Post by Admin on Jan 28, 2021 20:24:40 GMT
Discussion
It has clearly been established that the transformation from the LBK, which is characterized by a homogeneous material culture over a large area, to the later more diverse Neolithic societies in Europe was accompanied by genetic admixture3. However, the population interactions underlying this transformation have not yet been fully resolved. The admixture events were geographically highly localized and involved various populations with different ancestry components3. These processes likely led to the increase in HG ancestry proportions and mtDNA lineages that were observed in Middle to Late Neolithic communities1,7,35,36. It is currently not known what might have influenced these widespread demographic and genomic processes in Europe, but climate change and/or social processes may be considered contributing factors37.
Here we investigated a community of 42 Late Neolithic farmers excavated from the WBC gallery grave in Niedertiefenbach, Germany16,17,38. The radiocarbon dates (3300–3200 cal. BCE) placed the site only a few hundred years before the arrival of the steppe ancestry in central Europe. Interestingly, we did not observe any genetic evidence for an admixture with steppe components (e.g., no feasible two-way models with steppe ancestry or the absence of the Y haplogroup R1b). The Niedertiefenbach population exhibited a mixture of genomic components from western HGs and early farmers. The continuous range (34–58%) of the relatively high genetic HG proportion is surprising. Admixture dating indicated that the mixing of the two components occurred around 3860–3550 cal. BCE. From these results, it cannot be inferred to what extent the contributing populations themselves were already admixed or which subsistence economy they practiced. But interestingly, the estimated admixture date coincides with farming expansion phases and social changes during the Late MC (3800–3500 BCE)39. Archaeologically, there is a well-documented continuity from Late MC to WBC9. mtDNA data from two MC sites in France40 and Germany41 indicate that the analyzed individuals belonged to an already admixed population comprising haplotypes typical of both farmers and HGs40. Human genome-wide datasets from clear archaeological MC contexts are not available yet. A possible exception could be the data of four individuals from Blätterhöhle that may be chronologically (based on their radiocarbon dates of 4100–3000 BCE) and geographically linked with Late MC and/or WBC6. However, it has to be kept in mind that the remains were found in a cave without any definite cultural assignment. Our analyses showed that the Niedertiefenbach population appeared most closely related to the Blätterhöhle collective whose large HG component (39–72%)3 falls into the range observed for Niedertiefenbach. Moreover, they are a good proxy for the HG component in the Niedertiefenbach sample. In addition, our admixture date is very similar to the one obtained for Blätterhöhle that yielded 18–23 generations before the average sample date of 3414 ± 84 cal. BCE3. Thus, there is a possible genetic link between the people buried in Blätterhöhle and those in the gallery grave of Niedertiefenbach.
The WBC-associated population in Niedertiefenbach represents a genetically diverse group with a very broad range of HG proportions (as seen in Fig. 2, Supplementary Fig. 3, and in the qpAdm two-way models for each individual in Supplementary Fig. 9). This finding suggests that the admixture was still in progress at that time or had taken place a few generations before. This scenario is tentatively supported by the admixture dating analysis (Supplementary Information). Given the surprisingly large HG component, it seems conceivable that the admixture included also individuals who had exclusive or near-exclusive genetic HG ancestry. Taking into account all available lines of evidence, we hypothesize that the increase in the HG component likely occurred during the consolidation of the MC and/or the beginning of the WBC and could have involved also direct gene flow from unadmixed local western HGs into expanding farming populations.
The genetic data of the Niedertiefenbach sample, along with information obtained from archaeological and osteological analyses, shed light on the community that used this gallery grave. In total, the skeletal remains of a minimal number of 177 individuals were recovered from the 7 m2 site, reflecting a very high occupancy rate for a collective WBC burial38. The genetic sex distribution in the sample indicated a considerable excess of males (70%) among adults and subadults, which has not been described for other Neolithic populations42. As we followed a random sampling strategy, such an excess is noteworthy and may reflect a burial bias. Regarding age, we did not observe a numerical deficit of children that is often recorded for Neolithic cemeteries in Germany43,44. The phenotype reconstruction revealed that the examined individuals had a predominantly dark complexion and were genetically not yet adapted to digest starch-rich food or lactose. These phenotypes have typically been described for HGs and early farmers3.
