Grace O'Malley
06-12-2024, 07:42 AM
This new paper a pre-print is just out a couple of months ago. There is quite a bit in this paper and it will take a few readings to pick up some of the findings. There is quite a bit about about each of the different Isles populations and some of the findings are the same as previous i.e. the most isolated community in both Britain and Ireland are the Orkneys, Manx and Welsh.
ABSTRACT
Background While subtle yet discrete clusters of genetic identity across Ireland and Britain have been identified, their demographic history is unclear.
Methods Using genotype data from 6,574 individuals with associated regional Irish or British ancestry, we identified Irish-like and British-like genetic communities using network community detection. We segregated Identity-by-Descent (IBD) and Runs-of-Homozygosity (ROH) segments by length and approximated their corresponding time periods. Through this, we inferred the regional Irish and British demographic histories in these time periods by (1) estimating genetic relatedness between communities, (2) estimating changes in effective population sizes, (3) inferring recent migration rates across Ireland and Britain, and (4) estimating changing affinities to regional European populations. For a subset of the Irish communities, we determined the enrichment/depletion of surnames within the genetic communities.
Results Through patterns of IBD-sharing and ROH, we find evidence of recent population bottlenecks in the Orcadian, Manx and Welsh communities. While the structure in Ireland is subtler, the communities share relatively more IBD segments that are shorter in length, and the genetic differences between the Irish communities are more subtle on average, when compared to the British communities. Regional effective population size trajectories indicate a similar demographic history throughout the island of Ireland. Further, we observe a stable migration corridor between north-east Ireland and south-west Scotland while there is a recent migration barrier between South-Eastern Ireland and Western Ireland. We observed an enrichment of Anglo-Norman and English surnames in the Wexford community while within the West Ulster-Argyll community, we saw an enrichment of Gallowglass and Scottish surnames.
Conclusions Using well-annotated Irish and British reference genotypes, we observed temporal changes in genetic affinities within and between genetic communities in Ireland and Britain. In addition, using effective population size estimates and levels of haplotype-sharing, we detected varying degrees of genetic isolation in some Irish and British genetic communities across time. Using these new insights into the regional demographic history of Ireland and Britain across different time periods, we hope to understand the driving forces of rare allele frequencies and disease risk association within these populations.
https://www.biorxiv.org/content/10.1101/2024.03.08.584042v1.full.pdf
Also interesting is the section on European ancestry contributions to British and Irish.
Continental European ancestry in Irish and British communities
We also looked into the European ancestry contributions to our genetic communities across time using PCA of European IBD sharing (Fig. 6 and Supplemental Table S8) to complement the previous results. In the oldest [1,3cM) IBD bin, we observe that English genetic groups separate out from Irish communities on axes driven by Germanic-Swedish-Norwegian ancestries. Scottish/Northern Irish communities demonstrate more Swedish influence while there appears to be strong North and North-Western Norwegian influence in the Manx and Orcadian groups (Fig. 6a and Supplemental Fig.9-12a-c). In the recent-history bin (>5cM) however, there appears to be more of a West-Germany ancestry signal in the English communities while there is more of a Swedish-Finnish-Norwegian component in the Scottish groups. The Norwegian signal persists in the Manx and Orcadian groups (Fig. 6b and Supplemental Fig.9-12a-c).
Focussing on the contributions of European ancestry to Ireland over time, we find a strong signal from north Norway and western France and to a lesser extent from Sweden in the Irish communities in the [1-3cM) IBD bin (Supplemental Figs. 9-12). There appears to be a more recent contribution of ancestry in the [3,5cM) IBD bin from North-North-West Norway and Sweden in Ireland, specifically in the W.Leinster community (Supplemental Figs. 9-12).
By estimating contributions of European ancestries in the Irish and British genetic communities across timescales, we found evidence of gene flow between Scandinavia and the English, Scottish and Irish groups in the smaller IBD bins but across all IBD bins within the Orcadian and Manx communities. We also detected an affinity between modern populations in northwest Germany and the English communities in the smaller IBD bins, consistent with the influence of Germanic migrants in the Migration Period in the region. Further, by separating out signals of sharing with European groups, extending previous findings using haplotype “painting” of chromosomes, we shed light on the changing landscape of European affinity across the islands. This particular analysis touches again upon the question of the genetic legacy of Norse Viking activity on the modern Irish genetic landscape. We observed a higher similarity between Irish genetic communities and modern Norwegian haplotypes in smaller IBD segment
bins that is concurrent to the signal in Orkney and the Isle of Man and consistent with a Norse-Viking origin. Recent work with ancient DNA in Scandinavia has demonstrated significant gene flow from Ireland and the British Isles into Viking-era Scandinavia9,10 including the regions of Norway previously shown to have an excess sharing in Ireland3,8. Our results here are consistent with an inflation of present-day Norwegian sharing to present day Ireland due to this historical Irish gene flow to Viking-era Norway.
