Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans

Abstract

Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual-that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.Many studies have demonstrated that human population genetic structuring in Europe correlates with geography; for instance, a two dimensional representation of the genetic variation with principal component analysis (PCA) essentially mirrors a geographical map of Europe 1,2 . Several ancient DNA (aDNA) studies have shown that the overall genetic structure was shaped by three ancestral and over-imposed genomic components respectively deriving from the Mesolithic hunter-gatherers, the Early Neolithic farmers, and the steppe nomads that entered Europe from the East around 5,000 years ago 3-7 . However, it is expected that the genetic homogenisation of the European populations during the last two millennia complicates our ability to discern subtle changes in ancestry by using some common population genetic tools.Complementary to these analyses, the distribution of so-called identity by descent (IBD) genomic stretches, which are co-inherited genetic segments delimited by recombination events, can provide information on more recently shared ancestry among individuals [8][9][10] . Such genomic block characterization in current populations has demonstrated the presence of co-ancestry across geographically distant Europeans shared over the last few thousand years, and revealed more recently shared co-ancestry in neighboring populations 11 . Nevertheless, most IBD blocks are not expected to be recognizable after a few hundreds of years because they are being broken by recombination during meiosis. Since the far majority of ancient human genomes sequenced to date are >2,...

Revealing the recent demographic history of Europe via haplotype sharing in the UK Biobank

“…Maltese genetic differentiation is expanded upon in IBD-segment analysis ( Fig. 3 ) and agrees with previous IBD estimates from a smaller Maltese sample ( 40 ). Malta has a slightly lower average within-cluster total IBD length than Finland, although the average Maltese IBD-segment is longer (Malta IBD segment = 3.17 cM, Finland = 2.07 cM), suggesting a more recent source of this elevated sharing.…”

“…We therefore already identify recent migrants to the island who do not represent the historical ancestry there. The collective genetic profile of the Malta cluster is also consistent with previous literature, where Maltese uniparental data ( 43 ) and limited autosomal STR data ( 44 ), as well as analysis ( 40 ) of a small sample of Maltese SNP-array genotypes from the Human Origins dataset ( 30 ) have shown evidence of an island genetic isolate. Indeed, these Human Origin Maltese genotypes colocate with our sample in the projected PCA ( SI Appendix , Fig.…”

ancIBD - Screening for identity by descent segments in human ancient DNA

“…The promise of haplotype sharing signals in aDNA research has been acknowledged [Racimo et al, 2020], but so far only a few exceptional applications to comparably high-quality aDNA data have been published [see e.g. Sikora et al, 2017, Ferrando-Bernal et al, 2020]. First efforts to identify IBD based on imputed data have been fruitful [Kivisild et al, 2021, Allentoft et al, 2022, Ariano et al, 2022, Severson et al, 2022a], but those earlier works require higher coverage not routinely available for aDNA.…”

Patterns of genetic connectedness between modern and medieval Estonian genomes reveal the origins of a major ancestry component of the Finnish population

“…2 While ancient DNA work has become pivotal for addressing questions about the genetic ancestry in European prehistory, the use of IBD-based methods has been limited so far because of the fact that these require good-quality genotype calls, which can be made directly only from high-quality data. A study of a late-medieval 11.33 genome from Barcelona 3 showed, intriguingly, an excess of IBD sharing locally with the present-day Spanish population, highlighting the potential of IBD sharing measures to be informative in ancient DNA analyses in historical time depths. However, most ancient genomes that are currently available have low coverage and are routinely assessed via haploid genotype calls.…”