Scientists were able to sequence the complete human genome of an ancient hunter gatherer through a 5,700-year old saliva sample.
The researchers called the individual “Lola,” and through analysis, they were able to tell that she lived around 3,700 BC on an island in the Baltic Sea. Through the sample, the researchers were even able to study the microbes that lived inside Lola, finding that she suffered from lactose intolerance and might have suffered from gum disease.
Like many ancient European hunter-gatherers, Lola likely had dark skin and hair and blue eyes. Some of her meals also included ducks and hazelnuts. Despite this wealth of information, researchers are not able to tell how long she lived or the details of her death because all they knew comes from DNA locked in a wad of birch pitch that Lola once chewed on.
This marks the first time researchers have been able to reconstruct a complete human genome from a non-human material rather than physical remains.
The international team of researchers was able to identify the DNA of flora and fauna that she had likely recently consumed. They were also able to study the DNA of countless microbes inside her mouth, her oral microbiome.
According to Hannes Schroeder, co-author of the study and an associate professor of evolutionary genomics at the University of Copenhagen’s Globe Institute, this is the first time a complete ancient human genome has been reconstructed without the use of human bone. Through the material they have, the individual’s microbial DNA can also be studied.
What is so important about understanding the human microbiome? Researchers believe that it plays a very important role in our health. The variations that occur in the microbiome can affect a person’s susceptibility to infections and other diseases, even changes in behavior.
Schroeder believes that sequencing ancient DNA together with the microbiome might help us understand how the human microbiome has evolved over time. It may also reveal whether our shift from hunting and gathering to agriculture had a positive or negative impact on our microbiome and health.
Birch pitch and genome
Birch pitch, or tar, made by heating birch bark, is a glue-like substance used by people 750,000 to 125,000 years ago to fasten stone blades to handles. Because blobs of pitch were found imprinted with human teeth marks, archaeologists assume that pitch was softened before using by chewing. It is also believed that birch bark had medicinal properties.
These unremarkable wads of pitch have been long thought of to be a good source of ancient DNA, but it is not until recently when researchers had the tools needed to extract genomic data from it.
Lola’s DNA and microbiome were extracted from a wad of birch pitch from the site of Syltholm on the Danish island, Lolland. Radiocarbon dated to around 5,700 years ago, the pitch came from the Neolithic period in Denmark, a time when Mesolithic hunter-gatherers started being disrupted by the introduction of agriculture.
However, Lola does not show any of the genetic markers associated with the farming populations entering Europe. This supports the idea that genetically distinct hunter-gatherers were able to survive in the region for a longer time than previously believed. Because Lola’s genome also shows that she was lactose intolerant, it supports the theory that European populations only developed the ability to digest lactose later on when they started consuming dairy products from domesticated animals.
The majority of the bacteria identified in her oral microbiome are considered normal, although some would be associated with severe periodontal disease. She also had Streptococcus pneumoniae in her system, but it is still impossible to tell if she had been suffering from pneumonia.
What’s next for DNA studies
Through the DNA sample in the wad of birch pitch, researchers were also able to identify Lola’s diet, particularly pointing out the DNA of mallard ducks and hazelnuts. Because of the ability to isolate specific plant and animal DNA from a human DNA sample, researchers are able to see and understand the ancient peoples’ dietary habits. According to Steven LeBlanc, former director of collections at Harvard’s Peabody Museum of Archaeology and Ethnology, this information is new and previously unseen in usual archaeological records.
He believes that understanding the dietary information and microbiome from a non-human material will now set a new standard for understanding how ancient human populations lived, how their health was, and how they changed over time.