  5. Cut into strips and use as bookmarks.
  6. Use as scratch paper.
  7. Use in the garden between rows to minimize weeds.
  8. Make into a paper airplane.
  9. Roll, along with other excess paper, into logs for the fireplace.
  10. Frame, and display along with your other antiques.

Yes, it’s really that old and outdated!

Transfer DNA Results or Retest at Family Tree DNA?

confusionThe recent announcement by Ancestry.com that they are discontinuing their Y and mtDNA products and associated data bases, combined with the opportunity to transfer your Y and autosomal Y DNA results to Family Tree DNA has raised the question of whether it’s best to transfer or retest.  Let’s look at the various options, pluses and minuses, for each product involved.  As it turns out, one size does not fit all.  In other words, it depends…

Autosomal

The cost of an autosomal test transfer to Family Tree DNA is $69 and you can transfer either Ancestry.com’s autosomal test results or 23andMe’s v3 results to Family Tree DNA for that price.

However, the cost of retesting at Family Tree DNA, utilizing the Father’s Day sale, and yes, it’s valid for females too, not just men, is just $79.

So, should you transfer existing results or retest?

  1. If you retest at Family Tree DNA, you’ll have the added benefit of having your DNA archived there, available to you for other tests in the future. Archiving is free and is part of the service.
  2. If you retest at Family Tree DNA, you don’t have to deal with downloading files from Ancestry or 23andMe and then uploading them to Family Tree DNA. If you’re not a techie, this is a benefit.
  3. Ancestry has never been known for quality, so in terms of Ancestry, for a $10 difference, I would certainly retest.
  4. At 23andMe, if you tested either early (the v2 chip) or since November/December of 2013 (the v4 chip) you have no choice but to retest, because the results aren’t compatible.

In a nutshell, for a $10 difference, my vote would be to retest, unless, of course, the person isn’t available to retest then by all means, transfer the results.

If you’re going to retest, do it now while the price is still $79.  The sale ends on 6-17-2014.

Don’t forget, the Big Y, which is a nearly full sequence of the Y chromosome, is also on sale for Father’s Day for only $595.  The newly announced SNP matching in addition to the regular marker matching promises to add a second tool to those who are trying to determine family lineages.  I suggest that someone from each of your primary family surname lines take this test.  Mutations are being found every 90-150 years so this test holds great promised in combination with regular STR (37, 67 and 111 marker) testing.

Y DNA

You can transfer your Ancestry Y DNA results to Family Tree DNA for $19, and then upgrade to the Family Tree DNA standard marker test for another $39, for a total of $58.

If you transfer Ancestry’s 33 marker results, the $58 upgrade price buys you an upgrade to the 25 marker test.  If you transfer Ancestry’s 46 marker test, the upgrade buys you a standard 37 marker test.  Both of these upgrades include DNA matching to other participants.  The $19 transfer alone, does not, just the ability to join projects.

The standard 37 marker test at Family Tree DNA today costs $169 without the transfer, so transferring is definitely the way to go on Y DNA.  You save $111.  Plus, with the upgrade, you will have the added benefit of having your DNA archived at Family Tree DNA.

For Y DNA, a transfer with the upgrade is definitely your best value.  Don’t forget to do this before Sept. 5th because the Ancestry data base disappears that day.  In fact, the sooner, the better, because some of Ancestry’s DNA data base features have already been discontinued.

Mitochondrial DNA

Ancestry’s mtDNA test results weren’t compatible with Family Tree DNA’s, so you don’t have a transfer option.  The mtDNA plus at Family Tree DNA which provides you with your haplogroup and matches in the HVR1+HVR2 regions is $59, but the full sequence mitochondrial DNA test is only $199.  The full sequence test provides you with fully sequenced mitochondrial DNA results, about 10 times more locations than the HVR1+HVR2 regions, a full haplogroup designation and matching at the highest level.  It’s definitely the best value and then you’re done with mtDNA because there are no upgrades beyond the full sequence.

My recommendation would be to purchase the Full Sequence test for $199 as the best value.

The Net-Net

In short, here’s what we have:

  • Autosomal – you can retest at Family Tree DNA for $79, $10 more than the $69 transfer price, which has several benefits.
  • Y DNA – the transfer plus upgrade for $58 is your best value, saving you over $100.
  • Mitochondrial DNA – there is no transfer option, so retesting is necessary.

Click here to order.

Drunken Sailors and a Porcupine

I should have known when I heard the ship groaning in the night as it shifted from side to side.  But I knew unquestionably when I sat up in the morning and began to sway back and forth.  I remembered someone telling me once about falling out of the shower on a cruise ship.  I doubted it at the time, but as of this minute, I believe that entirely.

One crew member said that it’s always cold in these northern British Isles ports, even in summer, often wet and the water in the fall especially is “choppy.”  If this is just choppy, I’d hate to see worse.

So today, I’ve gained an appreciation for drunken sailors.  You see, they may not be drunk at all, simply seasick and staggering around trying to find and maintain their footing – or the closest bathroom.  Last night, John, the cruise director said he can always tell the drunks when it gets rough.  The people who are normally sober are all staggering around, but the drunks, they are all walking in a straight line, referred to, appropriately, as “the line of experience.”  Obviously, I simply don’t drink enough!

In any case, it’s been an exceedingly rough day at sea. I spent the morning staring out the window at the horizon trying to keep the Dramamine down.  I called the spa to cancel my “happy birthday to me” massage for today since I “wasn’t feeling well.”  When I called, they told me that acupuncture cures seasickness, right after they told me that the cancellation charge was the same amount as the original spa charge.  I had my doubts, believe me, but I was so sick and miserable I was willing to try just about anything, so off to the spa I staggered – plus I was paying for it whether I went or not – so why not try acupuncture.  I couldn’t feel much worse.

Actually, I had my husband deliver me.  The wind was blowing so hard they had the outside decks closed.  The wind is howling like an unhappy banshee in the deepest Michigan winter blizzard.  That’s on the inside, sheltered deck with the open roof that can’t be closed over the pool area.  The outside is worse and unsafe, which is why it’s closed. The spa is on the other side so you have to walk through the open roof area.  If I was going to blow away, I wanted him to be with me.  I figured two of us stood a much better chance of hanging on and well, we were much heavier together and more difficult to get aloft like giant inflatable kites.

These ships were not made for winter, in fact, they have no heaters for the rooms.  You can have A/C or “regular air” which is whatever the air temperature is, recycled.  It’s in the 50s today.  I’ve taken to sleeping in my sweatshirt and wool socks with the bathrobe thrown on top of the blankets for extra warmth and I was finally warm enough last night.  If they were selling parkas, they would make a fortune because it wouldn’t matter how much they cost.  I swear to you, I saw a crew member today wearing gloves.

Tell me why I’m doing this again???  Oh yes, it’s a DNA trip, to find my ancestor’s lands and share their experiences.  And yes, some of them were mariners.  Probably, knowing my family, the ones walking in a straight line.  Ugh.  I could have passed on this particular shared experience, but no, this had to be authentic.

So after arriving at the spa, off with most of the clothes (brrrr) and in with the acupuncture needles.  There were needles in my face, in my ears and in my hands and feet including between my eyebrows and between my toes.  As I lay there, looking like a distant relative of the porcupine family and afraid to move for fear of impaling myself, the thought crossed my mind that not only did I do this of my own choosing, but worse yet, I’m paying for the opportunity.  I tried to fall asleep, which is difficult with a bunch of needles sticking in your skin.  Basically, they poke you like a pin cushion, turn the lights off, come back in about an hour and collect money for doing so.

Now the good news is that I did and do feel better.  I’m still staggering around like a drunken sailor, or what I previously thought was a drunken sailor, but I’m not sick. By mid-afternoon, after my spa treatment, food even sounded good, so I went up to the lounge deck with floor to ceiling windows and had a snack.  Yes indeed, things are improving for the old porcupine.  But the sea is quite rough again as we have left the shelter of the Isle of Skye and other islands off Ireland and are in the open North Atlantic now.  It may be rough, but it’s still exceedingly beautiful.

rough seas

This reminded me of another time, years ago, when my kids were young and we had saved enough to take everyone salmon fishing in Lake Michigan.  We chartered a boat for the day, and we invited my Mom and (step)Dad to join us.  For my Dad, who loved to fish, this was a wonderful opportunity he had never enjoyed before – and maybe he’d catch something more interesting than catfish and bluegill in the farm pond at home.

We spent the night before in a local bed and breakfast and got up early to begin our much-anticipated adventure.  I gave everyone in the family Dramamine, everyone that was, except my mother.  She refused, saying that she didn’t get sea sick.  I encouraged her to take it anyway, but she would have none of that.

You know what happened don’t you?  She turned green as pea soup – and not only was she miserable – so were the rest of us.  It’s hard to have fun when someone is so ill.  So we went back to shore, Mom and Dad departed for home, despite our protests, and the rest of us went fishing.  We caught and froze some salmon for Dad, but it just wasn’t the same as catching those fish himself.

However, this made me wonder – is motion sickness hereditary?  I have suffered with it all of my life.  My first memories of it are riding in a car when I was quite young, pre-school.  I still suffer from this same problem.  Mine is much worse than Mom’s was.

According to 23andMe, indeed motion sickness is hereditary.

In a paper presented at the 2012 ASHG Meeting, they state that:

Roughly one in three individuals is highly susceptible to motion sickness; the remaining two-thirds of the population may experience motion sickness if the conditions are extreme.

It’s estimated that up to 70% of a person’s risk for motion sickness is due to genetics, but the genetics of motion sickness has been very poorly understood … until now.

23andMe scientist Bethann Hromatka presented results from a genetic study of nearly 37,000 customers who were surveyed about motion sickness. The analysis identified 14 genetic associations with motion sickness that fall into a few different biological categories. Three genetic variants are involved in development, including development of the eye and ear. Other variants are involved neurological processes and glucose/insulin regulation.

Aha, I knew it. I get to blame my mother, and maybe my father for this unfortunate inherited trait – but I’m guessing my Estes mariner ancestors didn’t carry it – or they wouldn’t have been mariners.  But, according to Mother, she wasn’t motion sick, she simply had “an inner ear problem.”  Uh, yea, Mom, you did.  A rose by any other name…

Now, I wonder why acupuncture helps relieve the symptoms?  The crew, who also take these treatments because they have to keep working, says that one acupuncture treatment works for days too.  Although truthfully, I don’t care why.  I’m just glad that it does.  Given that the condition is genetic, I’ll probably be blessed with it the rest of my life so it’s nice to have a tool, any tool.

