Genes mirror geography in the British Isles.

<p>(A) fineSTRUCTURE clustering dendrogram for combined Irish and British data. Data principally split into Irish and British groups before subdividing into a total of 50 distinct clusters, which are combined into cluster groups for clusters that formed clades in the dendrogram, overlapped in principal component space (B) and were sampled from regions that are geographically contiguous. Names and labels follow the geographical provenance for the majority of data within the cluster group. Details for each cluster in the dendrogram are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s002" target="_blank">S2 Fig</a>. (B) Principal component analysis (PCA) of haplotypic similarity based on the ChromoPainter coancestry matrix, coloured by cluster group with their median locations labelled. We have chosen to present PC1 versus PC4 here as these components capture new information regarding correlation between haplotypic variation across Britain and Ireland and geography, while PC2 and PC3 (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.g004" target="_blank">Fig 4</a>) capture previously reported splitting for Orkney and Wales, respectively, from Britain [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.ref007" target="_blank">7</a>]. A map of Ireland and Britain is shown for comparison, coloured by sampling regions for cluster groups, the boundaries of which are defined based on the Nomenclature of Territorial Units for Statistics (NUTS 2010), with some regions combined. Sampling regions are coloured by the cluster group with the majority presence in the sampling region; some sampling regions have significant minority cluster group representations as well, for example the Northern Ireland sampling region (UKN0; NUTS 2010) is majorly explained by the NICS cluster group but also has significant representation from the NLU cluster group. The PCA plot has been rotated clockwise by 5 degrees to highlight its similarity with the geographical map of the Ireland and Britain. NI, Northern Ireland; PC, principal component. Cluster groups that share names with groups from <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.g001" target="_blank">Fig 1</a> (NLU; SMN; CLN; CNN) have an average of 80% of their samples shared with the initial cluster groups. The map and administrative boundaries were produced using data from the database of Global Administrative Areas (GADM; <a href="https://gadm.org/" target="_blank">https://gadm.org</a>), note some boundaries have been subsumed or modified to better reflect sampling regions.</p

Principal components 2 and 3 of combined Irish and British coancestry matrix.

<p>(<b>A</b>) fineSTRUCTURE clustering dendrogram for combined Irish and British data, with cluster groups defined as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.g002" target="_blank">Fig 2</a>. Immediately following the principal inter-island split, Orkney and Wales branch in sequence, consistent with previous observations. (<b>B</b>) Principal component analysis (PCA) of haplotypic similarity based on the ChromoPainter coancestry matrix, coloured by cluster group with their median locations labelled. PC2 captures an Orkney split, while PC3 captures a Welsh split.</p

All-Ireland GLOBETROTTER admixture date estimates for European and British surrogate admixing populations.

<p>A summary of the date estimates and 95% confidence intervals for inferred admixture events into Ireland from European and British admixing sources is shown in (<b>A</b>), with ancestry proportion estimates for each historical source population for the two events and example coancestry curves shown in (<b>B</b>). In the coancestry curves <i>Relative joint probability</i> estimates the pairwise probability that two haplotype chunks separated by a given genetic distance come from the two modelled source populations respectively (i.e. FRA(8) and NOR-SG); if a single admixture event occurred, these curves are expected to decay exponentially at a rate corresponding to the number of generations since the event. The green fitted line describes this GLOBETROTTER fitted exponential decay for the coancestry curve. If the sources come from the same ancestral group the slope of this curve will be negative (as with FRA(8) vs FRA(8)), while a positive slope indicates that sources come from different admixing groups (as with FRA(8) vs NOR-SG). The adjacent bar plot shows the inferred genetic composition of the historical admixing sources modelled as a mixture of the sampled modern populations. A European admixture event was estimated by GLOBETROTTER corresponding to the historical record of the Viking age, with major contributions from sources similar to modern Scandinavians and northern Europeans and minor contributions from southern European-like sources. For admixture date estimates from British-like sources the influence of the Norman settlement and the Plantations could not be disentangled, with the point estimate date for admixture falling between these two eras and GLOBETROTTER unable to adequately resolve source and proportion details of admixture event (fit quality FQ_B< 0.985). The relative noise of the coancestry curves reflects the uncertainty of the British event. Cluster labels (for the European clustering dendrogram, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s004" target="_blank">S4 Fig</a>; for the PoBI clustering dendrogram, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s003" target="_blank">S3 Fig</a>): FRA(8), France cluster 8; NOR-SG, Norway, with significant minor representations from Sweden and Germany; SE_ENG, southeast England; N_SCOT(4) northern Scotland cluster 4.</p

Fine-grained population structure in Ireland.

