Ancient DNA Is Newest Tool in Genetic Genealogy


Eran Elhaik

Eran Elhaik

Eran Elhaik is a faculty member at the Department of Animal and Plant Sciences at the University of Sheffield in England specializing in genetic epidemiology, population genetics, molecular evolution, epigenetics and personalized medicine. He is the lead author of a paper on DREAM, a new microarray for second and third-generation tests like GPS ORIGINS and Primeval DNA Test. That work was published last year in GENOME BIOLOGY AND EVOLUTION. He is also head of a team of scientists who recently defined the concept of ancient ancestry informative markers, or aAIMs (U. Esposito et al., “ANCIENT ANCESTRY INFORMATIVE MARKERS FOR IDENTIFYING FINE-SCALE ANCIENT POPULATION STRUCTURE IN EURASIANS,” Genes 2018, 9, 625; doi:10:3390/genes9120625). In addition, he is also known for challenging popular notions about Jewish origins with EVIDENCE THAT ASHKENAZI JEWS ARE OF MIXED IRANO-TURKO-SLAVIC AND SOUTHERN EUROPEAN DESCENT rather than Levantine and Central European ancestry.

Millions of consumers have taken advantage of SNP chip technology and received their ancestry results from DNA testing companies. But not all are happy campers in this next-generation DNA testing wonderland.

The reason is a sort of lack of belief in the so-called hard science of it all, a reluctance to take a leap of faith and embrace precise percentages comparing modern-day people and bygone populations. “What is the meaning of telling me I am 50% English or 30% Jewish or 0.5% Asian,” said one user of a well-known ancestry service that sells for less than $69 on the web.

“The missing element,” according to Donald N. Yates, Ph.D., principal investigator of DNA Consultants, “has been a control, a sort of time machine that would yield a picture of what our DNA was actually like at points in the past rather than theoretical projections and extrapolations.”

“Customers have sometimes been incredulous, even defiantly so, about the picture of autosomal ancestry they receive—especially those exploring their Native American heritage,” says Yates. “Between the reliability of different microarray versions, which are very expensive for companies to maintain, and the validity of the predictive algorithms behind modern ancestry informative markers, the rate of accuracy could be as low as 40 percent, less than the odds of guessing heads or tails on a coin flip.”
Eran Elhaik, Ph.D., a young Israeli-American lab director and genetics professor in England, is hoping to change those odds. He is one of the authors of a new paper in the journal Genes proposing a definition of “ancient ancestry informative markers.” At the same time, he is the inventor of the algorithms behind DNA Consultants’ new family of Primeval DNA [link to page on site] tests.

After obtaining a doctorate in molecular evolution under the supervision of Dan Graur at the University of Houston, Elhaik completed two postdoctoral research fellowships at The Johns Hopkins University School of Medicine and School of Public Health before becoming a faculty member at Johns Hopkins and later, a lecturer at the University of Sheffield. Since that time, he has published papers with other genetic luminaries that have become some of the most cited in their respective areas of research.
There has been no way to check the true error rate of ancestry tests, Elhaik notes, because no other approach has been compared with them (for instance, forensics). “It’s as though we were dependent on rudimentary blood group studies for human prehistory, as indeed everyone was in the early days before the human genome project arrived,” he says. “All the test subjects up until recently have been living persons in a fairly confined cohort group.”

“With ancient DNA we have studies from different times and places,” he says. “It is difficult to correlate ancient history with the simplistic trajectories we have got used to in modern-day DNA data.”
“Modern-day results are naturally biased toward privileged societies and supposedly prestigious ancestries,” Elhaik claims. “By contrast, since we do not know where the next skeleton will pop up, ancient DNA introduces a more democratic and inclusive approach, which happens to be more free of assumptions.”

The ancient DNA revolution is upon us, and the shockwaves are amazing.

Ancient DNA testing allows anyone to compare their genome to that of a real person who lived in the past and see the degree of genetic similarity, one on one. Tests can include skeletons from ancient cemeteries, mummies from Egyptian tombs and fossils of early humans. The Primeval DNA Test series, launching this January, offers tests for an initial group of seven: Britons under the Roman Empire, Ancient Israelites, medieval Vikings, Ice Age humans, Stone Age hunter-gatherers, Egyptian Mummies and Paleo-Indians.

