A groundbreaking study on ancient human DNA has provided the most precise estimate yet regarding the time period when Neanderthals interbred with modern humans. This significant new research confirms that the interbreeding between Homo sapiens and Neanderthals began approximately 50,500 years ago and continued for about 7,000 years, until Neanderthals began to disappear. The analysis of ancient genomes has refined our understanding of when and how these two human species interacted, shedding new light on human evolution and the genetic legacy of Neanderthals in modern populations.
Modern humans and Neanderthals, two distinct species within the genus Homo, coexisted in Eurasia for several millennia. Though they evolved separately, their paths inevitably crossed, leading to interbreeding. This contact left a lasting mark on the DNA of non-African humans, with modern populations outside Africa carrying between 1% and 2% Neanderthal genetic material in their genomes. The latest research, based on an extensive analysis of both contemporary human genomes and 58 ancient genomes sequenced from human bones across Eurasia, provides a more accurate timeline of when these interbreeding events occurred.
The study’s findings, published in the journal Science on December 13, offer a new, more precise date for the interbreeding between Homo sapiens and Neanderthals, with an average date of approximately 47,000 years ago. This estimate is a significant refinement from earlier studies, which had placed the interbreeding period between 54,000 and 41,000 years ago. The updated timeline also suggests that the initial migration of modern humans out of Africa into Eurasia was essentially completed by 43,500 years ago.
The precise timing of this interbreeding is crucial because it has direct implications for our understanding of early human migration and settlement patterns. Priya Moorjani, an assistant professor at the University of California, Berkeley, and one of the study’s senior authors, emphasized the importance of these findings, stating that the timing of Neanderthal gene flow plays a vital role in understanding the broader process of human migration. Most non-Africans today inherit 1-2% of their ancestry from Neanderthals, and the new analysis of ancient genomes enhances our ability to trace the specific periods when these gene exchanges took place.
Moorjani’s work in collaboration with other researchers, including Benjamin Peter from the University of Rochester and the Max Planck Institute for Evolutionary Anthropology (MPI-EVA), focused on the sequencing of ancient DNA to model the complex process of interbreeding. For this study, the team used genomes from 58 ancient Homo sapiens who lived in Europe, Western and Central Asia over the past 45,000 years. By combining these ancient samples with the genetic data of 275 modern humans from around the world, the researchers were able to pinpoint a more specific date for the interbreeding events—47,000 years ago. This marked a major advancement over previous methods, which used single ancient genomes or the DNA of contemporary humans to infer the timing of gene flow.
One of the key insights of the study is the realization that the period of Neanderthal gene flow was not a short-term event but rather a complex, extended process lasting about 7,000 years. Earlier studies had assumed that the gene flow occurred over a single generation or in brief bursts, but the new model developed by the research team suggests that interbreeding was a prolonged event, with different human groups in various regions potentially experiencing these gene exchanges at different rates. This prolonged interaction between Homo sapiens and Neanderthals helps explain why some populations, such as East Asians, have a higher proportion of Neanderthal genes compared to Europeans or West Asians. According to Peter, the longer duration of interbreeding may account for the higher percentage of Neanderthal DNA observed in certain populations.
The genetic legacy of Neanderthals is not uniform across the human genome, however. The research team also explored the concept of “Neanderthal deserts”—regions of the human genome where Neanderthal genes are conspicuously absent. These regions likely represent parts of the genome where Neanderthal genetic variants were maladaptive or even harmful to modern humans. According to the study, these Neanderthal deserts likely formed rapidly after interbreeding, suggesting that some Neanderthal gene variants must have been detrimental to Homo sapiens’ survival. For instance, certain genes may have conferred resistance to environmental conditions or diseases faced by Neanderthals, but these very same genes might have been disadvantageous or even lethal to modern humans.
This phenomenon is evident in ancient human samples older than 40,000 years, such as those found in caves in Romania, Russia, the Czech Republic, China, and Bulgaria. These early Homo sapiens from around 40,000 years ago show clear signs of Neanderthal deserts in their genomes, implying that the process of gene flow and subsequent purging of harmful Neanderthal genes occurred relatively swiftly after the interbreeding events.
In contrast, some Neanderthal gene variants that were advantageous to Homo sapiens, such as those related to immune function, skin pigmentation, and metabolism, appear to have persisted and even increased in frequency over time. These beneficial traits, inherited from Neanderthal ancestors, likely provided early modern humans with adaptive advantages. For example, certain Neanderthal-derived genes associated with immune function have been shown to play a protective role against certain diseases. Notably, one such gene variant inherited from Neanderthals is believed to provide some protection against the coronavirus that causes COVID-19. Similarly, other Neanderthal genes linked to skin pigmentation and adaptation to cold environments likely helped early humans survive in harsh climates.
The study’s findings also shed light on the complex relationship between modern humans and their Neanderthal cousins. While some Neanderthal genes were beneficial and passed on through generations, others were gradually phased out due to their negative effects on survival and reproduction. This process of natural selection ensured that only the most advantageous Neanderthal traits remained in modern human populations, shaping the genetic diversity we see today.
The analysis of Neanderthal ancestry in East Asian populations is another interesting aspect of the study. East Asians tend to have more Neanderthal DNA than Europeans, and this has been a subject of much interest among researchers. Moorjani, in particular, is now exploring the genetic data of East Asians to better understand the specific Neanderthal genes that contributed to this higher proportion of Neanderthal ancestry. In addition to Neanderthal genes, East Asians also have small amounts of DNA inherited from another archaic hominin group, the Denisovans, further complicating the picture of human evolution in Eurasia.
The combination of Neanderthal and Denisovan genes in East Asians provides a unique glimpse into the complex evolutionary history of modern humans. The genetic traces left by these ancient human species reveal how different human populations were shaped by their interactions with other hominin groups over thousands of years. By studying these ancient genetic legacies, scientists can gain new insights into the biological and environmental factors that influenced the survival and adaptation of early humans.
As the research team continues to analyze the Neanderthal sequences found in the genomes of people from different regions, they are gaining a deeper understanding of how Neanderthal and Denisovan genes changed over time. By reconstructing the genetic history of modern populations, scientists can unravel the mysteries of human evolution and the complex interactions between early human species.
The findings of this study not only enhance our understanding of the timing and extent of interbreeding between Neanderthals and Homo sapiens but also offer valuable insights into the genetic makeup of contemporary humans. The Neanderthal genes that remain in our genomes today provide us with a direct connection to our ancient ancestors, offering a window into the past that has the potential to transform our understanding of human evolution.
More information: Leonardo N. M. Iasi et al, Neandertal ancestry through time: Insights from genomes of ancient and present-day humans, Science (2024). DOI: 10.1126/science.adq3010. www.science.org/doi/10.1126/science.adq3010
Arev Sümer, Earliest modern human genomes constrain timing of Neanderthal admixture, Nature (2024). DOI: 10.1038/s41586-024-08420-x. www.nature.com/articles/s41586-024-08420-x