Overall, the genomic data indicate that the gallery grave was mainly used by not closely related people who may have lived in various neighboring locations. This observation is supported by the large number of mtDNA haplogroups. However, also related individuals were interred. In one case, we observed inhumations of first-degree relatives (Supplementary Fig. 8). In addition, the presence of only one frequent Y chromosome haplotype (I2c1a1) suggests a patrilineage.
In line with studies investigating the health status of Neolithic populations in central Europe45, the Niedertiefenbach individuals showed numerous unspecific skeletal lesions that are indicative of physical stress, including malnutrition, and infections38. Interestingly, we did not detect any pathogens. This observation is consistent with aDNA-based findings describing only relatively few sporadic cases of infectious diseases for the Neolithic period46.
The HLA class I and II dataset generated for Niedertiefenbach was relatively small and thus precluded sophisticated statistical analysis. However, relative to contemporary German populations some striking shifts in allele frequencies could be observed (Table 1 and Supplementary Data 3). Interestingly, several of the alleles that are less common today (e.g., A*02:01, B*27:05, C*01:02, DQB1*03:01, and DRB1*08:01) are associated with higher resistance to viral pathogens (e.g., HIV, HCV, influenza A, and herpesvirus)47,48,49,50 and often also with higher susceptibility to bacterial infections or complications thereof50,51,52. When we traced the most frequent alleles of the class I and class II loci through time (by checking their proxy SNP alleles in published aDNA datasets), it became apparent that five HLA-B, -C, and -DRB1 alleles were a hallmark of HGs, but not of later-dating farmers (Fig. 3a and Supplementary Data 4). Their high frequencies in Niedertiefenbach may thus reflect the considerable HG-related ancestry proportion in the population. The alleles were potentially maintained at this frequency at that time because of their functional uniqueness, including a higher sequence divergence as well as a unique repertoire of presented antigens. Both of these properties should confer an advantage in fighting diverse viruses and other pathogens53. Later on, they may have lost their relative fitness advantage, e.g., because pathogens adapted to these most common alleles in a process of negative frequency-dependent selection54 and were replaced by alleles beneficial against newly emerging human pathogenic bacteria, such as Yersinia pestis. For the once common allele HLA-C*01:02, no protective effect against an infectious agent is known today. Thus, it is tempting to speculate that it had evolved in defense of a pathogen that is no longer virulent or that went extinct as has been described for Neolithic HBV lineages55.
Another notable difference concerns the HLA allele DRB1*15:01. It is widespread in present-day Europeans (ca. 15%), but absent in Niedertiefenbach samples. This allele predisposes to mycobacterial infections (tuberculosis and leprosy)56. In disease studies, the SNP allele rs3135388-T is often used as a marker for DRB1*15:0157. In published aDNA datasets25, rs3135388-T was also found to be absent in all European Paleolithic, Mesolithic, and Neolithic populations analyzed. It seemed to appear for the first time only during the Bronze Age. Since then, its initially high frequency (~20%) has decreased to the present low levels (Supplementary Fig. 10). This finding raises the intriguing possibility that the allele might have been incorporated into the European gene pool as part of the steppe-related ancestry component in the Final Neolithic and Bronze Age. Given the limited size of the ancient sample, these considerations remain speculative and await corroboration, as HLA data from further ancient populations become available.
The advent of farming and subsequent shifts in pathogen exposure are thought to have radically changed the immune genes in early agriculturalists25. The immune response of the Niedertiefenbach collective appears geared towards fighting viral agents. To what extent this HLA profile was due to the specific demographic history of the Niedertiefenbach population (i.e., the high HG ancestry proportion) or typical of Neolithic communities in the fourth millennium remains to be clarified. Overall, our study showed that the HLA-repertoire of modern Europeans was established quite recently, sometime during the last 5000 years, and may also have been shaped by population admixture.
By applying a comprehensive genomics approach to individuals interred in the WBC-associated collective burial in Niedertiefenbach, we discovered that the community, which used this site for about 100 years, was genetically heterogeneous and carried both Neolithic and HG ancestry. The mixture of these two components likely occurred at the beginning of the fourth millennium, indicating important demographic and cultural transformations during that time in western Europe. This event may also have affected the immune status of the admixed population and its descendants for generations to come.
