How Environmental DNA Could Transform Our Understanding of Human History
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Chapter 1: The Challenges of Human Fossilization
Humans do not preserve well as fossils. As a result, the fossil record for Homo sapiens and other human species is relatively sparse. When I refer to "humans," I'm encompassing the entire genus Homo, similar to how "canine" refers to wolves and "feline" to lions.
It's noteworthy that Charles Darwin's limited discussion on human evolution wasn't due to religious concerns, but rather the lack of substantial fossil evidence available to him. His reasonable inferences about our relationship to apes and origins in Africa were grounded primarily in observations of chimpanzees.
As we delve into the fossil record, we find that the first Neanderthal remains were unearthed in the Neander Valley in 1857, although it was merely a partial skull that went unrecognized as a significant find. The discoverers mistakenly believed it belonged to a recent early European tribesman. When Darwin authored The Descent of Man, he had no fossils to analyze. It wasn't until 1886 that more Neanderthal fossils were found, which were easier to date and more complete, confirming their distinctiveness.
Throughout the 20th century, we uncovered additional fossils that illustrated the evolution of both apes and humans. A significant breakthrough occurred in Russia's Denisova Cave—a name worth remembering.
In the 1970s, a few teeth and bone fragments were discovered there, leading to the identification of another human relative known as the Denisovans. Genetic studies revealed their close relation to both us and Neanderthals, potentially aligning them more closely with the latter. A 2018 DNA analysis revealed that a woman had DNA comprising 50% Neanderthal and 50% Denisovan ancestry, indicating that a Neanderthal woman had a child with a Denisovan man. This child, informally referred to as "Denny," suggests that such interspecies relationships, which likely occurred among all three species, were consensual.
Nevertheless, our understanding remains incomplete due to a lack of Denisovan fossils, while Neanderthal burials have been more common.
Chapter 1.1: The Role of Environmental DNA
What exactly is environmental DNA (eDNA)? It refers to genetic material found in our surroundings, as we continuously shed skin and other biological materials. Archaeologists are particularly interested in remnants found in middens and latrines.
Currently, eDNA is primarily utilized to monitor biodiversity. However, in the fields of paleontology and archaeology, it can serve an additional purpose. eDNA can sometimes be preserved in various sedimentary deposits, including those found in lakes, marine environments, and terrestrial sites.
One remarkably well-preserved site for eDNA analysis is Denisova Cave. Its unique configuration allows for sediment accumulation, providing a richer understanding of the site's history. Humans have occupied this cave intermittently for an astonishing 300,000 years.
At first, the Denisovans settled in this area for about 170,000 years before disappearing. The reasons remain unclear, but soon after, another group of Denisovans took their place. The changing climate, which became colder, also facilitated the arrival of Neanderthals. Different groups occupied the cave at various times, occasionally overlapping.
Did Denny's mother integrate into a Denisovan clan? Did they regard their differences in species as significant? Approximately 45,000 years ago, modern humans arrived at the cave, possibly coexisting with Neanderthals and Denisovans.
Thanks to eDNA, we now understand that this single location was home to three distinct human species, potentially all present simultaneously.
The first video, "Science at Cal Lecture – Uncovering the Past: Using Genetic Data to Understand Human History," explores how genetic analysis can provide insights into our ancient past.
Chapter 1.2: The Future of Environmental DNA in Research
Sites with preserved ancient eDNA hold immense potential for expanding our knowledge. While my focus has been on human DNA, eDNA from the Denisova Cave also reveals information about the fauna inhabiting the region at that time. Furthermore, eDNA recovered from middens could offer insights into the dietary habits of ancient peoples, supplementing current methods like bone fragment analysis and pollen studies.
The extraction of environmental DNA represents a significant advancement beyond fossil analysis, and I am genuinely excited about the possibilities it brings. The knowledge we stand to gain is boundless.
The second video, "Deep history within the human genome," discusses the implications of genetic findings on our understanding of human history.