Tuesday, January 5, 2016

Finding Your Roots, Season Three Premieres Tonight on PBS

Don't miss out, Season Three of "Finding Your Roots with Henry Louis Gates, Jr." premieres tonight on PBS (check your local listings) and will run every Tuesday night for ten weeks. The first episode features actor Ty Burrell, artist Kara Walker and author/political analyst Donna Brazile. I have written an article on some of the DNA analysis used for the show that should be posted in the next couple of days on the PBS site.

Read this great review of the series by Cal Thomas from the Washington Times. He writes, "Next to 'Downton Abbey,' which is again pulling large audiences for its sixth and final season, Mr. Gates' program (premiering Jan. 5th) is the best and most compelling television you will ever see."

I also have a new public Facebook page here. Please follow me there for more updates if you are on Facebook. 

Thursday, November 26, 2015

AncestryDNA's $69 Black Friday/Cyber Monday Sale Starts Tonight at 9pm Pacific!

AncestryDNA's Black Friday Sale = Only $69!

This is 30% off the regular price of $99 and is the best price of the year. It will run tonight at 9pm Pacific thorough the 30th at 9pm Pacific. (I have been advised that the free shipping code FREESHIPDNA will not work with this sale.)  Click on the link or image below to access the sale after 9 pm Pacific tonight -- 30% off AncestryDNA Nov 27-30. 

I hope this brings in many more testers to help us all with our research!


Wednesday, November 18, 2015

Ancestry.com Files a Trademark Case Against DNA Diagnostics Center for the Marketing of "AncestryByDNA"

I became aware today of a trademark case recently filed by Ancestry.com vs. DNA Diagnostics Center.

Although DDC's "AncestryByDNA" test has been around in one form or another for many years prior to the launch of "AncestryDNA" by Ancestry.com in 2012, I have seen significant market confusion due to the way AncestrybyDNA has been marketed through sites such as LivingSocial and GroupOn since that time. I wrote about this back in 2012 here.  In fact, I am the "third party" mentioned in the complaint: "On our about July 29, 2012, Ancestry was contacted by a third party who was concerned about consumer confusion resulting from an online 'LivingSocial' advertisement for 'Ancestry DNA.' Confusingly, the LivingSocial ad was entitled 'AncestryDNA' and advertised DDC's services at the website AncestrybyDNA.com." Since this time the confusion has continued and, as a result, we have seen many people who intended to purchase the AncestryDNA product extremely disappointed upon receiving their AncestrybyDNA results. It is such a shame to see people spending their hard-earned money and receiving a product that is virtually useless for genealogical purposes. In some cases, this was the only opportunity an individual had to test a family member, which as genetic genealogist know is of great importance to our research.  It is also an unfortunate and unnecessary deterrent for those who might otherwise have become more involved in our community since this test may discourage them from any further participation in genealogy/ancestry DNA testing.

Ancestry.com vs DDC Filing

In the very large genetic genealogy and unknown parentage-focused groups that I administer, we are seeing this brand confusion increasingly often -- almost on a daily basis lately -- and so I am very glad to see this addressed. All of my team spends a significant amount of time trying to clarify the difference between the two tests and save people from the impending disappointment of purchasing a product they believed was something else entirely.

Some people may argue that this is Ancestry using their vast resources to bury a smaller competitor, but DDC is a large, successful paternity testing company and the product in question is only a very small part of their business. I am quite confident that they make plenty of money without the extra income generated by people purchasing a test in error. I am not an intellectual property legal expert (unlike my friend and colleague Blaine Bettinger), so I will refrain from technical analysis of this case. However I will say that after reading the complaint thoroughly and from my own experience observing the marketplace, I believe that Ancestry.com is in the right and has a very strong and persuasive case. They addressed all of the misgivings I had about their position in the complaint. While it is true that DDC was using "AncestrybyDNA" before Ancestry started using "AncestryDNA," the market confusion due to their promotional methods is significant and very damaging. (All you have to do is read the comment section of my original blog post on the subject to see the evidence.) I hope this suit will put a stop to that.