It has clearly been established that the transformation from the LBK, which is characterized by a homogeneous material culture over a large area, to the later more diverse Neolithic societies in Europe was accompanied by genetic admixture3. However, the population interactions underlying this transformation have not yet been fully resolved. The admixture events were geographically highly localized and involved various populations with different ancestry components3. These processes likely led to the increase in HG ancestry proportions and mtDNA lineages that were observed in Middle to Late Neolithic communities1,7,35,36. It is currently not known what might have influenced these widespread demographic and genomic processes in Europe, but climate change and/or social processes may be considered contributing factors37.
Here we investigated a community of 42 Late Neolithic farmers excavated from the WBC gallery grave in Niedertiefenbach, Germany16,17,38. The radiocarbon dates (3300–3200 cal. BCE) placed the site only a few hundred years before the arrival of the steppe ancestry in central Europe. Interestingly, we did not observe any genetic evidence for an admixture with steppe components (e.g., no feasible two-way models with steppe ancestry or the absence of the Y haplogroup R1b). The Niedertiefenbach population exhibited a mixture of genomic components from western HGs and early farmers. The continuous range (34–58%) of the relatively high genetic HG proportion is surprising. Admixture dating indicated that the mixing of the two components occurred around 3860–3550 cal. BCE. From these results, it cannot be inferred to what extent the contributing populations themselves were already admixed or which subsistence economy they practiced. But interestingly, the estimated admixture date coincides with farming expansion phases and social changes during the Late MC (3800–3500 BCE)39. Archaeologically, there is a well-documented continuity from Late MC to WBC9. mtDNA data from two MC sites in France40 and Germany41 indicate that the analyzed individuals belonged to an already admixed population comprising haplotypes typical of both farmers and HGs40. Human genome-wide datasets from clear archaeological MC contexts are not available yet. A possible exception could be the data of four individuals from Blätterhöhle that may be chronologically (based on their radiocarbon dates of 4100–3000 BCE) and geographically linked with Late MC and/or WBC6. However, it has to be kept in mind that the remains were found in a cave without any definite cultural assignment. Our analyses showed that the Niedertiefenbach population appeared most closely related to the Blätterhöhle collective whose large HG component (39–72%)3 falls into the range observed for Niedertiefenbach. Moreover, they are a good proxy for the HG component in the Niedertiefenbach sample. In addition, our admixture date is very similar to the one obtained for Blätterhöhle that yielded 18–23 generations before the average sample date of 3414 ± 84 cal. BCE3. Thus, there is a possible genetic link between the people buried in Blätterhöhle and those in the gallery grave of Niedertiefenbach.
The WBC-associated population in Niedertiefenbach represents a genetically diverse group with a very broad range of HG proportions (as seen in Fig. 2, Supplementary Fig. 3, and in the qpAdm two-way models for each individual in Supplementary Fig. 9). This finding suggests that the admixture was still in progress at that time or had taken place a few generations before. This scenario is tentatively supported by the admixture dating analysis (Supplementary Information). Given the surprisingly large HG component, it seems conceivable that the admixture included also individuals who had exclusive or near-exclusive genetic HG ancestry. Taking into account all available lines of evidence, we hypothesize that the increase in the HG component likely occurred during the consolidation of the MC and/or the beginning of the WBC and could have involved also direct gene flow from unadmixed local western HGs into expanding farming populations.
The genetic data of the Niedertiefenbach sample, along with information obtained from archaeological and osteological analyses, shed light on the community that used this gallery grave. In total, the skeletal remains of a minimal number of 177 individuals were recovered from the 7 m2 site, reflecting a very high occupancy rate for a collective WBC burial38. The genetic sex distribution in the sample indicated a considerable excess of males (70%) among adults and subadults, which has not been described for other Neolithic populations42. As we followed a random sampling strategy, such an excess is noteworthy and may reflect a burial bias. Regarding age, we did not observe a numerical deficit of children that is often recorded for Neolithic cemeteries in Germany43,44. The phenotype reconstruction revealed that the examined individuals had a predominantly dark complexion and were genetically not yet adapted to digest starch-rich food or lactose. These phenotypes have typically been described for HGs and early farmers3.
