Post by Admin on May 20, 2021 3:52:58 GMT
Discussion
The deep sequencing of the Peștera Muierii 1 woman enabled us to identify a surprising genetic diversity in pre-LGM populations, which brings a new understanding of the early European population of AMH. These data propose a novel paradigm, in which early AMH populations after migration out of Africa were much more diverse than previously believed, and the bottlenecks associated with loss of diversity were caused by glacial climatic periods in northern latitudes. In line with the high diversity observed in EUP genomes, the burden of damaging variants in these individuals was largely the same as in modern-day individuals. This is clearly a different pattern from the high burden of deleterious variants found in small isolated populations,26 which may help us understand the different views of genetic load in humans.21,22,24, 25, 26 However, these ancient high-coverage genomes represent a very small sample size, and it is unclear whether the results can be extrapolated to the entire populations living during these time periods. Finally, using novel methodologies employed in medical genomics, we mined the genomes of ancient individuals for potential pathogenic variants. We have identified several interesting rare variants with medical consequences in the EUP genomes. In the case of other variants identified, such as the AIPL1 (p. (His82Tyr)) described in a sporadic case of Leber congenital amaurosis 4, we propose that they are unlikely to be pathogenic based on insufficient literature evidence. Additionally, one could argue that living completely blind would have been very challenging in the Palaeolithic. However, we also note that care for individuals with congenital disorders or injuries is present in the archaeological record since the Middle Pleistocene,54, 55, 56 and if the variant was verified as causing blindness, we could add another example of early human care for an individual with a severe disorder. This example shows that analysis of ancient genomes can also help in the pathogenicity assessment of rare genetic variants in modern-day patients.
This study opens the door to a new approach to the study of ancient genomes, in which classical population genetics can be combined with medical genomics to draw conclusions about demographics and disease epidemiology. Future research challenges will extend to broaden these medical genetics observations in larger populations, to study patterns of selection in ancient populations, and to directly identify the refugia and human populations from which the hunter-gatherers resurged after the LGM.
Definition of the mitochondrial haplotype of PM1
The mitogenome of PM1 was previously identified as a basal haplogroup U6∗, with a private mutation at position T10517A which had not previously been found in any ancient or modern human.36 Since then U6 has been identified in one more ancient specimen, PM2, the sample originating from the same cave as PM1,14 now also suggested to be related to or the same individual as PM1 (Data S1D). To call a consensus sequence for the mitochondrial genome of PM1, we used mpileup and vcfutils provided by samtools59 requiring mapping and base qualities of at least 30. We reanalyzed the mitogenome from PM1, now at 1492 X coverage, and confirm the same private mutation as previously found (Data S1D).
The Bayesian phylogenetic re-analysis was performed to infer the phylogenetic position of PM1. The best-fit model of evolution was selected using jModeltest 267 under AIC, BIC, and AICc criteria prior to Bayesian analyses. Bayesian analyses were carried out using BEAST 2.68 Two simultaneous runs of 50 million generations were conducted for the datasets and trees were sampled every 1,000 generations, with the first 25% discarded as burn-in. Samples from the posterior were checked for acceptable effective sample sizes (> 200) and the adequate convergence of the MCMC chains was checked using Tracer 1.69
The phylogenetic reanalysis was performed using the complete mitogenomes of 245 modern Homo sapiens, including 61 individuals from the Upper Palaeolithic (15 individuals have been added to the previous analysis in Hervella et al.,36 41 humans from the Neolithic, one individual from the 15th century and 143 modern samples (Data S1E). The modern humans were selected from all the individuals with published mitogenomes and covered the whole phylogenetic diversity within the N hg lineage, with special emphasis in the U lineage. The analysis was carried out using the HKY+G+I substitution model, strict molecular clock and coalescent constant population tree prior, indicating the tip dates of the samples (Figure S2A).
We confirm the basal U6 mitochondrial haplogroup for the PM1 genome as described in Hervella et al.,36 and increase the coverage in 1492X. Our estimates of the haplogroup U6 TMRCA that incorporate ancient genomes (including PM1) set the formation of the U6 lineage back to 49.6 ky BP (95% HPD: 42–58 ky) (using a mutation rate of 2.06∗ 10−8 SD = 1.94 ∗ 10−9). Our estimates are almost identical in age to that by Secher et al.111 (45.1 ± 6.9 ky). Moreover, our conclusion has been supported by a recent study38 who presented genomic data from seven ∼15,000-year-old modern humans from Morocco, defined six sub –haplogroup U6 (U6a1b, U6a6b and U6a7), this being the most ancient signal of the back to Africa migration from Eurasia in Africa. They estimated a divergence time of the haplogroup U6 with a value similar to Hervella et al.36 and Secher et al.111
In summary, given the presence of a basal U6 mitogenome in Romania 34 ky BP, the presence of U6 haplotype derived in Northern Africa ̴15ky,38 and the estimated TMRCA for U6 haplogroup, we can support the view that the PM1 mitochondrial lineage of South East Europe is an offshoot that can be traced to the Early Upper Palaeolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified. However, the timing and geographical direction for the spread of the U6 haplotypes, and their association with a back-to-Africa migration, remains poorly understood.