During the rest of the day, we were treated to a rainbow several times.  The end of the rainbow always seemed to wind up in the restrooms on the lower decks.  Not sure what to make of that pot-o-gold.  I guess it was near the casino.  The rainbow didn’t photograph well through the glass, but you get the idea.  It was pleasant and hopeful to see after not feeling so well.

OLYMPUS DIGITAL CAMERA

Our towel guy tonight has, what else…no, not acupuncture needles, although that certainly would have been appropriate.  Ginger snaps to help with seasickness, Bonine (which also costs far more on this ship than an outfit at Kohl’s) and chocolate covered strawberries – the last 3 on the ship.  Well, after all, it was my belated birthday present.  Acupuncture, ginger snaps and chocolate-covered strawberries. Who could ask for more!

Tomorrow, solid ground again.  We’re going to Urquhart Castle.  Hope you’re coming along!

OLYMPUS DIGITAL CAMERA

Finding Native American Ethnic Results in Germanic People

I’m often asked about the significance of small percentages of autosomal DNA in results.  Specifically, the small percentages are often of Native American or results that would suggest Native admixture.  One of the first questions I always ask is whether or not the individual has Germanic or eastern European admixture.

Why?

Take a look at this map of the Invasion of the Roman Empire.  See the Huns and their path?

Hun map

It’s no wonder we’re so admixed.

Here’s a map of the Hunnic empire at its peak under Attila between the years 420-469.

Hun emplire

But that wasn’t the end of the Asian invasions.  The Magyars, who settled in Hungary arrived from Asia as well, in the 800s and 900s, as shown on this map from LaSalle University.

magyar map

Since both the Hungarians and some Germanic people descend from Asian populations, as do Native Americans, albeit thousands of years apart, it’s not unrealistic to expect that, as populations, they share a genetic connection.

Therefore, when people who carry heritage from this region of the world show small amounts of Native or Asian origin, I’m not surprised.  However, for Americans, trying to sort out their Native ethnic heritage, this is most unhelpful.

Let’s take a look at the perfect example candidate.  This man is exactly half Hungarian and half German.  Let’s see what his DNA results say, relative to any Asian or Native heritage, utilizing the testing companies and the free admixture tools at www.gedmatch.com.

He has not tested at Ancestry, but at Family Tree DNA, his myOrigins report 96% European, 4% Middle Eastern.  At 23andMe in speculative view, he shows 99.7 European and .2 sub-saharan African.

Moving to the admixture tools at GedMatch, MDLP is not recommended for Asian or Native ancestry, so I have excluded that tool.

Eurogenes K13 is the most recently updated admixture tool, so let’s take a look at that one first.

Eurogenes K13

 JK Eurogenes K13 v2

Eurogenes K13 showed 7% West Asian, which makes perfect sense considering his heritage, but it might be counted as “Native” in other circumstances, although I would certainly be very skeptical about counting it as such.

However, East Asian, Siberian and Amerindian would all be amalgamated into the Native American category, for a combined percentage of 1.31.

jk eurogenes k13 chart

However, selecting the “admixture proportions by chromosome” view shows something a bit different.  The cumulative percentages, by chromosome equate to 10.10%.  Some researchers mistakenly add this amount and use that as their percentage of Native ancestry.  This is not the case, because those are the portions of 100% of each individual chromosome, and the total would need to be divided by 22 to obtain the average value across all chromosomes.  The total is irrelevant, and the average may not reflect how the developer determines the amount of admixture because chromosomes are not the same size nor carry the same number of SNPs.  Questions relative to the functional underpinnings of each tool should be addressed to the developers.

Dodecad

I understand that there is a newer version of Dodecad, but that it has not been submitted to GedMatch for inclusion, per a discussion with GedMatch.  I can’t tell which of the Dodecad versions on GedMatch is the most current, so I ran the results utilizing both v3 and 12b.

jk dodecad v3

jk dodecad v3 chart

I hope v3 is not the most current, because it does not include any Native American category or pseudocategory – although there is a smattering of Northeast Asian at .27% and Southwest Asian at 1%.

Dodecad 12b below

jk dodecad 12b

The 12b version does show .52% Siberian and 2.6% Southwest Asian, although I’m not at all sure the Southwest Asian should be included.

HarappaWorld

jk harappaworld

jk harappaworld chart

Harappaworld shows .09 Siberian, .27% American (Native American), .23% Beringian and 1.8% Southwest Asian, although I would not include Southwest Asian in the Native calculation.

In Summary

Neither Family Tree DNA nor 23andMe find Native ancestry in our German/Hungarian tester, but all 3 of the admixture tools at Gedmatch find either small amounts of Native or Asian ancestry that could certainly be interpreted as Native, such as Siberian or Beringian.

Does this mean this German/Hungarian man has Native American ancestry?  Of course not, but it does probably mean that the Native population and his ancestral populations did share some genes from the same gene pool thousands of years ago.

While you might think this is improbable, or impossible, consider for a minute that every person outside of Africa today carries some percentage of Neanderthal DNA, and all Europeans also carry Denisovan DNA.  Our DNA does indeed have staying power over the millennia, especially once an entire population or group of people is involved.  We’ve recently seen this same type of scenarios in the full genome sequencing of a 24,000 year old Siberian male skeleton.

Our German/Hungarian man carries 2.4% Neanderthal DNA according to 23andMe and 2.7% according to the Genographic Project, which also reports that he carries 3.9% Denisovan.  The European average is about 2% for Neanderthal.

The net-net of this is that minority admixture is not always what it seems to be, especially when utilizing autosomal DNA to detect small amounts of Native American admixture.  The big picture needs to be taken into consideration.  Caution is advised.

When searching for Native admixture, when possible, both Y DNA and mitochondrial DNA give specific answers for specific pedigree lines relative to ancestry.  Of course, to utilize Y or mtDNA, the tester must descend from the Native ancestor either directly paternally to test the male Y chromosome, or directly matrilineally to test the mitochondrial line.  You can read about this type of testing, and how it works, in my article, Proving Native American Ancestry Using DNA.  You can also read about other ways to prove Native ancestry using autosomal DNA, including how to unravel which pedigree line the Native ancestry descends from, utilizing admixture tools, in the article, “The Autosomal Me.”

Ethnicity Percentages – Second Generation Report Card

Recently, Family Tree DNA introduced their new ethnicity tool, myOrigins as part of their autosomal Family Finder product.  This means that all of the major players in this arena using chip based technology (except for the Genographic project) have now updated their tools.  Both 23andMe and Ancestry introduced updated versions of their tools in the fall of 2013.  In essence, this is the second generation of these biogeographical or ethnicity products.  So lets take a look and see how the vendors are doing.

In a recent article, I discussed the process for determining ethnicity percentages using biogeographical ancestry, or BGA, tools.  The process is pretty much the same, regardless of which vendor’s results you are looking at.  The variant is, of course, the underlying population data base, it’s quality and quantity, and the way the vendors choose to construct and name their regions.

I’ve been comparing my own known and proven genealogy pedigree breakdown to the vendors results for some time now.  Let’s see how the new versions stack up to a known pedigree.

The paper, “Revealing American Indian and Minority Heritage using Y-line, Mitochondrial, Autosomal and X Chromosomal Testing Data Combined with Pedigree Analysis” was published in the Fall 2010 issue of JoGG, Vol. 6 issue 1.

The pedigree analysis portion of this document begins about page 8.  My ancestral breakdown is as follows:

Geography Pedigree Percent
Germany 23.8041
British Isles 22.6104
Holland 14.5511
European by DNA 6.8362
France 6.6113
Switzerland 0.7813
Native American 0.2933
Turkish 0.0031

This leaves about 25% unknown.

Let’s look at each vendor’s results one by one.

23andMe

23andme v2

My results using the speculative comparison mode at 23andMe are shown in a chart, below.

23andMe Category 23andMe Percentage
British and Irish 39.2
French/German 15.6
Scandinavian 7.9
Nonspecific North European 27.9
Italian 0.5
Nonspecific South European 1.6
Eastern European 1.8
Nonspecific European 4.9
Native American 0.3
Nonspecific East Asian/Native American 0.1
Middle East/North Africa 0.1

At 23andMe, if you have questions about what exact population makes up each category, just click on the arrow beside the category when you hover over it.

For example, I wasn’t sure exactly what comprises Eastern European, so I clicked.

23andme eastern europe

The first thing I see is sample size and where the samples come from, public data bases or the 23andMe data base.  Their samples, across all categories, are most prevalently from their own data base.  A rough add shows about 14,000 samples in total.

Clicking on “show details” provides me with the following information about the specific locations of included populations.

23andme pop

Using this information, and reorganizing my results a bit, the chart below shows the comparison between my pedigree chart and the 23andMe results.  In cases where the vendor’s categories spanned several of mine, I have added mine together to match the vendor category.  A perfect example is shown in row 1, below, where I added France, Holland, Germany and Switzerland together to equal the 23andMe French and German category.  Checking their reference populations shows that all 4 of these countries are included in their French and German group.

Geography Pedigree Percent 23andMe %
Germany, Holland, Switzerland & France 45.7451 15.6
France 6.6113 (above) Combined
Germany 23.8014 (above) Combined
Holland 14.5511 (above) Combined
Switzerland 0.7813 (above) Combined
British Isles 22.6104 39.2
Native American 0.2933 0.4 (Native/East Asian)
Turkish 0.0031 0.1 (Middle East/North Africa)
Scandinavian 7.9
Italian 0.5
South European 1.6
East European 1.8
European by DNA 6.8362 4.9 (nonspecific European)
Unknown 25 27.9 (North European)

I can also change to the Chromosome view to see the results mapped onto my chromosomes.

23andme chromosome view

The 23andMe Reference Population

According to the 23andMe customer care pages, “Ancestry Composition uses 31 reference populations, based on public reference datasets as well as a significant number of 23andMe members with known ancestry. The public reference datasets we’ve drawn from include the Human Genome Diversity ProjectHapMap, and the 1000 Genomes project. For these datasets as well as the data from 23andMe, we perform filtering to ensure accuracy.

