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Friday, December 28, 2012

AncestryDNA and a Possible Faux Pa: Part Deux

My mother's genetic journey began with one mystery, and led to another.

My mother's late father was a Cyr, but the family had long suspected that he was fathered by his mother's eventual second husband, a Levesque. The most pressing reason for my taking an autosomal DNA test was to find evidence of her father's paternity. I had researched both the Cyr and Levesque pedigrees, and hoped that among my genetic matches would be a cousin whom I could tie to one of the branches of one of these trees.

That mystery has since (tentatively) been solved, but another popped up when my AncestryDNA results came back. As I discussed in my earlier post, the results showed no evidence of my French ancestry. I speculated that the test could have missed (i.e. misidentified) my French genes, or else my grandmother could have been unfaithful. When AncestryDNA opened to the public in early November, I ordered a test for my mother, and two-and-a-half weeks later the results were in.

Recall that this was my "Genetic Ethnicity Summary":


My mother's summary is a bit more interesting:


Her mother was born to Finnish immigrants; her father was Franco-American. I've concluded that the Finnish/Volga-Ural came from her mother, along with the Eastern European and some of the Scandinavian. The rest came from her father. The test didn't recognize her Frenchness, though almost all of her matches who shared their family trees were of French-Canadian ancestry. In fact, two of her matches were 4th to 6th cousins through her Cyr line, making it less likely that her biological grandfather was "Grampa Levesque."

One mystery was fading, but the other deepened. Was her summary reflecting her father's "deep ancestry," or was it simply mistaken?

It wasn't AncestryDNA that helped me solve this mystery, but its rival 23andMe. I was able to apply that company's recently announced Ancestry Composition feature to test results I had previously obtained for my maternal uncle. To a point, the feature is similar to AncestryDNA's Genetic Ethnicity Summary. Beyond that point, AncestryDNA's weaknesses become apparent.

Ancestry Composition provides three resolutions: Global, Regional and Sub-regional. Sub-regional Resolution gives a summary much like AncestryDNA's:


This shows at least some French ancestry, which is better than AncestryDNA did for my mom. But notice that, whereas AncestryDNA assigned 99% of my mother's DNA to more or less specific regions, 23andMe assigns only about 77% of her brother's—the rest is labeled "Nonspecific European" or "Unassigned." 23andMe also seems hesitant to recognize Scandinavian ancestry. Obviously AncestryDNA is the better company!

But wait. I always try to be careful when expressing genealogical conclusions to couch them with words like "probably," "apparently," or "possibly." How certain is AncestryDNA of its conclusions? It provides confidence percentages for DNA matches, but not for its ethnicity calculations. We are told simply that the latter results are held to "an extremely high standard of accuracy," and (by implication) should not be doubted. Why not? Because SCIENCE!
There are a few reasons why your ethnicity may not be exactly what you expected:
  • Your genetic ethnicity may go back further than your family tree.
  • While your ancestors lived in a certain country, there may have been genetic influence from other places.
  • You don’t necessarily share common DNA with all of your ancestors.
In other words, if our conclusions don't match your expectations, your expectations were wrong.

Blaine Bettinger quotes a concession that I can't find on the Ancestry.com website:
Right now, your genetic ethnicity may not look quite right, with some ethnicities under or over-represented. As scientists gain a deeper understanding of the data, our prediction models will evolve to provide you with more accurate and relevant information about your family history.
The website concedes only that the ethnicity summaries "may update over time as new genetic signatures are discovered," and that they might someday be able to show "more granular ethnic regions." It promises refinement—something less than correction.

To be clear, my issue isn't with the quality of AncestryDNA's prediction models, but with the presentation of its predictions. To present a prediction without qualification is to imply that we should trust that prediction without reservation. "A hard rain's a-gonna fall" is a very different statement from "There is a 60 percent chance of precipitation."

Let's compare AncestryDNA's approach with 23andMe's. Just above my uncle's Ancestry Composition percentages is a drop-down box that allows me to adjust the estimate.