The deep sequencing of the Peștera Muierii 1 woman enabled us to identify a surprising genetic diversity in pre-LGM populations, which brings a new understanding of the early European population of AMH. These data propose a novel paradigm, in which early AMH populations after migration out of Africa were much more diverse than previously believed, and the bottlenecks associated with loss of diversity were caused by glacial climatic periods in northern latitudes. In line with the high diversity observed in EUP genomes, the burden of damaging variants in these individuals was largely the same as in modern-day individuals. This is clearly a different pattern from the high burden of deleterious variants found in small isolated populations,26 which may help us understand the different views of genetic load in humans.21,22,24, 25, 26 However, these ancient high-coverage genomes represent a very small sample size, and it is unclear whether the results can be extrapolated to the entire populations living during these time periods. Finally, using novel methodologies employed in medical genomics, we mined the genomes of ancient individuals for potential pathogenic variants. We have identified several interesting rare variants with medical consequences in the EUP genomes. In the case of other variants identified, such as the AIPL1 (p. (His82Tyr)) described in a sporadic case of Leber congenital amaurosis 4, we propose that they are unlikely to be pathogenic based on insufficient literature evidence. Additionally, one could argue that living completely blind would have been very challenging in the Palaeolithic. However, we also note that care for individuals with congenital disorders or injuries is present in the archaeological record since the Middle Pleistocene,54, 55, 56 and if the variant was verified as causing blindness, we could add another example of early human care for an individual with a severe disorder. This example shows that analysis of ancient genomes can also help in the pathogenicity assessment of rare genetic variants in modern-day patients.
This study opens the door to a new approach to the study of ancient genomes, in which classical population genetics can be combined with medical genomics to draw conclusions about demographics and disease epidemiology. Future research challenges will extend to broaden these medical genetics observations in larger populations, to study patterns of selection in ancient populations, and to directly identify the refugia and human populations from which the hunter-gatherers resurged after the LGM.
Definition of the mitochondrial haplotype of PM1
The mitogenome of PM1 was previously identified as a basal haplogroup U6∗, with a private mutation at position T10517A which had not previously been found in any ancient or modern human.36 Since then U6 has been identified in one more ancient specimen, PM2, the sample originating from the same cave as PM1,14 now also suggested to be related to or the same individual as PM1 (Data S1D). To call a consensus sequence for the mitochondrial genome of PM1, we used mpileup and vcfutils provided by samtools59 requiring mapping and base qualities of at least 30. We reanalyzed the mitogenome from PM1, now at 1492 X coverage, and confirm the same private mutation as previously found (Data S1D).
The Bayesian phylogenetic re-analysis was performed to infer the phylogenetic position of PM1. The best-fit model of evolution was selected using jModeltest 267 under AIC, BIC, and AICc criteria prior to Bayesian analyses. Bayesian analyses were carried out using BEAST 2.68 Two simultaneous runs of 50 million generations were conducted for the datasets and trees were sampled every 1,000 generations, with the first 25% discarded as burn-in. Samples from the posterior were checked for acceptable effective sample sizes (> 200) and the adequate convergence of the MCMC chains was checked using Tracer 1.69
The phylogenetic reanalysis was performed using the complete mitogenomes of 245 modern Homo sapiens, including 61 individuals from the Upper Palaeolithic (15 individuals have been added to the previous analysis in Hervella et al.,36 41 humans from the Neolithic, one individual from the 15th century and 143 modern samples (Data S1E). The modern humans were selected from all the individuals with published mitogenomes and covered the whole phylogenetic diversity within the N hg lineage, with special emphasis in the U lineage. The analysis was carried out using the HKY+G+I substitution model, strict molecular clock and coalescent constant population tree prior, indicating the tip dates of the samples (Figure S2A).
We confirm the basal U6 mitochondrial haplogroup for the PM1 genome as described in Hervella et al.,36 and increase the coverage in 1492X. Our estimates of the haplogroup U6 TMRCA that incorporate ancient genomes (including PM1) set the formation of the U6 lineage back to 49.6 ky BP (95% HPD: 42–58 ky) (using a mutation rate of 2.06∗ 10−8 SD = 1.94 ∗ 10−9). Our estimates are almost identical in age to that by Secher et al.111 (45.1 ± 6.9 ky). Moreover, our conclusion has been supported by a recent study38 who presented genomic data from seven ∼15,000-year-old modern humans from Morocco, defined six sub –haplogroup U6 (U6a1b, U6a6b and U6a7), this being the most ancient signal of the back to Africa migration from Eurasia in Africa. They estimated a divergence time of the haplogroup U6 with a value similar to Hervella et al.36 and Secher et al.111
In summary, given the presence of a basal U6 mitogenome in Romania 34 ky BP, the presence of U6 haplotype derived in Northern Africa ̴15ky,38 and the estimated TMRCA for U6 haplogroup, we can support the view that the PM1 mitochondrial lineage of South East Europe is an offshoot that can be traced to the Early Upper Palaeolithic back migration from Western Asia to North Africa, during which the U6 lineage diversified. However, the timing and geographical direction for the spread of the U6 haplotypes, and their association with a back-to-Africa migration, remains poorly understood.