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PCA Based Ethnic Origins – Part 7, Autosomal SNP Genetics 101

Sometimes, I read something, and it is so very wrong, I feel somehow responsible for the person who wrote it not knowing better. Not that I have caused it mind you, but that I am falling short as a genealogy and genetic genealogy educator. This was the case when I read some text on one of the testing companies websites a few weeks ago. Below is the text.

What if myOrigins results are not what I expected?

People sometimes feel their results are not accurate because they do not see a specific country or population reported. Please keep in mind that myOrigins uses regional percentages (not nationality/specific countries), as DNA mutates regionally rather than across man-made borders. It is also common for some individuals not to see certain reference populations, as they may not have received enough genetic “markers” for that particular population throughout the generations.

From Explore your ancestry with Family Finder – Family Tree DNA January 7, 2019 (Archived in the Wayback Machine)

Let me back up to the very basics of DNA and genetics.

DNA Review

What are mutations?

Mutations are changes in our DNA code. Researchers prefer to call these mutations variants. They reserve the word mutation for variants that cause disease. In genetic genealogy, we use both words about the same way.

How do mutations happen?

Mutations happen as part of the human cell copying process. A small copy mistake is made in the DNA passed to a new cell. Most of the time, these mistakes are purely random.

Are mutations bad?

Most mutations, the variants, do not cause any functional change. A small number of mutations are either helpful or harmful. A helpful mutation would be one that caused lactose tolerance. That is, the ability to drink and digest milk as an adult. A harmful mutation would be one that caused cystic fibrosis. Cystic fibrosis is a serious illness that affects lung and other organ function.

Are all mutations clearly good, bad, or harmless?

No. There are some variants that partly change the way our DNA code works. This type of change might make us more prone to cancer or depression or more likely to do well in math. It does not cause Yes / No or On / Off changes like a light switch though.

Are mutations inherited?

New variants, mutations, come in two types. There are ones that happen in different parts of our bodies throughout our lives. Then, there are ones that happen in our reproductive sperm and eggs. Only the second type from sperm and eggs can be inherited.

What DNA is used for Ethnic Origins tests?

Most Ethnic Origins tests today use our autosomal DNA.

How is autosomal DNA inherited?

We inherit 50% of our autosomal DNA from each parent. We inherit our autosomal DNA in DNA segments.

If we get 50% of our autosomal DNA from each parent, does that mean we get 25% from each grandparent?

No. How much we get from each grandparent falls in a range. This is due to the randomness of inheritance and the DNA segment based system.

Is it possible to get no DNA from some ancestors?

Yes, it is. Four to five generations, back, we might get no DNA or very little DNA from some of our ancestors. For other ancestors, we get much more than expected.

Does PCA Ethnic Origins testing use DNA segments?

No, it does not. It uses individual SNP markers. These are a type of mutation or variant.

What is a SNP marker?

A SNP marker is a mutation or variant where exactly one letter of DNA code is changed to exactly one different letter of DNA code.

What is the source of the SNP markers tested for Ethnic Origins?

The variants (mutations) used on SNP chips for Ethnic Origins come from global testing projects like the International HapMap project, the HGDP, and the 1K Genomes project.

How are the SNP markers selected for chip tests?

The markers are selected to be usually around 5% of the global population. Some more recent chips have added markers as low frequency as 1%.

What is the impact of this selection criteria?

The selection criteria used means that the SNPs on chips are usually thousands or tens of thousands of years old.

Why does this matter for Ethnic Origins?

Because PCA based Ethnic Origins tests use individual SNP markers and the markers on the chips are usually old, the population migrations they detect are usually also old.

Are there exceptions to this?

Yes, there are a few populations such as the Finnish people and Ashkenazi Jews that have highly distinctive genetic signatures. This is due to extreme population size reductions in the past 2,000 years. Here too though, the distinctness is harder to detect after 2 to 3 generations of mixture with other populations.

Evaluating the quote

People sometimes feel their results are not accurate because they do not see a specific country or population reported.

People may feel like results are inaccurate. This is because they are not presented clearly to explain the close recent ancestry of all people and the limitations of the test.

Please keep in mind that myOrigins uses regional percentages (not nationality/specific countries), as DNA mutates regionally rather than across man-made borders.

DNA does not mutate regionally. No. DNA mutates in individuals. It is because the DNA variants used for current Ethnic Origins tests are so old that they are found across broad regions today.

It is also common for some individuals not to see certain reference populations, as they may not have received enough genetic “markers” for that particular population throughout the generations.

It is true that you may share only small amounts of DNA with your ancestors who lived four to five generations ago. That is one of the limitations of DNA testing for personal ancestry.

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