Ancient human DNA: Modern science of our ancient past

At-home genetic tests have become popular in recent years as they allow a glimpse into the geographic past of our ancestors. They’re based on comparing genetic markers to current populations around the world. But what if we were to go back in time and get our distant family members to spit into a tube? What would that reveal? How are they related to their geographic past?

The new science of ancient DNA gives us the tools to answer some of these questions. But obviously, getting our long-dead ancestors to spit into a tube is not an option. So, how do we get DNA from ancient people?

Ancient DNA extraction

After we die, we decompose, including our DNA. Fortunately, some DNA can survive in pockets of our bodies, primarily bones. One of the richest sources of ancient DNA comes from one of the densest bones in our bodies, the petrous bone surrounding the inner ear [1]. The petrous bones can yield 100 times more DNA than other bones, including teeth.

Bones are ground into a powder, mixed with a solution to remove proteins and minerals; the DNA is extracted, sequenced and compared. But it’s not that easy. The DNA extracted from ancient bones can easily be contaminated with DNA from people working with the samples. Even the slightest touch can overwhelm the DNA signal. So, the work is done in “clean” rooms subjected to UV radiations, bleach decontamination, and positive air pressure, and the researchers don protective suits and face masks.

There is also contamination from ancient microbes that were on the body before or after death. And on top of that, DNA itself can degrade through spontaneous fragmentation and deamination of cytosine to uracil [2]. In the end, the amount of actually ancient human DNA is tiny.

To enrich these samples, the researcher took a page from medical genomics and isolated the parts of the DNA most interesting for analysis. They washed the DNA over a series of human DNA primers, or bait sequences, and sequenced only those parts relevant to human biological history [3]. These advances have led to an explosion in ancient DNA research studying everything from the human past to animals, plants, and microbes.

Human Past

Migration

While archeology typically analyzes objects left by ancient people, ancient DNA allows us to study the people themselves. One of the fascinating lessons from analyzing ancient human DNA isolated from carbon-dated skeletons describes how ancient people populated the earth.

In western Europe, a recent study demonstrated that the people who built the famous Stonehenge were farmers who originated in Anatolia or modern-day Turkey [4]. Before 8000 years ago, there were four distinct groups, the Western and Eastern European foragers and farmers from Iran and the middle east [5]. But by 5000 years ago, farmers migrated out of Anatolia and had thoroughly mixed with local groups creating a more homogeneous population.

There was, however, a third subsequent migration into Europe that replaced the builders of Stonehenge. These people migrated from the steppe region north the Black and Caspian Seas called the Yamnaya or Beaker people [6]. They had advanced the horse and wagon use and expanded into Europe, either replacing or mixing with local groups. So, over the past 8000 years, Europe has been transformed by two massive migrations, and the people living there today are a mix of multiple groups.

Likewise, early middle east farmers spread east into India 8500 years ago and were subsequently mixed with the Yamnaya people [3,7]. And farther to the east, farmers from south China spread into Southeast Asia around 5000 years ago. Current peoples in the area are four distinct ancient populations, including people from northeast Asia [8,9].

Ancient DNA isolated from burials in Alaska to Patagonia, representing over 10,000 years of genetic history, revealed that ancient populations of people spread rapidly across the Americas 13,000 years ago [10,11]. And entirely new was evidence of large-scale movements between North and South America, including a population turnover in South America around 9000 years ago.

And recently, DNA isolated from two 31,000-year-old milk teeth in Siberia identified a previously unknown group now call the Ancient North Siberians [12]. These people mixed with a group of East Asians living on the Bering land bridge that connected Asia to North America, producing a genetically distinct group dubbed Ancient Palaeo-Siberians. It was some of these people that move east to populate North America.

Evolution

Genetic analysis of modern humans led scientists to propose the “out-of-Africa” model for human expansion from Africa to the rest of the world. But recent discoveries in ancient DNA have shown that non-Africans are not 100% African.