One other very interesting thing to me is that Ancestry.com states in the filing that ConnectMyDNA, (the other useless "ancestry" DNA test that Judy Russell wrote about here) has also been marketed by DDC, "Previously, DDC apparently advertised its services through LivingSocial under the trademark CONNECTMYDNA and the website www.connectmydna.com." I checked the site registration and sure enough, the site is registered by DDC.

Thank you to Ancestry.com for taking action to clear up this confusion. It is my sincerest wish that consumers will no longer be fooled into spending money on these products that do not fulfill the purpose for which they were purchased.

Friday, October 9, 2015

DNA.Land Launches

DNA.Land was launched today by scientists from the New York Genome Center and Columbia University. I was asked to advise on this project several months ago and have been excitedly anticipating its launch. 

Posted by Dr. Yaniv Erlich on Facebook today:

After long months of work, DNA.Land (https://dna.land) is finally on air.

We developed a platform to massively crowd source genetic, genealogy, and health information from millions of people. Our goal is to help our participants know more about their genome and help science. By uploading their genome data to our website, participants will be able to find genetic relatives, learn about their ancestry, and get a more complete version of their genome data. During this process, they will also be able to contribute to cutting-edge genetic research...

To quantify their level of contribution to science, the website will also present to each participant a badge with a score that corresponds to the amount of data he or she contributed and the percentile of data contribution...

If you were tested with 23andMe, Family Tree DNA, or Ancestry - take a look at https://dna.land/

The website is not-for-profit and was developed by scientists from Columbia University and the NY Genome Center.

We would love to hear your feedback.

Anyone who has tested at 23andMe, Family Tree DNA or AncestryDNA may participate by uploading the raw data to the site. There are very good instructions on DNA.Land for completing the raw data upload process. Please make sure to use a valid email address or you will not be able to access your results. Due to consent and privacy issues, DNA.Land currently does not support multiple uploads to a single account, so you if you have consent from family members to perform the upload to DNA.Land, it will require a different email address/account to do so. 

The raw data upload and the imputation step will take about two hours and the ancestry reports will be ready in about 24 hours. (Imputation is the act of inferring the base -- ATCG -- at a location that has not been tested. More info here and here.)

I have received my reports and am sharing screen shots from my account below. Right now there are only two, but there will be more features added in the future. 

Relative Matching:

I really like that DNA.Land classifies the shared segments as either "ancient" (green) or "recent" (orange), which we have not seen previously on other sites. Not surprisingly, shorter segments are more likely to be designated as "ancient," but you cannot always tell just by looking at the chromosome graph. This is because in some regions, the rate of recombination is slower than others, resulting in a lower centiMorgan value versus nucleotide count (megabase pairs). You can see this in my screenshots above where DNA.Land has classified the segment on Chromosome 9 in my matches 1, 4 and 5 as "ancient" even though it appears to be relatively large in comparison to some of the other "recent" segments. This is because it is crossing the centromere and the recombination rate is expected to be slower there. At this point, you cannot see the start and stop points of the shared segments on the site, but I am advised you can do so by viewing the HTML source. (Hopefully, this will be surfaced later.)

Since I was one of the first ones to upload to the database, most of my matches are from OpenSNP. For these, no email address is provided (column one), but for most of your matches, there should be an email address for contact. I have some concerns with the closeness of the relationship estimates shown in column two because I would not expect to see so many close relatives in such a small database, but I am confident the team will reassess this during this beta phase. I think the "Relationship Likelihood" graph in column five is a good addition to demonstrate the uncertainty of the relationship predictions. 

Ancestral Origins Report:

As you can see these reports are pretty basic right now, but they will continue to develop and improve. Knowing how much the genetic genealogy community likes to see the predictions of the small percentage ancestral origins, I have recommended that this be expanded. 

