2024-12-12 マックス・プランク研究所
<関連情報>
- https://www.mpg.de/23832006/1205-evan-new-timeline-for-neandertal-gene-flow-event-150495-x
- https://www.science.org/doi/10.1126/science.adq3010
ネアンデルタール人の祖先:古代人と現生人類のゲノムから判明したこと Neanderthal ancestry through time: Insights from genomes of ancient and present-day humans
Leonardo N. M. Iasi, Manjusha Chintalapati, Laurits Skov, Alba Bossoms Mesa, […], and Priya Moorjani
Science Published:13 Dec 2024
DOI:https://doi.org/10.1126/science.adq3010
Editor’s summary
Gene flow from archaic hominins into modern humans, and vice versa, has been amply demonstrated in recent years. However, many questions remain about how selection has acted on introgressed variants as well as the diversity of hominin individuals who contributed to this admixture. Iasi et al. identified Neanderthal ancestry in genomic data from 59 ancient and 275 present-day human samples. They found that gene flow likely happened over a period of about 6000 years, and that positive and negative selection acted within about 100 generations on these introgressed segments. Surprisingly, the authors didn’t find evidence for a second pulse of introgression into East Eurasians despite the increased levels of introgression found in modern individuals. —Corinne Simonti
Structured Abstract
INTRODUCTION
Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. Most non-Africans living today derive ~1 to 2% of their ancestry from Neanderthals. Across the genome, some genomic regions harbor a high frequency of Neanderthal variants and are identified as “candidates of adaptive introgression,” whereas others are devoid of any Neanderthal ancestry and are referred to as “deserts.” However, the timing and evolutionary processes, for example, genetic drift or natural selection, that have shaped the landscape of Neanderthal ancestry remain elusive. Most of the previous studies have focused on genomes of present-day individuals, where separating the effects of past demography and selection is challenging. Ancient DNA analyses have transformed research into human evolutionary history by enabling the direct observation of genetic variation patterns that existed in the past.
RATIONALE
In this study, we analyzed genomic data from 59 ancient individuals sampled between 45,000 and 2200 years before present and 275 diverse present-day individuals to study the evolutionary history of Neanderthal ancestry throughout time. We examined the frequency, length, and distribution of Neanderthal ancestry segments over time to answer the following questions: (i) How is Neanderthal ancestry shared among individuals, by geography and time? (ii) When did Neanderthal gene flow occur and for how long did it last? and (iii) What is the functional legacy of Neanderthal ancestry in modern humans?
RESULTS
We generated a catalog of Neanderthal ancestry in ancient and present-day modern humans and found that the majority of the Neanderthal ancestry segments are shared across populations and that the sharing of Neanderthal ancestry segments mirrors the population structure among non-Africans. The comparison with sequenced Neanderthals, for example, Vindija, Altai, and Chagyrskaya, suggests that the gene flow occurred from a single or multiple closely related Neanderthal groups. By contrast, the earliest modern humans—Oase, Ust’-Ishim, Zlatý kůň, and Bacho Kiro—possess substantial unique Neanderthal ancestry and a distinct matching profile to the sequenced Neanderthals, indicating that some Neanderthal ancestry in these early individuals is not shared with modern humans after 40,000 years.
By studying the distribution and lengths of the Neanderthal ancestry segments in ancient individuals, we found evidence for a single extended period of Neanderthal gene flow that occurred ~47,000 years ago and lasted for ~7000 years. This is consistent with archaeological evidence for the potential overlap of early modern humans and Neanderthals in Europe.
Finally, we examined the frequency of Neanderthal ancestry across the genome and over time. We uncovered new candidates of adaptive introgression, including regions that were immediately adaptive for modern humans and some that became adaptive more recently from introgressed standing variation. Most Neanderthal deserts—on the autosomes and the X chromosome—were formed rapidly after the gene flow and were also evident in the earliest modern human genomes. Notably, the X chromosome exhibits a nonuniform and nonrandom distribution of Neanderthal ancestry, with large Neanderthal ancestry deserts overlapping previously identified signals of sweeps in non-Africans.
CONCLUSION
Our study provides insights into the complex history of Neanderthal gene flow into modern humans. We found strong support for a single extended period of Neanderthal gene flow into the common ancestors of all non-Africans that occurred between 50,500 and 43,500 years ago. These dates provide a lower bound for the timing of the out-of-Africa migration and settlement of regions outside Africa. The majority of natural selection—positive and negative—on Neanderthal ancestry happened very quickly after the gene flow and left clear signals in the genetic diversity of the earliest modern humans outside Africa.
Neanderthal ancestry in modern humans.
Using Neanderthal (red) and present-day Africans as references, we identified regions of Neanderthal ancestry in >300 ancient and present-day modern humans (gray). We assessed the sharing of Neanderthal segments between populations, inferred the mean time and duration of the gene flow, and examined the variation in frequency across the genome to identify candidates of positive and negative selection. ya, years ago. [Figure created with BioRender.com]
Abstract
Gene flow from Neanderthals has shaped genetic and phenotypic variation in modern humans. We generated a catalog of Neanderthal ancestry segments in more than 300 genomes spanning the past 50,000 years. We examined how Neanderthal ancestry is shared among individuals over time. Our analysis revealed that the vast majority of Neanderthal gene flow is attributable to a single, shared extended period of gene flow that occurred between 50,500 to 43,500 years ago, as evidenced by ancestry correlation, colocalization of Neanderthal segments across individuals, and divergence from the sequenced Neanderthals. Most natural selection—positive and negative—on Neanderthal variants occurred rapidly after the gene flow. Our findings provide new insights into how contact with Neanderthals shaped modern human origins and adaptation.