Neanderthals bones were used first to identify them as recent human cousins. Retrieving DNA from Neanderthal bones not only confirmed our evolutionary relationship but also showed that ancient humans and Neanderthals had children that became ancestors to all Europeans [13]. That is, genomes from modern Europeans contain about 2% Neanderthal DNA.

Ancient DNA was also used to identify a previously unknown species of archaic humans, the Denisovans [14]. Isolated from a tiny finger bone found in the Denisova Cave in the Altai Mountains in southern Siberia, the DNA showed these humans were similar yet distinct from Neanderthals. It appears that while Neanderthals dominated western Eurasia, the Denisovans lived in eastern Eurasia. And like Neanderthals, Denisovans also interbreed with ancient modern humans, leaving their genetic traces in people of Asia today, about 6%.

One interesting finding from a study comparing the Y chromosome of Neanderthals to modern humans found that this chromosome is absent in modern humans. This suggested that Neanderthal males may not have produced viable male offspring with ancient human females [15].

Disease

Microbial contamination is a problem when analyzing ancient DNA unless it’s the microbe of interest. Isolating DNA from deadly pathogens present on ancient skeletons can give insights into the history of these diseases.

DNA from the malaria parasite, an infectious pathogen that currently kills over 400,000 people each year, has been identified in 4000 old Egyptian mummies from different kingdoms [16] as well as remains from 2000-year-old ancient Rome [17].

Genetic analysis of Y. pestis, the bacterium responsible for the Black Plague, isolated from the bones of plague victims, revealed that this microbe was once a harmless stomach bacterium that becomes a killer following the acquisition of a single gene named pla [18].

Tuberculosis (TB) was identified in bones excavated from a 9000-year-old Pre-Pottery Neolithic village in Israel [19]. This particular strain of TB, however, was missing DNA that is present in modern-day stains. But, ancient skeletons from Europe and Britain dating to the second–nineteenth centuries showed that different strains of TB existed, in single locations, and one case, a single person [20].

Ötzi – The Ice Man

Ötzi is the well-preserved 5200 years old mummy of a may found buried in the ice in the Ötztal Alps in 1991. By the following year, his complete genome was determined and published [21]. Analysis revealed he was most closely related to the people of southern Europe, in particular, the Mediterranean islands of the Tyrrhenian Sea, including Sardinia and Corsica. And Ötzi still has distant relatives in the region. DNA analysis also showed he was lactose intolerant, was at risk for cardiovascular disease, and was infected with Lyme disease. All these are familiar to the modern world.

Ethics

Extracting ancient DNA from burial sites can raise ethical questions such as who controls the human remains? Many of these finds are removed from the country of origin for analysis without permission. Advances in ancient DNA extraction and the fast pace of this new science mean destroying more bones. Which means more control of specimen allocation?

There are other potential negative consequences to ancient DNA analysis. The results may complicate territorial claims or repatriation efforts, contradict oral histories, harm identity, or even stigmatize communities due to genetic susceptibility to diseases.

Fortunately, there are calls within the scientific community for better integration of data and the requirement to make the data public. More and more, journals are printing statements on ethics, museums are creating guidelines, and researchers are consulting with indigenous peoples and defining sampling best practices.

[1] https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0129102

[2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3685887/

[3] https://www.nature.com/articles/nature14317#ref8

[4] https://www.nature.com/articles/s41559-019-0871-9

[5] https://www.nature.com/articles/nature19310

[6] https://www.nature.com/articles/nature25738

[7] https://www.biorxiv.org/content/10.1101/292581v1

[8] https://science.sciencemag.org/content/361/6397/88

[9] https://science.sciencemag.org/content/361/6397/92

[10] https://science.sciencemag.org/content/362/6419/eaav2621

[11] https://www.sciencedirect.com/science/article/pii/S0092867418313801

[12] https://www.nature.com/articles/s41586-019-1279-z