Please remember that this is an early beta version and DNA.Land will be refined as they work through issues and add additional features. Feedback and questions should be sent to info@dna.land.

This is a wonderful way to contribute to genetic research, so please check it out! 

FAQ are here.
Facebook page where you can ask questions here.
More information from the Nature news article here

Friday, August 21, 2015

Do You Have Lupus? Join 23andMe's Lupus Study

Click here to enroll: 23andMe Lupus Study

23andMe, Pfizer, and the Lupus Research Institute are collaborating to study the genetics of lupus in a research initiative that is designed to recruit and genotype 5,000 individuals from the U.S. who have the disease. The partners aim to discover the underlying genetics involved in lupus, with the hope that this knowledge will lead to new or improved treatments. 

Eligible enrollees will receive the 23andMe Personal Genome Service® at no cost, including reports on their ancestry and their raw genetic data. Additionally, enrollees may receive up to $50 in compensation for completing five short bi-monthly surveys plus one final survey that will be delivered within the 12 months after joining the study. For current 23andMe customers, eligible enrollees will receive a $20 Amazon gift card for joining the study and agreeing to the terms. Learn more about the study here.  

See if you are eligible:
Lupus is characterized by the body’s immune system attacking normal, healthy tissues almost anywhere in the body. People with lupus might have symptoms that include inflammation of the joints, or skin rashes, sores or damage to the kidneys, or heart or lungs. 
In order to participate in the first study within the lupus community, you must meet all of the following criteria: 
• You've been diagnosed with lupus by a qualified physician. 
• You consent to have 23andMe (via a partner) contact your physician to obtain your medical records. 
• You're willing to submit a saliva sample for DNA testing and complete online surveys related to your condition. 
• You are at least 6 years old (minors under 18 require parental consent to enroll). 
• You have access to the Internet. 
• You reside in the United States.

Questions: If you have additional questions about the lupus study, please email 23andMe directly at lupus-help@23andme.com. 

Friday, February 27, 2015

Switched at Birth: Unraveling a Century-Old Mystery with DNA

The following is a guest post by Alice Plebuch demonstrating the potential of DNA testing. When Alice first contacted me about two and a half years ago with the beginning of this incredible tale, I knew that the answer was just waiting to be discovered one day through genetic genealogy. Many of you may have heard part of her family's story already, but I thought it only made sense for Alice to share it from the beginning through to its completion since it was her DNA test that started the unraveling of this mystery and her persistence that, finally, led to the resolution. (The final piece of evidence just arrived this week and, with it, the confirmation needed by Alice's family to finally share their story.)

Three years ago I blithely took a DNA test at AncestryDNA. At the time, the fact that it was in beta, somewhat alleviated my concern when I first saw my results. I was three quarters Irish with the remainder being a English/Scottish mix, but the test claimed I was half Jewish. It was as if half my ancestry was wrong. The results had to be wrong! I was expecting to see Mc and Mac relatives, but the names were overwhelming Eastern European, Russian, and Jewish. I can assure you, they weren't any of my relatives, or were they?

Alice's Unexpected Ethnicity Estimate

I have six siblings strewn all over the United States. By chance, two brothers visited within days of my receiving the perplexing DNA report. Their reactions ranged from finding the Jewish component mildly interesting, but wrong, to outright ridicule. How could I ever imagine we were anything but Irish, they asked? Nothing makes me take an opposite position faster than being mocked. I defended the test, even as I harbored huge doubts. Looking at the family trees of my matches became a daily endeavor and I wondered, could I really be related to these people?

I called my only sister, Gerry, and shared the disturbing results. Her immediate and intense reaction was that the DNA test was correct. Gerry thought it just felt right. I had conducted some research on genetic testing companies so when Gerry decided to test, I recommended 23andMe where I knew we'd have direct access to our genomes. I also retested at 23andMe.

