Summary: New genomic analyses narrow the window of interbreeding between modern humans and Neanderthals. The evidence indicates gene flow began roughly 50,500 years ago, with the main pulse centered near 47,000 years ago and continuing for about 7,000 years—ending by approximately 43,500 years ago. This admixture left most non‑African populations with about 1–2% Neanderthal ancestry and introduced genetic variants that influenced immune response, skin pigmentation and metabolic traits.
Researchers also identified so‑called Neanderthal “deserts”—stretches of the modern human genome that remained free of Neanderthal DNA. Those deserts appear to have formed quickly after admixture, consistent with the idea that some Neanderthal variants were deleterious or incompatible with modern human biology. Together, these findings clarify the timing, duration and evolutionary consequences of contact between Homo sapiens and Neanderthals.
Key Facts
- Timeline: Admixture began around 50,500 years ago; the core period centers on ~47,000 years ago and lasted about 7,000 years, concluding by ~43,500 years ago.
- Genetic Impact: Modern non‑African genomes retain roughly 1–2% Neanderthal ancestry; introgressed variants affected immunity, skin pigmentation and metabolic traits.
- Genome Deserts: Regions devoid of Neanderthal ancestry emerged rapidly after gene flow, likely due to harmful or lethal incompatibilities.
Source: UC Berkeley
A comprehensive analysis of ancient and present‑day human genomes has produced the most precise timeline yet for Neanderthal–Homo sapiens interbreeding. By jointly examining genomes from 58 ancient modern humans sampled across Europe and Asia alongside 275 contemporary genomes, the team reconstructed when and how long Neanderthal gene flow affected the ancestors of today’s non‑African populations.
The genomic reconstruction yields an average date near 47,000 years ago for admixture events, refining earlier estimates that ranged from roughly 41,000 to 54,000 years ago. In practical terms, the results support a model in which modern humans and Neanderthals overlapped in Eurasia for several thousand years, during which repeated or prolonged interbreeding left a lasting genetic legacy across non‑African populations.
“Precise timing alters how we interpret the out‑of‑Africa migration and subsequent settlement of Eurasia,” said Priya Moorjani, assistant professor of molecular and cell biology at the University of California, Berkeley, and a senior author of the study. The findings also align with archaeological evidence for co‑occupation of the same regions by early modern humans and Neanderthals for about 6,000–7,000 years.
The study was co‑led by Benjamin Peter of the University of Rochester and the Max Planck Institute for Evolutionary Anthropology (MPI‑EVA). Lead authors include Leonardo Iasi (MPI‑EVA) and Manjusha Chintalapati (formerly a UC Berkeley postdoctoral fellow, now at Ancestry DNA). The paper appears in the December 13 print issue of Science, with an independent MPI‑EVA study in Nature reporting similar timing based on newly sequenced 45,000‑year‑old genomes.
Rather than modeling admixture as a single generation pulse, the researchers tested more complex scenarios and found the data best support an extended period of gene flow lasting several thousand years. This prolonged contact helps explain observed geographic differences in Neanderthal ancestry—for example, why East Asian populations tend to carry roughly 20% more Neanderthal DNA than Europeans and West Asians. Populations that moved eastward already carried mixed Neanderthal variants acquired during the extended admixture period.
Neanderthal deserts in the genome
Using methods developed for working with fragmentary ancient genomes, the team cataloged Neanderthal ancestry segments across ancient and present‑day individuals. They mapped both high‑frequency introgressed regions and deserts lacking Neanderthal DNA. The deserts, which appear on autosomes and the X chromosome, were already present in very early modern human samples older than 40,000 years—such as Oase, Ust‑Ishim, Zlatý kůň, Tianyuan and Bacho Kiro—indicating that many deserts formed rapidly after initial admixture.
