A collaborative team from The University of Texas at Austin and the University of California, Los Angeles has conducted a distinctive statistical analysis on ancient DNA sourced from human skeletal remains. Their findings shed light on how ancient Europeans adjusted to their surroundings throughout 7,000 years of history in Europe. This research was recently published in the journal Nature Communications.
“By examining ancient DNA, we can delve into the past and trace evolutionary shifts in historical populations,” stated Vagheesh Narasimhan, the lead researcher and assistant professor of integrative biology and statistics at UT Austin. “We are uncovering genetic indicators that have largely been erased or obscured in today’s genomes.”
The research team analyzed over 700 samples from archaeological locations in Europe and parts of modern Russia, covering a timeline from the Neolithic era (approximately 8,500 years ago) to the late Roman period (around 1,300 years ago). They discovered evidence of natural selection—indications of genetic adaptations to environmental pressures—etched into the DNA of ancient Europeans but undetectable in contemporary DNA. These revelations not only offer a glimpse into the distant past but also highlight how advantageous genetic traits for survival can fade over time.
Modern genetic studies often struggle to identify signs of ancient natural selection. The subtle remnants of natural selection can dissipate across generations due to recombination, where DNA segments are mixed and diluted. Moreover, genetic drift—random changes in gene frequency—and population intermingling can obscure historical adaptive traits from the gene pool. Ancient DNA offers a direct examination of the genomes of individuals who lived closer to these key events, enabling scientists to observe evolutionary progress before it was lost. Thus, ancient DNA serves as a crucial tool for piecing together the historical patterns of human adaptation.
The research utilized a new statistical methodology that is particularly adept at analyzing ancient DNA data. With this innovative technique, the team could more effectively identify signs of natural selection compared to traditional approaches. They categorized the samples into four distinct eras: Neolithic, Bronze Age, Iron Age, and Historical, which allowed for tracking genetic modifications in response to lifestyle changes, such as the shift from hunting and gathering to agriculture.
“Our approach offers a clearer understanding of how and when certain traits became advantageous, particularly where those clues have been lost in modern genomes,” mentioned Devansh Pandey, a graduate student in cell and molecular biology and co-first author of the study.
Through investigations into human adjustments during the shift from foraging to farming and the rise of state-level societies, the researchers could see how genes evolved as humans began living in closer quarters with each other and domesticated animals.
The study identified 14 regions in the genome that showed significant natural selection over the analyzed periods. For instance, genes linked to early Europeans’ abilities to produce vitamin D and digest milk in adulthood displayed strong indicators of selection, particularly in more recent eras. While the lighter skin pigmentation may have helped early farmers produce vitamin D in less sunny environments, the capacity to digest milk allowed individuals to benefit from milk as a food source once dairy farming became prevalent in Europe.
“This ability to digest dairy was likely crucial for survival during times of crop failures, food shortages, and sickness,” Narasimhan explained.
The analysis also revealed that genes related to immune responses experienced selective pressures across various periods, likely as ancient populations adjusted to newly introduced diseases stemming from agriculture and subsequent migrations. Notably, approximately half of these adaptive signals were only found in the earliest periods, suggesting they later diminished due to genetic drift or were obscured by widespread population mixing.
This study offers a groundbreaking perspective on how European populations overcame environmental challenges through the centuries, enhancing our understanding of the persistence, disappearance, or modification of certain traits over time. The findings underscore the significance of ancient DNA in reconstructing human history, illustrating how traits that once provided a survival edge in early Europeans have become obscured in today’s genetic framework.
Mariana Harris and Nandita Garud from UCLA also contributed to this research. Funding for the study was provided by the Paul G. Allen Family Foundation, the Good Systems Fellowship for Ethical AI at UT Austin, the Paul G. Allen Foundation, the Research Corporation for Science Advancement, the University of California Hellman Fellowship, the National Science Foundation, and the National Institutes of Health.