Waiting on the second round of testing gave me time to imagine incredible scenarios, most notably, "I was adopted" and "Mom had an affair"! Gerry laughingly dismissed those notions by reminding me of how much we all resemble Dad. Everyone in the family has Dad's distinctive eyes and I certainly have his flat feet and massive bones. Nevertheless, it was a real relief when the first thing I saw in my DNA family list was a nephew with the proper relationship. Shortly thereafter, Gerry's results were posted. We were full sisters and both half Ashkenazi! Another brother casually mentioned he also tested at 23andMe. His profile was neither public nor had he even looked at his ancestry composition. We quickly shared genomes and it was three for three.

To be on the safe side, I sent a copy of my genome to Doug McDonald, a retired professor at the University of Illinois, noted for calculating accurate ancestry admixtures. His analysis was quite pointed. "It can't be any clearer. One of your parents is Jewish."

23andMe's Ancestry Composition Feature Shows Fully Jewish Chromosomes for One Parent

Now that the Ashkenazi component was verified, the question of which parent remained. Our prime suspect was Dad. Mom had an extremely well documented family tree, but more importantly, we personally knew many of her huge extended family and they were definitely not Jewish. We had pictures of Mom's family extending back over a hundred years. Dad's parents died while he was young, and kin did not raise him.

So together, my sister and I worked out a plan where we would test first cousins from both sides of the family. Our cousins are considerably older than us and we were concerned they wouldn't be open to DNA testing. We were pleasantly surprised when they eagerly agreed to spit for us. Their one request was that their identities be kept private.

We also asked our brother, Jim, to take a Y-DNA test through National Geographic. His test came back, indicating his genotype is the predominate type in southern Ireland where our grandfather was born. Almost as a footnote, it was mentioned that a small number of Ashkenazi Jews shared the genotype.

23andMe has a facility called Countries of Ancestry that displays areas on a person's chromosomes that are associated with Ashkenazi Jews. Those areas are displayed in blue, the rest in white. Once again, I found myself staring at a computer screen trying to make sense of what I was seeing. I kept flipping back and forth between the chromosomes of Bill, Gerry and myself, when suddenly I had a "Eureka!" moment. Males inherit their X-chromosome exclusively from their mothers while females get one allele from their mother and the other from their father. Blue permeated each and every single chromosome for Gerry and me, but there wasn't a single dot of blue on our Bill's X-chromosome. Dad was Jewish!

Alice's X-chromosomes show Jewish DNA

Bill's X-chromosome shows no Jewish DNA

Armed with the knowledge that the Ashkenazi genes came from Dad, Gerry and I made a friendly bet. I wagered that our paternal cousin would also be Jewish. My sister was just as sure he wouldn't be related to us. She had come to the seemingly ludicrous conclusion that "Dad was switched at birth!"

More waiting provided time to research Dad's parents; after all, they could have been Irish Jews or Jews that assumed Irish persona so they could more easily enter the United States. Now that everything is on the Internet, it was relatively easy to verify that our grandparents came from Irish Catholic families, marrying into other Irish Catholic families, for quite some time. There was no hint that they were anything other than Irish.

It was almost as Loki, the trickster, was having fun with us. One cousin's kit had the correct address on it, but it was delivered it to the wrong address and the person just kept it, unopened. The other cousin's saliva didn't yield sufficient DNA and had to be reprocessed. At last the results arrived. 

Mom's nephew was almost classic 1st cousin match. I went cold when I ran the comparison for Dad's nephew. None of us had any genetic relationship with him, whatsoever. He was as Irish as we were Jewish! I lost the bet with Gerry, but more importantly, was left with the unenviable task of telling our beloved cousin that we weren't genetically related.

The family was stunned. Our brothers were no longer laughing. My sister and I swung into high gear to find our biological grandparents.

The big question was how could Dad become separated from his family. In 1913, most women had home births, but Dad's birth certificate clearly states he was born in a hospital. Even today, with high-tech monitoring, occasionally babies are misidentified. Imagine a hospital that has just started delivering babies and didn't foresee mix-ups, much less DNA. We knew when and where the other baby was born so we turned to The New York City Birth Index, in which we identified thirty male infants born in the Bronx within a day of Dad.

