Angela
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"A unified genealogy of modern and ancientgenomes"
Anthony Wilder Wohns1,2,*, Yan Wong1, Ben Jeffery1, AliAkbari2,3,6, Swapan Mallick2,4, Ron Pinhasi5, Nick Patterson2,3,4,6,David Reich2,3,4,6, Jerome Kelleher1,+, and Gil McVean
https://www.biorxiv.org/content/10.1101/2021.02.16.431497v1.full.pdf
All the big labs got together for this. So far, the analysis doesn't change the big picture, but there "are" changes.
"The sequencing of modern and ancient genomes from around the world hasrevolutionised our understanding of human history and evolution1,2. However,the general problem of how best to characterise the full complexity of ancestralrelationships from the totality of human genomic variation remains unsolved.Patterns of variation in each data set are typically analysed independently, andoften using parametric models or data reduction techniques that cannot capture the full complexity of human ancestry3,4. Moreover, variation in sequencingtechnology5,6, data quality7 and in silico processing8,9, coupled with complexities of data scale10, limit the ability to integrate data sources. Here, we introducea non-parametric approach to inferring human genealogical history that overcomes many of these challenges and enables us to build the largest genealogyof both modern and ancient humans yet constructed. The genealogy providesa lossless and compact representation of multiple datasets, addresses the challenges of missing and erroneous data, and benefits from using ancient samplesto constrain and date relationships. Using simulations and empirical analyses,we demonstrate the power of the method to recover relationships between individuals and populations, as well as to identify descendants of ancient samples.Finally, we show how applying a simple nonparametric estimator of ancestor geographical location to the inferred genealogy recapitulates key events in humanhistory. Our results demonstrate that whole-genome genealogies are a powerful means of synthesising genetic data and provide rich insights into humanevolution."
The real meat is going to be in the Supplements, but here is one nugget: the paper includes four new high coverage genomes from Afanasievo.
"For the Afanasievo family, we find the greatest amount of descent from theirproxy ancestral haplotypes among individuals in Western Eurasia and SouthAsia (Extended Data Fig. 6a), consistent with findings from the geneticallysimilar Yamnaya peoples36. Notably, the most frequent descendant blocks inExtended Data Fig. 6b all contain geographically disparate modern samples.These cosmopolitan patterns of descent support a contemporaneous diffusion ofAfanasievo-like genetic material via multiple routes36."
Anthony Wilder Wohns1,2,*, Yan Wong1, Ben Jeffery1, AliAkbari2,3,6, Swapan Mallick2,4, Ron Pinhasi5, Nick Patterson2,3,4,6,David Reich2,3,4,6, Jerome Kelleher1,+, and Gil McVean
https://www.biorxiv.org/content/10.1101/2021.02.16.431497v1.full.pdf
All the big labs got together for this. So far, the analysis doesn't change the big picture, but there "are" changes.
"The sequencing of modern and ancient genomes from around the world hasrevolutionised our understanding of human history and evolution1,2. However,the general problem of how best to characterise the full complexity of ancestralrelationships from the totality of human genomic variation remains unsolved.Patterns of variation in each data set are typically analysed independently, andoften using parametric models or data reduction techniques that cannot capture the full complexity of human ancestry3,4. Moreover, variation in sequencingtechnology5,6, data quality7 and in silico processing8,9, coupled with complexities of data scale10, limit the ability to integrate data sources. Here, we introducea non-parametric approach to inferring human genealogical history that overcomes many of these challenges and enables us to build the largest genealogyof both modern and ancient humans yet constructed. The genealogy providesa lossless and compact representation of multiple datasets, addresses the challenges of missing and erroneous data, and benefits from using ancient samplesto constrain and date relationships. Using simulations and empirical analyses,we demonstrate the power of the method to recover relationships between individuals and populations, as well as to identify descendants of ancient samples.Finally, we show how applying a simple nonparametric estimator of ancestor geographical location to the inferred genealogy recapitulates key events in humanhistory. Our results demonstrate that whole-genome genealogies are a powerful means of synthesising genetic data and provide rich insights into humanevolution."
The real meat is going to be in the Supplements, but here is one nugget: the paper includes four new high coverage genomes from Afanasievo.
"For the Afanasievo family, we find the greatest amount of descent from theirproxy ancestral haplotypes among individuals in Western Eurasia and SouthAsia (Extended Data Fig. 6a), consistent with findings from the geneticallysimilar Yamnaya peoples36. Notably, the most frequent descendant blocks inExtended Data Fig. 6b all contain geographically disparate modern samples.These cosmopolitan patterns of descent support a contemporaneous diffusion ofAfanasievo-like genetic material via multiple routes36."