What is the Primeval DNA Test

Measurements of genetic distances

Ever since the first human population genetics paper in 1965, geneticists have been concerned with developing methods to measure genetic distances between species, populations, and people and modelling the genetic structure of the population. For example, in 1972, Lewontin1 showed that the differences between human continental groups  (Africans, Asians, and Europeans) are too small to constitute genetic “races,” a finding confirmed by Elhaik2 later on using a database of 3M mutations. Measures of genetic distances and similarity were not limited to humans. In 2010 scientists reported that all Europeans share between 1 and 4% Neanderthal DNA3. This study, which launched the era of Paleogenomics, was followed by the development of new methods to measure distances, now between modern and ancient people. For example, by comparing the ancestry of ancient South American individuals to modern individuals, Posth and colleagues4 concluded that all the Ancient South Americans descended from the same Eurasian source population. In summary, there are different ways to measure genetic distances (and genetic similarity) between people and populations. These tests differ in their assumptions and resolution, but they all aim to answer similar questions that eventually allow us to reconstruct past demographic history.

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The Figure was obtained from5.

Obtaining ancient DNA from skeletons

There is rich literature on the process of extracting and sequencing ancient DNA from skeletons5,7,8 and what can it tell us about the individual, culture, and metapopulations and various aspects of their lives including their environmental adaptations and disease susceptibility.

Ancient DNA supports cultural conservation efforts

In recent years, local communities and geneticists started to work together to sequence DNA from remains that were taken from their homelands decades ago and return them home. 

Obtained from Nature.

The identification of the museum specimen as coming from a certain population is done by sequencing its ancient genome and measuring the genetic distance to that of modern-day communities. If a mummy is found to be the closest to Native Americans, for example, then under the US 1990 Native American Graves Protection and Repatriation Act (NAGPRA) and similar state legislation, museums have to return what they can in the way of ancestral remains and sacred objects to Native American communities.

Measurements of genetic distances in the Primeval DNA Test

The Primeval DNA Test operates in a similar way to other genetic distance measures. It compares the participant’s DNA to that of DNA obtained from ancient people and reports the genetic similarity. The comparison is done by looking at a unique group of mutations that we recently identified and termed ancient Ancestry Informative Markers (aAIMs)6. These mutations show variation between past populations and are therefore informative to determine ancient ancestry. We introduced this concept and the method of comparison in our recent paper6.

The ancient DNA was recovered from skeletons (usually the ear bone) found in various archeological digs around the world and published in the archaeological or paleogenetics literature. All the ancient individuals were given a nickname that fits their culture and origins. For instance, the ancient Israelite Gal was named after Gal Gadot – Israeli actress in Hollywood who played Wonder Woman), whereas a man who led a group of Turkish migrants to Israel around the Patriarch period was, unsurprisingly, named Abraham. The test also reports the age of each ancient person, their burial site, and their mitochondria and Y chromosomal haplogroups.

To take the test, the user uploads a zipped file of their raw autosomal DNA results, such as those provided by half a dozen companies, or orders a DNA kit and selects the tests that they wish to take. The file is then unzipped, run through our pipeline and analyzed for the requisite ancient populations. The results show the percentage of similarity to each of the ancient people within each test, much like how a contemporary test will show the percentage of Neanderthal in one’s genome.

Interpretation of the results

Analysis of the genetic similarities is expressed in percentage of genetic admixture between the DNA strands of the two individuals being compared (modern person and ancient skeleton). After finding out the degree of similarity, the user can compare their results to the range of results obtained for other populations (e.g., English populations, modern-day Egyptians, North Africans and Ashkenazic Jews). All this happens in an interactive fashion in the account.

All the tests were developed by Dr. Eran Elhaik. Dr. Elhaik’s laboratory also developed the public website Ancient DNA Hub as a source of knowledge on archeological sites from which ancient skeletons were found and sequenced.

The purpose of the Primeval DNA Test was to create a realistic and accurate ancestry test with minimal assumptions that will distinguish it from contemporary tests that compare peoples’ genomes to other modern peoples’ genomes who reported having four grandparents from certain populations – at best – under the assumptions that the latter represent the true genetic diversity of their population. This assumption is, of course, very problematic, as all populations have mixed over time, and the extent of conclusions that one can draw from these results about the past is extremely limited. These tests were simply developed at a time when ancient DNA was not around so they had to make these assumptions, but we have seen time and time again, how incorrect they are. The Primeval DNA test compares the person’s results directly to the ancient skeletons from cultures of interest. The comparison is 1:1, meaning one person:one skeleton and no assumptions are made on what each ancient skeleton represents except for what is known from the scientific literature. Obviously, the older the skeleton, the less genetic similarity can be expected.

In that respect, the Primeval DNA test is unique. For once, it is unbiased like modern-day ancestry tests that are based on modern-day people taking the test (mostly Europeans). The test includes ancient people from all over the world, with the obvious physical limitations of extracting ancient DNA from certain areas. Second, it reflects one’s true genetic similarity to people of the past, which is what standard ancestry tests ask us to believe is true but is not. Finally, it allows people access to the vast Paleogenomic data and knowledge accumulated over the past decade in an unbiased and educated manner, that is to say, the results are not calibrated according to people’s liking.

The Primeval DNA test allows testing some of the most profound beliefs in our society concerning nationality and identity. Are contemporary English 100% Vikings? Are modern-day Jews fully ancient Israelites? But there are some questions that no test can answer, such as the concerns of the everyday lives of the ancient people or the meaning of our similarity to them.

 

References

[1] R.C. Lewontin, in Evolutionary Biology, Vol 6, T.G. Dobzhansky, M.K. Hecht, W.C. Steere, Eds. (Appleton Century Crofts, New York, 1972), pp. 381-398.

[2] E. Elhaik (2012), Empirical distributions of FST from large-scale Human polymorphism data, PLoS One 7, e49837.

[3] R.E. Green et al. (2010), A draft sequence of the Neandertal genome, Science 328, 710-722.

[4] C. Posth et al. (2018), Reconstructing the Deep Population History of Central and South America, Cell 175, 1185-1197 e1122.

[5] I. Morozova et al. (2016), Toward high-resolution population genomics using archaeological samples, DNA Res. 23, 295-310.

[6] U. Esposito et al. (2018), Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians, Gene 9, 625.

[7] I. Lazaridis et al. (2016), Genomic insights into the origin of farming in the ancient Near East, Nature 536, 419-424.

[8] A. Prohaska et al. (2019), Human Disease Variation in the Light of Population Genomics, Cell 177, 115-131.

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