Our untested brothers dutifully spit into test tubes so we'd have a better chance of finding a match. Then, all our genomes were transferred to Family Tree DNA and GedMatch to widen our dragnet. Although Jim already took a Y-DNA test, it only reported on 12 markers; far too few for genealogical purposes. Bill volunteered to take the more expensive, but much more accurate, "111-marker Y-DNA" test at FTDNA. Although Bill had the same genotype as Jim, his matches were with Ashkenazi men of Eastern European ancestry, with the notable exception of an Irish man with our surname! We choose to discount the Irish match as being a NPE after talking with the family. Bill had a single "extremely significant" match that predicts a common ancestor within 4 generations. We were hopeful and dared wonder, "Had we found our father's true surname?" Unfortunately, autosomal DNA tests indicated a more distant relationship.

It was suggested that what we should look for a Jewish baby with a surname similar to ours. In fact, there was a male infant with a very close, but distinctively Jewish, surname. Thanks to a birth announcement in the NY Times we were able to trace the family into the present. DNA testing showed he couldn't be the Irish child. Our hopes for a quick and easy resolution were crushed.

Thus began the tedious work of the next two and a half years. On behalf of the family, Gerry and I sent out over a thousand invitations to share genomes at 23andMe. We also contacted many of our approximately 3,000 DNA cousins (each, for a collective total of 7,000 unique cousins) at FTDNA. The overwhelming majority of DNA cousins never responded, a few hurt our feelings by refusing to even speak to us, but enough accepted to build an excellent search base. A few of our Jewish DNA cousins have become fast friends and marvelous co-researchers.

As more and more match data accumulated, it became obvious to Jim, that the spreadsheets we used were unwieldy. Jim used his skills as a developer to create an iPad application, DNAMatch, which easily and efficiently managed the 300,000 plus overlap segments our large family has generated. Real analysis was finally possible.

Jim's DNAMatch Automated Spreadsheet Feature

We had massive amounts of information on the location and surnames of our DNA cousins and were able to make some predictions. Minsk, Vilna and Ukraine were clearly geographic "hot spots", yet some of our closest matches traced their families to Romania. Many were related to us on both sides of their families. While the majority of our contacts knew their ancestors came from Russia, they weren't sure of the town or even the name of the current country. Ancestral surnames changed at a dizzying pace or they simply didn't exist. I hate to admit I was getting depressed over the probability of finding our grandparents, but...

Dad's Irish nephew has always been supportive of our quest and I provide him with updates. His 23andMe DNA Relatives list doesn't change frequently, so I'd fallen into the habit of checking his matches monthly instead of daily. In the middle of my most current update, rather than report a lack of progress, I stopped and signed on to his profile. OMG! OMG! There, right below his name, was an anonymous woman listed as a second cousin. In my heart-of-hearts, I knew she was the key. With my heart pounding and my hands shaking, I wrote her a personalized invitation, explaining that I managed my cousin’s account. Would she would compare genomes with him to help me solve a 100-year-old mystery concerning my father.

When she accepted, I wrote, “Thank you for responding so quickly. P N [his posted name] is helping me discover who my real grandparents were. Theoretically, we are first cousins, but I found out, through a DNA test that my Irish father is, in fact, fully Ashkenazi Jewish. We tested all our first cousins and he doesn't match my family at all, which is impossible if we were genetic first cousins. Every expert that has looked at the evidence is convinced, as are we, that Dad was accidentally switched at birth with the Irish child.”

Jessica, the young woman, in turn responded, “I was actually expecting to be much more Ashkenazi than I am. My father died when I was very young, but I was always told that both his parents were descended from Eastern European Jews. Through this test I've found that I am only about 2% Ashkenazi and that I am actually Irish, which I had not expected at all. So I'm not really sure what is going on.”

