March 29, 2021
Science

Ancient DNA - How It Works and Ancient DNA Reports

Ancient DNA provides a powerful way to explore humanity's past. Plus, a simple DNA test can show you which ancient groups you come from!
By
Tomohiro Takano
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If you think it’s cool that science can match two people on opposites sides of the world based on the DNA strands they carry, you’ll be really impressed to learn what scientists have been able to do with Ancient DNA from Neanderthals, Vikings, and other ancient groups of humans! 


Never heard of Ancient DNA? That’s okay, too! In this post, we’ll take a look at what ancient DNA is, where it comes from, how they analyze it, and how a simple genetic analysis can see which ancient populations you are related to! Check it out!

What is Ancient DNA (aDNA)?

Ancient DNA - aDNA for short - is any DNA that has been recovered from an organism that lived a long time ago. While this article will mostly discuss human aDNA, there are many other sources of ancient DNA from plants, animals, and microorganisms that lived hundreds or thousands of years ago. These sources of DNA come from many different sources and are absolutely instrumental in determining evolutionary relationships between different groups of organisms and ancient peoples. For instance, in evolutionary ecology, researchers can use ancient DNA to develop models of which species were present at the same time in North America (or Siberia, or the Australian outback) thousands of years ago.


When it comes to hominin and human aDNA, there are many different sources that can yield ancient DNA. By and large, the greatest source of ancient human DNA comes from bones. These bones can come from archeological dig sites (like the Denisova cave or Viking burial sites) that contain the remains of ancient humans. Many of these places have low humidity, low temperature, and low oxygen content - all things that help preserve the DNA in human remains. However, even well-stored museum specimens can contain small amounts of untainted ancient DNA.


While the DNA in specimens buried in ideal conditions can last for 1.5 million years (or more!), most DNA becomes damaged, oxidized, and destroyed long before 400,000 years. Still, considering that most human (and hominins) evolution happened within the last million years in the (Pleistocene), there are many ancient human remains that still contain ancient DNA. In fact, researchers have gathered, extracted, and sequenced aDNA samples from thousands of ancient archeological specimens!

Ancient DNA Analysis and Human Evolution

The techniques required to process and analyze ancient human DNA are much more complex than those used to gather, analyze, and sequence the nucleotides from living human populations. For starters, you can’t just get a Neanderthal to spit in a tube and send it to the lab at 23andMe. DNA extraction and DNA preservation techniques on ancient genomes are much more complex.


The techniques used to extract and process ancient DNA have been pioneered by researchers like Pääbo, Haak, Higuchi, Gilbert, Krause, Reich, Poinar, Wilson, and many other evolutionary biologists searching for ways to better understand the Earth’s evolutionary history. You can look up the hundreds of papers on ancient DNA that have been published by searching PubMed, PLOS, or Google Scholar.


In general, these researchers needed to devise ways to extract the incredibly small amount of DNA present in ancient samples. While most fresh DNA sources can contain micrograms of DNA for analysis, ancient sources may contain as little as a few picograms. In other words, if ancient DNA contains 1 unit of DNA, a similar fresh source would contain 100,000 units. Even with techniques of DNA amplification (like PCR - polymerase chain reactions), DNA from ancient bones is hard to recover. This makes it very hard to accurately estimate the admixture of ancient populations, and additional steps must be taken to ensure that ancient DNA studies are not contaminated with any DNA sources from the lab. 


However, once this tiny bit of DNA has been analyzed and sequenced, it can provide a huge amount of information about evolutionary relationships. Sources of ancient DNA sequences include teeth, the petrous bone (in the skull), and large bones like the femur. Teeth are covered in enamel, a very hard substance that helps protect the fragile DNA inside. The petrous bone is uniquely situated to protect genome sequences, while the femur is large enough that plenty of bone marrow can remain safely stored inside. Still, the amount of DNA used in ancient DNA studies is very small. Though these datasets are smaller and the genetic material has been degraded, geneticists can still develop accurate representations of ancient populations using skeletal remains from the early Holocene and late Pleistocene.


For example, one of the most common forms of ancient DNA is mitochondrial DNA (mtDNA). Mitochondrial genome sequences are only inherited from a person’s mother, so they can be used to track maternal haplogroups. By sequencing and comparing mtDNA samples from ancient groups like the Neandertals, Denisovans, and other neolithic peoples from European, Egyptian, and Eurasian sources, researchers have been able to better understand the complex relationships between these groups. While it was once assumed that hominins like Neandertals and Denisovans were completely separate from modern humans, it is now clear that these groups share a common ancestry with present-day humans and likely interbred with many ancient human groups. If researchers are lucky, they can also harvest Y-chromosome DNA and autosomal DNA from ancient samples, giving them many more base pairs and genome sequences to match with modern genetic loci.

Matching Your Genome to Ancient DNA

If you are familiar with DNA ancestry testing and population genetics, you know that DNA testing companies can easily match you to living people and living populations of people from different ethnicities, simply based on the unique variations that you carry in your DNA. Using similar techniques, scientists can also match your DNA sample to ancient populations!


When enough samples have been gathered and analyzed from an ancient population, a large-scale study can create an ancient “reference population” - similar to those created for ethnicity estimates - that can roughly estimate the various genetic variations that were present in an ancient population during the Pleistocene. By measuring the genetic diversity you carry and comparing these variations to these ancient reference populations, scientists can estimate how much these groups contributed to your genome!


While the process is similar to the way that ethnicity estimates are created, there are a few caveats with Ancient DNA testing. First off, the further back in time an ancient population lived, the more likely it is that you will carry at least some of the same genetic variations. (This is because humans share a common ancestor, so ancient human genomes likely contributed to many modern ethnicities). However, certain variations (like Neanderthal, Viking, Siberian, and Native American variants), contain more recent and unique mutations from human history that can be more easily traced across time and populations. This is what makes it possible to compare your genome to groups like Native Americans and Vikings. It all depends on the specific variants that researchers are looking at and the unique data they have used to define ancient populations. 

Do You Have Ancient DNA?

If you have already taken a DNA test (from 23andMe, Ancestry, or MyHeritage), you can use your raw DNA data file to find out how much ancient DNA you have from different sources. It doesn’t really matter if you live in New York, Orlando, or Tokyo - you likely have inherited DNA from a diverse arrangement of ancient populations. In fact, Genomelink offers two unique reports that compare your DNA to different groups of ancient people:


Ancient Ancestry Report

The Genomelink Ancient Ancestry Report compares your DNA to 7 different ancient groups of people: Hunter-gatherers, the First Farmers, Steppe Pastoralists, Indigenous Americans, West Africa, East Asians, and South Asians. For each group, you will see how much they contributed to your genome, a brief history, and a map that shows how they migrated across the ancient world!


Viking Index Report

Did you know that there were several distinct groups of Vikings that contributed to modern ethnicities all over the world? These include the Scandinavian Vikings, Finnish Vikings, Slavic Vikings, and British Vikings. Considering how widespread Viking culture became at its height, many people are surprised to find that they are related to at least one of these groups! This report gives a brief description of each one of these groups and estimates which groups contributed most to your unique genomic data.



Tomohiro Takano
Tomohiro Takano
Co-Founder and CEO