Using DNA to Put Cracks in a Brick Wall

One of my long-time brick walls is my 3rd great-grandfather Jacob Garber. He is an ancestor on my Dad’s side. I have written about the rather sparse information I have been able to gather on him and the challenges in finding his parents in the brick wall section of my website. [Here is the link: bit.ly/jacob-garber-bw]

This is essentially what I know about him. He was born circa 1802, probably in the area of Amity or Douglassville, Berks County, Pennsylvania. He married Ann Campbell on 13 Nov 1825. Ann died in 1850 and was survived by six children – five daughters and one son. Despite the oldest daughter Mary Ann being born in Oct of 1825, all of Ann Campbell Garber’s children are presumed to be fathered by Jacob. At this point I am not sure when Jacob died. It is possible that he remarried after Ann’s death and fathered additional children.

So what’s the big break through with DNA? Well I have a AncestryDNA match who also has Jacob Garber and Ann Campbell in his tree. I have been in contact with him, but unfortunately he doesn’t know the parents of Jacob either. If my match would not have uploaded his DNA test results to GEDMatch that would be the end of the story – at least for now. But because of the chromosome-level matching information that we get through GEDMatch we now have a triangulation group that points to possible parents for Jacob!!

But there’s a twist. As I mentioned in an earlier post, I have created paternal and maternal side kits on GEDMatch by phasing my original kit with my Mom’s. When I do a one to one comparison between my paternal & maternal side kits I get a 21.3 cM match on Chromosome 11. I was not surprised (nor upset) by this because I have known for several years that both my Mom and Dad descend from Valentine Keely & wife Susanna Mueller as well as from George Bechtel & Hannah Yocum. Both of these couples lived in the 1700s. Thus, in one case my parents are 5th cousins once removed and in the other case 6th cousins once removed.

As you have probably guessed by now, my Jacob Garber-Ann Campbell match (let’s call him EK) matches me on that very same segment where my two chromosome 11s match each other. EK, of course, also matches my Mom on that segment and matches my maternal uncle on part of the segment. So the main triangulation group is my Dad (via the segment I inherited from him), my Mom and EK. How awesome is that! (Note that recently my brother and a maternal Aunt tested and they share this segment as well!)

We first need to look at the match itself. I have a couple of graphics from GEDmatch to illustrate the match from the perspective of my paternal side as well as my maternal side. The first graphic shows the match based on what I inherited from my Dad. Leaving my Uncle out of the equation (for the moment), it is easy to see that EK has the exact same match to my paternal side kit as my Mom and I. It is also obvious that the matching segment crosses over the centromere and I’ll address that shortly.The second graphic shows the match based on what inherited from my Mom. I think the interesting thing to note is that this match to EK is slightly longer than the match based on my Dad’s side.

Getting back to the centromere. If you have ever seen a graphic with a chromosome represented by an X-like figure, the centromere would be where the legs of the X connect. It is represented by the pinkish colored vertical band. It is also a region where recombination doesn’t generally occur and could be passed down unchanged for many, many generations. So a match on that area of the chromosome is usually considered a false positive in that it may not indicate a common ancestor in a genealogical time frame.

That being said the matching segments as pictured above extend well beyond the centromere and I believe they represent true IBD segments. In fact the Ancestry matching algorithm, which is supposed to be designed to subtract false positive areas, classifies my match to EK as 4th-6th cousin with shared DNA being a total of 18.6 cM across 2 segments. Kind of curiously, it classified both my Mom’s and Uncle’s match to EK as 5th-8th cousin, with a total of 15.6 cM across 2 segments and 14.9 across 2 segments, respectively. Given the results shown on GEDmatch, I would have expected my Mom’s match to EK to have been closer in length to mine, but for one reason or another Ancestry has not calculated it that way.

So getting back to the Garber connection. As it turns out, there are Garbers in my mother’s ancestry. One of her 3rd great-grandparents (my 4th great) are Conrad Garber and Anna Maria Bechtel. From Chester County, Pennsylvania estate documents we know that Conrad had a brother named John who died prior to 1837 leaving 12 children. The children are named in the probate file of their bachelor uncle Johan Adam Garber, as are the children of Conrad.

I have found baptism records for some of John Garber’s children, but not all of them. One of the children for whom I have not located a baptism record is the son named Jacob. For several years I have been wondering if Jacob, son of John, was the Jacob who married Ann Campbell. The approximate age is right and the location is right, but with multiple Garber families in the area I have felt that more evidence was needed to make that call. This DNA match is nudging me closer.

