Using Hot and Cold Segments to Identify Distant Cousin Matches

by Jane Horvath and Frank Paukowits

Originally Published in THE BURGENLAND BUNCH NEWS – No. 286
April 30, 2018, © 2018 by The Burgenland Bunch

The Chromosome Browser is one of the more important tools available to people researching their genealogy through the testing of autosomal DNA. Applied correctly, it can provide critical information to help verify relationships in your family tree. Moreover, once you get comfortable using this tool, it is not complicated to deploy with reasonable expectations for successful outcomes.

FamilyTreeDNA (FTDNA), which sponsors the Burgenland DNA Project, provides each person who has had an autosomal test with information related to their chromosomal structure. This data is included in the Chromosome Browser, to which there is a link on the participant’s homepage. The Browser enables participants to compare their DNA with known relatives and other members who have been found to share matching DNA.

Through this process, someone can find out, in graph format, where matches occur in the chromosomes. It will show the length of the matches in centiMorgans (cM), along with their locations, at varying thresholds. Further, you can secure details on up to five people at a time, which may help to locate common relatives among your matches. This can be very helpful in researching your family connections. While locating a 2nd cousin shouldn’t require much more than comparing your own family tree to the surnames of your match’s great-grandparents, the Chromosome Browser can prove quite useful to help identify the connection to predicted 4th cousins …or even further.

However, there are some limitations. Since a large portion of our matches will fall into this “4th to distant” category, and many people haven’t located their 7th, let alone 19th great-grandparents, one should first try to figure out if these matches are genetically relevant. Fortunately, geneticists have identified hot and cold regions within the chromosomes that may help estimate how far back someone needs to look to find a shared ancestor. The hot spots are the areas where recombination occurs with a high degree of frequency, and conversely, the cold spots recombine at a much less frequent rate.

Recombination refers to the way portions of DNA change with each generation. For example, if you and your son each submit a DNA sample and view your shared matches, you’ll notice that (with some exceptions) a given chromosome segment you share with a particular match will be the same size or larger than the segment your son may share with that same person.

For example, if you share a 15 cM segment with person A and your son shares that identical 15 cM segment with A, odds are that the segment is in a cold spot. It’s cold because it hasn’t changed at all from your generation to his. This particular segment could indicate a common ancestor with person A going back much further than normally expected. Conversely, if you share a 50 cM segment match with person B and your son shares only 30 cM of that same segment with B, it can be projected by the loss of 20 cM that this segment exists in a hot region. Under these circumstances it would much more likely be from a recent ancestor.

A 2013 study1 of genetic divergence conducted by researchers at Penn State University produced a map2 of these regions, as shown below:

Unfortunately, this image in its original state isn’t very useful for genealogical comparisons. For the purpose of analyzing group member data, the map has been altered to match the proportions of the Chromosome Browser on the FamilyTreeDNA site. The neutral regions have been removed and only the hot and cold regions remain, as shown in the next image.

Though these regions do not always behave as expected, for the most part, understanding which regions are hot and which are cold may help to identify which 4th cousins are likely to be found and which are not. For the sake of identifying 3rd and 4th cousins, small segments occurring in the blue regions are theoretically less significant than similarly-size segments in red regions. However, if you have been able to trace your lineage back to 5th and 6th great-grandparents, you may be lucky enough to identify a distant cousin in one of these cold spots where recombination is less frequent.

When comparing different relatives on the Chromosome Browser, a process called triangulation is used to calculate common ancestors. In this process, the place where the matching bits of DNA appear in the graph is critical. Invariably, you will have many people who have matches with you in different places on the graph. While these people would all be related to you, they won’t necessarily be related to one another.

The key to performing a successful triangulation is ensuring that each person in the comparison shares an overlapping segment in the same place on the same chromosome. True triangulation uses at least three people who are not very close relatives and who all match each other on the same place on a particular segment of DNA.

When working with medium to large segments (>15 cM), these bits of DNA merely need a significant overlap, but trying to find a 4th cousin may require comparing smaller segments. In this case, a good indicator of a true match is a segment with identical start and/or endpoints. (Note: this will only occur if you and your matches have all tested with the same company. In the example, all three participants submitted their DNA samples directly to FTDNA.)


An analysis was done comparing Project members Linda Issowits and Frank Seier to group administrator Frank Paukowits. All three participants had the Jautz name from Tobaj in their family lineages and FTDNA predicted they were DNA matches to each other. By comparing where their DNA matched on the Chromosome Browser, a common segment was found to be shared by all three.

The segment shared by Frank P and Frank S is 17.6 cM and Linda’s segment is 7.6 cM, but all three participants share the same identical endpoint on this segment. As previously mentioned, a shared identical start and/or endpoint is very important when analyzing these smaller segments. This match not only shows an overlapping segment, but also shows a bit of common DNA that ends at the same exact genetic location.

Because all three participants had adequate family trees, it has been ascertained that Frank P, Linda, and Frank S, are all fourth cousins to one another, and that their common ancestors are 3rd great-grandparents György Jautz (1788-1871) and Theresia Heiliman (1788-1848). Indeed, the use of the Chromosome Browser, coupled with the analysis of the family trees, enabled this result. Below is how this triangulation looks with all three family trees combined into one.


* The green lines in the chart represent the flow of common DNA from generation from generation.

The next step would be to download the cM data for all matches and search for any others with identical start or end points on chromosome 4. They very likely share a Jautz and/or Heiliman ancestor.

  1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3767554/
  2. http://science.psu.edu/news-and-events/2013-news/Makova8-2013

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