I explained when and where Dad was born and within 20 minutes Jessica wrote to say, “Just glancing quickly through internet records, it looks like my dad's father, Philip, was born on September 24, 1913, so you may well be on to something.” She later confirmed that her grandfather was actually born a day earlier, just like Dad. Her grandfather’s name was on my list of “suspects”, but his surname was misspelled!

It was late at night when we finally emailed our “good nights”. Sleep was impossible, making the wait until morning, and sharing of the joyous news, sheer agony.

We received email photographs of our grandparents the following afternoon. What an incredible feeling it was to look at old snapshots and see those familiar, smiling, faces. There was Dad’s hairline, his nose, his ears, and eyes on his father. Dad’s mother graced him with her marvelous facial bone structure. There is no denying — we’re related.

Alice's parents on their wedding day

Alice's newly discovered biological grandparents Sam and Ida

Alice's father

Our wonderful Jewish DNA cousins constructed our family tree within hours. With a real tree, my closest DNA match at Ancestry found we share the same 2X great grandparents and, today, the DNA test on Jessica’s Jewish grand aunt — my presumed 1st cousin — confirms we ARE indeed first cousins! Dad really was switched at birth!

Matching DNA between Alice and her new
first cousin plus four of Alice's siblings

And now our Irish family is Jewish. Our "Swap Cousins" are Irish and are trying to adjust to this shocking news. We’re all hungry to learn about each other's family and how to intertwine the two families, Irish and Jewish, into one tree.

Despite all our careful planning and matching of cousins, our final success is attributable to a one-in-a-million, unpredicted match. I’m not a particularly religious person, but the inexplicable events that lead us on this remarkable odyssey, and its unexpected and spectacular conclusion, are sure having an effect on my belief system!

Wednesday, December 3, 2014

The Folly of Using Small Segments as Proof in Genealogical Research

Responsible genealogists adhere to high standards of proof in their research, in the evidence that they present and in the conclusions they reach. I strongly believe that genetic genealogists should as well. When we make claims that are not supported by sound science, then we undermine the credibility of our field.

Experience has demonstrated to me that there is great folly in claiming small segments can be used as proof (yes, even supporting) in genealogical research. When I use the term "small segments" in this article,  I am referring to unphased "matching" segments under 5 centiMorgans and I am addressing their use in matching, not admixture.  A few genetic genealogists have argued that there are certain instances when small segments are not only helpful in our genealogical research, but reliable. I strongly disagree.

One of the many problems with utilizing small segments is that, in general, people tend to see evidence that supports their theories and reject evidence that does not. Because the nature of small segments is so random, as I will demonstrate, it is possible that an individual will see patterns where none exist in reality, such as in a cluster of tiny, meaningless "matching" segments. This also holds true for admixture analysis.

Blaine Bettinger already wrote a great blog explaining the work that has already been done on this issue along with some of his own comparisons, so I am going to concentrate on the multi-generational data to which I have access. Angie Bush has kindly allowed me access to her family's extensive data while she is unable to collaborate on this post since she is on a genealogy cruise. (Thanks, Angie!)

All of these examples are the first ones I looked at, so they are randomly chosen and not selected with bias. There is a huge amount of analysis that can still be performed on this data set. Since Gedmatch was down when I wrote this, I concentrated on Family Tree DNA data. When I am able to access Gedmatch again, I will add to my analysis.

First let's look at this simple chart of my data compared to James, a confirmed paternal fourth cousin, and then my father's data compared to that same cousin. As you can see, both my father and I have one substantial matching segment with James on Chromosome 4 (in purple). Some would argue that because we have one longer matching segment, that this makes the matching small segments reported more valid and thus can be more responsibly attributed to our known common ancestor.

Notice the segments highlighted in red in my chart. Those are all segments that were reported to be matching between me and James that do not show up as matches with my father. So, right off the bat, we can eliminate eight segments of what some might claim is supporting evidence of the known relationship with James.  That is 66.6% of the segments under 5 cM, which is in line with what was found in the 23andMe study.