Standard Estimate is the default, but I can also see a Speculative Estimate and a Conservative Estimate. Here's the speculative estimate of my uncle's ancestral ethnicity:


Based on this estimate (and assuming a genetic Maginot Line that kept out any German genes), he's at least a quarter French, which seems closer to the truth than 3.3%.[1] Even when speculating, 23andMe leaves a sizable chunk of his ancestry somewhat vague (though the "Nonspecific European" portion has shrunk considerably). The company provides a white paper that explains exactly how they arrive at these estimates, and what "speculative," "standard" and "conservative" mean. (Briefly, they indicate 50 percent, 75 percent and 90 percent "confidence thresholds.") Scroll down to the "Testing & Validation" section and you'll see that French and German ancestry is by far the most difficult to determine.
In the worst case, the French & German population, the recall is 7%, meaning that 93% of the actual French & German DNA was not labeled as such.
Scroll back up and you'll learn that "Finns are so distinct from other populations, they actually get their own reference population in Ancestry Composition." So, my mother's ancestry demonstrates the best- and worst-case scenarios for identifying specific European ancestries.[2] I would not have learned this from the AncestryDNA website. When your competitor is educating your customers, that's a problem.

With the introduction of the Ancestry Composition tool at 23andMe, there is one less reason to recommend AncestryDNA. I hope that Ancestry.com is reconsidering its decision to "dumb down" its test results, and will begin providing more and better data for us to evaluate. It needs to pull its scientists out of the lab to tell us where these percentages are coming from. What reference populations are they using? How confident are they in their estimates? I would rather be confused by too much information than by too little. Blind me with science!

[1]The Iberian ancestry fits with my uncle's Y chromosome haplogroup, which is most prevalent on the Iberian peninsula and southern France.

[2]Having such distinct maternal and paternal ancestries provides an opportunity to distinguish which of each chromosome pair comes from the mother, and which from the father. (In labspeak, this is part of the "phasing" process.) 23andMe's new tool lets me view which of my uncle's chromosomal segments come from which part of Europe. The Eastern European shows up as part of his X chromosome, indicating that it came from his Finnish mother. I'm also able to see that those segments identified as Scandinavian in every case share a chromosome with those identified as Finnish. That means that these Scandinavian genes (if phased correctly) most likely came through Sweden rather than Normandy.

Wednesday, June 13, 2012

AncestryDNA and a Possible Faux Pa

Having received free admission to the AncestryDNA Beta and gained some knowledge as a result, I feel obliged to offer a review of the service.

Through my father, I expected my genetic ancestry to be about 47% British Isles, 3% Dutch. Some portion of my British genes might in fact be Scandinavian, due to the notoriously indiscriminate dating practices of Vikings. But barring some non-paternity hanky panky not reflected in the records or family tradition, my father's heritage is pretty well settled.

My mother's family was even more a settled fact. Her mother was the child of Finnish immigrants. mtDNA tests taken by me and a maternal uncle were both consistent with a Finnish maternal ancestry. My mother's father was French, and her brother's Y chromosome is consistent with a French paternal ancestry. So I expected my genetic profile to come back 25% French and 25% Finnish/Scandinavian (the Finnish/Swedish border being historically permeable). Imagine my surprise when I received these results:


WTF! Pardon my French, but . . . where's the French?

Let's say my paternal ancestry accounts for the 36% British Isles, maybe 3% of the Uncertain, and perhaps 11% of the Scandinavian. (My scant Dutch ancestry might have been classified as Uncertain, or else misidentified as British Isles; Vikings also left some genetic traces in the Netherlands.) That leaves me with a maternal genetic ancestry which is 16% Finnish and maybe 31% Scandinavian, 3% Uncertain. Which leaves me uncertain who the hell that guy was that I used to call "Grampa."

I can think of three possible explanations:
  1. My French grandfather wasn't French.
  2. The test results are wrong.
  3. My grandmother fooled around.

1. My French grandfather wasn't French
Not likely. He didn't often speak French, but he did curse in French. He was born in Presque Isle in northern Maine, and all of his known ancestors came through the French regions of New Brunswick and Quebec. He was either French or the mastermind of a very elaborate hoax.