Populations are selected for Ancestry Composition by studying the cluster plots of the reference individuals, choosing candidate populations that appear to cluster together, and then evaluating whether we can distinguish the groups in practice. The population labels refer to genetically similar groups, rather than nationalities.”

Additional detailed information about Ancestry Composition is available here.

Ancestry.com

ancestry v2

Ancestry is a bit more difficult to categorize, because their map regions are vastly overlapping.  For example, the west Europe category is shown above, and the Scandinavian is shown below.

ancestry scandinavia

Both categories cover the Netherlands, Germany and part of the UK.

My Ancestry percentages are:

Ancestry Category Ancestry Percentage
North Africa 1
America <1
East Asia <1
West Europe 79
Scandinavia 10
Great Britain 4
Ireland 2
Italy/Greece 2

Below, my pedigree percentages as compared to Ancestry’s categories, with category adjustments.

Geography Pedigree Percent Ancestry %
West European 52.584 (combined from below) 79
Germany 23.8041 Combined
Holland 14.5511 Combined
European by DNA 6.8362 Combined
France 6.6113 Combined
Switzerland 0.7813 Combined
British Isles 22.6104 6
Native American 0.2933 ~1 incl East Asian
Turkish 0.0031 1 (North Africa)
Unknown 25
Italy/Greece 2
Scandinavian 10

Ancestry’s European populations and regions are so broadly overlapping that almost any interpretation is possible.  For example, the Netherlands could be included in several categories – and based up on the history of the country, that’s probably legitimate.

At Ancestry, clicking on a region, then scrolling down will provide additional information about that region of the world, both their population and history.

The Ancestry Reference Population

Just below your ethnicity map is a section titled “Get the Most Out of Your Ethnicity Estimate.”  It’s worth clicking, reading and watching the video.  Ancestry states that they utilized about 3000 reference samples, pared from 4245 samples taken from people whose ethnicity seems to be entirely from that specific location in the world.

ancestry populations

You can read more in their white paper about ethnicity prediction.

Family Tree DNA’s myOrigins

I wrote about the release of my Origins recently, so I won’t repeat the information about reference populations and such found in that article.

myorigins v2

Family Tree DNA shows matches by region.  Clicking on the major regions, European and Middle Eastern, shown above, display the clusters within regions.  In addition, your Family Finder matches that match your ethnicity are shown in highest match order in the bottom left corner of your match page.

Clicking on a particular cluster, such as Trans-Ural Peneplain, highlights that cluster on the map and then shows a description in the lower left hand corner of the page.

myorigins trans-ural

Family Tree DNA shows my ethnicity results as follows.

Family Tree DNA Category Family Tree DNA Percentage
European Coastal Plain 68
European Northlands 12
Trans-Ural Peneplain 11
European Coastal Islands 7
Anatolia and Caucus 3

Below, my pedigree results reorganized a bit and compared to Family Tree DNA’s categories.

Geography Pedigree Percent Family Tree DNA %
European Coastal Plain 45.7478 68
Germany 23.8041 Combined above
Holland 14.5511 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
British Isles 22.6104 7 (Coastal Islands)
Turkish 0.0031 3 (Anatolia and Caucus)
European by DNA 6.8362
Native American 0.2933
Unknown 25
Trans-Ural Peneplain 11
European Northlands 12

Third Party Admixture Tools

www.GedMatch.com is kind enough to include 4 different admixture utilities, contributed by different developers, in their toolbox.  Remember, GedMatch is a free, meaning a contribution site – so if you utilize and enjoy their tools – please contribute.

On their main page, after signing in and transferring your raw data files from either 23andMe, Family Tree DNA or Ancestry, you will see your list of options.  Among them is “admixture.”  Click there.

gedmatch admixture

Of the 4 tools shown, MDLP is not recommended for populations outside of Europe, such as Asian, African or Native American, so I’ve skipped that one entirely.

gedmatch admix utilities

I selected Admixture Proportions for the part of this exercise that includes the pie chart.

The next option is Eurogenes K13 Admixture Proportions.  My results are shown below.

Eurogenes K13

Eurogenes K13

Of course, there is no guide in terms of label definition, so we’re guessing a bit.

Geography Pedigree Percent Eurogenes K13%
North Atlantic 75.19 44.16
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.74 combined East Asian, Siberian, Amerindian and South Asian
Turkish 0.0031 1.78 Red Sea
Unknown 25
Baltic 24.36
West Med 14.78
West Asian 6.85
Oceanian 0.86

Dodecad K12b

Next is Dodecad K12b

According to John at GedMatch, there is a more current version of Dodecad, but the developer has opted not to contribute the current or future versions.

Dodecad K12b

By the way, in case you’re wondering, Gedrosia is an area along the Indian Ocean – I had to look it up!

Geography Pedigree Percent Dodecad K12b
North European 75.19 43.50
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 3.02 Siberian, South Asia, SW Asia, East Asia
Turkish 0.0031 10.93 Caucus
Gedrosia 7.75
Northwest African 1.22
Atlantic Med 33.56
Unknown 25

Third is Harappaworld.

Harappaworld

harappaworld

Baloch is an area in the Iranian plateau.

Geography Pedigree Percent Harappaworld %
Northeast Euro 75.19 46.58
Germany 23.8041 Combined above
British Isles 22.6104 Combined above
Holland 14.5511 Combined above
European by DNA 6.8362 Combined above
France 6.6113 Combined above
Switzerland 0.7813 Combined above
Native American 0.2933 2.81 SE Asia, Siberia, NE Asian, American, Beringian
Turkish 0.0031 10.27
Unknown 25
S Indian 0.21
Baloch 9.05
Papuan 0.38
Mediterranean 28.71

The wide variety found in these results makes me curious about how my European results would be categorized using the MDLP tool, understanding that it will not pick up Native, Asian or African.

MDLP K12

mdlp k12

The Celto-Germanic category is very close to my mainland European total – but of course, many Germanic people settled in the British Isles.

Second Generation Report Card

Many of these tools picked up my Native American heritage, along with the African.  Yes, these are very small amounts, but I do have several proven lines.  By proven, I mean both by paper trail (Acadian church and other records) and genetics, meaning Yline and mtDNA.  There is no arguing with that combination.  I also have other Native lines that are less well proven.  So I’m very glad to see the improvements in that area.

Recent developments in historical research and my mitochondrial DNA matches show that my most distant maternal ancestral line in Germany have some type of a Scandinavian connection.  How did this happen, and when?  I just don’t know yet – but looking at the map below, which are my mtDNA full sequence matches, the pattern is clear.

mitomatches

Could the gene flow have potentially gone the other direction – from Germany to Scandinavia?  Yes, it’s possible.  But my relatively consistent Scandinavian ethnicity at around 10% seems unlikely if that were the case.

Actually, there is a second possibility for additional Scandinavian heritage and that’s my heavy Frisian heritage.  In fact, most of my Dutch ancestors in Frisia were either on or very near the coast on the northernmost part of Holland and many were merchants.

I also have additional autosomal matches with people from Scandinavia – not huge matches – but matches just the same – all unexplained.  The most notable of which, and the first I might add, is with my friend, Marja.

It’s extremely difficult to determine how distant the ancestry is that these tests are picking up.  It could be anyplace from a generation ago to hundreds of generations ago.  It all depends on how the DNA was passed, how isolated the population was, who tested today and which data bases are being utilized for comparison purposes along with their size and accuracy.  In most cases, even though the vendors are being quite transparent, we still don’t know exactly who the population is that we match, or how representative it is of the entire population of that region.  In some cases, when contributed data is being used, like testers at 23andMe, we don’t know if they understood or answered the questions about their ancestry correctly – and 23andMe is basing ethnicity results on their cumulative answers.  In other words, we can’t see beneath the blanket – and even if we could – I don’t know that we’d understand how to interpret the components.

So Where Am I With This?

I knew already, through confirmed paper sources that most of my ancestry is in the European heartland – Germany, Holland, France as well as in the British Isles.  Most of the companies and tools confirm this one way or another.  That’s not a surprise.  My 35 years of genealogical research has given me an extremely strong pedigree baseline that is invaluable for comparing vendor ethnicity results.

The Scandinavian results were somewhat of a surprise – especially at the level in which they are found.  If this is accurate, and I tend to believe it is present at some level, then it must be a combined effect of many ancestors, because I have no missing or unknown ancestors in the first 5 generations and only 11 of 64 missing or without a surname in generation 6.  Those missing ancestors in generation 6 only contribute about 1.5% of my DNA each, assuming they contribute an average of 50% of their DNA to offspring in each subsequent generation.

Clearly, to reach 10%, nearly all of my missing ancestors, in the US and Germany, England and the Netherlands would have to be 100% Scandinavian – or, alternately, I have quite a bit scattered around in many ancestors, which is a more likely scenario.  Still, I’m having a difficult time with that 10% number in any scenario, but I will accept that there is some Scandinavian heritage one way or another.  Finding it, however, genealogically is quite another matter.

However, I’m at a total loss as to the genesis of the South European and Mediterranean.  This must be quite ancient.  There are only two known possible ancestors from these regions and they are many generations back in time – and both are only inferred with clearly enough room to be disproven.  One is a possible Jewish family who went to France from Spain in 1492 and the other is possibly a Roman soldier whose descendants are found within a few miles of a Roman fort site today in Lancashire.  Neither of these ancestors could have contributed enough DNA to influence the outcome to the levels shown, so the South European/Mediterranean is either incorrect, or very deep ancestry.

The Eastern European makes more sense, given my amount of German heritage.  The Germans are well known to be admixed with the Magyars and Huns, so while I can’t track it or prove it, it also doesn’t surprise me one bit given the history of the people and regions where my ancestors are found.

What’s the Net-Net of This?

This is interesting, very interesting.  There are tips and clues buried here, especially when all of the various tools, including autosomal matching, Y and mtDNA, are utilized together for a larger picture.  Alone, none of these tools are as powerful as they are combined.

I look forward to the day when the reference populations are in the tens of thousands, not hundreds.  All of the tools will be far more accurate as the data base is built, refined and utilized.

