The Endogamy Files: What Is Endogamy?

Endogamy is a word that gets bandied around a lot in genetic genealogy circles, but what it means and how it affects our work is less clear. This post is the first in a series about what endogamy is, why it matters, how to detect it, and how to work with it.

Endogamy is the practice of mating within a specific group.  All human populations have practiced endogamy to one extent or another.  Some still do.  Endogamy can occur because the group is geographically isolated from other people, like Native Hawaiians were; because they prefer to marry within their religion, ethnicity, language, and/or social caste, as most cultures do; or for other reasons, like consolidating power among royalty.

Key to endogamy is that the group is small enough that, over time, marriages occur between cousins.  Not necessarily first or even second cousins (although that can occur), but between third, fourth, and more distant cousins.  Over and over.  And over.

It’s important to remember that endogamy is not incest, which is sexual relations between close relatives, like a father and daughter or uncle and niece.  Incest is associated with a substantial risk of early death or genetic disorders in the child, while marriages between even first cousins are much safer.

I’ll discuss the health implications of incest and endogamy in a later post.


Endogamy and Pedigree Collapse

Endogamy causes something called pedigree collapse, but not all pedigree collapse rises to the level of endogamy.

Consider the example below.  The home person (at the bottom) is the child of parents who were third cousins to one another.  That is, the parents shared a pair of great-great grandparents.  As a result, their child (the home person in the diagram) has 30 unique great-great-great grandparents instead of the expected 32.  One set of 3-great grandparents shows up twice in the child’s tree.  We say the pedigree is “collapsing” rather than doubling in number with each generation back, as we’d expect.


But pedigree collapse is not endogamy.  Pedigree collapse is one or a few isolated incidents of cousin marriage, while endogamy occurs repeatedly over many, many generations.

This is endogamy:

Note that this second diagram also incorporates birth year, so the generations are not aligned with one another vertically like they were in the hypothetical example above.  To see your own tree this way, use the Exploring Family Trees tool.


This is my mother’s tree.  She’s Cajun, a culture that was geographically and culturally isolated in southern Louisiana and, before that, in what is now Nova Scotia.  Cajuns have been marrying mainly within their own population since the 1600s.

My mother’s parents were fourth cousins.  I don’t think they knew, because my grandmother’s father was born out of wedlock.  My grandfather’s parents were third cousins; they definitely knew.  There’s no known incest in this tree, but the cousin marriages go on and on, back to the earliest settlers in Port-Royal, Acadia (now Annapolis Royal, Nova Scotia) in the early 1600s, because there simply weren’t a lot of options for marriage partners.

The closest cousin marriages I’ve identified in this tree are between first cousins.  Consider Isaure Marie Guidry (1863–1933), my mother’s great grandmother.  In the diagram above, she is the left-most female (pink) ancestor just below the horizontal line for 1850.  Her parents, Alexis Onésime Guidry and Palmire Dupré, were first cousins through their shared grandparents Louis–David Guidry and Marie Modeste Borda.

To complicate matters even more, Onésime had been widowed before marrying Palmire.  His previous wife, Celestine, was Palmire’s older sister, and Celestine had a daughter named Marie.  So Marie and Isaure were half sisters their father Onésime, and first cousins through their mothers Celestine and Palmire.  (This combination is often termed three-quarter siblings.)  But they were also second cousins through Onésime and their mothers.  Each unique relationship path is shown in red below.


Technically, Marie and Isaure were second cousins twice over, once through Onésime and Celestine and once through Onésime and Palmire, but you get the picture.  It’s enough to make your head spin!


How Does Endogamy Affect Genetic Matching?

Isaure and Marie died more than 75 years before the advent of genetic genealogy using autosomal DNA, but what would their match to one another look like if we could analyze their genomes today?  As half sisters, we’d expect them to share about 1750 cM, as first cousins another 850 cM or so, and as double second cousins roughly 200 cM twice over.  In many parts of their genomes, they’d match on both copies of their two chromosomes, much like full siblings do.  In fact, they might well be indistinguishable from full sisters using the methods we use for genealogy.

While Isaure and Marie are an extreme case, DNA matching is affected to some degree in all endogamous populations.  People who are no closer than fourth cousins might share enough DNA to be predicted as third cousins, because they’re picking up “extra” shared DNA through their other relationships.

For example, my mother shares 184 cM with D.M.  If you were to plug that number into the DNA Painter SCP tool, you’d see a combined probability of 89.1% that they were either in the second cousin group (38.8% chance) or the second cousin once removed group (50.3%).


In fact, their closest relationship is third cousins, who average only about 50 cM. On the other hand, Mom and D.M. are also third cousins once removed twice over, fourth cousins once removed, and fifth cousins … that we know of.  All those distant relationships add to the shared centimorgan tally.

Thus, the overall effect of endogamy is to make many of our DNA matches appear to be more closely related than they really are.  This complicates everything, from basic relationship prediction to more advanced and powerful techniques, like the Leeds method and the What Are the Odds? tool.


In subsequent posts, we’ll address how to identify endogamy in a family tree, how to identify it using only DNA match lists, gauging how much endogamy is present, best practices for genetic genealogy, and some health implications.