Going back a generation, the parents of Conrad, John and Johan Adam Garber were Johan Adam Garber and Anna Maria Schleicher. Assuming for now that Jacob is the son of John, my relationship to EK via my Mom’s side is sixth cousin once removed. The relationship on my Dad’s side is fourth cousin. A nagging issue is why my maternal side kit seems to share slightly more DNA with EK even though the relationship is more distant. I have a few thoughts on this. First, the randomness of DNA inheritance and recombination causes you to share more (or less) than the average amount expected at a given cousin level. Second, the fact that this matching segment crosses the centromere could have the effect of making it more “sticky” than if it were located elsewhere on the chromosome. Also, the Ancestry algorithm calculated a larger shared DNA amount between EK and me than between EK and my Mom and that is consistent with the actual relationships. So maybe whatever it does to strip out false positive regions is working in this case.

The bottom line is that I am cautiously optimistic that I have found Jacob’s parents – and a third common ancestor couple for my parents. However, there is still more work to be done to be sure the match is not inherited from Jacob’s wife Ann. While I have fairly good information on her paternal side, her maternal side is yet another brick wall. There is always the possibility, however remote, that Ann’s mother connects back to one of my known pedigree intersections – i.e. Valentine Keely/Susannah Mueller or George Bechtel/Hannah Yocum or an as yet unknown common ancestor shared by my parents. (Note that because EK descends from a daughter of Jacob & Ann who moved west (not the one born prior to the marriage), the chance of a link through another of EK’s ancestors is extremely remote.)

That all being said, I’m not a DNA expert so if someone reading this has other ideas or thinks I’m off-base, I would love to hear from you!

Gedmatch, Phasing and Losing Matches

As I mentioned in my last post, I have joined the autosomal DNA bandwagon and have uploaded my raw DNA data from Ancestry into Gedmatch. I have also had my Mom tested and have uploaded her results to Gedmatch as well. And now things are getting interesting!

One of the first things I did was to phase my DNA with my Mom’s. The phasing process compares my DNA to my Mom’s and determines which of my genetic information comes from her. The half that doesn’t come from her is assumed to come from my Dad. (He is no longer living, so I cannot phase directly with him.) As a result, in addition to my original Gedmatch kit, I now have a paternal-side kit and a maternal-side kit as well.

Before I jump into my DNA findings, I need to mention a bit about my heritage. Pretty much all of my ancestors on both sides were in the southeastern Pennsylvania counties of Montgomery, Chester and Berks since colonial times. Some arrived as early as the 1600s. Many were Pennsylvania German, but some were Welsh, Scottish, Swedish and a few other nationalities. The communities in which they lived were small and relatively isolated. As you might imagine there were cousin marriages.  This occurred within the lines of both my parents and also between their respective lines. So it’s possible, maybe even probable, that some of the phenomena I am finding with my DNA matches is a result of endogamy.

With that being said, here’s what happened. First I ran a 1-to-many match on my full kit using the default parameters. This should return all the people in gedmatch with whom I share a DNA match of 7 cM (centiMorgans) or greater, sorted largest to smallest. I got 1500 matches that were all 8.1 cM or longer. 1500 is the cut off for the number of matches that Gedmatch returns in the the 1-to-many results. Thus I hit the Gedmatch maximum before I reached the 7 cM threshold. To circumvent this, I decided to run the 1-to-many match on my paternal-side and maternal-side kits. My thinking was that this would not only sort my matches, but that by splitting them I would see the ones I missed due to the 1500 limit. So I ran a 1-to-many on my paternal-side kit, again using the default parameters, and got 389 matches. Then I ran a 1-to-many on my maternal-side kit and got 481 matches. A grand total of 870 matches!? Yes, I lost matches! Lots of them!

So what happened? I am not totally sure, but I have a possible explanation. The first step is to understand how gedmatch determines matches. Basically, the process of matching is comparing the respective values at certain locations (SNPs) on chromosomes of two people. But since our chromosomes come in pairs – with one coming from Mom and the other coming from Dad – we have 2 values at each location as does the person to whom we are comparing. In order to be a match at a given location only one of our values needs to match one of theirs. But when it makes these comparisons, gedmatch does not have the information to know which of the two values is contributed by which parent. To have a true IBD (identical by descent) segment, the matching values culled from my pairs must all come from either my mom or my dad, but not a combination of the two. Same for the other individual in the match. Thus, it would seem that the matches that disappeared were actually false matches and the result of one or more small segments inherited from my Dad combining with one or more small segments inherited from my Mom to form one larger segment that matched someone else. At least this the explanation I have come up with at this point.

What is still unclear to me is whether or not my results are typical. Does my genetic background and the fact that I have cousin marriages and pedigree collapse in my 8 generation pedigree chart make me more prone to these types of false matches? Is losing over 40% of their matches something most people can expect when they phase their kit to their parent(s)? I would be interested to hear what others think and what their experiences are regarding this.