Until then, I’ll continue to follow each release and watch for more tips and clues – and will compare the various tools.  For example, I’m very pleased to see Family Tree DNA’s new ethnicity matching tool incorporated into myOrigins.

I’ve taken the basic approach that my proven pedigree chart is the most accurate, by far, followed by the general consensus of the combined results of all of the vendors.  It’s particularly relevant when vendors who don’t use the same reference populations arrive at the same or similar results.  For example, 23andMe uses primarily their own clients and Nat Geo of course, although I did not include them above because they haven’t released a new tool recently, uses their own population sample results.

National Geographic’s Geno2

Nat Geo took a bit of a different approach and it’s more difficult to compare to the others.  They showed my ethnicity as 43% North European, 36% Mediterranean and 18% Southwest Asian.

nat geo results

While this initially looks very skewed, they then compared me to my two closest populations, genetically, which were the British and the Germans, which is absolutely correct, according to my pedigree chart.  Both of these populations are within a few percent of my exact same ethnicity profile, shown below.

Nat geo british 2

The description makes a lot of sense too.  “The dominant 49% European component likely reflects the earliest settlers in Europe, hunter-gatherers who arrived there more than 35,000 years ago.  The 44% Mediterranean and the 17% Southwest Asian percentages arrived later, with the spread of agriculture from the Fertile Crescent in the middle East, over the past 10,000 years.  As these early farmers moved into Europe, they spread their genetic patterns as well.”

nat geo german

So while individually, and compared to my pedigree chart, these results appear questionable, especially the Mediterranean and Southwest Asian portions, in the context of the populations I know I descend from and most resemble, the results make perfect sense when compared to my closest matching populations.  Those populations themselves include a significant amount of both Mediterranean and Southwest Asian.  Looking at this, I feel a lot better about the accuracy of my results.  Sometimes, perspective makes a world of difference.

It’s A Wrap

Just because we can’t exactly map the ethnicity results to our pedigree charts today doesn’t mean the results are entirely incorrect.  It doesn’t mean they are entirely correct, either.  The results may, in some cases, be showing where population groups descend from, not where our specific ancestors are found more recently.  The more ancestors we have from a particular region, the more that region’s profile will show up in our own personal results.  This explains why Mediterranean shows up, for example, from long ago but our one Native ancestor from 7 or 8 generations ago doesn’t.  In my case, it would be because I have many British/German/Dutch lines that combine to show the ancient Mediterranean ancestry of these groups – where I have many fewer Native ancestors.

Vendors may be picking up deep ancestry that we can’t possible know about today – population migration.  It’s not like our ancestors left a guidebook of their travels for us – at least – not outside of our DNA – and we, as a community, are still learning exactly how to read that!  We are, after all, participants on the pioneering, leading edge of science.

Having said that, I’ll personally feel a lot better about these kinds of results when the underlying technology, data bases and different vendors’ tools mature to the point where there the differences between their results are minor.

For today, these are extremely interesting tools, just don’t try to overanalyze the results, especially if you’re looking for minority admixture.  And if you don’t like your results, try a different vendor or tool, you’ll get an entirely new set to ponder!

What Does “Sharing Genomes” at 23andMe Mean?

underpantsOne of the comments to my posting about 23andMe Producing a 10% Response Rate when contacting matches mentioned that the phrase “share genomes” was really an “overly dramatic, scary and inaccurate phrase.” I never really thought about that before, but that commenter is right. And fear of the unknown is likely frightening some people. Comments since then have conveyed the same concerns. Are people you “share genomes” with going to see you in your genetic underpants???

I’ve condensed another commenter’s statements below:

“I would like to know in advance how much of my info will be available to strangers. The process needs to be better explained to newbies, to reassure us about what is public and what can be kept private, while still participating in the sharing. A bridge is needed between the DNA-for-dummies introductory videos apparently made by the producers of Sesame Street, and the over-our-heads fine detail in the white paper. There’s a wide gap there.”

I agree, and so I’d like to show the basics of what “sharing genomes” means.

Big caveat and disclaimer – I don’t’ work for 23andMe nor do I have any relationship with them other than as a consumer and as a consultant who has recommended their tests in the past generally relative to health and sometimes for ancestry. I have no inside information. This is accurate, to the best of my knowledge, but 23andMe could change their website and/or internal processes at any minute and it might not be accurate anytime in the future. Furthermore, I could have missed something. If so, and if it is brought to my attention, I will update this information.

The titles for each of these sections indicate the various series of clicks you’ll need to do to access the data shown below the title.

When you choose to share your genome with someone, they will be able to see the following information about you, arranged by tab at 23and Me. Note that their tabs for Ancestry information show up in two areas:

My Results, Ancestry Overview 

Sharing genomes 1

Family and Friends, then DNA Relatives and Family Traits

sharing genomes 2

Several of these are rather frivolous.  Gene Comparison has been obsoleted/removed.  However,  there are a couple that are very important to genealogists.

My Results, Ancestry Overview, Ancestry Tools

Countries of Ancestry

Countries of ancestry shows where you match someone whose 4 grandparents were from the same location.

Sharing genomes 3

23andMe provides the following caveat about your data.

sharing genomes 4

If you elect to download the data for the person you’ve selected, it looks like this.

sharing genomes 4.1

As you can see, many people remain anonymous. This is a list of the people who match this person selected, and the segments that are listed as entirely Spanish, or UK, for example. This could be useful to you if you find the names of some of your matches, or if you would decide to include this information in your matching spreadsheet. I don’t utilize this information in my spreadsheet, because I don’t feel that grandparents living in one location is terribly useful, although at least one of my matches is utilizing this information. This does not mean that your ancestors or the DNA you inherited in this location (on half of the chromosome in question) is from this location, but it could provide a clue. I can say without a doubt that in the case of some of the Netherlands segments, those did come from my mother’s Dutch lines. Please note that these measurements are in mega-base pairs, NOT in centiMorgans, and will not match up with your spreadsheet segments exactly for that reason.

My Results, Ancestry Overview, Ancestry Tools

Family Inheritance: Advanced (FIA)

This is the primary tool utilized by genealogists.

Utilizing the FIA tool, you can see how up to three different people’s DNA compares against yours. Below, my half-sister’s granddaughter on my father’s side (blue) is compared with my first cousin (once removed) on my mother’s side (green). Of note, they both share with me on some of the same segments, specifically chromosome 5, 7, 11 and 17. That’s not unexpected, because both halves of my chromosomes are showing here, Moms and Dads.

Sharing genomes 5

To see if they actually do match each other, or if their matches are to me on Mom’s and Dad’s side, separately, we check to see if they also match each other.

They do, on one segment, suggesting that they may share a common ancestor that is likely not shared with me. How do we know this? Because their match to each other is on chromosome 19, and their matches in common to me are not on chromosome 19. This means that their matches to me on common chromosomes are simply because one is matching me on Mom’s side and one on Dad’s. Their match to each other on chromosome 19 would need to be investigated separately. As it turns out, I did notice a surname in common in both of their trees, a line that is not shared with me.

Sharing genomes 6

From the above screen, you can’t see segment start and stop numbers, but utilizing the www.dnagedcom.com utility, below, you can download your matches segments to each other by entering your name in the profile (exactly including capital letters) and the person you want to see in the FIA match field. This means you will see all of the matches of your matches to each other. You will NOT see matches for this person outside of those they match in common with you and only for those who are sharing their genomes. You will NOT see anyone who is not sharing genomes.

sharing genomes 7

My cousin’s downloaded match file looks like this, minus the green shading, and plus full names, which I’ve redacted.

Sharing genomes 8

This is extremely useful because it allows me to see exactly where on the segments that my matches match each other. These are shaded green. This allows me to compare exactly where they match each other, and me. If they match each other, and me, on the same segment, that indicates that we share a common ancestor at that location. So, in this case, my cousin, whose FIA record this is, matches me, William and Diana on a common segment of chromosome 4. She matches me, Sean and Sheila on 5. They don’t have to match exactly, just on some overlapping piece.

Note that this tells us that the segments that I colored green are true matches, as my cousin matches both me and these other individuals at these locations, indicating we share a common ancestor. In some cases, based on genealogy or knowing the person in question, I can tell you exactly from looking at the common matches which lines the people who match come from. This is the goal and the power of chromosome mapping.

My Results, Ancestry Overview, Ancestry Tools

Global Similarity Map

You can see the Global Similarity Map of the people you are sharing genomes with.

sharing genomes 9

My Results, Ancestry Overview, Ancestry Tools

Neanderthal Ancestry

Your matches can, gasp, see your percentage of Neanderthal ancestry.

Sharing genomes 10

Maternal Line, Paternal Line and DNA Relatives Page

People with whom you share can see your haplogroup on both the maternal and paternal line, page (under the My Results, Ancestry Overview tab,) and they can also see it on the DNA Relatives main match page (under the Family and Friends tab.) Mine is shown below, but if I were a male, it would also include the Y haplogroup. One useful feature on the Maternal and Paternal pages is that you can see your matches sorted by haplogroup which in some cases, especially with a rare haplogroup, maybe a clue as to how you are related, either matrilineally or patrilineally.

Sharing genomes 11

Family and Friends, Family Traits

You can see if you match someone by selecting between traits, such as bitter taste, circadian rhythm, endurance, etc. to see if you share any of the genes for a specific trait such as bitter tasting ability, circadian rhythm, endurance, female fertility, immune system compatibility, non-bitter tasting, pigmentation and weight/body mass index or any set of genes you enter specifically by number.

This shows me compared to my sister’s granddaughter for weight/BMI.

Sharing genomes 12

23andMe Discusses Genome Sharing

What does 23andMe have to say about genome sharing? Here are links

How does genome sharing work? https://customercare.23andme.com/entries/21242872

Learn more and what should I know? https://23andme.zendesk.com/entries/21251933

Family and Friends, Manage Sharing

You can see who you are sharing with. I never share health reports, although I would consider it if someone had a good reason for asking.

Sharing genomes 14

You can manage your sharing by clicking on the green “share your genome” button in the upper right hand corner or by simply accepting a share request.

In Summary

I hope this quick spin-through of “sharing genomes” at 23andMe has been helpful. There is nothing frightening about sharing your genome at 23andMe and if you want to be able to make a sound genealogical connection, it’s necessary. You’re not sharing your entire genome, or your raw data, only selected parts where you match people with whom you are related.

