Angela
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Another new paper on British genomics:
Iron Age and Anglo-Saxon genomes from East England reveal British migration history
http://www.nature.com/ncomms/2016/160119/ncomms10408/full/ncomms10408.html
"British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain."
This is the paper and the samples that resulted in quite a kerfuffle when we tried to analyze them.
They give an estimate of 38% for Anglo-Saxon admixture into eastern England. Leslie et al gave 35%, yes? So, it's virtually the same.
For more nuance:
"By this measure the East England samples are consistent with 38% Anglo-Saxon ancestry on average, with a large spread from 25 to 50%, and the Welsh and Scottish samples are consistent with 30% Anglo-Saxon ancestry on average, again with a large spread (Supplementary Table 4). These numbers are lower on average if we exclude the low-coverage individual HS3 from the Anglo-Saxon group (35% for East English samples). A similar result is obtained when we analyse modern British samples from the 1,000 Genomes Project, which exhibit a strong substructure (Supplementary Note 4, Supplementary Fig. 4). We find that samples from Kent show a similar Anglo-Saxon component of 37% when compared against Finnish and Spanish outgroups, with a lower value for samples from Cornwall (Supplementary Fig. 5a, Supplementary Table 4)."
"An alternative and potentially more direct approach to estimate these fractions is to measure rare allele sharing directly between the modern British and the ancient samples. While being much noisier than the analysis using Dutch and Spanish outgroups, this yields consistent results (Supplementary Fig. 5b, Supplementary Note 3). In summary, this analysis suggests that on average 25–40% of the ancestry of modern Britons was contributed by Anglo-Saxon immigrants, with the higher number in East England closer to the immigrant source. The difference between groups within Britain is surprisingly small compared with the large differences seen in the ancient samples. This is true for both the UK10K samples and for the British samples from the 1,000 Genomes project, although we note that the UK10K sample locations may not fully reflect historical geographical population structure because of recent population mixing."
"There are striking differences in the sharing patterns of the samples, illustrated by the ratio of the number of rare alleles shared with Dutch individuals to the number shared with Spanish individuals (Fig. 2a). The middle Anglo-Saxon samples from Hinxton (HS1, HS2 and HS3) share relatively more rare variants with modern Dutch than the Iron Age samples from Hinxton (HI1 and HI2) and Linton (L). The early Anglo-Saxon samples from Oakington are more diverse with O1 and O2 being closer to the middle Anglo-Saxon samples, O4 exhibiting the same pattern as the Iron Age samples, and O3 showing an intermediate level of allele sharing, suggesting mixed ancestry."
"The ancient samples fall within the range of modern English and Scottish samples, with the Iron Age samples from Hinxton and Linton falling closer to modern English and French samples, whereas most Anglo-Saxon era samples are closer to modern Scottish and Norwegian samples. Overall, though, population genetic differences between these samples at common alleles are small."
Iron Age and Anglo-Saxon genomes from East England reveal British migration history
http://www.nature.com/ncomms/2016/160119/ncomms10408/full/ncomms10408.html
"British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain."
This is the paper and the samples that resulted in quite a kerfuffle when we tried to analyze them.
They give an estimate of 38% for Anglo-Saxon admixture into eastern England. Leslie et al gave 35%, yes? So, it's virtually the same.
For more nuance:
"By this measure the East England samples are consistent with 38% Anglo-Saxon ancestry on average, with a large spread from 25 to 50%, and the Welsh and Scottish samples are consistent with 30% Anglo-Saxon ancestry on average, again with a large spread (Supplementary Table 4). These numbers are lower on average if we exclude the low-coverage individual HS3 from the Anglo-Saxon group (35% for East English samples). A similar result is obtained when we analyse modern British samples from the 1,000 Genomes Project, which exhibit a strong substructure (Supplementary Note 4, Supplementary Fig. 4). We find that samples from Kent show a similar Anglo-Saxon component of 37% when compared against Finnish and Spanish outgroups, with a lower value for samples from Cornwall (Supplementary Fig. 5a, Supplementary Table 4)."
"An alternative and potentially more direct approach to estimate these fractions is to measure rare allele sharing directly between the modern British and the ancient samples. While being much noisier than the analysis using Dutch and Spanish outgroups, this yields consistent results (Supplementary Fig. 5b, Supplementary Note 3). In summary, this analysis suggests that on average 25–40% of the ancestry of modern Britons was contributed by Anglo-Saxon immigrants, with the higher number in East England closer to the immigrant source. The difference between groups within Britain is surprisingly small compared with the large differences seen in the ancient samples. This is true for both the UK10K samples and for the British samples from the 1,000 Genomes project, although we note that the UK10K sample locations may not fully reflect historical geographical population structure because of recent population mixing."
"There are striking differences in the sharing patterns of the samples, illustrated by the ratio of the number of rare alleles shared with Dutch individuals to the number shared with Spanish individuals (Fig. 2a). The middle Anglo-Saxon samples from Hinxton (HS1, HS2 and HS3) share relatively more rare variants with modern Dutch than the Iron Age samples from Hinxton (HI1 and HI2) and Linton (L). The early Anglo-Saxon samples from Oakington are more diverse with O1 and O2 being closer to the middle Anglo-Saxon samples, O4 exhibiting the same pattern as the Iron Age samples, and O3 showing an intermediate level of allele sharing, suggesting mixed ancestry."
"The ancient samples fall within the range of modern English and Scottish samples, with the Iron Age samples from Hinxton and Linton falling closer to modern English and French samples, whereas most Anglo-Saxon era samples are closer to modern Scottish and Norwegian samples. Overall, though, population genetic differences between these samples at common alleles are small."