118 | Nature | Vol 637 | 2 January 2025
Article
High-resolution genomic history of early 
medieval Europe
Leo Speidel1,2,3 ✉, Marina Silva1, Thomas Booth1, Ben Raffield4, Kyriaki Anastasiadou1, 
Christopher Barrington5, Anders Götherström6,7, Peter Heather8 & Pontus Skoglund1 ✉
Many known and unknown historical events have remained below detection thresholds 
of genetic studies because subtle ancestry changes are challenging to reconstruct. 
Methods based on shared haplotypes1,2 and rare variants3,4 improve power but are not 
explicitly temporal and have not been possible to adopt in unbiased ancestry models. 
Here we develop Twigstats, an 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 1,556 available ancient whole genomes from Europe in the historical 
period. We are able to model individual-level ancestry using preceding genomes to 
provide high resolution. During the first half of the first millennium ce, we observe  
at least two different streams of Scandinavian-related ancestry expanding across 
western, central and eastern Europe. By contrast, during the second half of the first 
millennium ce, ancestry patterns suggest the regional disappearance or substantial 
admixture of these ancestries. In Scandinavia, we document a major ancestry influx  
by approximately 800 ce, when a large proportion of Viking Age individuals carried 
ancestry from groups related to central Europe not seen in individuals from the early 
Iron Age. Our findings suggest that time-stratified ancestry analysis can provide a 
higher-resolution lens for genetic history.
Ancient genome sequencing has revolutionized our ability to recon-
struct expansions, migrations and admixture events in the ancient past 
and understand their impact on human genetic variation today. How-
ever, tracing history using genetic ancestry has remained challenging, 
particularly in historical periods for which the richest comparative 
information from history and archaeology often exists. This is because 
ancestries in many geographical regions are often so similar as to be 
statistically indistinguishable with current approaches. One example is 
northern and central Europe since the start of the Iron Age around 500 
bce, a period for which many long-standing questions remain, such as 
the nature of large-scale patterns of human migration during the fourth 
to sixth centuries ce, their impact on the Mediterranean world and later 
patterns of human mobility during the Viking Age (around 750–1050 ce).
Several recent studies have documented substantial mobility and 
genetic diversity in these time periods, suggesting stable population 
structure despite high mobility5, and have revealed genetic variation 
in Viking Age Scandinavia6–8, early medieval England3,9, early medieval 
Hungary10,11 and Iron Age and medieval Poland12. However, previous 
studies mostly used large modern cohorts to study ancestry change 
through time and space. This is because the differentiation between 
Iron Age groups in central and northern Europe is an order of magnitude 
lower (fixation index (FST) = 0.1–0.7%; Extended Data Fig. 1) than, for 
example, the more commonly studied hunter-gatherer, early farmer 
and steppe-pastoralist groups that shaped the ancestry landscape of 
Stone Age and Bronze Age Europe13–16 (FST = 5–9% (refs. 13,17)). Modern 
populations provide more power to detect differences, but their genetic 
affinity to ancient individuals may be confounded by later gene flow, 
that is, after the time of the ancient individual(s)18. The most principled 
approach is thus to build ancestry models in which source and ‘out-
group/reference’ populations are older than, or at least contemporary 
with, the target genome or group that we are trying to model18. However,