What is Ancient DNA (aDNA)?
Ancient DNA or aDNA, is DNA that has been recovered from biological remains that are hundreds to thousands of years old. The methods of extraction were first pioneered by researchers at the University of California Berkeley by the laboratory of professor Allan Wilson. In 1984, their team published the successful extraction of mitochondrial DNA from 140 year old remains of a Quaga— an extinct zebra like Animal that was last documented as seen in an Amsterdam zoo in 1883.
Wilson’s team recovered DNA from dried muscle tissue in amounts approaching 1% of that expected from fresh muscle. From that small fraction collected, they sequenced a mere 229 base pairs — a tiny window into a genome that, in a living zebra, contains over 2 billion. For reference, the human genome contains 3 billion base pairs. A mere 229 base pairs — a sequence so short it would be invisible under any microscope. — held enough signal to place the quagga’s divergence from other zebras 3 to 4 million years ago.
In 1984, the landscape of biology was vastly different than today. The Sanger method of DNA sequencing (invented in 1977), could only read short stretches of DNA at a time. PCR, a standard method of today which allows the reproduction of genetic material for sequencing, favoring higher signal to noise ratios for greater accuracy, would not be published until 1987. The Human Genome Project did not exist yet, and it would not until 1990 — with the full human genome not being declared complete until 2003.
The sequencing of the extinct Quagga genome, as well as the development of scientific methods throughout the 80s, eventually empowered others to pursue ancient DNA from human remains. But before it could move forward, the field of ancient DNA research faced a crisis. Between 1985 and 1990, contamination was discovered in many of the field’s pivotal studies — including the quagga sequence itself. The setbacks made it clear that ancient DNA research required standards.
The contamination crisis wasn’t a series of individual failures—it was a problem the field had to solve collectively, and also how science naturally flows. Discoveries are announced, scientists discuss to validated or contest, and methods and standards are updated to ensure accuracy. At the 5th International Ancient DNA Conference in Manchester (2000), researchers formally articulated the criteria that are now standard: isolated work areas, control amplifications, inverse correlation between fragment length and amplification efficiency, and reproducibility across independent extracts.
Beyond the contamination criss, the field was also limited by the natural process of DNA degradation. Remember, the quagga tissue yielded only about 1% of the DNA expected from fresh muscle — meaning that most of the information it once held was lost, broken down by time and chemistry. But what remained was also a signal. By studying the breakdown of DNA, scientists have discovered that degradation occurs in predictable patterns. Today, through bioinformatics, scientists can reconstruct what an original DNA molecule likely looked like.
Throughout the 2000s and 2010s, the field produced a flood of studies. The Neanderthal genome was sequenced in 2010, revealing that modern humans outside Africa carry 1–4% Neanderthal ancestry. That same year, a previously unknown hominin—the Denisovans—was identified from a single finger bone in Siberia. Many more ancient human genomes followed: a 4,000-year-old Paleo-Eskimo in 2010, a high-coverage Denisovan genome in 2012, hundreds more. But this success created a new problem. Each study published its data in its own format, with its own metadata conventions. There was no shared compendium, no way to easily compare results across papers. The field had the data, but the lack of organization limited the analysis that could be synthesized.
These developments yielded the first public release of the Allen Ancient DNA Resource in 2019 — a publicly available resource that in 2022, through partnerships with various countries and sovereign tribal nations, announced over 10,000 genomes of ancient and contemporary people… available for the public to freely access. You can find the AADR here [insert link].
The AADR did more than organize data. It changed who could use it. For the first time, a student, an independent researcher, or a community member could download the same curated dataset that professional population geneticists work with — the same individuals, the same positions, the same standardized formats. What had once required institutional access, personal connections, or years of manual data wrangling was now a single download away. The field of ancient DNA research was no longer just producing knowledge. It was beginning to share the means of producing it.