What Does Archaic DNA Reveal About Human Ancestry?

The study of archaic DNA, genetic material from extinct hominin species, has reshaped our understanding of human history by merging fossil studies with molecular science. This analysis offers a direct view into the genetic makeup of our ancestors, revealing deep connections between them and modern humans. It illuminates the complex evolutionary journey that led to who we are today.

Recovering Ancient Genetic Material

Archaic DNA is primarily sourced from ancient remains, with bones and teeth being the most common reservoirs. The dense petrous bone of the inner ear and the cementum of teeth are particularly good at preserving DNA. In some cases, genetic material can even be extracted from sediment layers in caves where hominins once lived, capturing environmental DNA shed through skin, hair, or waste.

Extracting this genetic material presents significant technical hurdles. Over thousands of years, DNA degrades into short fragments. Another major issue is contamination from modern DNA from microbes or humans, meaning often less than one percent of the DNA extracted from a sample is genuinely ancient.

To overcome these obstacles, scientists use specialized techniques. Research is conducted in ultra-clean laboratories to prevent contamination. Chemical extraction methods are optimized to isolate short, damaged DNA fragments, and advanced computational tools piece together the genetic code while filtering out contaminating sequences.

Key Archaic Hominin Genomes Sequenced

Among the breakthroughs in ancient genetics has been the sequencing of genomes from Neanderthals and Denisovans. Neanderthals (Homo neanderthalensis) lived across Europe and western Asia from about 400,000 to 40,000 years ago and were adapted to colder climates. The initial drafts of the Neanderthal genome were made possible by DNA from bones found in Vindija Cave in Croatia.

The Denisovans are a more enigmatic group, identified almost entirely through their DNA. In 2010, scientists analyzed a tiny finger bone from Denisova Cave in Siberia, expecting it to be Neanderthal. Instead, the DNA revealed a distinct hominin lineage that was a sister group to Neanderthals, identifying a previously unknown archaic human group from its genetic signature alone.

The sequencing of these genomes provided a detailed genetic baseline for these archaic peoples. This created a reference point to compare against the DNA of modern humans and uncover the history of their interactions.

Revelations About Human Ancestry

Comparing archaic and modern human genomes reveals that as anatomically modern humans (Homo sapiens) migrated out of Africa, they interbred with archaic populations they encountered, such as Neanderthals and Denisovans.

Analysis of these genomes allows scientists to estimate when and where these mixing events occurred. The primary admixture between Neanderthals and modern humans likely took place in the Middle East between 50,000 and 60,000 years ago. The genetic data also reveals interbreeding between different archaic groups themselves, as DNA from Denisova Cave shows that Neanderthals and Denisovans interbred.

Archaic genomes also offer insights into the lives of these ancient peoples. Genetic analysis suggests that Neanderthal populations were often small and isolated, leading to lower genetic diversity compared to modern humans. By studying the genes within these populations, scientists can identify adaptations they possessed for their environments, such as those related to metabolism or immunity.

The Archaic Inheritance in Modern Populations

The legacy of these ancient encounters is written in the DNA of people alive today. Virtually all non-African populations carry traces of Neanderthal DNA, making up around 1-2% of their genome. Denisovan DNA is less evenly distributed, found at significant levels primarily in populations in Oceania and to a lesser extent in parts of East and South Asia.

This inherited archaic DNA has functional consequences, a concept known as adaptive introgression. Some ancient gene variants were beneficial to modern humans as they expanded into new environments. For example, specific archaic gene variants found in modern humans are linked to:

• The immune system, providing defenses against local pathogens.
• Skin and hair characteristics.
• Fat metabolism.
• Adaptation to high altitudes, as seen in Tibetans who inherited a helpful Denisovan gene variant.

However, not all inherited archaic DNA is beneficial in modern contexts. Some Neanderthal-derived gene variants are associated with an increased risk for conditions like type 2 diabetes, depression, and certain autoimmune diseases like Crohn’s disease.