A Fun Thought Experiment

Is the entire human population endogamous?  After all, we only mate (well, mate successfully) with other humans and have been doing so for ten thousand years or more, since the last archaic humans, like Denisovans and Neanderthals, died out.  Technically, we’re all (very distant) cousins, and all of our pedigrees collapse eventually.

What do you think?

21 thoughts on “The Endogamy Files: What Is Endogamy?”

  1. That’s interesting. Here in Canada earlier today by chance I was watching this: It’s a mini history lesson about Acadia.

    I have a lot of East Frisians and have wondered about endogamy in that group. I haven’t heard about it… but I wouldn’t be too surprised if it’s a factor.

    1. The expulsion was barbaric. Thousands died, and families were separated forever.

      It would be interesting to look at endogamy in East Frisians. Unfortunately, not many Germans have tested yet.

  2. I have DNA matches which suggests endogamy. My daughter and I have matches where we share the same amount of centimorgans or very close amounts with the match. I also have matches which are shared with both my parents.
    Looking forward to learning more

    1. If you and your daughter share just one segment with those matches, it might not be endogamy. It’s possible the same segment simply got passed down to you intact rather than being whittled down by crossing over. In an upcoming post, I’ll show how to gauge the amount of endogamy in your match list.

  3. Thank you for this very interesting post. I look forward to the rest of the series. I have encountered much difficulty over the years attempting to solve some NPEs in the New Mexican branch of my family tree as my efforts continue to be complicated by endogamy.

    I am grateful for the information you’ve posted about the amount of atDNA Isaure and Marie might have been expected to share. If I have read it correctly, you appear to be saying that the amount of DNA they would have been expected to share is roughly the sum of all of the amounts of shared DNA from each of their different reationships to each other combined. This is something I have often wondered but have had difficulty finding expressly stated. Thank you.

    1. In most cases, you can assume that the total shared amount of DNA is roughly the sum of the individual relationships (assuming you can identify all the relationships, and also allowing for the fact that DNA inheritance is messy). However with three-quarter siblings, there’s an added complication that I only alluded to in the post.

      Full siblings have spots in their genomes where they don’t match at all (roughly 25%), spots where they match on one of their two chromosome copies (roughly 50%; called “half identical”), and spots where they match on both (25%; called “fully identical”). Most testing sites treat half identical and fully identical segments exactly the same. In other words, a fully identical segment of 100 cM would only count as 100 cM toward the total, even though it’s really two 100-cM segments.

      The presence of fully identical regions (FIRs) is a characteristic of full siblings, but we also see them in three-quarter siblings to a lesser extent. I haven’t thought through how much FIRs Isaure and Marie would have had given the additional 2nd cousin relationships.

  4. Thanks for this, Leah. I am looking forward to the rest of series. As you know, I have found endogamy a real stumbling block to using DNA to further my genealogy research.

  5. Pedigree collapse and endogamy get brought up pretty often, as you mentioned, when discussing DNA. Thank you for this clear post on how they are alike and how they are different. And, the graphs are particularly helpful. I’ve meaning to chart my own family’s pedigree collapse, so thanks for the reminder!

  6. Thank you for this series. I have French Canadians as well as some Germans in Southwest Virginia who have made my DNA matches difficult.

  7. Thank you for this article. The line that It will make your head spin is 100% true! I have a lot of French Canadian and Colonial American ancestors- nothing surprises me on who’s related anymore!

  8. Leah, many thanks! This puts a finer point on my unstanding of the topic. I posted this at the FTDNA Forum. Think I got your permission to do this previously.

  9. Thank you so much for this information! I’ve been struggling with the endogamy and pedigree collapse throughout my Dad’s paternal line for years. I’ve traced the group back to their arrival in New Amsterdam and their migration patterns from that point. I’ve narrowed it down to basically three groups that went separate directions but each group falls into the endogamy relationship pattern for a number of generations. My Dad’s branch managed to break out of the group around 1850 when they moved from Illinois to Minnesota. In addition to the endogamy, I believe there is at least one pedigree collapse in his direct line where two brothers or cousins (we can not be certain of whether they were brothers or cousins at this point!) but they married two sisters and as a result, the descendants of both lines show up as much closer dna connections… that could also be due to the endogamy within the groups!

    1. We see the same pattern over and over with immigrants and emigrants. People tended to migrate in groups of relatives and friends, and they often married within that group until they became established in their new locations.

  10. I have a situation with two families that immigrated to the US from Alsace Loraine. Siblings of one family had been marrying siblings of the other family for several generations. Now, in trying to solve an NPE by triangulating DNA matches, all roads lead to both families, though cM numbers are higher for matches to one family than the other. With this situation be considered endogamy?

    1. The difference between endogamy and pedigree collapse is one of degree: an isolated cousin marriage is pedigree collapse. When it occurs repeatedly over many generations, it’s endogamy. There’s no sharp line between the two. Your case sounds like endogamy to me.

  11. “ENDOGAMY”… What an interesting topic!
    I thoroughly enjoyed reading about this topic and looking forward to learning more about this informative area of genealogy.

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