Genomic signals of migration and continuity in Britain before the Anglo-Saxons

Abstract

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Insular Celtic population structure and genomic footprints of migration

“…In contrast to the west of Ireland, eastern individuals exhibited relative homogeneity; a similar pattern was observed in the PoBI study [7], in which all samples in a large region in To explore this, we estimated the extent of admixture per individual in the Irish dataset from Britain, using samples from the PoBI dataset as a reference [7], along with eighteen ancient British individuals from the Iron Age, Roman and Anglo-Saxon periods in northeast and southeast England [16,17]. Using an unsupervised ADMIXTURE analysis [18], we observed…”

“…To estimate the proportion of British admixture into Irish clusters, ADMIXTURE [18] was run on the combined PoBI and Irish datasets, alongside eighteen ancient individuals from the Iron Age, Roman and Anglo-Saxon periods of northeast and southeast England [16,17].…”

Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph

“…To evaluate whether the improvements seen in the previous section mitigate reference bias in real ancient DNA data, we selected 34 previously published ancient DNA samples (Table 1), including Iron Age, Roman, and Anglo-Saxon period samples shotgun sequenced to low-medium coverage [20,21], high-coverage Yamnaya and Botai culture individuals [22], and target captured samples from South America [23]. These are representative of the different types of data produced in the field of aDNA, as they are of variable genomic coverage, they were generated as part of SNP array target capture or whole-genome shotgun sequencing experiments, and were subject to different enzymatic treatments.…”

“…In order to compare read mapping between vg and bwa, we compiled a dataset of sequencing reads from previously published ancient individuals (Table 1). Adapter trimming was done with AdapterRemoval [29] for [22] and [30] for [20]. Unaligned fastq data from the other two datasets [21,23] were already provided with trimmed adapters.…”

The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods

“…In order to harness the power of haplotype-based methods to investigate substructure in our ancient samples, we imputed missing genotypes in 10 out of 14 ancient Portuguese together with 57 published ancient DNA genomes, choosing those with >0.75X coverage and using the 1000 Genomes phase 3 reference haplotypes [2,3,5,11,[14][15][16][17][18][19][20][21][22].…”