The most frightening part of genetic genealogy is if you discover that you’re related to someone you wish you weren’t, or you’re not related to someone you thought you were. But if you’re playing in the genealogy field, especially the genetic genealogy field, that is a constant consideration and one we’re all aware of.

Happy Ancestor Hunting through genome sharing.

Haplogroup Comparisons Between Family Tree DNA and 23andMe

Recently, I’ve received a number of questions about comparing people and haplogroups between 23andMe and Family Tree DNA.  I can tell by the questions that a significant amount of confusion exists about the two, so I’d like to talk about both.  In you need a review of “What is a Haplogroup?”, click here.

Haplogroup information and comparisons between Family Tree DNA information and that at 23andMe is not apples and apples.  In essence, the haplogroups are not calculated in the same way, and the data at Family Tree DNA is much more extensive.  Understanding the differences is key to comparing and understanding results. Unfortunately, I think a lot of misinterpretation is happening due to misunderstanding of the essential elements of what each company offers, and what it means.

There are two basic kinds of tests to establish haplogroups, and a third way to estimate.

Let’s talk about mitochondrial DNA first.

Mitochondrial DNA

You have a very large jar of jellybeans.  This jar is your mitochondrial DNA.

jellybeans

In your jar, there are 16,569 mitochondrial DNA locations, or jellybeans, more or less.  Sometimes the jelly bean counter slips up and adds an extra jellybean when filling the jar, called an insertion, and sometimes they omit one, called a deletion.

Your jellybeans come in 4 colors/flavors, coincidentally, the same colors as the 4 DNA nucleotides that make up our double helix segments.  T for tangerine, A for apricot, C for chocolate and G for grape.

Each of the 16,569 jellybeans has its own location in the jar.  So, in the position of address 1, an apricot jellybean is always found there.  If the jellybean jar filler makes a mistake, and puts a grape jellybean there instead, that is called a mutation.  Mistakes do happen – and so do mutations.  In fact, we count on them.  Without mutations, genetic genealogy would be impossible because we would all be exactly the same.

When you purchase a mitochondrial DNA test from Family Tree DNA, you have in the past been able to purchase one of three mitochondrial testing levels.  Today, on the website, I see only the full sequence test for $199, which is a great value.

However, regardless of whether you purchase the full mitochondrial sequence test today, which tests all of your 16,569 locations, or the earlier HVR1 or HVR1+HVR2 tests, which tested a subset of about 10% of those locations called the HyperVariable Region, Family Tree DNA looks at each individual location and sees what kind of a jellybean is lodged there.  In position 1, if they find the normal apricot jellybean, they move on to position 2.  If they find any other kind of jellybean in position 1, other than apricot, which is supposed to be there, they record it as a mutation and record whether the mutation is a T,C or G.  So, Family Tree DNA reads every one of your mitochondrial DNA addresses individually.

Because they do read them individually, they can also discover insertions, where extra DNA is inserted, deletions, where some DNA dropped out of line, and an unusual conditions called a heteroplasmy which is a mutation in process where you carry some of two kinds of jellybean in that location – kind of a half and half 2 flavor jellybean.  We’ll talk about heteroplasmic mutations another time.

So, at Family Tree DNA, the results you see are actually what you carry at each of your individual 16,569 mitochondrial addresses.  Your results, an example shown below, are the mutations that were found.  “Normal” is not shown.  The letter following the location number, 16069T, for example, is the mutation found in that location.  In this case, normal is C.  In the RSRS model of showing mitochondrial DNA mutations, this location/mutation combination would be written as C16069T so that you can immediately see what is normal and then the mutated state.  You can click on the images to enlarge.

ftdna mito results

Family Tree DNA gives you the option to see your results either in the traditional CRS (Cambridge Reference Sequence) model, above, or the more current Reconstructed Sapiens Reference Sequence (RSRS) model.  I am showing the CRS version because that is the version utilized by 23andMe and I want to compare apples and apples.  You can read about the difference between the two versions here.

Defining Haplogroups

Haplogroups are defined by specific mutations at certain addresses.

For example, the following mutations, cumulatively, define haplogroup J1c2f.  Each branch is defined by its own mutation(s).

Haplogroup Required Mutations  
J C295T, T489C, A10398G!,   A12612G, G13708A, C16069T
J1 C462T, G3010A
J1c G185A, G228A,   T14798C
J1c2 A188G
J1c2f G9055A

You can see, below, that these results, shown above, do carry these mutations, which is how this individual was assigned to haplogroup J1c2f. You can read about how haplogroups are defined here.

ftdna J1c2f mutations

At 23andMe, they use chip based technology that scans only specifically programmed locations for specific values.  So, they would look at only the locations that would be haplogroup producing, and only those locations.  Better yet if there is one location that is utilized in haplogroup J1c2f that is predictive of ONLY J1c2f, they would select and use that location.

This same individual at 23andMe is classified as haplogroup J1c2, not J1c2f.  This could be a function of two things.  First, the probes might not cover that final location, 9055, and second, 23andMe may not be utilizing the same version of the mitochondrial haplotree as Family Tree DNA.

By clicking on the 23andMe option for “Ancestry Tools,” then “Haplogroup Tree Mutation Mapper,” you can see which mutations were tested with the probes to determine a haplogroup assignment.  23andMe information for this haplogroup is shown below.  This is not personal information, meaning it is not specific to you, except that you know you have mutations at these locations based on the fact that they have assigned you to the specific haplogroup defined by these mutations.  What 23andMe is showing in their chart is the ancestral value, which is the value you DON’T have.  So your jelly bean is not chocolate at location 295, it’s tangerine, apricot or grape.

Notice that 23andMe does not test for J1c2f.  In addition, 23andMe cannot pick up on insertions, deletions or heteroplasmies.  Normally, since they aren’t reading each one of your locations and providing you with that report, missing insertions and deletions doesn’t affect anything, BUT, if a deletion or insertion is haplogroup defining, they will miss this call.  Haplogroup K comes to mind.

J defining mutations

J1 defining mutations

J1c defining mutations

23andMe never looks at any locations in the jelly bean jar other than the ones to assign a haplogroup, in this case,17 locations.  Family Tree DNA reads every jelly bean in the jelly bean jar, all 16,569.  Different technology, different results.  You also receive your haplogroup at 23andMe as part of a $99 package, but of course the individual reading of your mitochondrial DNA at Family Tree DNA is more accurate.  Which is best for you depends on your personal testing goals, so long as you accurately understand the differences and therefore how to interpret results.  A haplogroup match does not mean you’re a genealogy match.  More than one person has told me that they are haplogroup J1c, for example, at Family Tree DNA and they match someone at 23andMe on the same haplogroup, so they KNOW they have a common ancestor in the past few generations.  That’s an incorrect interpretation.  Let’s take a look at why.

Matches Between the Two

23andMe provides the tester with a list of the people who match them at the haplogroup level.  Most people don’t actually find this information, because it is buried on the “My Results,” then “Maternal Line” page, then scrolling down until your haplogroup is displayed on the right hand side with a box around it.

Those who do find this are confused because they interpret this to mean they are a match, as in a genealogical match, like at Family Tree DNA, or like when you match someone at either company autosomally.  This is NOT the case.

For example, other than known family members, this individual matches two other people classified as haplogroup J1c2.  How close of a match is this really?  How long ago do they share a common ancestor?

Taking a look at Doron Behar’s paper, “A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root,” in the supplemental material we find that haplogroup J1c2 was born about 9762 years ago with a variance of plus or minus about 2010 years, so sometime between 7,752 and 11,772 years ago.  This means that these people are related sometime in the past, roughly, 10,000 years – maybe as little as 7000 years ago.  This is absolutely NOT the same as matching your individual 16,569 markers at Family Tree DNA.  Haplogroup matching only means you share a common ancestor many thousands of years ago.

For people who match each other on their individual mitochondrial DNA location markers, their haplotype, Family Tree DNA provides the following information in their FAQ:

    • Matching on HVR1 means that you have a 50% chance of sharing a common maternal ancestor within the last fifty-two generations. That is about 1,300 years.
    • Matching on HVR1 and HVR2 means that you have a 50% chance of sharing a common maternal ancestor within the last twenty-eight generations. That is about 700 years.
    • Matching exactly on the Mitochondrial DNA Full Sequence test brings your matches into more recent times. It means that you have a 50% chance of sharing a common maternal ancestor within the last 5 generations. That is about 125 years.

I actually think these numbers are a bit generous, especially on the full sequence.  We all know that obtaining mitochondrial DNA matches that we can trace are more difficult than with the Y chromosome matches.  Of course, the surname changing in mitochondrial lines every generation doesn’t help one bit and often causes us to “lose” maternal lines before we “lose” paternal lines.

Autosomal and Haplogroups, Together

As long as we’re mythbusting here – I want to make one other point.  I have heard people say, more than once, that an autosomal match isn’t valid “because the haplogroups don’t match.”  Of course, this tells me immediately that someone doesn’t understand either autosomal matching, which covers all of your ancestral lines, or haplogroups, which cover ONLY either your matrilineal, meaning mitochondrial, or patrilineal, meaning Y DNA, line.  Now, if you match autosomally AND share a common haplogroup as well, at 23andMe, that might be a hint of where to look for a common ancestor.  But it’s only a hint.

At Family Tree DNA, it’s more than a hint.  You can tell for sure by selecting the “Advanced Matching” option under Y-DNA, mtDNA or Family Finder and selecting the options for both Family Finder (autosomal) and the other type of DNA you are inquiring about.  The results of this query tell you if your markers for both of these tests (or whatever tests are selected) match with any individuals on your match list.

Advanced match options

Hint – for mitochondrial DNA, I never select “full sequence” or “all mtDNA” because I don’t want to miss someone who has only tested at the HVR1 level and also matches me autosomally.  I tend to try several combinations to make sure I cover every possibility, especially given that you may match someone at the full sequence level, which allows for mutations, that you don’t match at the HVR1 level.  Same situation for Y DNA as well.  Also note that you need to answer “yes” to “Show only people I match on all selected tests.”