2. The test results are wrong
Possibly. AncestryDNA is still in Beta, so refinements and improvements can be expected. But could they have mislabeled a quarter of my genetic makeup? Could my French genes somehow have been misidentified as Scandinavian and/or British? Others have been surprised by the nonFrenchness of their AncestryDNA results, and many have noted an apparent overestimation of Scandinavian ancestry. So maybe when the Francophobic Viking lover in AncestryDNA's laboratory is discovered and fired I'll get fresh results that will again make my grandfather French.

3. My grandmother fooled around
Well, Grampa fooled around, but that's not relevant to this discussion. When I told my mother about the test results, she was unexpectedly pleased. She had always felt more Finnish than French, and the percentages do suggest that her biological father could have been Finnish/Scandinavian. (If her mother did fool around, it was probably with another Finn.) Her siblings looked more French than she ever did. She is now on the waiting list for a $99 AncestryDNA test of her own, which she hopes will confirm that she is 100% Finnish/Scandinavian. Once she has those results (and after we've given AncestryDNA some time to refine its process), she'll broach the subject with her maternal aunt—likely the only person alive with knowledge of any possible extramarital activity.

My criticisms of AncestryDNA are the same that have been leveled elsewhere. The superficial presentation of test results makes it impossible to know what parts of my genome I share with each of my "Member Matches." Further, I have two matches in the fourth-sixth cousin range, but I can't contact them through the site without an active subscription.* (One of my matches' username is her first and last name, which allowed me to identify her and through some stalking snooping ingenious genealogical research determine that she is my fifth cousin once removed. I was able to identify the other match as well (she uses the same username on Twitter), but haven't been able to find a common ancestor.)

I join the chorus asking that AncestryDNA make raw data available and test results portable, i.e. let users export their data and upload it to third-party sites. The graphs and maps are pretty and all, but some users want to get under the hood and get their hands dirty. Being matched with a previously unknown fifth cousin and finding that our pedigrees intersect gives me some confidence that the science behind AncestryDNA is sound. But allowing experienced genetic genealogists to compare the raw data from this and other tests would go a long way toward establishing widespread confidence in a service that is, so far, a black box.

*I have been offered 6 months free access to "Ancestry Connections" which would allow me to contact them, but will paying customers be offered this deal as the service moves out of Beta? I can understand restricting access to member trees and other features, but shouldn't potential cousins be allowed to make contact without continued contributions to Ancestry.com's bottom line?

Thursday, April 29, 2010

A Contrary Code of Conduct

Like Thomas MacEntee, I think a GeneaBloggers' Code of Conduct is long overdue. From now on, any blogger wishing to appear in my Genealogy Blog Finder must adhere to the following guidelines:

  1. Follow best genealogical practices at all times. Or else learn to fake it like the rest of us.
  2. Hateful language will not be tolerated unless directed at people I also hate.
  3. When attacking religions, lay off the Mormons because you'll probably need their help someday.
  4. Politics should never, ever be discussed on a genealogy blog because Obama is the Antichrist.
  5. Always give proper attributions for the stuff you rip off from better blogs.
  6. Your grandchildren are not as cute as you think they are, so stop writing about them.
  7. Never accept money or gifts from companies in return for favorable reviews of their products without first offering to cut me in.
  8. As Ernest Hemingway once told my grandfather over a bottle of absinthe while celebrating the liberation of Paris, "Do not embellish your family history to attract readers."
  9. Periodically post your blog's traffic statistics so those of us with more visitors can feel superior.
  10. Ask for help when you need it. But don't ask me to help you move, because I'm busy that weekend.
Note: Being listed in the Genealogy Blog Finder constitutes membership in the community and acceptance of the preceding terms. Retroactive membership fees of $50 per year may be sent via PayPal to the email address in my profile.

Monday, April 19, 2010

Ménage à Trois in a Test Tube Revisited

I first wrote about scientists producing human embryos with the DNA of three people in 2008. The new issue of Nature has an article on the researchers' progress.

