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

The authors acknowledge support from the National Genomics Infrastructure in Stockholm funded by Science for Life Laboratory, the Knut and Alice Wallenberg Foundation and the Swedish Research Council, and SNIC/Uppsala Multidisciplinary Center for Advanced Computational Science for assistance with massively parallel sequencing and access to the UPPMAX computational infrastructure. We used resources from projects SNIC 2022/23-132, SNIC 2022/22-117, SNIC 2022/23-163, SNIC 2022/22-299, and SNIC 2021-2-17. This research was supported by the Swedish Research Council project ID 2019-00849_VR and ATLAS (Riksbankens Jubileumsfond). Part of the modern dataset was supported by a research grant from Science Foundation Ireland (SFI), grant number 16/RC/3948, and co-funded under the European Regional Development Fund and by FutureNeuro industry partners.Peer reviewedPublisher PD

The population genomic legacy of the second plague pandemic

Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.1 It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).2 Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17th-19th century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics

Author Correction: The Anglo-Saxon migration and the formation of the early English gene pool.

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The Anglo-Saxon migration and the formation of the early English gene pool

The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2,3,4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans—including 278 individuals from England—alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6

The Y-chromosome point mutation rate in humans.

Mutations are the fundamental source of biological variation, and their rate is a crucial parameter for evolutionary and medical studies. Here we used whole-genome sequence data from 753 Icelandic males, grouped into 274 patrilines, to estimate the point mutation rate for 21.3 Mb of male-specific Y chromosome (MSY) sequence, on the basis of 1,365 meioses (47,123 years). The combined mutation rate for 15.2 Mb of X-degenerate (XDG), X-transposed (XTR) and ampliconic excluding palindromes (rAMP) sequence was 8.71 × 10(-10) mutations per position per year (PPPY). We observed a lower rate (P = 0.04) of 7.37 × 10(-10) PPPY for 6.1 Mb of sequence from palindromes (PAL), which was not statistically different from the rate of 7.2 × 10(-10) PPPY for paternally transmitted autosomes. We postulate that the difference between PAL and the other MSY regions may provide an indication of the rate at which nascent autosomal and PAL de novo mutations are repaired as a result of gene conversion.Rannis, Icelandic Student Research Fund/1103340061 info:eu-repo/grantAgreement/EC/FP7/29034

The genetic structure of Norway

Abstract The aim of the present study was to describe the genetic structure of the Norwegian population using genotypes from 6369 unrelated individuals with detailed information about places of residence. Using standard single marker- and haplotype-based approaches, we report evidence of two regions with distinctive patterns of genetic variation, one in the far northeast, and another in the south of Norway, as indicated by fixation indices, haplotype sharing, homozygosity, and effective population size. We detect and quantify a component of Uralic Sami ancestry that is enriched in the North. On a finer scale, we find that rates of migration have been affected by topography like mountain ridges. In the broader Scandinavian context, we detect elevated relatedness between the mid- and northern border areas towards Sweden. The main finding of this study is that despite Norway’s long maritime history and as a former Danish territory, the region closest to mainland Europe in the south appears to have been an isolated region in Norway, highlighting the open sea as a barrier to gene flow into Norway

Supplementary Figure 1. Relatedness among HJ’s descendants.

A boxplot of autosomal IBD proportions estimated for pairs of HJ descendants by category of relationship, abbreviated as follows: first cousins (FC), full siblings (FS), grandparent - grandchild (GP-GC), great-grandparent-grandchild (Great-GP-GC), half-first cousins (H-FC), half-uncle/aunt-niece/nephew (H-UA-NN), half-siblings (HS), parent offspring (PO) and uncle/aunt-niece/nephew (UA-NN)

Supplementary Figure 15. wIBS and IBD (Affymetrix)

Plots showing the mean and 95% CIs for (a) wIBS and (b) IBD values between HJ’s reconstructed maternal genome and African reference populations with more than 10 genotyped individuals. For estimating IBD proportions, we used the following thresholds to identify IBD fragments with HJ: i) a minimum length of 1cM, ii) a minimum number of 40 loci with matching alleles, iii) no mismatches and iv) a maximum of 5 loci with missing genotypes

Supplementary Figure 9. Transmission of HJ’s X and Y chromosome

<div>(a) A genealogical tree showing the transmission of HJ’s X and Y chromosome. This tree represents a subset of the genealogy used in the study, with two different paths connecting a 5th descendant (HJD_5_85, represented by a filled circle), who carries part of HJ's X chromosome and a 6th generation descendant (HJD_6_274, represented by a filled square), who carries HJ's Y chromosome. (b) Beside this tree, the ancestry results as estimated by HAPMIX in the haploid mode, for the pair of X chromosomes from HJD_5_85 is shown.</div><div>The Y chromosome haplogroup of the direct male line descendant (HJD_6_274) was determined to be I2a2a3a2. Of the two X chromosome fragments in HJD_5_85, neither were shared with any of the 150,832 genotyped Icelanders who were not descendants of HJ. The longer 10.21 Mb fragment was carried by only HJD_5_85, while the smaller 3.86 Mb fragment was found to be shared with 3 other HJ’s descendants (two children and a grandchild of HJD_5_85). These two African fragments in HJD_5_85 are very likely to have been derived from HJ’s X chromosome. HJ’s Y chromosome is of European origin, while his maternal X chromosome seems to be of African origin, which agrees with the historical reports that his mother was African and his father European.</div><div><br></div

Supplementary Figure 12. PCA plots with African reference populations

Plots showing the first two eigen-vectors of a PCA with HJ’s reconstructed maternal genome along with (a) African reference populations and (b) West African reference populations