Rapid formation of deserts suggests some introgressed Neanderthal alleles were strongly disadvantageous or lethal in modern human genetic backgrounds. In contrast, other introgressed regions rose in frequency over time, consistent with adaptive introgression: many of these high‑frequency segments involve immune function, skin pigmentation and metabolism. For instance, several Neanderthal‑derived immune variants influence susceptibility or response to modern pathogens, and one variant has been linked to altered outcomes for the coronavirus that causes COVID‑19.
“Neanderthals were adapted to the harsh, Ice Age environments and their local pathogens,” said Iasi. “When modern humans left Africa and interbred with Neanderthals, they occasionally acquired variants that helped them adapt to cold climates or local disease pressures.” Some of those variants appear to have been beneficial immediately after introgression, while others became advantageous only later as environments and disease landscapes changed.
Moorjani is continuing to investigate Neanderthal and Denisovan sequences in East Asian populations, which not only show elevated Neanderthal ancestry but also small contributions (up to ~0.1% of the genome) from Denisovans—another archaic human lineage. Together, these admixture events illuminate how interactions with archaic hominins shaped the genetic diversity and adaptive potential of modern humans outside Africa.
Funding: Additional co‑authors on the Science paper include postdoctoral fellow Laurits Skov (UC Berkeley) and Alba Bossoms Mesa and Mateja Hajdinjak (MPI‑EVA). Moorjani’s research received support from the Burroughs Wellcome Fund and the National Institutes of Health (R35GM142978).
About this evolution and neuroscience research news
Author: Robert Sanders, UC Berkeley
Source: UC Berkeley
Contact: Robert Sanders – UC Berkeley
Image: Image credited to Neuroscience News
Original Research: Closed access. DOI: 10.1126/science.adq3010 — “Neandertal ancestry through time: Insights from genomes of ancient and present‑day humans” by Priya Moorjani et al., Science
Abstract
Neandertal ancestry through time: Insights from genomes of ancient and present‑day humans
INTRODUCTION
Gene flow from Neanderthals has left a measurable imprint on modern human genomes. Most non‑African individuals today inherit about 1–2% of their genomes from Neanderthals. Across the genome, some regions show high frequencies of introgressed Neanderthal variants—candidates for adaptive introgression—while other regions are conspicuously absent of Neanderthal DNA and are called deserts. Disentangling the roles of demography, genetic drift and natural selection in shaping this landscape requires direct observation of ancient genomes.
RATIONALE
This study analyzes genomic data from 59 ancient individuals dated between 45,000 and 2,200 years before present, together with 275 diverse present‑day genomes, to reconstruct how Neanderthal ancestry changed over time. By examining the frequency, length and distribution of Neanderthal segments, the researchers addressed three questions: how Neanderthal ancestry is shared across geography and time; when and how long Neanderthal gene flow occurred; and what functional legacy these introgressed segments carry in modern humans.
RESULTS
The study produced a catalog of Neanderthal ancestry segments shared among ancient and present‑day individuals. Most introgressed segments are shared across populations and reflect non‑African population structure. Comparison with sequenced Neanderthal genomes suggests admixture involved a single Neanderthal group or multiple closely related groups. Some very early modern humans retain unique Neanderthal ancestry not found in later populations, indicating partial loss of certain introgressed segments over time. Analysis of segment lengths and distributions supports a single extended period of gene flow centered around ~47,000 years ago and lasting about 7,000 years. Many deserts formed rapidly after admixture and were detectable in the earliest genomes outside Africa. Several introgressed regions show evidence of positive selection, particularly those related to immunity, skin pigmentation and metabolism.
CONCLUSION
These results support a model of a single, extended episode of Neanderthal gene flow into the ancestors of all non‑African populations between roughly 50,500 and 43,500 years ago. The majority of selection—both positive and negative—acting on Neanderthal ancestry appears to have occurred soon after admixture, leaving detectable signatures in the genomes of the earliest modern humans outside Africa. This refined timeline provides a clearer lower bound for the out‑of‑Africa migration and offers new insight into how interactions with archaic hominins shaped human evolution.