Periodic Reporting for period 4 - 100 Archaic Genomes (Genome sequences from extinct hominins)
Reporting period: 2021-05-01 to 2021-10-31
At the beginning of this project, a single high-coverage Neandertal genome and a single high-coverage Denisovan genome had been generated. Although several novel insights had emerged from the analysis of these genomes, our knowledge about the extent of genetic variation among Neandertals was still very limited. In addition, DNA retrieval had so far been restricted to late Neandertals. The amount of information about Denisovans was even more limited. The project has substantially extended the knowledge about genetic variation among Neandertals, Denisovans and their ancestors across time and space and has generated insights into how Neandertals, Denisovans and modern humans mixed with each other. It has also generate genomic data from older specimens.
We have drastically increased the number of Neandertals for which genome sequences are available.
Analyses of these data show that Neandertals carried fewer differences among them than present-day humans, suggesting that Neandertal populations were of small size. Genetic similarity among late Neandertals is predicted by their geographical location and a population turnover is likely to have occurred towards the end of Neandertal history.
The bulk of Neandertal gene flow into early modern humans originated from one or more Neandertal populations that were more closely related to the Neandertals we have sequenced in this project than the previously sequenced Neandertal from Siberia. This allows us to identify 10 to 20% more Neandertal DNA in present-day humans, including variants involved in medically significant traits such as low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
From one site in the Altai Mountains of southern Siberia we generated genetic data from 11 Neandertals, the first social group of Neandertals extensively studied. All individuals were closely related and included a father-daughter pair. The patterns of variation in the genomes show that these individuals were part of a small community and that female migrated between communities more than males.
From Denisova Cave we have identified several new Neandertal and Denisovan specimens, in several cases thanks to our collaboration with the PalaeoChron project of Prof. Thomas Higham (ERC: grant 324139). One of these specimens turned out to come from an individual who had a Neandertal mother and a Densiovan father, showing that these two groups met and interacted in the region. We also have generated a Neandertal genome from Denisova Cave of high coverage that is between 130-150 thousand years old. It is being analyzed at the moment and will yield insights into the deep history of Neandertals. In addition, we have sequenced five additional Neandertal genomes from Belgium, Poland, the Caucasus and Siberia to high quality. They will illuminate the history of Neandertals and help identifying genetic features that were typical of Neandertals.
We have identified several new Denisovan specimens from Denisova Cave and generated genomic sequences from them. One is of high quality and about 110,000 years old. Four others are of moderate quality and vary in age 55,000 and approximately 200,000 years. They are being analyzed at the moment and will allow an unprecedented detailed view of Denisovan history.
To understand how the gene flow from Neandertals into early modern humans occurred, we have studied the genomes of some early modern humans that lived before ~30,000 years ago. In one case, we analyzed a new genome we studied from Mongolia as well as one we previously sequenced from China and showed that they carried genomic segments of Denisovan ancestry deriving from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians. In another study, we generated genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bulgaria. We found that they belonged to a modern human migration into Europe that was not previously known from the genetic record. Strikingly, all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed frequently with Neandertals.
One technical breakthrough has been the demonstration that it is possible to retrieve hominin DNA from archaeological sediments. This opens the possibility to demonstrate that Neandertals and Denisovans have been present at a site even when no recognizable physical remains of these groups are found at a site. We applied this at a large scale to Denisova Cave in the Altai Mountains, and recently developed methods for microsampling sediments, which will allow DNA from single individuals from defined contexts to be isolated.
Analyses of these data show that Neandertals carried fewer differences among them than present-day humans, suggesting that Neandertal populations were of small size. Genetic similarity among late Neandertals is predicted by their geographical location and a population turnover is likely to have occurred towards the end of Neandertal history.
The bulk of Neandertal gene flow into early modern humans originated from one or more Neandertal populations that were more closely related to the Neandertals we have sequenced in this project than the previously sequenced Neandertal from Siberia. This allows us to identify 10 to 20% more Neandertal DNA in present-day humans, including variants involved in medically significant traits such as low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
From one site in the Altai Mountains of southern Siberia we generated genetic data from 11 Neandertals, the first social group of Neandertals extensively studied. All individuals were closely related and included a father-daughter pair. The patterns of variation in the genomes show that these individuals were part of a small community and that female migrated between communities more than males.
From Denisova Cave we have identified several new Neandertal and Denisovan specimens, in several cases thanks to our collaboration with the PalaeoChron project of Prof. Thomas Higham (ERC: grant 324139). One of these specimens turned out to come from an individual who had a Neandertal mother and a Densiovan father, showing that these two groups met and interacted in the region. We also have generated a Neandertal genome from Denisova Cave of high coverage that is between 130-150 thousand years old. It is being analyzed at the moment and will yield insights into the deep history of Neandertals. In addition, we have sequenced five additional Neandertal genomes from Belgium, Poland, the Caucasus and Siberia to high quality. They will illuminate the history of Neandertals and help identifying genetic features that were typical of Neandertals.
We have identified several new Denisovan specimens from Denisova Cave and generated genomic sequences from them. One is of high quality and about 110,000 years old. Four others are of moderate quality and vary in age 55,000 and approximately 200,000 years. They are being analyzed at the moment and will allow an unprecedented detailed view of Denisovan history.
To understand how the gene flow from Neandertals into early modern humans occurred, we have studied the genomes of some early modern humans that lived before ~30,000 years ago. In one case, we analyzed a new genome we studied from Mongolia as well as one we previously sequenced from China and showed that they carried genomic segments of Denisovan ancestry deriving from the same Denisovan admixture event(s) that contributed to present-day mainland Asians but are distinct from the Denisovan DNA segments in present-day Papuans and Aboriginal Australians. In another study, we generated genome-wide data from three individuals dated to between 45,930 and 42,580 years ago from Bulgaria. We found that they belonged to a modern human migration into Europe that was not previously known from the genetic record. Strikingly, all three individuals had Neanderthal ancestors a few generations back in their family history, confirming that the first European modern humans mixed frequently with Neandertals.
One technical breakthrough has been the demonstration that it is possible to retrieve hominin DNA from archaeological sediments. This opens the possibility to demonstrate that Neandertals and Denisovans have been present at a site even when no recognizable physical remains of these groups are found at a site. We applied this at a large scale to Denisova Cave in the Altai Mountains, and recently developed methods for microsampling sediments, which will allow DNA from single individuals from defined contexts to be isolated.
We have extended the knowledge about genetic variation in Neandertals and Denisovans.
We have generated several new genomes from both groups, some of a quality similar to genomes from present-day individuals.
We have studied one site where several Neandertals who were contemporaneous with each other are found, allowing a first view of relationships within Neandertal groups.
We have generated several new genomes from both groups, some of a quality similar to genomes from present-day individuals.
We have studied one site where several Neandertals who were contemporaneous with each other are found, allowing a first view of relationships within Neandertal groups.