ABUTTING SEGMENT BOUNDARIES (ASBs)


 A discovery was made which from the outset seemed promising but a little hard to understand. To explain, 'abutting segment boundaries' or ASBs are a type of segment boundary coincidence in which 2 segment matches abut (we first reported 2 such cases here in which the Cr2 8099555 event is accompanied by the additional 8442248 event). Initially we (mistakenly) saw an explanation of ASBs in meiosis, for 4 gametes are produced from one set of parental chromosomes. Complementary gametes show a parent's DNA rejected on one side of a recombination appearing on the other side, thus producing an abutting boundary coincidence which can survive to later generations. With some excitement our presentation 'Fun with Autosomal DNA' used this 'insight' to claim a Baruch Lousada connection across 4 family branches. However Andrew Millard pointed out that the statistics of sperm and egg utilization do not favour our 'insight'. After our first 2 ASBs, new ones were discovered making 20 ASBs in total from a total of 1963 segment matches arising from a 12-relative set using Qmatch set at 3cM with P = 3.

From what follows, it seemed that the terminal SNP of any reported segment normally lies outside the actual segment. For as GEDmatch advised on 24 Oct 2025: 'The boundaries of a segment are practically impossible to get exactly correct. There are alleles in positions which are not SNPs and the crossover is likely not exactly at a SNP. So the mismatch at the front of the segment is before the segment actually starts and the mismatch after the end of the segment is after the segment ends. There is also the possibility that the SNPs after the beginning of the mismatch at the beginning of the segment happen by chance and the segment might actually start after the first aligned SNP following the match. For example if the first SNP inside the segment is AC then it will match what ever is in the other kit but the crossover may be further in. The same is true at the end of the segment. Finally if the two kits are not from the same vendor chip set there are SNPs which do not align and had those SNPs been available the mismatch SNPs which bound the segment may be different'. 

From those comments, it appears that ASBs should be reported as having a 1 or 2 SNP overlap. But they aren't, so - in Qmatch - we infer that GEDmatch reports a segment boundary halfway between the last misaligned and the first aligned SNP. That is, as we belatedly realised, the GEDmatch comments above refer to normal matching, and not Qmatch which is a proprietary product the details of which are kept secret as it is behind a (Tier 1) paywall. Qmatch was recommended to us by GEDmatch for use with small matches, and we have indeed found that without it ASBs do not appear (at least readily). In Qmatch it was easy for us to notice ASBs unaided, because the end of one segment is reported as numerically identical to the beginning of the other abutting segment! A computer search will be needed for sets larger than our 12 relatives to avoid missing any ASBs, and this would also allow a search for ASBs showing small overlaps or misses eg of a few hundred nucleotide positions (should Qmatch methodology change and inadvertently remove exact ASB matching which is currently so beneficial).

The following diagram shows in essence what causes ASBs - starting with 3-person ASBs (3pASBs). Thus, where an ancestral crossover in one sibling is carried forward into a present-day descendant and is accompanied (in 2 further present-day descendants) by a stretch of each parent's DNA which bridges the crossover, ASBs can result under favourable circumstances. By this is meant that they will obviously not be detectable in cases where the ancestral parents match in the region surrounding the crossover. In any event, it is important to consider whether the ancestors defining an ASB are 'parents' as shown in the diagram and not immediate ancestors thereof - which may not be a concern for us because our 3cM match threshhold size makes it likely that the ancestral family is no earlier than that of Amador de Lousada (11 generations back):


Of the 17 3pASBs we found, the following chart shows how 16 of them fit the model. The 17th raises the question of whether Je descends from 2 ancestral siblings and not just Fernando. In any case, our insight allows us to also understand the small number of 4-person ASBs as well - for here, a pair of relatives from the same family branch can act as a surrogate for Relative 1 in the chart. That is, both of the relatives in the pair carry the ancestral crossover - a situation which of course is not common given the many reproductive events which might have eliminated the crossover of interest. The significance of the following chart is that every one of the 3pASBs describes at least one interbranch connection. Further we have evidence that MD does descend from his own ancestral sibling, but of course at least 8 of our set of 12 relatives descend from more than one ancestral sibling (and so might Je) and we can't tell them apart.








We can now see the potential of ASBs, for in the following chart of proven matches, we have added the 24 extra 3pASB connections from the previous chart to our small match procedure. We have also added the 5 extra 4pASB connections. It can be seen that the ASB contribution greatly outnumbers the 5 matches from RSBCs and the 10 from Qmatch. More importantly they vastly strengthen the interbranch connections.