Y-DNA at 23andMe

Y-DNA works pretty much the same at 23andMe as mitochondrial meaning they probe certain haplogroup-defining locations.  They do utilize a different Y tree than Family Tree DNA, so the haplogroup names may be somewhat different, but will still be in the same base haplogroup.  Like mitochondrial DNA, by utilizing the haplogroup mapper, you can see which probes are utilized to determine the haplogroup.  The normal SNP name is given directly after the rs number.  The rs number is the address of the DNA on the chromosome.  Y mutations are a bit different than the display for mitochondrial DNA.  While mitochondrial DNA at 23andMe shows you only the normal value, for Y DNA, they show you both the normal, or ancestral, value and the derived, or current, value as well.  So at SNP P44, grape is normal and you have apricot if you’ve been assigned to haplogroup C3.

C3 defining mutations

As we are all aware, many new haplogroups have been defined in the past several months, and continue to be discovered via the results of the Big Y and Full Y test results which are being returned on a daily basis.  Because 23andMe does not have the ability to change their probes without burning an entirely new chip, updates will not happen often.  In fact, their new V4 chip just introduced in December actually reduced the number of probes from 967,000 to 602,000, although CeCe Moore reported that the number of mtDNA and Y probes increased.

By way of comparison, the ISOGG tree is shown below.  Very recently C3 was renamed to C2, which isn’t really the point here.  You can see just how many haplogroups really exist below C3/C2 defined by SNP M217.  And if you think this is a lot, you should see haplogroup R – it goes on for days and days!

ISOGG C3-C2 cropped

How long ago do you share a common ancestor with that other person at 23andMe who is also assigned to haplogroup C3?  Well, we don’t have a handy dandy reference chart for Y DNA like we do for mitochondrial – partly because it’s a constantly moving target, but haplogroup C3 is about 12,000 years old, plus or minus about 5,000 years, and is found on both sides of the Bering Strait.  It is found in indigenous Native American populations along with Siberians and in some frequency, throughout all of Asia and in low frequencies, into Europe.

How do you find out more about your haplogroup, or if you really do match that other person who is C3?  Test at Family Tree DNA.  23andMe is not in the business of testing individual markers.  Their business focus is autosomal DNA and it’s various applications, medical and genealogical, and that’s it.

Y-DNA at Family Tree DNA

At Family Tree DNA, you can test STR markers at 12, 25, 37, 67 and 111 marker levels.  Most people, today, begin with either 37 or 67 markers.

Of course, you receive your results in several ways at Family Tree DNA, Haplogroup Origins, Ancestral Origins, Matches Maps and Migration Maps, but what most people are most interested in are the individual matches to other people.  These STR markers are great for genealogical matching.  You can read about the difference between STR and SNP markers here.

When you take the Y test, Family Tree DNA also provides you with an estimated haplogroup.  That estimate has proven to be very accurate over the years.  They only estimate your haplogroup if you have a proven match to someone who has been SNP tested. Of course it’s not a deep haplogroup – in haplogroup R1b it will be something like R1b1a2.  So, while it’s not deep, it’s free and it’s accurate.  If they can’t predict your haplogroup using that criteria, they will test you for free.  It’s called their SNP assurance program and it has been in place for many years.  This is normally only necessary for unusual DNA, but, as a project administrator, I still see backbone tests being performed from time to time.

If you want to purchase SNP tests, in various formats, you can confirm your haplogroup and order deeper testing.

You can order individual SNP markers for about $39 each and do selective testing.  On the screen below you can see the SNPs available to purchase for haplogroup C3 a la carte.

FTDNA C3 SNPs

You can order the Geno 2.0 test for $199 and obtain a large number of SNPs tested, over 12,000, for the all-inclusive price.  New SNPs discovered since the release of their chip in July of 2012 won’t be included either, but you can then order those a la carte if you wish.

Or you can go all out and order the new Big Y for $695 where all of your Y jellybeans, all 13.5 million of them in your Y DNA jar are individually looked at and evaluated.  People who choose this new test are compared against a data base of more than 36,000 known SNPs and each person receives a list of “novel variants” which means individual SNPs never before discovered and not documented in the SNP data base of 36,000.

Don’t know which path to take?  I would suggest that you talk to the haplogroup project administrator for the haplogroup you fall into.  Need to know how to determine which project to join, and how to join? Click here.  Haplogroup project administrators are generally very knowledgeable and helpful.  Many of them are spearheading research into their haplogroup of interest and their knowledge of that haplogroup exceeds that of anyone else.  Of course you can also contact Family Tree DNA and ask for assistance, you can purchase a Quick Consult from me, and you can read this article about comparing your options.

23 Ways To Be a PITA

PITANo, not PETA, the People for the Ethical Treatment of Animals, but PITA – Pain In The Arm….yes….arm…what are you thinking???

For most people, being a PITA doesn’t come naturally….so you might need some help knowing how to be one, or perhaps perfecting your PITA skills.  Yes, in case you’re wondering….my tongue is firmly implanted in my cheek.

For genetic genealogists, there are special ways to be a PITA.  Let me share some of these with you, just so you can fine tune and add to your PITA skills.

First and maybe the best ways to be a PITA, right off the bat.

1. Send e-mails with no subject or punctuation and an indecipherable topic, especially to someone you’ve never communicated with before.  Here’s an example.  You can just copy and paste this and send it to anyone you want to irritate or confuse.

“i would love to have any information you could give me…..thanks…..”

I so want to send this person something about penile implants.  Is this wrong?

2. Send e-mails with no capitals or punctuations.  This is always a wonderful way to impress people.

i just wanted to let you know that i have no idea how to type or how to use the period or comma keys or how to use the shift button i’m also using the fact that i’m using my phone as an excuse not to use punctuation however I can manage to type half of my life story for you to try to decipher so get out your special decoder ring

3. BETTER YET, SEND THE ENTIRE MESSAGE, INCLUDING SEVERAL PAGES OF YOUR ANCESTORS NAMES WITH NO DATES OR OTHER IDENTIFYING INFORMATION IN ALL CAPITALS.  THEN ASK FOR ANY INFORMATION THAT PERSON MIGHT HAVE ABOUT THOSE ANCESTORS.  THIS IS ESPECIALLY USEFUL WHEN FIRST INTRODUCING YOURSELF AND LETS YOUR NEW CONTACT KNOW JUST HOW IMPORTANT THEY ARE AND HOW MUCH FUN IT’S GOING TO BE TO COMMUNICATE WITH YOU.

4. When a match asks you for genealogy information, just send them a link to your Ancestry.com tree.  You can then sit back and laugh, knowing that they have no idea where to search in your 35,723 people for a common ancestor without looking for every surname they have.  Plus, you have the added benefit that Ancestry will help you be a PITA by attaching your tree to their account like a giant kudzu vine that they can’t disentangle without knowing the secret handshake.

5. When a match asks you for genealogy information, never, ever send them something actually useful, like a pedigree chart with an index.  Instead send them rambling e-mails with disconnected tidbits from both sides of your family, or that link to your Ancestry tree.  Go to sleep then, knowing they will be up all night trying to figure this out.

6. Ask for, or better yet, demand free consulting.  Select someone at random (not me please, I already receive more than my share – 17 yesterday alone) and send them a rambling stream-of-consciousness e-mail several pages long.  At the end, tell them that you can’t afford to pay anything, but ask if they would tell you “what they think.”  Before sending these to anyone in the genetic genealogy community, send several to other professionals, physicians or lawyers in your community and see how that works out?

Now, if someone is a project volunteer, that’s a bit different.  They still don’t “owe” you free consulting, but they have set themselves forth as a volunteer resource.  Still, try to be respectful of their time and be brief and concise in your requests.

In other words, the 21 page e-mail I received this week from Person Unknown demanding that I, as a project administrator, figure out how the “requester” was related to three people in the large Cumberland Gap project (also persons unknown) was, well, ahem, a bit over the top, to put it mildly.  No, I confess, I did not read all 21 pages and the only reason I know it WAS 21 pages long is because I wanted to use it as a bad example.  If that was your e-mail and I’ve just offended you, well, I’m sorry you’re offended, but that is not the way to win friends and influence people, nor to get your questions answers or your problems solved.  It is, however, a great way to be a PITA.  In fact, you win this week’s PITA award!

Here’s an example of a reasonable, concise question from my blog:

“Thanks for that explanation, I needed that information. Still would like to know what a “back mutation” is.”

And the answer:

“A back mutation is when a mutations happens, like from A to C, and then the reverse happens, a mutation from C to A. It initially looks like no mutation happened, unless you are aware of the intermediate step and that two mutations actually happened.”

There’s a big difference between a simple one or two line general DNA question and a multi-page personal epistle that the receiver has to read three times and make charts to even begin to unravel or understand, so, to be a PITA – always make yourself annoying and then you can wonder why you never receive replies from people.  Then complain about not receiving replies.

Oh, and if you do write to a project administrator, never, ever tell them how or why you are writing specifically to them – it’s much more fun to leave them guessing.  The sender of the 21 page epistle did not SAY it was the Cumberland Gap project – they left that for me to decipher.

7. Skim articles, don’t click on the links, and then ask questions of the author that would have been answered if you had clicked on the links they provided in the first place.  They love receiving several of these e-mails every day!

Now, if you have DNA tested at any of the three major testing companies, there special ways for you to be a PITA with each one.  Let me give you some fresh ideas.

At Family Tree DNA

8. Join a DNA project, any project.  Then, when the administrator sends you a welcome message, introducing themselves and asking for genealogy information, send them a nasty note.  Here’s one I received recently.  You can just use it.

“Who the hell are you and why are you contacting me.  Don’t ever contact me again.”

9. Family Tree DNA does you the very large favor of providing you with the e-mail addresses of your contacts instead of forcing you to go through a message system like at 23andMe and Ancestry.

When sending an e-mail to someone you match, be sure to never include the name of the person you match, or what kind of a test you took that matches.  This will confuse them and make them really want to answer your inquiry.  Many people manage test kits for several people and if you don’t put the name of the person you match in your e-mail, they will probably think it’s their kit, and then they will either spend a lot of time looking for matches and/or putting together genealogy info to send to you that is not useful.  Then, after you receive the info, tell them you’re sorry, but the match was to a different person.  That will truly endear you to them.