The British team carrying out the study used fertilized eggs donated by couples undergoing fertility treatment, and which were unsuitable for in vitro fertilization (IVF). At this early stage the sperm and egg nuclei, which contain most of the parental genes, have not yet fused. The researchers removed these nuclei and transferred them into another fertilized egg cell which had had its own nuclei removed.

As very little cytoplasm was transferred with the nuclei, the transfer left behind almost all the mitochondria from the donor egg.
Neurologist Doug Turnbull doesn't think a contributor of mitochondria should be considered a parent.
Turnbull compared mitochondria to the power source for a laptop. “All the characteristics of the computer are stored on the computer. We’re just changing the battery,” he said. [Link]
For genealogists, it's a bit more complicated than that. Mitochondrial DNA has become a convenient way to trace maternal ancestry, and that only works if the DNA was contributed in the natural way. Someday we might have to distinguish between OEM batteries and those provided by third-party manufacturers.

Saturday, April 10, 2010

Genealogy: Another Reason for Your Family to Hate You

Not only is genealogy a worthless pursuit, it can lead to family discord.

Illegitimate children, hidden affairs, troubled finances and deceit all await those determined to piece together their family's past, found Dr Anne-Marie Kramer of Warwick University.

When she interviewed more than 220 people across the country who had looked into their past, she discovered it had led to conflict with relatives in more than one in eight cases. [Link]
So, in about 7 out of 8 cases, family history research did not lead to conflict. Those are pretty good odds. And the odds might be even better, as there's no telling from the article what exactly constitutes a "conflict," and whether these conflicts can be fairly attributed to genealogy. Some of the problems described here and elsewhere—neglecting family, pestering reticent relatives—are more about being unpleasant human beings than about making unpleasant discoveries. Someone who neglects her children because she's obsessed with genealogy would probably do the same if obsessed with Sudoku. And someone who badgers a relative for information is probably a jerk in his non-genealogical life as well.

As for uncovering secrets, I love finding illegitimate children, hidden affairs, troubled finances and deceit in my family. (I'm certainly not British enough to ever be disturbed by the discovery of an ancestor's "previously unknown humble origins.") All four show up in the family of one of my grandparents. In fact, we're planning a DNA test to settle a paternity question in the family. No conflicts here, just questions waiting for answers.

There are families with legitimately disturbing secrets, disclosure of which would embarrass or anger the living. And I have no problem with Dr. Kramer warning of the (meager) risks. Personally, I'd rather know an unhappy truth than live in happy ignorance, but if others want to cling to myths, that's up to them. That said, in some cases discretion should keep us from publishing the truth. But nothing should keep us from ethically discovering and recording it.

Wednesday, April 07, 2010

Every Family Has a Story, And Yours Probably Sucks

The Times has another of those "genealogists are (and should be) only interested in famous ancestors" articles, this time by Sathnam Sanghera.

Genealogists also have a habit of remarking that “every family has a story”. But it’s not necessarily a story worth telling.
Given the huge number of worthless family stories in the world, how fortuitous that Sanghera found his own worth telling.
And before anyone points out the hypocrisy of a memoirist slagging off genealogy, life writing and genealogy are completely different. One being the equivalent of an interest in music, the other the equivalent of an interest in hi-fi equipment.
No, one is the equivalent of the narcissist who talks of nothing but himself, the other the equivalent of the empathic person who shows legitimate interest in the stories of others. You know, the kind of person who might actually buy and enjoy Sanghera's memoirs.

Friday, April 02, 2010

They Were Practically War Buddies

Chris Staats finds five degrees of separation between himself and George Washington. I think I can beat him.

I knew my great-aunt Gladys (died when I was 25), who knew her grandfather Lemuel Dunham (died when she was 10), who knew his grandfather Moses Dunham (died when he was 15). Moses served in the Continental Army under Washington for a couple of years, and was by his own account present at the surrender of Cornwallis. I would imagine he was in the front row and met the general himself, which would leave four degrees of separation between me and Washington.

If you think you can beat me, I preemptively doubt your evidence and ridicule your logic.

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