The genetic history of Scandinavia from the Roman Iron Age to the present

Rodríguez-Varela, Ricardo; Moore, Kristjan H. S.; Ebenesersdóttir, S. Sunna; Kılınç, Gülşah Merve; Kjellström, Anna; Papmehl-Dufay, Ludvig; Alfsdotter, Clara; Berglund, Birgitta; Alrawi, Loey; Kashuba, Natalija; Sobrado, Verónica; Lagerholm, Vendela Kempe; Gilbert, Edmund; Cavalleri, Gianpiero L.; Hovig, Eivind; Kockum, Ingrid; Olsson, Tomas; Alfredsson, Lars; Hansen, Thomas; Werge, Thomas; Munters, Arielle R.; Bernhardsson, Carolina; Skår, Birgitte; Christophersen, Axel; Turner‐Walker, Gordon; Gopalakrishnan, Shyam; Daskalaki, Eva; Omrak, Ayça; Pérez-Ramallo, Patxi; Skoglund, Pontus; Gunnarsson, Fredrik; Hedenstierna-Jonson, Charlotte; Gilbert, Martin; Lidén, Kerstin; Jakobsson, Mattias; Einarsson, Lars; Victor, Helena; Krzewińska, Maja; Zachrisson, Torun; Storå, Jan; Stefánsson, Kári; Helgason, Agnar; Götherström, Anders

doi:10.1016/j.cell.2022.11.024

Cited by 14 publications

(22 citation statements)

References 75 publications

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“…This could be due to a lack of statistical power to distinguish these closely related sources with standard methods, as well as through potential biases introduced by using modern surrogate populations that have since been influenced by later gene flow (such as gene flow into Britain). We illustrate this by replicating analyses of Refs 13,44 (Supplementary Figure 7). Similarly, a previous study has suggested the presence of southern European ancestry at sites such as Kärda in southern Sweden 13 .…”

Section: Origins Of Viking Age Mobility Into Scandinaviamentioning

confidence: 82%

“…Previous studies had suggested a major influx of ancestry related to Britain into Viking Age Scandinavia 13,44 . While we detect this ancestry in some individuals (8 individuals in Norway, 12 in Denmark, 8 in Sweden), including some individuals whose ancestry appears to be entirely derived from Iron Age Britain, its overall impact appears reduced compared to previous reports.…”

Section: Origins Of Viking Age Mobility Into Scandinaviamentioning

confidence: 96%

“…We additionally remove 17 individuals that did not have a feasible model in Ref. 44 . Supplementary Figure 8 Ancestry models of Viking Age individuals in Scandinavia a, MDS of each Scandinavian Viking group plotted on top of preceding Iron age and Roman individuals.…”

Section: Clustering Using Qpwavementioning

confidence: 99%

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High-resolution genomic ancestry reveals mobility in early medieval Europe

Speidel,

Silva,

Booth

et al. 2024

Preprint

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Ancient DNA has unlocked new genetic histories and shed light on archaeological and historical questions, but many known and unknown historical events have remained below detection thresholds because subtle ancestry changes are challenging to reconstruct. Methods based on sharing of haplotypes and rare variants can improve power, but are not explicitly temporal and have not been adopted in unbiased ancestry models. Here, we develop Twigstats, a new approach of time-stratified ancestry analysis that can improve statistical power by an order of magnitude by focusing on coalescences in recent times, while remaining unbiased by population-specific drift. We apply this framework to 1,151 available ancient genomes, focussing on northern and central Europe in the historical period, and show that it allows modelling of individual-level ancestry using preceding genomes and provides previously unavailable resolution to detect broader ancestry transformations. In the first half of the first millennium ~1-500 CE (Common Era), we observe an expansion of Scandinavian-related ancestry across western, central, and southern Europe. However, in the second half of the millennium ~500-1000 CE, ancestry patterns suggest the regional disappearance or substantial admixture of these ancestries in multiple regions. Within Scandinavia itself, we document a major ancestry influx by ~800 CE, when a large proportion of Viking Age individuals carried ancestry from groups related to continental Europe. This primarily affected southern Scandinavia, and was differentially represented in the western and eastern directions of the wider Viking world. We infer detailed ancestry portraits integrated with historical, archaeological, and stable isotope evidence, documenting mobility at an individual level. Overall, our results are consistent with substantial mobility in Europe in the early historical period, and suggest that time-stratified ancestry analysis can provide a new lens for genetic history.

