Ancient DNA comes from early human fossils and ancient remains around the world. It is recovered from human graves, cemeteries and skeletal remains from the past, often dating from hundreds to thousands of years ago and prehistoric. It is sometimes distinguished from archaic DNA on the one hand (such as Neanderthal and Denisovan) and modern DNA from living humans and contemporary populations, on the other. Archeologists work with geneticists to publish aDNA findings in scientific journals. The first ancient genomes were published in 2010.
It depends on the test you have already taken. You can upload autosomal SNP test results from HomeDNA (GPS Origins), 23andme, Ancestry.com, National Geographic Geno Next Gen, Family Tree DNA Family Finder, My Heritage and Living DNA. We will analyze them for whichever ancient peoples you have selected (Ancient Israelites, Chumash Paleo-Indians etc.). Just upload your file of results into your account area and the relevant personal reports will be generated for you. You will receive an email notification when they are available. Then you can download, print and share them.
Download your results from 23andme or the company you tested with. Then upload them to your DNA Consultants account. Go here for more detailed instructions.
We use the program called mini-DREAM, with about 200,000 nucleotide positions in the DNA raw data file. The paper by Eran Elhaik et al. describing this test was published in the journal GBE: Genome Biology and Evolution in December 2017. It was titled, “The Diversity of REcent and Ancient huMan (DREAM): A New Microarray for Genetic Anthropology and Genealogy, Forensics, and Personalized Medicine.”
Advanced molecular biology laboratories like David Reich’s at Harvard University or Svante Pääbo’s at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, painstakingly extract and sequence genomic data from preserved specimens. Recent modifications of the process have eliminated contamination, increased the success of efforts and lowered the cost by a factor of 10,000. This great leap forward is called the “ancient DNA revolution.”
In 2010, a team led by Eske Willerslev sequenced the first-ever ancient genome from a 4,000-year-old Greenland man’s hair. DNA of Mal’ta Boy, who proved to be a 28,000-year-old link between Europe and America, was sequenced from an arm bone in a Russian museum. Important aDNA has come from brains, teeth and a fossilized pinky toe bone (50,000-year-old Neanderthal woman). In 2015, Ron Pinhasi, a Canadian anthropologist now at the University of Vienna in Austria, showed that the optimal place to look for DNA in ancient bones was the inner ear part of the skull. This discovery made DNA sampling and analysis a thousand times more cost-effective.
The first ancient human remains studied in this way came from northern regions, such as Siberia and Greenland. Because warm climates increase chemical reactions, DNA from southern locations is more decayed and harder to tease out. Many ancient lands have largely remained beyond our ken. Scientists have not yet recovered aDNA from before fourteen thousand years ago from southeastern Europe and the Near East. Since most paleogeneticists are Europeans or Americans of European ancestry, there is a bias in the archeological sites that have been placed on the record. Few historical-era sites have been typed. However, there is hope for more universal coverage with time. Blockbuster additions to the picture are coming from the Levant, the Americas and Africa.
Although it is still possible to recover mitochondrial, Y chromosome and X chromosome readings from aDNA as in the early days, the overweening goal now is the prize of the whole genome—the full set of genetic code each of us inherits from our parents. Just as the first companies promised customers their “haplotype” (history of their mother’s direct female lineage or father’s direct male lineage), since 2006 the emphasis both in science and its applications, including genetic counseling and consumer testing, has been on autosomal DNA.
Commercial companies typically sequence only a small part of one’s DNA. The final file contains 80,000 or more nucleotide positions (nps) mapped across all your chromosomes. It can be downloaded from the website of the company which provided the service. The results for each nucleotide are labeled A, G, C or T, the names of chemicals found in sequences and strands that intertwine through your genome. This personal database reflects your entire ancestry. It can be compared with another person’s or with a specimen of ancient DNA to gauge relatedness. At DNA Consultants, you can upload your raw genomic data for free. Then purchase individual comparisons with ancient peoples on a pay-as-you-go basis.
