Genetic Analysis of Fossil DNA Opens a Window to the Past

Most analyses of DNA focus on what is, and what’s to come. But for a certain group of scientists, DNA also opens a window to what used to be. Thanks to modern genomic analysis, researchers have taken deep dives into the traits and behaviors of our ancestors.

Just last week, scientists reported new findings about a skull found in northeastern China that dates back at least 146,000 years. Known as “Dragon Man,” the skull resisted previous attempts to identify its place in the evolutionary history of ancient hominins. Now, analysis of both mitochondrial DNA and proteins makes clear that the skull comes from a group of prehistoric humans known as Denisovans.

Anyone who has watched Jurassic Park might assume that this kind of analysis is straightforward — easy, even — but the reality is very different. I remember attending some of the earliest conference talks from scientists pursuing these ancient DNA investigations, and their presentations were filled with reports of roadblocks and obstacles. DNA and proteins degrade easily; they aren’t meant to last for tens of thousands of years. The genetic materials found in fossils are fragmented, split into tiny pieces that represent just a fraction of the original. It’s as if you stumbled across the remains of a 10,000-piece puzzle and all that’s left is a water-damaged corner piece.

For the past 20 years or so, scientists around the world have been honing the unique skills needed to conjure up useful insights from these sources of ancient DNA. From meticulous sample preparation techniques to carefully crafted genome analysis tools designed for the purpose, the field of ancient genome analysis is thriving.

Denisovans, for example, were first identified at the genomic level from bone fragments found in a Russian cave bearing that name. The newly analyzed Dragon Man sample is the first skull ever linked to this ancient population, which has genetic ties to both Neanderthals and to Homo sapiens. As one scientist put it, “After 15 years, we give the Denisovan a face.”

Studies of ancient humans have given us a lot more than that. Here are some highlights from recent discoveries:

• Some 6,000 years ago, a previously unknown group of hunter-gatherers lived in the area near the land bridge connecting North and South America — close to the current site of Bogotá.

• Advances in data analysis allowed scientists to more finely map migration of populations across Europe around the first millennium AD. Groups from Scandinavia and northern parts of Germany moved south, where they left a lasting imprint in the genomes of current residents.

• The ancestors of modern humans, Neanderthals, and Denisovans co-existed for hundreds of thousands of years, with sporadic interaction and interbreeding. For reasons that are still unknown, Neanderthals and Denisovans vanished about 40,000 years ago while the Homo sapiens species thrived. People descended from the groups that migrated out of Africa carry some elements of Neanderthal genes in their genomes, and some people of Asian descent have markers carried over from Denisovans. Scientists have identified certain markers as conferring risk for various diseases, but they’ve also been shown to be helpful in some cases, such as allowing people to digest the lactose in milk more easily.

• About 8% of our genomes today are relics of ancient viral infections. Some of these genetic elements have been linked to neurodegenerative disorders, but they’ve also been shown to help us store memories more effectively.

Paleontologist and anthropologist John Hawks tracks studies of ancient DNA, and reported late last year that scientists have now generated genomic information from at least 10,000 individuals. For context, it took many years after the Human Genome Project to produce genomic data for 10,000 modern individuals. This is a stunning amount of information from mostly prehistoric times, and it provides a strong foundation for even more exciting discoveries in the future.