“Gordon” (not his real name) is an adoptee who recently contacted me to help decipher a new DNA match named Rafael. Another genealogist had previously identified Gordon’s birth mother. Based on her family tree, Rafael should have been a first cousin once removed (1C1R) through Gordon’s birth mother, but the amount of shared DNA was unusually high at 762 cM. Another maternal 1C1R, Beryl, shared 997 cM, which is beyond the known range for that relationship. Something unexpected was clearly afoot.
My first thought was that Gordon’s parents were related to one another. I ran his DNA results through the Are Your Parents Related (AYPR, for short) tool at GEDmatch, and indeed they were. Closely.
The ‘Are Your Parents Related’ Tool
AYPR looks for so-called runs of homozygosity (ROH), which is a geeky way of saying ‘sections of DNA that were inherited from both parents’. ROH are not uncommon in people from endogamous populations, where spouses are often distant cousins to one another. For example, my mother is Cajun, and this is a portion of her results:
She has a single ROH of 8.3 cM. It’s the solid yellow chunk on chromosome 2 in the image above. Kitty Cooper shared a great rule of thumb in a recent blog post about AYPR: multiply the total amount of ROH by four to get an estimate of how closely related the parents are. In my mom’s case, 8.3 x 4 = 33.2. Her parents were, in fact, fourth cousins to one another, which fits the amount of ROH pretty well.
That’s not what was going on with Gordon, though. His AYPR results look like this:
All told, he had 20 ROH segments totaling 791.9 cM. Using Kitty’s multiplier, 791.9 x 4 = 3167.6 cM, suggesting that his parents were full siblings to one another. Or father–daughter. It was a shock.
Gordon is a man with intrinsic grace, and he took the news well. He feels blessed to belong to his adoptive family. He is healthy. And these results explained the message relayed by the adoption agency: His birth mother declined contact with Gordon because the experience was too painful for her.
After some time to process, Gordon decided that he wanted to know who his birth father was. And since he did not want to intrude on his birth mother to ask, we took another approach.
Gordon’s Biological Family
Gordon’s biological mother was Helene Mills, born in 1942. Helene’s parents were Oscar Mills and Florence Mattieson. Florence died when Helene was only 7 years old.
Helene has two older brothers, Chris and Tony, and one younger brother, Michael. Grandchildren of two of her siblings have tested; those are the matches that first tipped me off that Gordon’s parents might be related. The numbers below Rafael’s and Beryl’s names indicate how much DNA they share with Gordon (total cM / number of segments), and the color indicates the testing company (green for AncestryDNA; red for FTDNA, with segments below 7 cM excluded).
From a purely genetic standpoint, there are four possibilities for Gordon’s biological father: Helene’s father Oscar or one of her brothers, Chris, Tony, or Michael. We can eliminate two of those brothers as candidates based on other evidence, though.
Gordon was probably conceived in December 1957, when Helene was 15 years old and Michael was only 13. Michael is unlikely to be Gordon’s father given his age at the time.
Rafael is Chris’ grandson, and he shares 762 cM with Gordon. If Chris were Gordon’s father, Rafael would be Gordon’s half nephew through Chris (average, ≈850 cM) plus Gordon’s first cousin once remove through Helene (average, ≈425 cM). If this were the case, Gordon and Rafael would share much more DNA than they do. Thus, we can rule Chris out, too.
Only Oscar and Tony remain as possible candidates to be Gordon’s birth father.
I considered three factors in answering Gordon’s question:
- The number of ROH Gordon has.
- The total amounts of DNA Gordon shares with his DNA matches.
- Whether Gordon’s ROH segments are shared with paternal relatives, maternal ones, or both.
Number of ROH
Our DNA is packaged into units called chromosomes. We have 22 pairs of so-called autosomal chromosomes, plus one set of sex-determining chromosomes, the X and the Y. (Most genetic women have two copies of the X chromosome, while most genetic men have one X and one Y.)
A child inherits one copy of autosomal DNA from each parent, for a total of two copies of each one. Each copy in a pair contains the same sets of genes, but usually different versions of those genes. That is, the copy of chromosome 3 from the mother is not genetically identical to the copy of chromosome 3 from the father. (Think of gene versions like recipes: your apple pie recipe might be different from mine, but they both make apple pie.)
When close relatives have a child together, some segments of DNA will be genetically identical on both copies. These are the ROH we saw in Gordon’s AYPR results above. The total of ROH is a measure of how closely Gordon is related to himself through his two parents. Unfortunately, the total cannot distinguish between a father–daughter scenario and a brother–sister one.
With every generational step, DNA segments along each chromosome get broken down in size in a process called “crossing over”. Because there are more generational steps in the brother–sister scenario than in the father–daughter one, we would expect the former to result in more ROH segments on average than the latter, regardless of the total amount of shared DNA. If we know how many segments of DNA to expect in each case, we can compare Gordon’s actual number of ROH segments (20) to the expectations.
Dr. Andrew Millard is a professor at Durham University in the UK. He has developed a computer program that can simulate genealogical scenarios, and he generously agreed to do some simulations for Gordon’s situation. Simulations allow us to compare Gordon’s results to thousands of similar cases, even when we don’t have access to that many real-life data points.
First, consider the total amount of ROH and the number of ROH segments for the child of a father–daughter pairing versus a brother–sister one. The simulated data shows that the total amount of ROH in centimorgans is essentially indistinguishable in the two cases (left-hand image), but a father–daughter pairing will results in fewer ROH segments, on average (right-hand image).