Ancient peoples are at the root of modern peoples, and ancient percentages underpin modern percentages. In terms of modern-day matches, if an African American male is reported to have 80 percent West African and 20 percent European ancestry, a conclusion is being hazarded that about five hundred years ago, prior to the population migrations and mixtures set in motion by European colonialism, 80 percent of his ancestral threads were found in West Africa and the remainder in Europe. With the Primeval DNA Test, percentages are calculated based on the number of mutations (variations) that are shared between you and the ancient specimen you are compared with. An example: You take the Ice Age European Test and receive a 15% match. This suggests 15% of your ancestry traces back to a population of hunter gatherers who lived in Ice Age Europe.
Of course, there are numerous challenges associated with this “genetic similarity” approach, not to mention the fact that all populations are mixed to begin with, and that we cannot always trace back to the direct ancestors. Sometimes we have a “missing link” with individuals who are mixed from ancient populations A and B, none of which exists or can be found among ancient peoples. In this instance, neighboring populations (A’ and B’) are ascertained and reported. The approach continues to be refined as more ancient DNA is uncovered, allowing us to better identify those links. The full universe of ancestral populations is not known. But all those identified were mixed and remixed. Many, apparently, went extinct. Every pioneering phase of knowledge starts small and builds to more and more certainty, comprehensiveness and precision. A philosopher once said, “We are dwarfs standing on the shoulders of giants.”
A microchip array (“SNP chip”) pinpoints the individual’s variation and differences (mutations) in terms of single nucleotides, sequences, strands of DNA or, loosely speaking, genes. These data are then compared to the ancient genomes sequenced on a similar microchip or using a complete-genome approach that attempts to recover a sample’s entire DNA (not just 0.5-1.0 million bases). As of the end of 2017, the total number of ancient DNA reference samples was over 2,000.
By November 2017, 711 samples from ancient peoples or archeological sites had been published. That is only about 15% of the total number of ancient genomes known. Most are unpublished. With breakthroughs in technology reducing the costs of extraction and sequencing, and with automation creating a factory-like setting, efforts have shifted from generating more data to using and interpreting what we have. The heroic age of excavation and discovery has yielded to the building of museums and the pleasures of visiting their vast collections. Ancient DNA labs like that of Eran Elhaik at the University of Sheffield in England are now producing new analytical tools so fast that their publication lags far behind. The pace of invention is only expected to accelerate, for that is where the greatest prestige lies for professional geneticists. Online publication and informal networks, it is hoped, will take up the slack. DNA Consultants’ original Primeval DNA Test is the first stand-alone, comprehensive ancient DNA test series sold directly to consumers. It was introduced at the end of 2018. At that time, the company had around 50 ancient samples on line available for comparison with customer’s results. Under the curatorship of Eran Elhaik, this number is expected to grow to 2,000 by the end of the following year.
If we go back 15 generations each person alive today has 32,768 ancestors. Only two of them contributed the mitochondrial and Y chromosome lines which your parents gave you—the focus of DNA testing companies’ earliest haplotype assignments (H, R1b, L etc.). Y chromosomes and mitochondrial DNA reflect information only from the entirely male or entirely female lines. Autosomal genomes, on the other hand, carry recombining segments inherited from tens of thousands of others. Even though the two sex-linked haplotypes are important—and may indeed be typical of all the other populations you incorporate from the past—they are by no means the whole story.
As we go back deeper in time, a person’s genomic DNA gets chopped up each generation and scattered into more and more bits of fragments attributable to ever-larger numbers of ancestors. Projecting fifty-thousand years ago, as Europe was being colonized and the Neanderthals were becoming extinct, our modern-day genome can be seen as a mosaic composed of more than one hundred thousand ancestral pieces of DNA. Much of this information has likely disappeared over time or remains unknown to us in the absence of a reference genome. We cannot make sense of it. The purpose of ancient DNA testing is to bring into relief and restore the outlines and details of that mosaic as much as possible. To a greater or lesser degree, we inherit DNA from nearly everyone in our ancestral populations. It is just a matter of measuring the amount derived from each ancestral population once data from the population become available. As Walt Whitman wrote, “I am large, I contain multitudes.”
