Founder Effect | DNA and Endogamy

Jayne Ekins

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Founder effect and endogamy are different, but they can occur concurrently in your family tree. Read more from Jayne about the founder effect, what it is, an example of it, and how it differs from endogamy.

Both founder effect and endogamy can lead to reduced diversity in your DNA. However, they are not the same thing. Continue reading to learn more about the founder effect in historical populations (like your ancestors’ communities) and how it is different from endogamy (which also may have affected those same communities).

What is founder effect?

Founder effect is a principle from population genetics that describes the reduced diversity seen in a group of descendants who come from an isolated group that was established by just a few people. It makes sense that an isolated population that was established by three couples would have less genetic diversity than a population that was established by 200 couples. Founder effect can make the people from this descendant cohort genetically distinct in a way that is detectable by DNA analysis. 

Founder effect: The original population (left) could give rise to different founder populations (right). Public domain image.

What’s an example of founder effect?

One example of the possibility of founder effect can be seen in early American colonists, namely the Mayflower passengers who arrived in North America in1620. They began with a small population–102 original passengers–but only 53 survived the first winter. 

If they had remained isolated and only had children with other Mayflower passengers, their genetic characteristics would be magnified and accentuated in future generations. This could have then led to a real possibility of founder effect in the Mayflower community. However, additional colonists, many of whom were unrelated to the Mayflower passengers, arrived the following years and expanded the gene pool.

There is, however, a potential to detect a more general “Puritan genetic community” for the New England region, as this population separated and continued to generally isolate themselves for generations. You can read more about “Mayflower DNA” here

Does founder effect happen everywhere?

A recent study of small isolated rural communities in Illinois put this idea to the test. They investigated whether 157 people from four different small rural communities tested on 999,259 genetic markers were able to represent groups that were distinguishable from one another using DNA. 

Said another way, are these four groups from rural Illinois genetically different enough to be detectable, or do they share too much common DNA today due to other relatively recent common shared ancestry? Researchers compared the four rural Illinois groups to a public database with genetic representatives from world populations called the 1000 Genomes database.

Most of the 157 Illinois individuals were all clustered together with others of European descent from 1000 Genomes, without showing differentiation to one of the four rural groups. When comparing the Illinois people to just the 503 individuals from 1000 Genomes of European origin, two sub groups within Illinois were able to be distinguished: those of British descent, and another group from the more broad European landscape.

These results demonstrate the ability to recognize source populations of contemporary rural Illinois groups. However, researchers did not find that they could completely distinguish the four rural populations genetically, implying that the founder effect on these groups was not profound enough to leave a distinct genetic legacy.

The Illinois population that lived isolated in the countryside for two to four generations didn’t result in a detectable level of genetic distinctiveness or elevated DNA sharing among descendants. 

Are founder effect and endogamy the same thing?

No, founder effect and endogamy are not the same thing. It will help to clarify our definition of endogamy here. For most of the world, endogamy just means the practice of marrying inside a tradition, ethnicity, etc. This can be in effect for just one generation and still be called endogamy. Here at Your DNA Guide, where the context is genetic genealogy, what we really mean when we talk about endogamy is the genetic effects of prolonged endogamy (when a community marries within its defined culture or location for many, many generations).

A founder effect may kick off a scenario for reduced genetic diversity in a community. But for endogamy to come into play with your DNA analysis, that community would have to remain genetically isolated for a long time. Both can operate concurrently in small isolated populations and contribute to elevated DNA sharing in descendants.

It really takes time for the genetic signature of endogamy to develop–hundreds or thousands of years of extended endogamous practice–or a splinter group that comes off of an extended endogamous context in the first place. You can read more about endogamy in detail here and in our unique and popular Endogamy and DNA Course.

Your DNA ethnicity results may identify your ancestry with increasingly specific and accurate historical communities, including those that may have experienced founder effect and/or endogamy. Learn more in our free guide to DNA ethnicity.

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<a href="" target="_self">Jayne Ekins</a>

Jayne Ekins

Jayne has been in the field of genetic genealogy since its beginnings as part of the Sorenson Molecular Genealogy Foundation. She has lectured throughout the United States and international venues on the applications of molecular biology to elucidating ancient and recent genealogical connections. She has authored and co-authored many peer-reviewed scientific publications, as well as general articles on genetic genealogy. It is a pleasure for her to see the accelerating developments in genetic genealogy, and the wide accessibility and application it has for the average human curious about their origins.


  1. Heather

    Where can I read the original “recent study” involving the four rural Illinois communities?

  2. Doug Bank

    This explanation was not completely clear. I think it would be better if it also included a clear cut example of a true founder effect – like you would see with genetic mutations like BRCA in Ashkenazi Jews. How did three specific mutations survive to be present in 1 in 40 people in this population? Also, aside from specific mutations, how else does the founder effect differ from endogamy?

    • Diahan Southard

      The founder effect has to do with how many couples were there in the beginning. The few beginning couple or couples who started a DNA line that was isolated for a long period of time are founders. Endogamy happens when members of a family intermarry/have children over time and those children intermarry/have children over time. Sometimes there is overlap. But in terms of population genetics, the definitions begin with how many couples were the entire group descended from.

  3. Alva Balter

    I thought my maternal side was pedigree collapse but now I wonder if its founder effect. My mom’s side is from Virginia most of her parents relatives are from the same 2 or 3 towns close to each other. My 3rd great grandfather founded one of the towns. Many have married 2nd or 3rd cousins over the last 200 years.


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