10. Don’t ever update your e-mail address…then complain online and loudly about how you never receive contacts from either your project administrator or your contacts/matches.

11. Don’t upload your GEDCOM file either, because someone might accidentally discover a common surname match or a common ancestor, and that would be just awful.  It would also provide Family Tree DNA with the information to bold matching surnames on your autosomal match list for you, AND you’d get a $10 coupon…all of which would be just terrible.

12. Volunteer to be a project administrator, then do nothing at all.  Leave your project entirely ungrouped, and refuse any assistance.  In this case, you really don’t have to DO anything to be a PITA.

Better yet, create an off-site (non-FTDNA) website instead of using the one at Family Tree DNA and remove any information that could be useful to someone searching for their ancestral line.  Here’s an example.

Private project no useful info

Don’t want to create your own website?  Well, you can be almost as large a PITA by using the Family Tree DNA page and simply disabling anything useful, like, you know, most distant ancestor.  That way people can see that there is a project and their line MIGHT be hidden in there, but they have no way to find out other than contacting you.  Then, don’t answer, of course.

ftdna project no names

At 23andMe

13. Give yourself a really innovative “screen name,” like, say “Your cousin” or “3rd cousin” or better yet, “My Mother.”  That way when you send contact requests or sharing requests to people, it looks like it is coming from their mother…and if their mother has already passed over…well…let’s just say your contact request could be really startling.  Worse yet, if that person matches two people who are equally as creative and both named themselves “My Mother,” how will they ever tell you apart???  And can you really have two mothers?  OMG, I feel an identity crisis coming on…

14. Tell your contact that you are really interested in genealogy, provide a little bit of genealogy info, just a couple tidbits, maybe a juicy morsel, but then refuse to share your DNA.

15.  Don’t provide any surname or location information.  That might give someone a clue as to how you connect – so don’t ever do that.

16.  I’d tell you to never upload your GEDCOM file, or create one, but you can actually be a larger PITA by uploading your file at 23andMe, because their file reader interface works so poorly that your match will be more frustrated trying to read the file than by not finding one at all.  So you can be a PITA whether you upload your file or not.  How’s that for good luck!

17.  Don’t ever reply to contact or sharing requests.  I know this one is already quite popular.  About 90% of the people there already do this, so you’ll be in good company.  If people at 23andMe aren’t interested in genealogy, there is an opt-out, but don’t opt out because you can be much more of a PITA by leaving yourself in the genealogy pool but never replying to anyone, especially close matches.  Drives them crazy!

At Ancestry

18. First and foremost, never, ever reply to messages.  I know that this one is very popular, because many of my DNA matches, including my closest match at Ancestry has implemented this scheme.  She, I assume, due to the name (unless I’m related to the boy named Sue) and I share a common great-grandfather.  In this case, I have photos she might really like to have.  Too bad she is being a PITA.

19. Make your tree private, AND never reply to requests.  This is the ultimate tease, because your match KNOWS the information is there, right there, hiding just out of reach, and can’t get to it.

20. Copy and paste several trees together because, after all, the names match and, hello, it wouldn’t BE on Ancestry if it wasn’t RIGHT.  Right?  You can then scare the bejesus out of someone when they discover that their non-Mormon grandfather had 7 wives and 35 kids….all while married to their grandmother.  That’s always fun.  Then, when they frantically contact you to ask about it, don’t even think about replying to that message.

21. Insist that because you and your Ancestry DNA match have a shakey leaf and a common ancestor in your tree, that you KNOW that’s your DNA match because Ancestry SAYS SO.  When your match tries to explain that connection might be incorrect, may not be your DNA match and that there is no way to prove it, at least not without utilizing tools from either GedMatch or Family Tree DNA, don’t reply to them anymore.  That will certainly solve the problem!

22.  Send random people invitations to your Ancestry tree – and be positive your tree name has absolutely no identifying words in it.  Like the one I received recently, for example, named “A Global Tree of Life.”  Yep, I can tell you right away who sent that to me and why!!!

23. Oh yes, and in true PITA-esque fashion, never, ever say “Thank you,” to anyone, ever, for anything.  Thank you is such an easy thing to say and it makes the person on the receiving end feel good about whatever it was they did for you – even if was “just” answering your question.  So don’t slip up and do this!  Otherwise, you’ll certainly be thrown out of the PITA Club!

Thank you collage

Added PITAs

24. Instead of being grateful for free things, like blogs and webpages, and simply unsubscribing or ignoring them if you don’t like them, make nasty comments.  That will certainly confirm your PITA membership and make the person providing the free content feel warm and fuzzy about the time they invest.

“How about I unsubscribe to your boring emails about your family I have been getting the last year. Ms PITA.”

 

What If You Die?

coffinWell, it’s not exactly a what-if question, it’s a given.  You’re going to.  The only real question is when, and will you be prepared?

By prepared, I’m not talking about your will, I’m talking about your DNA.

The unspeakable happened this past weekend.  A long time researcher and close friend, Aleda, died, rather unexpectedly.  She has been chronically ill for some time, but not critically.  On Saturday, she read my blog, worked with her research group on the Autosomal DNA Segment Analyzer and ordered Emily’s book.  Then, in the afternoon, she said she didn’t feel well and got into her chair to take a nap.  Nothing unusual about that.  Aleda didn’t feel well a lot, but she persevered anyway, always helping and guiding her research group.  But this time was different.  Aleda was gone.

Her research group is wandering around like a group of lost souls.  It’s like someone shot a hole through the middle of all of us.  This isn’t a large well organized group with an official structure, but a small group of closely and not so closely related researchers trying to figure out their DNA and genealogy connections.

If you are a significant contributor, you will be sorely missed.  If you are reading this, and have had your DNA tested, you are one of the contributors.

The research group members are already asking, “What next?  How do we access the DNA records of the people Aleda had tested?”  Good question.  Let’s talk about preparing for the inevitable.

Aleda had given the kit passwords to a friend, who is now so upset she can’t find them.  As the project administrator of one of the projects that includes one of Aleda’s family member’s kits, I can see some of the information.

E-Mail

I can see that Aleda set up a special DNA e-mail address which I’m presuming she used for all of the kits.  Unfortunately, there is no alternate e-mail address.

When Family Tree DNA, and virtually all the companies, do a password reset, they send the password information to the e-mail address on file.

Does anyone, other than Aleda, have the password to that e-mail account?

Project administrators cannot change primary e-mail addresses.  Only the kit owner can do that.

If you change your password to your e-mail account, you’ll need to remember to provide the new password to your trusted other as well.

Passwords

If you share your password with someone, that’s fine, but if they can’t find it, or if you change it and don’t tell them, that won’t be helpful.  You might want to add their e-mail as an alternate.  You might want to provide this information to multiple people, just in case your chosen person predeceases you, or some other unfortunate situation exists, like a fire, system crash or losing the passwords.

At 23andMe, to download a raw data file, a password isn’t enough.  You also have to know the answer to the secret question.

Beneficiary Information

Family Tree DNA goes one step further and provides people with a beneficiary form for situations just like this.

Unfortunately, Aleda’s family member’s form is blank, and she protected his information by changing the setting to prevent project administrators from completing this form.

beneficiary form

Covering all the Bases

Don’t forget about 3rd party sites like GedMatch where you may also be registered.

What to do?

1. Family Tree DNA is the only company to provide the option of beneficiary information.  Take advantage of this and complete the form.  It’s only 3 lines – name, phone and e-mail of your beneficiary.  You can find it under the “My Account” tab on the blue/black bar at the top of your personal page.

beneficiary dropdown

2. Add an alternate e-mail address.

3. Provide password and e-mail password information to a trusted other, and maybe a few trusted others.

4. Remember to notify password holders when you change passwords to either e-mail or DNA kits.

5. If you are a project administrator, try your best to find a co-administrator and share information, such as genealogy provided by participants.

6. Provide a notification list for your family that includes important genealogy and DNA contacts, including Family Tree DNA if you are a project administrator.  Many times I’ve received an e-mail from someone’s account with their name as the subject.  I’ve learned to cringe when I see them, because I know what’s coming…but at least the family has taken the trouble to notify those of us who communicate electronically with that person instead of leaving us to wonder forever what happened.

7. Preparing for the inevitable doesn’t just apply to DNA testing, but to all aspects of online life.  Think about Facebook, for example.  My brother died 2 years ago, today, and no one has his password.  We post to his page from time to time, but like a ghost ship, his Facebook account will sail off into the indefinite captainless future.

That Unruly X….Chromosome That Is

Iceberg

Something is wrong with the X chromosome.  More specifically, something is amiss with trying to use it, the way we normally use recombinant chromosomes for genealogy.  In short, there’s a problem.

If you don’t understand how the X chromosome recombines and is passed from generation to generation, now would be a good time to read my article, “X Marks the Spot” about how this works.  You’ll need this basic information to understand what I’m about to discuss.

The first hint of this “problem” is apparent in Jim Owston’s “Phasing the X Chromosome” article.  Jim’s interest in phasing his X, or figuring out where it came from genealogically, was spurred by his lack of X matches with his brothers.  This is noteworthy, because men don’t inherit any X from their father, so Jim’s failure to share much of his X with his brothers meant that he had inherited most of his X from just one of his mother’s parents, and his brothers inherited theirs from the other parent.  Utilizing cousins, Jim was able to further phase his X, meaning to attribute portions to the various grandparents from whence it came.  After doing this work, Jim said the following”

“Since I can only confirm the originating grandparent of 51% my X-DNA, I tend to believe (but cannot confirm at the present) that my X-chromosome may be an exact copy of my mother’s inherited X from her mother. If this is the case, I would not have inherited any X-DNA from my grandfather. This would also indicate that my brother Chuck’s X-DNA is 97% from our grandfather and only 3% from our grandmother. My brother John would then have 77% of his X-DNA from our grandfather and 23% from our grandmother.”

As a genetic genealogist, at the time Jim wrote this piece, I was most interested in the fact that he had phased or attributed the pieces of the X to specific ancestors and the process he used to do that.  I found the very skewed inheritance “interesting” but basically attributed it to an anomaly.  It now appears that this is not an anomaly.  It was, instead the tip of the iceberg and we didn’t recognize it as such.  Let’s look at what we would normally expect.