Although there is a lot of overlap between the two scenarios on the right, when there are fewer ROH segments, the evidence weighs more heavily toward father–daughter, and when there are more ROH segments, it weighs more heavily toward brother–sister.
The blue arrow in the right-hand figure points to 20 ROH segments, the number in Gordon’s results. The figure suggests that it’s about 13 times more likely that Gordon’s parents were father–daughter than brother–sister.
DNA Shared with Other Matches
We can also consider how much DNA Gordon would be expected to share with his genetic cousins under each scenario. The figure below shows Gordon’s relationships to his closest known DNA matches.
Gordon’s direct line is in black bold text, and the people in red font appear twice in the tree. (Debbie is related to Gordon through both his Mills/Walton side and his Mattieson side). As before, the shading indicates where the match tested.
If Tony is Gordon’s father, the matches on the Mattieson side are double cousins rather than single cousins, because Gordon would be the grandchild of Florence Mattieson twice. On the other hand, if Oscar is Gordon’s father, Gordon’s DNA should reflect the fact that Oscar is more closely related to the matches on the Walton/Mills side than Tony is. The distinctions are subtle, however, which is why we must use simulations and evaluate all of Gordon’s matches as a whole.
For this analysis, Dr. Millard performed a bespoke simulation based on the relationships outlined above and then plotted the expected distributions of shared DNA amount for each of Gordon’s matches. As before, we can compare the real numbers (shown with blue arrows in the figures below) to the expected distributions to get a sense of which scenario is more likely.
Two of Gordon’s matches, Beryl (997 cM) and Rafael (762 cM), are grandchildren of Helene’s siblings. If Tony is Gordon’s father, each of them is a double first cousin once removed, once through Helene (average, â‰ˆ425 cM) and once through Tony (average, â‰ˆ425 cM). If Oscar is Gordon’s father, each of them would be a first cousin once removed through Helene (average, â‰ˆ425 cM) and a half great nephew/niece through Oscar (average, â‰ˆ425 cM). In both scenarios, the average is expected to be roughly 850 cM (425 + 425) of shared DNA.
The simulations confirm that the shared DNA amounts are the same regardless of which scenario applies; neither Rafael nor Beryl helps to answer Gordon’s question.
For Gordon’s other matches, the amounts of shared DNA have different distributions under the two scenarios. Although the distributions overlap, in each case, there are centimorgan amounts for which the father–daughter scenario is more likely (where the solid green line is higher than the dashed red one) and others for which the brother–sister scenario is more likely (vice versa).
In Gordon’s case, every one of these cousin matches shares a DNA amount that favors the father–daughter possibility. Dr. Millard calculated that it’s 85 times more likely that Gordon’s parents were father–daughter than brother–sister based on these DNA matches.
Mapping of ROH Segments
Runs of homozygosity are segments of DNA that are inherited from both parents who, in turn, inherited the segments from their parents. If Tony is Gordon’s father, roughly half of Gordon’s ROH should be segments that both Helene and Tony inherited from their father Oscar and roughly half should be segments that they both inherited from their mother Florence. In that case, we should be able to find relatives on Florence’s side who match Gordon on those ROH segments. If Oscar is Gordon’s father, none of Gordon’s ROH should map to Mattieson cousins (although some non-ROH regions will map to those relatives).
Of Gordon’s 20 ROH, I was able to map five to known relatives. All of them are related to Gordon on the Mills side. The odds of this happening by chance are only 3.125%, indicating that it’s 32 times more likely that Oscar was Gordon’s father than Tony.
I analyzed Gordon’s DNA results three different ways, and all three ways supported the scenario that Oscar was Gordon’s father. The father–daughter pairing was 13 times more likely given the number of ROH segments, 85 times more likely considering how much DNA Gordon shares with his cousin matches, and 32 times more likely when ROH segments were mapped to the ancestors Gordon share with Gordon’s DNA matches. Overall, it’s about 35,000 times more likely that Oscar was Gordon’s father than Tony.
Implications for Physical and Mental Health
Discovering that your parents were closely related can be a shock, even though the child of such a pairing is never to blame. This brochure, written specifically for people who discover they have high levels of ROH, refers you to resources that may be helpful. https://www.watersheddna.com/highrohinfosheet
Runs of homozygosity can sometimes lead to medical conditions. Normally, we have two variant copies of each gene, so if one copy is defective or less functional than average, the other copy can usually compensate, and the individual is healthy. Within ROHs, both copies of each gene are identical, so if one copy is defective, so is the other. There is no “backup”. Of course, it is also possible that both copies will be fine and the person will have no adverse effects.
Having high levels of ROH is not a guarantee of medical problems; it just increases the chances. Your doctor will be able to advise you if you have concerns.
Because ROHs only occur when a child’s parents are related, medical conditions that arise are not likely to be passed on to the next generation. In other words, Gordon’s own children and grandchildren will not have an increased risk of genetic conditions as long as Gordon’s spouse is not related to him. While Gordon may have two identical versions of Gene A, Gordon’s children will have inherited one version of Gene A from him and one from his wife, so even if his copies are faulty, the one they inherited from their mother can compensate.
If you discover that you have high ROH levels and have additional questions, you may wish to consult a genetic counselor. This brochure can direct you to resources that will help.
Gordon’s story was shared with his permission. To protect the family’s privacy, all given names were changed to tropical cyclone names from the U.S. National Hurricane Center, and the surnames were made up. Dr. Millard generously contributed his time and expertise to the case and pointed out that ROH could be mapped to cousins as evidence for who Gordon’s father was.
2 November 2021 — Clarified information on the sex-determining chromosomes.