Overall, the genomic data indicate that the gallery grave was mainly used by not closely related people who may have lived in various neighboring locations. This observation is supported by the large number of mtDNA haplogroups. However, also related individuals were interred. In one case, we observed inhumations of first-degree relatives (Supplementary Fig. 8). In addition, the presence of only one frequent Y chromosome haplotype (I2c1a1) suggests a patrilineage.
In line with studies investigating the health status of Neolithic populations in central Europe45, the Niedertiefenbach individuals showed numerous unspecific skeletal lesions that are indicative of physical stress, including malnutrition, and infections38. Interestingly, we did not detect any pathogens. This observation is consistent with aDNA-based findings describing only relatively few sporadic cases of infectious diseases for the Neolithic period46.
The HLA class I and II dataset generated for Niedertiefenbach was relatively small and thus precluded sophisticated statistical analysis. However, relative to contemporary German populations some striking shifts in allele frequencies could be observed (Table 1 and Supplementary Data 3). Interestingly, several of the alleles that are less common today (e.g., A*02:01, B*27:05, C*01:02, DQB1*03:01, and DRB1*08:01) are associated with higher resistance to viral pathogens (e.g., HIV, HCV, influenza A, and herpesvirus)47,48,49,50 and often also with higher susceptibility to bacterial infections or complications thereof50,51,52. When we traced the most frequent alleles of the class I and class II loci through time (by checking their proxy SNP alleles in published aDNA datasets), it became apparent that five HLA-B, -C, and -DRB1 alleles were a hallmark of HGs, but not of later-dating farmers (Fig. 3a and Supplementary Data 4). Their high frequencies in Niedertiefenbach may thus reflect the considerable HG-related ancestry proportion in the population. The alleles were potentially maintained at this frequency at that time because of their functional uniqueness, including a higher sequence divergence as well as a unique repertoire of presented antigens. Both of these properties should confer an advantage in fighting diverse viruses and other pathogens53. Later on, they may have lost their relative fitness advantage, e.g., because pathogens adapted to these most common alleles in a process of negative frequency-dependent selection54 and were replaced by alleles beneficial against newly emerging human pathogenic bacteria, such as Yersinia pestis. For the once common allele HLA-C*01:02, no protective effect against an infectious agent is known today. Thus, it is tempting to speculate that it had evolved in defense of a pathogen that is no longer virulent or that went extinct as has been described for Neolithic HBV lineages55.
Another notable difference concerns the HLA allele DRB1*15:01. It is widespread in present-day Europeans (ca. 15%), but absent in Niedertiefenbach samples. This allele predisposes to mycobacterial infections (tuberculosis and leprosy)56. In disease studies, the SNP allele rs3135388-T is often used as a marker for DRB1*15:0157. In published aDNA datasets25, rs3135388-T was also found to be absent in all European Paleolithic, Mesolithic, and Neolithic populations analyzed. It seemed to appear for the first time only during the Bronze Age. Since then, its initially high frequency (~20%) has decreased to the present low levels (Supplementary Fig. 10). This finding raises the intriguing possibility that the allele might have been incorporated into the European gene pool as part of the steppe-related ancestry component in the Final Neolithic and Bronze Age. Given the limited size of the ancient sample, these considerations remain speculative and await corroboration, as HLA data from further ancient populations become available.
The advent of farming and subsequent shifts in pathogen exposure are thought to have radically changed the immune genes in early agriculturalists25. The immune response of the Niedertiefenbach collective appears geared towards fighting viral agents. To what extent this HLA profile was due to the specific demographic history of the Niedertiefenbach population (i.e., the high HG ancestry proportion) or typical of Neolithic communities in the fourth millennium remains to be clarified. Overall, our study showed that the HLA-repertoire of modern Europeans was established quite recently, sometime during the last 5000 years, and may also have been shaped by population admixture.
By applying a comprehensive genomics approach to individuals interred in the WBC-associated collective burial in Niedertiefenbach, we discovered that the community, which used this site for about 100 years, was genetically heterogeneous and carried both Neolithic and HG ancestry. The mixture of these two components likely occurred at the beginning of the fourth millennium, indicating important demographic and cultural transformations during that time in western Europe. This event may also have affected the immune status of the admixed population and its descendants for generations to come.