Recombination

The X chromosome does recombine when it can, or at least has the capacity to do so.  This means that a female who receives an X from both her father and mother receives a recombined X from her mother, but receives an X that is not recombined from her father.  That is because her father only receives one X, from his mother, so he has nothing to recombine with.  In the mother, the X recombines “in the normal way” meaning that parts of both her mother’s and her father’s X are given to her children, or at least that opportunity exists.  If you’re beginning to see some “weasel words” here or “hedge betting,” that’s because we’ve discovered that things aren’t always what they seem or could be.

The 50% Rule

In the statistical world of DNA, on the average, we believe that each generation receives roughly half of the DNA of the generations before them.  We know that each child absolutely receives 50% of the DNA of both parents, but how the grandparents DNA is divided up into that 50% that goes to each offspring differs.  It may not be 50%.  I am in the process of doing a generational inheritance study, which I will publish soon, which discusses this as a whole.

However, let’s use the 50% rule here, because it’s all we have and it’s what we’ve been working with forever.

In a normal autosomal, meaning non-X, situation, every generation provides to the current generation the following approximate % of DNA:

Autosomal % chart

Please note Blaine Bettinger’s X maternal inheritance chart percentages from his “More X-Chromosome Charts” article, and used with his kind permission in the X Marks the Spot article.

Blaine's maternal X %

I’m enlarging the inheritance percentage portion so you can see it better.

Blaine's maternal X % cropped

Taking a look at these percentages, it becomes evident that we cannot utilize the normal predictive methods of saying that if we share a certain percentage of DNA with an individual, then we are most likely a specific relationship.  This is because the percentage of X chromosome inherited varies based on the inheritance path, since men don’t receive an X from their fathers.  Not only does this mean that you receive no X from many ancestors, you receive a different percentage of the X from your maternal grandmother, 25%, because your mother inherited an X from both of her parents, versus from your paternal grandmother, 50%, because your father inherited an X from only his mother.

The Genetic Kinship chart, below, from the ISOGG wiki, is the “Bible” that we use in terms of estimating relationships.  It doesn’t work for the X.

Mapping cousin chart

Let’s look at the normal autosomal inheritance model as compared to the maternal X chart fan chart percentages, above, and similar calculations for the paternal side.  Remember, the Maternal Only column applies only to men, because in the very first generation, men’s and women’s inheritance percentages diverge.  Men receive 100% of their X from their mothers, while women receive 50% from each parent.

Generational X %s

Recombination – The Next Problem

The genetic genealogy community has been hounding Family Tree DNA incessantly to add the X chromosome matching into their Family Finder matching calculations.

On January 2, 2014, they did exactly that.  What’s that old saying, “Be careful what you ask for….”  Well, we got it, but “it” doesn’t seem to be providing us with exactly what we expected.

First, there were many reports of women having many more matches than men.  That’s to be expected at some level because women have so many more ancestors in the “mix,” especially when matching other women.

23andMe takes this unique mixture into consideration, or at least attempts to compensate for it at some level.  I’m not sure if this is a good or bad thing or if it’s useful, truthfully.  While their normal autosomal SNP matching threshold is 7cM and 700 matching SNPs within that segment, for X, their thresholds are:

  • Male matched to male – 1cM/200 SNPs
  • Male matched to female – 6cM/600 SNPs
  • Female matched to female – 6cM/1200 SNPs

Family Tree DNA does not use the X exclusively for matching.  This means that if you match someone utilizing their normal autosomal matching criteria of approximately 7.7cM and 500 SNPs, and you match them on the X chromosome, they will report your X as matching.  If you don’t match someone on any chromosome except the X, you will not be reported as a match.

The X matching criteria at Family Tree DNA is:

  • 1cM/500 SNPs

However, matching isn’t all of the story.

The X appears to not recombine normally.  By normally, I don’t mean something is medically wrong, I mean that it’s not what we are expecting to see in terms of the 50% rule.  In essence, we would expect to see approximately half of the X of each parent, grandfather and grandmother, passed on to the child from the mother in the maternal line where recombination is a possibility.  That appears to not be happening reliably.  Not only is this not happening in the nice neat 50% number, the X chromosome seems to be often not recombining at all.  If you think the percentages in the chart above threw a monkey wrench into genetic genealogy predictions, this information, if it holds up in a much larger test, in essence throws our predictive capability, at least as we know it today, out the window.

The X Doesn’t Recombine as Expected

In my generational study, I noticed that the X seemed not to be recombining.  Then I remembered something that Matt Dexter said at the Family Tree DNA Conference in November 2013 in Houston.  Matt has the benefit of having a full 3 generation pedigree chart where everyone has been tested, and he has 5 children, so he can clearly see who got the DNA from which of their grandparents.

I contacted Matt, and he provided me with his X chromosomal information about his family, giving me permission to share it with you.  I have taken the liberty of reformatting it in a spreadsheet so that we can view various aspects of this data.

Dexter table

First, note that I have sorted these by grandchild.  There are two females, who have the opportunity to inherit from 3 grandparents.  The females inherited one copy of the X from their mother, who had two copies herself, and one copy of the X from her father who only had his mother’s copy.  Therefore, the paternal grandfather is listed above, but with the note “cannot inherit.”  This distinguishes this event from the circumstance with Grandson 1 where he could inherit some part of his maternal grandfather’s X, but did not.

For the three grandsons, I have listed all 4 grandparents and noted the paternal grandmother and grandfather as “cannot inherit.”  This is of course because the grandsons don’t inherit an X from their father.  Instead they inherit the Y, which is what makes them male.

According to the Rule of 50%, each child should receive approximately half of the DNA of each maternal grandparent that they can inherit from.  I added the columns, % Inherited cM and % Inherited SNP to illustrate whether or not this number comes close to the 50% we would expect.  The child MUST have a complete X chromosome which is comprised of 18092 SNPs and is 195.93cM in length, barring anomalies like read errors and such, which do periodically occur.  In these columns, 1=100%, so in the Granddaughter 1 column of % Inherited cM, we see 85% for the maternal grandfather and about 15% for the maternal grandmother.  That is hardly 50-50, and worse yet, it’s no place close to 50%.

Granddaughter 1 and 2 must inherit their paternal grandmother’s X intact, because there is nothing to recombine with.

Granddaughter 2 inherited even more unevenly, with about 90% and 10%, but in favor of the other grandparent.  So, statistically speaking, it’s about 50% for each grandparent between the two grandchildren, but it is widely variant when looking at them individually.

Grandson 1, as mentioned, inherited his entire X from his maternal grandmother with absolutely no recombination.

Grandsons 2 and 3 fall much closer to the expected 50%.

The problem for most of us is that you need 3 or 4 consecutive generations to really see this happening, and most of us simply don’t have data that deep or robust.

A recent discussion on the DNA Genealogy Rootsweb mailing list revealed several more of these documented occurrences, among them, two separate examples where the X chromosome was unrecombined for 4 generations.

Robert Paine, a long-time genetic genealogy contributor and project administrator reported that in his family medical/history project, at 23andMe, 25% of his participants show no recombination on the X chromosome.  That’s a staggering percentage.  His project consists of  21 people in with 2 blood lines tested 5 generations deep and 2 bloodlines tested at 4 generations

One woman’s X matches her great-great-grandmother’s X exactly.  That’s 4 separate inheritance events in a row where the X was not recombined at all.

The graphic below, provided by Robert,  shows the chromosome browser at 23andMe where you can see the X matches exactly for all three participants being compared.

The screen shot is of the gg-granddaughter Evelyn being compared to her gg-grandmother, Shevy, Evelyn’s g-grandfather Rich and Evelyn’s grandmother Cyndi. 23andme only lets you compare 3 individuals at a time so Robert did not include Evelyn’s mother Shay, who is an exact match with Evelyn.

Paine X

Where Are We?

So what does this mean to genetic genealogy?  It certainly does not mean we should throw the baby out with the bath water.  What it is, is an iceberg warning that there is more lurking beneath the surface.  What and how big?  I can’t tell you.  I simply don’t know.

Here’s what I can tell you.

  • The X chromosome matching can tell you that you do share a common ancestor someplace back in time.
  • The amount of DNA shared is not a reliable predictor of how long ago you shared that ancestor.
  • The amount of DNA shared cannot predict your relationship with your match.  In fact, even a very large match can be many generations removed.
  • The absence of an X match, even with someone closely related whom you should match does not disprove a descendant relationship/common ancestor.
  • The X appears to not recombine at a higher rate than previously thought, the previous expectation being that this would almost never happen.
  • The X, when it does recombine appears to do so in a manner not governed by the 50% rule.  In fact, the 50% rule may not apply at all except as an average in large population studies, but may well be entirely irrelevant or even misleading to the understanding of X chromosome inheritance in genetic genealogy.

The X is still useful to genetic genealogists, just not in the same way that other autosomal data is utilized.  The X is more of an auxiliary chromosome that can provide information in addition to your other matches because of its unique inheritance pattern.

Unfortunately, this discovery leaves us with more questions than answers.  I found it incomprehensible that this phenomenon has never been studied in humans, or in animals, for that matter, at least not that I could find.  What few references I did find indicated that the X seems to recombine with the same frequency as the other autosomes, which we are finding to be untrue.

What is needed is a comprehensive study of hundreds of X transmission events at least 3 generations deep.

As it turns out, we’re not the only ones confused by the behavior of the X chromosome.  Just yesterday, the New York Times had an article about Seeing the X Chromosome in a New Light.  It seems that either one copy of the X, or the other, is disabled cell by cell in the human body.  If you are interested in this aspect of science, it’s a very interesting read.  Indeed, our DNA continues to both amaze and amuse us.

A special thank you to Jim Owston, Matt Dexter, Blaine Bettinger and Robert Paine for sharing their information.

Additional sources:

Polymorphic Variation in Human Meiotic
Recombination (2007)
Vivian G. Cheung
University of Pennsylvania
http://repository.upenn.edu/cgi/viewcontent.cgi?article=1102&context=be_papers

A Fine-Scale Map of Recombination Rates and Hotspots Across the Human Genome, Science October 2005, Myers et al
http://www.sciencemag.org/content/310/5746/321.full.pdf
Supplemental Material
http://www.sciencemag.org/content/suppl/2005/10/11/310.5746.321.DC1