<p>(<b>A</b>) fineSTRUCTURE clustering dendrogram for 1,035 Irish individuals. Twenty-three clusters are defined, which are combined into cluster groups for clusters that are neighbouring in the dendrogram, overlapping in principal component space (B) and sampled from regions that are geographically contiguous. Details for each cluster in the dendrogram are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s001" target="_blank">S1 Fig</a>. (<b>B</b>) Principal components analysis (PCA) of haplotypic similarity, based on ChromoPainter coancestry matrix for Irish individuals. Points are coloured according to cluster groups defined in (A); the median location of each cluster group is plotted. (<b>C</b>) Map of Ireland showing the sampling location for a subset of 588 individuals analysed in (A) and (B), coloured by cluster group. Points have been randomly jittered within a radius of 5 km to preserve anonymity. Precise sampling location for 44 Northern Irish individuals from the People of the British Isles dataset was unknown; these individuals are plotted geometrically in a circle. The map and administrative boundaries were produced using data from the database of Global Administrative Areas (GADM; <a href="https://gadm.org/" target="_blank">https://gadm.org</a>). (<b>D</b>) “British admixture component” (ADMIXTURE estimates; k = 2) for Irish cluster groups. This component has the largest contribution in ancient Anglo-Saxons and the SEE cluster. (<b>E</b>) Linear regression of principal component 2 (B) versus British admixture component (r² = 0.43; p < 2×10⁻¹⁶). Points are coloured by cluster group. (Standard error for ADMIXTURE point estimates presented in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.s011" target="_blank">S11 Fig</a>.).</p

Inter-island exchange of haplotypes between the north of Ireland and northern Britain.

<p>The boxplots show the distribution of individuals on principal component (PC) 1 for each island and for specific sampling regions (Scotland/Northern Ireland) and cluster groups (SSC and NICS; see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.g002" target="_blank">Fig 2</a>). A substantial proportion of Northern Irish individuals fall within the expected range for Scottish individuals in PC space and <i>vice versa</i>. This exchange is particularly pronounced for Northern Irish and Scottish individuals that fall within the NICS and SSC cluster groups (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007152#pgen.1007152.g002" target="_blank">Fig 2</a>), respectively.</p

Patterns of hunter-gatherer haplotype donation to ancient Eurasians.

<p>This was estimated by subtracting the vector of haplotype donation of Hungarian HG from a vector of hunter-gatherer X, where X = {LaBrana, Bichon, Loschbour}. Legend: E—Early; M—Middle; L—Late; N—Neolithic; PT—Portugal; SP—Spain. Note: HG individuals were removed from the tree.</p

CHROMOPAINTER/fineSTRUCTURE analysis.

<p><b>(A)</b> PCA estimated from the CHROMOPAINTER coancestry matrix of 67 ancient samples ranging from the Paleolithic to the Anglo-Saxon period. The samples belonging to each one of the 19 populations identified with fineSTRUCTURE are connected by a dashed line. Samples are placed geographically in 3 panels (with random jitter for visual purposes): <b>(B)</b> Hunter-gatherers; (<b>C)</b> Neolithic Farmers (including Ötzi) and (<b>D)</b> Copper Age to Anglo-Saxon samples. The Portuguese Bronze Age samples (D, labelled in red) formed a distinct population (<i>Portuguese_BronzeAge</i>), while the Middle and Late Neolithic samples from Portugal clustered with Spanish, Irish and Scandinavian Neolithic farmers, which are termed “<i>Atlantic_Neolithic</i>” (C, in green).</p

Total variation distance between vectors of median haplotype donation from Bronze Age (purple) and Neolithic (green) samples from different regions in Europe to modern populations.

<p>Circle size varies according to the absolute difference between Neolithic and Bronze Age samples in terms of the number of haplotypes donated to present day populations. Regardless of the geographical locations of the ancient samples, Neolithic samples tend to donate comparatively more haplotypes to Southern populations, while Bronze Age show the opposite pattern, with an excess of haplotype contribution to Northern Europeans. This pattern is present, but distinctly weaker in the Portuguese Neolithic-Bronze Age comparison.</p

ADMIXTURE analysis of 1941 modern and 176 ancient individuals. Selected profiles of 227 ancient samples, alongside individuals from nine present-day Eurasian populations are displayed here for K = 10 ancestral clusters.

<p>Individuals are ordered within a grid, partitioned by approximate time period and geographic region. Where possible, ancient individuals have been grouped under common population labels, based on archaeological context. For populations containing three or less individuals, bar plots have been narrowed, leaving empty space within the grid box. Samples from the current study are highlighted in bold.</p

Extended haplotype homozygosity in regions under selection.

<p>Panels on the left represent the decay of EHH, or the probability of homozygosity at a certain base across 2 randomly chosen chromosomes in a population. Plots on the right represent existing haplotypes in a population, with the lower portion of the graph depicting haplotypes with the derived allele (red) and the upper part showing haplotypes carrying the ancestral allele (blue). Unique haplotypes in a population are not represented. Legend: CEU—Utah Residents (CEPH) with Northern and Western Ancestry; YRI—Yoruba in Ibadan, Nigeria; CHB—Han Chinese in Beijing, China; 1KG: 1000 Genomes Project. * Earliest appearance of the homozygous derived allele in the samples analysed.</p