Since I have no reason to believe that I inherited those segments from my mother, they are likely pseudo-segments. Pseudo-segments are spliced together by jumping between alleles from mom and dad, impersonating a matching stretch of DNA where one does not exist. The inability to distinguish these from authentic matching segments is a limitation of our current technology. Could they have actually come from my mother, you might be asking? My mother does not match James at the Family Tree DNA thresholds and I can't check Gedmatch to be sure, but there are no known common origins between them. (I am checking with James to see if he is willing to allow me to make that comparison for my next post.) Regardless, this analysis clearly disproves that the red segments are a result of the known paternal relationship. As such, there should be no argument to the conclusion that the majority of the small segments in this randomly chosen example cannot function as supporting evidence of the primary relationship in any way.

Next, look at the green segments. In this case, it appears that I inherited those from my father, but if you look closely, they are actually longer for me than for my father. This means that they are at least, partially, false positives or pseudo-segments. Incidentally, the one substantial matching segment we have in common (purple) is also reported to be a bit longer for me than for my father, which illustrates that it is questionable to rely too heavily on what appear to be exact assignments. In my list of matching segments, only the pink segments on chromosomes 2 and 3 are left as potentially fully IBD segments. Some will say that the fact that they persist from parent to child makes them more reliable indicators of a genealogical relationship. Perhaps, but there is no proof that that the pink segments weren't originally pseudo-segments interpreted as a match by the technology in my father's data and then passed to me through recombination of his two chromosomes. Does that sound far-fetched? Well let's see by looking at multi-generational data.

Please bear with me because this is going to take awhile. This chart is the matching DNA between Brynne and a known Bush cousin from her mother's father's father's branch of the family. The common ancestors are Frederick Bush and Martha White, so you can see that the expected path of inheritance for matching DNA between Brynne and this cousin is:
Brynne >> Angie >> Grandpa >> Great Grandpa

Here we are looking at the threshold set at 5 cM. Brynne's data compared to the Bush cousin is on the left and the comparison of her mother Angie to this same cousin is on the right.

This is her grandfather's (left) and great grandfather's (right) DNA compared to the same cousin.

These are nicely consistent with all of Brynne's matching segments being inherited from her great grandfather, as would be expected.

Now, let's look at the same comparisons with the threshold lowered to 1 centiMorgan.

Brynne and Angie:

Grandfather and great grandfather:

As you can see things got very messy at this level. We have all kinds of problems and inconsistencies with the data now. Let's look at just a few.

Chromosome 11:

As you can see Brynne has three small segments (under 5 cM) in common with her known Bush cousin on Chromosome 11. One is lost as we move to her mother Angie's comparison, but two persist. So, if the theory is correct that when a small segment persists over two generations that it is more likely to be identical by descent or attributable to the known common ancestor, then the two remaining ones should be IBD. However, look what happens - another is lost when we move the next generation back in time toward the common ancestor with the known cousin and then finally all three have disappeared by the time we get to the great grandfather. This is the opposite of what we should be seeing. Could these last two segments be attributable to another common ancestor on Brynne's grandmother's and great grandmother's branches of her tree? Possibly, but if so, that still doesn't support the claim that small segments help to prove the primary relationship responsible for the large matching segments. In fact, it refutes it because it demonstrates that even in families with no known pedigree collapse, such as this one, there still may be small segments inherited from distant common ancestors.

We saw other problems too. In some cases, like on Chromosomes 3 and 6, segments disappear at one generation and seemingly reappear at the next. That tells us one of two things - that coincidences happen and/or that the technology is not reliably picking up these small segments consistently. Either scenario does not instill confidence in genealogical conclusions based on small segment analysis.

Chromosome 3: Grandpa was "skipped" and the segment was almost three times larger in the most recent generation which is opposite of what we would expect to see if it was identical by descent.