Most scientists until the advent of ancient DNA conceived the history of prehistoric humans as part of a great tree. Once a population or species branched off it did not remix. If ancient DNA analysis has taught us anything, however, it is how wrong the metaphor of the family tree is for expressing the relationships between the member populations of modern humanity. When the floodgates of aDNA were opened beginning in 2015, scientists began to reexamine some of the time-honored theories about human history. They saw that most populations in the past, as are those in today’s genetic landscape, were mixed. Great mixtures of highly divergent populations have occurred over and over in prehistory. Instead of the standard tree model, one scientist suggests a trellis. Such a metaphor better captures the luxuriant branching, recombining and flowering far back into our past.
Although much of the epic is still unfolding, the big lesson of ancient DNA studies is that human migrations are very different from the simple models proposed after the first autosomal tests. We really knew very little about populations prior to the new technology. Ancient samples prove that the population in any given “homeland,” so far from being static and homogenous, has turned over many times. Mixtures have joined with new mixtures. Sometimes, there has been almost total population replacement. Cataclysmic events can be seen in the genetic records. Examples are the super-volcano near present-day Naples 39,000 years ago or spread of plague from Central Asia in prehistoric Europe. A new synthesis of genetics, archeology and linguistics is solving historical mysteries, overturning outdated theories and opening the eyes of DNA testing customers to little-known currents of deep history such as Basal Eurasian, Denisovan genes and the violent Yamnaya culture.
Each sample of ancient DNA corresponds to an archeological site or early find site and specific time, as characterized by one or more individuals or skeletons. Example: Early Farmers at Motza Tachtit, Israel, about 9,000 years before present, based on the genome of one skeleton and associated burials published by I. Lazaridis et al. in the magazine Nature in 2016.
It used to be thought that, as a tree took root, budded, branched and died, humanity predictably grew, spread and thrived, with few false starts or dead ends. The discovery of our archaic relatives, the Neanderthals and Denisovans, put an end to that thinking. Once science possessed complete genomes, statistical comparisons suggested not only that there were other archaic skeletons still waiting to be found, but many extinct populations and dead branches. “Ghost populations” are peoples dimly glimpsed in ancient DNA data who do not survive as a coherent population today. The prototype was Mal’ta Boy, who was predicted before he was discovered. His Siberian gene pool from 24,000 years ago (with U2 as his mitochondrial haplotype and R1b as his male lineage) is undoubtedly the source of Ancient North Eurasians, the European founder group responsible for the blond hair mutation. An eastern branch mixed with East Asians and produced Native Americans. This is one reason modern-day Finns and Native Americans have genetic similarities. But Mal’ta Boy’s DNA died out in Siberia. Today’s Siberians have none of it in their ancestry. It is a ghost population.
No. We are all accumulations of the mixing and re-mixing events of the past. As David Reich puts it in Who We Are and How We Got Here, “Ancient DNA has established major migration and mixture between highly divergent populations as a key force shaping human prehistory, and ideologies that seek a return to a mythical purity are flying in the face of hard science.” Despite population bottlenecks, inbreeding and even geographical isolation, there are few “dominant” populations that continue in our genes for long without becoming broken up and mixed anew. Examples of populations that have formed only in the last five hundred years are Hispanics, Ashkenazi Jews and African Americans.
Ancient DNA dispels a lot of the myths and assumptions about human origins and migrations popularized in the first generation of autosomal testing. It is rewriting human history in myriads of ways and shows no sign of disappointing with its surprises. On the medical front, it has already fingered the ancient sources of mutations that were not clear in previous genome-wide association studies. Its power is so great that the decade since 2010 has emerged in the minds of many researchers as the third phase of the Human Genome Project. Groups like Basal Eurasians are provoking more interest than shadowy non-Africans of yesteryear’s thinking, while whole new ancient cultures have grabbed our attention—like the Yamnaya people, the male-oriented, violence-celebrating herders of Central Asia who brought the horse, wheel and Indo-European languages to Europe. Ancient DNA is at the base of everything downstream from it. If “fundamental inquiry into who we are is at the pinnacle of what we as a species hope to achieve” (David Reich), then its pursuit is the greatest game of all. By suggesting who we were, it helps answer the question how we got to where we are now. But more than that, it teaches us about the achievements and mistakes of past cultures and what we can become in the future by embracing knowledge, diversity and change.