As this is done with IBD I think it is more reliable than previous studies.
ABSTRACT
Background While subtle yet discrete clusters of genetic identity across Ireland and Britain have been identified, their demographic history is unclear.
Methods Using genotype data from 6,574 individuals with associated regional Irish or British ancestry, we identified Irish-like and British-like genetic communities using network community detection. We segregated Identity-by-Descent (IBD) and Runs-of-Homozygosity (ROH) segments by length and approximated their corresponding time periods. Through this, we inferred the regional Irish and British demographic histories in these time periods by (1) estimating genetic relatedness between communities, (2) estimating changes in effective population sizes, (3) inferring recent migration rates across Ireland and Britain, and (4) estimating changing affinities to regional European populations. For a subset of the Irish communities, we determined the enrichment/depletion of surnames within the genetic communities.
Results Through patterns of IBD-sharing and ROH, we find evidence of recent population bottlenecks in the Orcadian, Manx and Welsh communities. While the structure in Ireland is subtler, the communities share relatively more IBD segments that are shorter in length, and the genetic differences between the Irish communities are more subtle on average, when compared to the British communities. Regional effective population size trajectories indicate a similar demographic history throughout the island of Ireland. Further, we observe a stable migration corridor between north-east Ireland and south-west Scotland while there is a recent migration barrier between South-Eastern Ireland and Western Ireland. We observed an enrichment of Anglo-Norman and English surnames in the Wexford community while within the West Ulster-Argyll community, we saw an enrichment of Gallowglass and Scottish surnames.
Conclusions Using well-annotated Irish and British reference genotypes, we observed temporal changes in genetic affinities within and between genetic communities in Ireland and Britain. In addition, using effective population size estimates and levels of haplotype-sharing, we detected varying degrees of genetic isolation in some Irish and British genetic communities across time. Using these new insights into the regional demographic history of Ireland and Britain across different time periods, we hope to understand the driving forces of rare allele frequencies and disease risk association within these populations.
https://www.biorxiv.org/content/10.1101/2024.03.08.584042v1.full.pdf
Also interesting is the section on European ancestry contributions to British and Irish.
Continental European ancestry in Irish and British communities
We also looked into the European ancestry contributions to our genetic communities across time using PCA of European IBD sharing (Fig. 6 and Supplemental Table S8) to complement the previous results. In the oldest [1,3cM) IBD bin, we observe that English genetic groups separate out from Irish communities on axes driven by Germanic-Swedish-Norwegian ancestries. Scottish/Northern Irish communities demonstrate more Swedish influence while there appears to be strong North and North-Western Norwegian influence in the Manx and Orcadian groups (Fig. 6a and Supplemental Fig.9-12a-c). In the recent-history bin (>5cM) however, there appears to be more of a West-Germany ancestry signal in the English communities while there is more of a Swedish-Finnish-Norwegian component in the Scottish groups. The Norwegian signal persists in the Manx and Orcadian groups (Fig. 6b and Supplemental Fig.9-12a-c).
Focussing on the contributions of European ancestry to Ireland over time, we find a strong signal from north Norway and western France and to a lesser extent from Sweden in the Irish communities in the [1-3cM) IBD bin (Supplemental Figs. 9-12). There appears to be a more recent contribution of ancestry in the [3,5cM) IBD bin from North-North-West Norway and Sweden in Ireland, specifically in the W.Leinster community (Supplemental Figs. 9-12).
By estimating contributions of European ancestries in the Irish and British genetic communities across timescales, we found evidence of gene flow between Scandinavia and the English, Scottish and Irish groups in the smaller IBD bins but across all IBD bins within the Orcadian and Manx communities. We also detected an affinity between modern populations in northwest Germany and the English communities in the smaller IBD bins, consistent with the influence of Germanic migrants in the Migration Period in the region. Further, by separating out signals of sharing with European groups, extending previous findings using haplotype “painting” of chromosomes, we shed light on the changing landscape of European affinity across the islands. This particular analysis touches again upon the question of the genetic legacy of Norse Viking activity on the modern Irish genetic landscape. We observed a higher similarity between Irish genetic communities and modern Norwegian haplotypes in smaller IBD segment
bins that is concurrent to the signal in Orkney and the Isle of Man and consistent with a Norse-Viking origin. Recent work with ancient DNA in Scandinavia has demonstrated significant gene flow from Ireland and the British Isles into Viking-era Scandinavia9,10 including the regions of Norway previously shown to have an excess sharing in Ireland3,8. Our results here are consistent with an inflation of present-day Norwegian sharing to present day Ireland due to this historical Irish gene flow to Viking-era Norway.
As this is done with IBD I think it is more reliable than previous studies.