Chromosome 6: Mom was "skipped". Notice the high number of SNPs (again many more in the most recent generation), which makes it seem less likely that it was simply missed by the technology.

These examples lend credence to the myth that DNA can skip a generation, which we all know to be untrue.

Most importantly, in this entire comparison, NOT ONE of Brynne's small segments shared with her known Bush cousin persisted consistently through all four generations on the path back to the known common ancestor.

When going through this data, I saw so many examples that fly in the face of the belief that small segments can, in any way, be reliable indicators of a genealogical relationship that I couldn't even begin to cover them all here. Since Gedmatch was down while I was writing this, I was unable to do some of the comparisons I had planned, so perhaps I will do that at a later time.

In the meantime, since I read a lot of comments over the last few days that people feel comfortable mapping small segments to their known ancestors using comparisons of their close relatives, I decided to see if that, at least, could stand up to analysis. Let's look at Brynne compared to her maternal grandparents.

We can see her DNA mapped to her grandfather in orange and her grandmother in blue. It is quite clean at the 5 cM threshold on the left with almost no overlap as we would expect, however when you drop the threshold to 1 cM, you can start to see issues on the right. Look at Chromosome 1, for example. There are three small segments from the grandparents that are directly in opposition to the obvious inheritance pattern. You can also see it on chromosomes 3, 5, 6, 10, 12 and 14 (click image to enlarge). If you only had one of the grandparents tested, you would map those small segments to the wrong grandparent and, thus, be "barking up the wrong" branch of the tree.

Brynne's DNA mapped to her maternal grandparents

Let's look more closely at Brynne's Chromosome 14 and the inheritance from her maternal grandparents through to her great grandfather Bush.

The pink in the image below is the comparison with her mother, Angie. Of course, they share across the length of the chromosome. Then, you can see, in green, the DNA she shares with her maternal grandfather and, in blue, the DNA she shares with her great grandfather from the same line. It appears that she has one long segment from her grandfather and then one small one that she inherited from her great grandfather through her grandfather. You would feel pretty safe mapping that small blue/green segment to her great grandfather, right? There is only one problem...the orange is the DNA she inherited from her maternal grandmother! That small segment falls right where the DNA she inherited from her mother came from her maternal grandmother, not her grandfather! She couldn't have inherited DNA from both her maternal grandmother and her maternal grandfather on that spot, so the small segment must be a false positive even though it persisted over multiple generations.

You can see similar problems on Chromosome 1, 5 and 6.

Remember she can't inherit DNA in the same spot from both grandma and grandpa.

Pink - mother, green = grandfather, blue = great grandfather (father of grandfather), orange = grandmother. 

All three of these chromosomes show small segments that fall in sections inherited from the opposite side of the family, proving they are false positives. Look at the colorful pile-up on Chromosome 6. Some of these segments are almost 5 cM!

There is so much more to say about the use of small segments in genealogical research and a huge amount of data to explore, but I will stop here for today. I think that these few examples should give any genetic genealogist who believes that small segments can, in any way, support genealogical theories serious pause for thought.

In a later article, we will examine the assertion that small segments can prove useful as "population specific" guides and if there is any support for the recent ancient genome comparison analysis. The fact that these segments are not consistently inherited certainly calls that type of analysis into question as well.

I encourage those of you with access to multi-generational data to perform a similar analysis and let us know what you find. The more data, the better!

[Note: In the future, I believe that we will be able to utilize smaller segments in our research and even assign them to specific ancestors through chromosome mapping, but this will only be possible when technology has advanced considerably and we are using higher resolution autosomal DNA testing and much improved phasing engines. The exception is Tim Janzen who is attempting to do so now through highly technical and advanced work. He is phasing his data through testing and comparison of large numbers of known relatives, many more than the vast majority of genealogists will ever test. To my knowledge, he has never claimed to have used small segments to break down any genealogical brick walls or to have proven anything in that regard, even as supporting evidence.]