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Iron Age and Anglo-Saxon Genomes From East England Reveal British Migration History

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Iron Age and Anglo-Saxon Genomes From East England Reveal British Migration History

Stephan Schiffels et al. Nat Commun.

Abstract

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.

Figures

Figure 1
Figure 1. Geographic and temporal context of the samples used in this study.
(a) Anglo-Saxon migration routes of people from the continental coast, as reconstructed from historical and archaeological sources. (b) The ancient samples used in this study were excavated at three archaeological sites in East England: Hinxton, Oakington and Linton. The towns Cambridge and Saffron Walden are also shown (black circles). Background green/brown shades indicate altitude. The colours of the four sample match the ones in c and Fig. 2. (c) The 10 ancient samples belong to three age groups. The sample from Linton and two samples from Hinxton are from the late Iron Age, the four Oakington samples from the early Anglo-Saxon period and three Hinxton samples are from the middle Anglo-Saxon period.
Figure 2
Figure 2. Relative rare allele sharing between ancient and modern samples.
(a) The ratio of the numbers of rare alleles shared with modern Dutch and Spanish samples as a function of the allele count in the set of modern samples. Ancient sample codes (left-hand and middle sections) are defined in Table 1. Results from present-day British individuals (right hand panel) are averaged over 10 individuals from each subpopulation. Results from a Dutch and a Spanish individual are shown for comparison. Error bars are calculated from raw count statistics and using s.e. propagation (Methods section). (b) The relative fraction of rare alleles shared with modern Dutch compared with Spanish alleles, integrated up to allele count five in the modern samples. Iron Age and Anglo-Saxon samples mark the two extremes on this projection, while modern samples are spread between them, indicating mixed levels of Anglo-Saxon ancestry, which is on average higher in East England than in Wales and Scotland, with a large overlap. Two Early Anglo-Saxon samples from Oakington have been excluded from computing the average, indicated by empty circles, because they show evidence for being admixed (O3) or of non-immigrant ancestry (O4). One modern sample from Scotland is also excluded, indidated as empty circle because it is a clear outlier with respect to all other Scottish samples. Samples are shown with a random vertical offset for better clarity. Error bars (Methods section) for the modern samples are omitted here, but of the same order of magnitude as for the ancient samples. Data for this figure is available as Supplementary Data 1.
Figure 3
Figure 3. Modelling European history with rarecoal.
(a) Rarecoal tracks the probabilities for the lineages of rare alleles (red) within a coalescent framework back in time, and approximates the distribution of non-derived alleles (dark blue) by its average. (b) By optimizing the likelihood of the data under the model, we can estimate population sizes and split times. Tested with simulated data, the estimates closely match the true values (in parentheses). (c) Applied to hundreds of European individuals, rarecoal estimates split times as indicated on the time axis and population sizes for each branch. (d) Same as c, but using samples from Kent instead of Cornwall as a proxy for the British population. The different tree topology between c and d reflects different population histories in Cornwall compared with Kent in the South of England.
Figure 4
Figure 4. Placing ancient samples into the European tree.
Given the European tree with Cornwall as British population branch, we map ancient samples onto this tree. We colour each point in the tree according to the likelihood that the ancestral branch of the ancient sample merges at that point. The maximum likelihood merge point is marked by a black circle. The analysis shows that Iron Age samples L, HI1 and HI2 have highest likelihood to merge onto the ancestral branch of all Northern European populations analysed, whereas the Anglo-Saxon samples merge into the Dutch and Danish branches, respectively. The low coverage samples L, HI1 and HS3 have the biggest spread in likelihood, but are consistent with the higher coverage samples.

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