Since a team led by Danish geneticist Eske Willerslev sequenced the first ancient genome from a 4,000-year-old Greenland man’s hair in 2010, ancient genomes have grown to encompass more than 6,000 profiles for peoples around the world, from the Stone and Ice Ages to the Middle Ages. Willerslev was also involved in sequencing the genes of the 24,000-YEAR-OLD MAL’TA BOY, part of a “ghost population” (link to that q&A in the Ancient FAQs). This heretofore-unknown population in Ice Age Siberia, identified only from its genetic traces, provided a link between Ancient North Eurasians like Finns and Saamis and Native Americans.

Willerslev’s initial findings were so controversial that his team held their conclusions for two years before daring to publish them. Many people believed that Mal’ta Boy’s Eurasian haplotypes—U2 and R2b—could only have been the effect of contamination with European scientists who handled the fossils. Neither archeologists nor the public was ready for the disruptions and complexities of aDNA.

The key to analyzing aDNA—and designing a product useful and accurate for genetic genealogists—is a set of smart ancient AIMs, or aAIMs. Elhaik and his team have laid down a blueprint for them in a recent paper published in the journal GENES (Basel, Switzerland).

Ancient ancestry informative markers are a strand of DNA sequences sufficiently distinctive to identify and classify an ancient population or culture—for instance, Paleo-Indians, Celts in the British Isles or Ice Age inhabitants of the Alps (like Ötzi the Ice Man, who lived more than 5,000 years ago).

While the framework of hunting out aAIMs are the same microarrays as those used for modern-DNA testing, two very challenging problems faced Elhaik and his collaborators in applying the traditional AIMs-finding approaches to aDNA AIMs—missingness and haploidy. The first is a technical term for the sparsity of ancient DNA. The second has to do with the age of DNA samples.

DNA has survived for four billion years, but it is not indestructible. Water and heat can break the molecule. Most of ancient DNA survives in shattered fragments that cannot be traced back and mapped onto their proper chromosomes but is full of holes and gaps and missing connectors.

“Unlike Jurassic Park,” Elhaik explains, “where scientists attempt to patch the holes with frog DNA, we just leave them open in ancient DNA sequences. But we can’t be certain when we encounter a mutation like A/C whether it is A or C or something collapsed. In haploidy, we are only seeing half or less of the picture.”

Despite this lack of clarity in reading aDNA sequences, it is clear that the diversity of ancient gene pools is greater than that of the present, much greater, and the challenges of cataloguing that diversity are accordingly large. Ancient populations turned over rapidly. People migrated thousands of miles in one or two generations. Events like the bubonic plague recast population structure overnight. Many new ruling hierarchies were heavily biased by sex or determined by other societal inequalities—what we may now call racism.

Just in the last month, ancient DNA studies have completely rewritten the story of the “peopling of the Americas.”

If ancient DNA analysis has taught us anything, it is how mixed, how mobile and how constantly changing human cultures have been. Ancestry tests that compare only living persons show an illusory sameness, homogeneity and uniformity.

“To make things worse,” says a customer outspokenly critical of next-generation ancestry testing, “the results are all very similar, no matter which company reports them, and let’s face it, uninformative and somewhat boring.”

The upshot? You can bracket for the time being your relatedness to people who are alive today. Thanks to Elhaik and his fellow paleogeneticists you can now start sticking pins in the map where your actual ancestors lived—or at least died and were buried—at different times and epochs.

In genetic genealogy as in other professions like poetry, the child is father to the man. The exciting discoveries and surprises of ancient DNA will only build and multiply as the field matures. Ready to discover your genetic relatedness to some of your remote ancestors like Romans, Vikings and Egyptians? Check out Primeval DNA.

Links

ERAN ELHAIK LAB (with links to publications and publicity)
Primeval DNA FAQs
“Where the Past Meets the Future” (news release, Dec. 13, 2018)
Ancient DNA Hub, a wiki of ancient peoples, sites and cultures from the Eran Elhaik Lab
“Slaying the Dragons of Genetic Dogma” (blog post, Sept. 21, 2016)
“GPS DNA Tracking with Dr. Eran Elhaik of University of Sheffield” (video, 7:09, Apr. 30, 2014) My browser is showing two embedded videos here.

The Time Traveler’s Suitcase (podcast, hosted by Pete Ferrand)
Explore the interface between history, archeology and ancient DNA.

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