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Section: Origins Of Viking Age Mobility Into Scandinaviamentioning

confidence: 82%

Section: Origins Of Viking Age Mobility Into Scandinaviamentioning

confidence: 96%

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High-resolution genomic ancestry reveals mobility in early medieval Europe

Speidel,

Silva,

Booth

et al. 2024

Preprint

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“…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][10][11][12].…”

Section: Continental European Ancestry In Irish and British Communitiesmentioning

confidence: 99%

A genetic perspective on the recent demographic history of Ireland and Britain

Shanmugam,

Merrigan,

O’Reilly

et al. 2024

Preprint

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BackgroundWhile subtle yet discrete clusters of genetic identity across Ireland and Britain have been identified, their demographic history is unclear.MethodsUsing 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.ResultsThrough 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.ConclusionsUsing 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.

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“…The data analysed in this study was obtained from the following archive study accessions: PRJEB54831 (ENA) 8 , PRJEB51180 (ENA) 9 , PRJCA005576 (GSA) 10 , PRJEB52849 (ENA) 11 , PRJEB42656 (ENA) 12 , PRJEB52230 (ENA) 13 , PRJNA786530 (SRA) 14 , PRJNA1005336 (SRA) 15 , PRJEB51440 (ENA) 16 , PRJEB56773 (ENA) 17 , PRJEB49291 (ENA) 18 , PRJEB42781 (ENA) 19 , PRJEB46734 (ENA) 20 , PRJNA798381 (SRA) 21 , PRJEB42269 (ENA) 22 , PRJEB47891 (ENA) 23 , PRJEB54899 (ENA) 24 , PRJEB43715 (ENA) 25 , PRJEB39134 (ENA) 26 , PRJEB46162 (ENA) 27 , PRJEB46875 (ENA) 28 , PRJEB44430 (ENA) 29 , PRJEB42199 (ENA) 30 , PRJEB38555 (ENA) 31 , PRJEB55327 (ENA) 32 , PRJEB56213 (ENA) 33 , PRJEB51862 (ENA) 34 , PRJEB58698 (ENA) 35 , PRJEB62503 (ENA) 36 , PRJEB66319 (ENA) 37 , PRJEB59008 (ENA) 38 , PRJEB61818 (ENA) 39 , PRJEB50368 (ENA) 40 , PRJEB50857 (ENA) 41 , PRJCA003870 (GSA) 42 , PRJCA003699 (GSA) 43 , PRJEB53475 (ENA) 44 , PRJEB37782 (ENA) 45 , PRJNA687817 (SRA) 46 , PRJEB42372 (ENA) 47 , PRJEB66422 (ENA) 48 , PRJEB57364 (ENA) 49 .…”

Section: Data Availabilitymentioning

confidence: 99%

Improving data archiving practices in ancient genomics

Bergström

2023

Preprint

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The sequencing of ancient DNA from preserved biological remains is producing a rich record of past genetic diversity in humans and other species. However, unless the primary data is made available in public archives in an appropriate fashion, its long-term value will not be fully realised. I surveyed publicly archived data from 28 recent ancient genomics studies. I found that half of the studies archived incomplete subsets of the generated genomic data, preventing accurate replication and representing a loss of data of potential use for future research. None of the studies met all archiving criteria that could be considered best practice. Based on these results, I make six recommendations for data producers: 1) archive all sequencing reads, not just those that can be aligned to a reference genome, 2) archive read alignments as well, but as secondary analysis files linked to the underlying raw read files, 3) provide correct experiment metadata on how samples, libraries and sequencing runs relate to each other, 4) provide informative sample metadata in the public archives, 5) publish and archive data from screening, low-coverage, poorly performing and negative experiments, and 6) review data archiving as part of peer review processes. Given the reliance on destructive sampling of finite material, I argue that ancient genomics studies have a particularly strong responsibility to ensure the longevity and reusability of generated data.

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The genetic history of Scandinavia from the Roman Iron Age to the present

Cited by 14 publications

References 75 publications

High-resolution genomic ancestry reveals mobility in early medieval Europe

High-resolution genomic ancestry reveals mobility in early medieval Europe

A genetic perspective on the recent demographic history of Ireland and Britain

Improving data archiving practices in ancient genomics

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