ena-STUDY-ESTONIAN BIOCENTRE, ESTONIA-07-07-2021-12:20:40:541-9
Patterns of genetic connectedness between modern and medieval Estonians reveal the origins of a major ancestry component of Finns
The Finnish population is a unique example of a genetic isolate affected by a recent founder event that has been extensively utilized in gene mapping studies. According to current genetic and archaeological synthesis the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1st millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness at historic time depths directly through ancient DNA we first assessed the efficacy of imputation of low coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23x) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1x coverage can be reliably used in principal component analyses without projection. By searching for long shared allele intervals (LSAI; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns and 14 imputed ancient genomes from Estonia, we  find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries that stand in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8th–10th cc AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine scale structure in large cohorts.
The Finnish population is a unique example of a genetic isolate affected by a recent founder event that has been extensively utilized in gene mapping studies. According to current genetic and archaeological synthesis the ancestors of Finnic-speaking Finns and Estonians reached the circum-Baltic region by the 1st millennium BC. However, high linguistic similarity points to a more recent split of their languages. To study genetic connectedness at historic time depths directly through ancient DNA we first assessed the efficacy of imputation of low coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23x) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1x coverage can be reliably used in principal component analyses without projection. By searching for long shared allele intervals (LSAI; similar to identity-by-descent segments) in unphased data for >143,000 present-day Estonians, 99 Finns and 14 imputed ancient genomes from Estonia, we  find unexpectedly high levels of individual connectedness between Estonians and Finns for the last eight centuries that stand in contrast to their clear differentiation by allele frequencies. High levels of sharing of these segments between Estonians and Finns predate the demographic expansion and late settlement process of Finland. One plausible source of this extensive sharing is the 8th–10th cc AD migration event from North Estonia to Finland that has been proposed to explain uniquely shared linguistic features between the Finnish language and the northern dialect of Estonian and shared Christianity-related loanwords from Slavic. These results suggest that LSAI detection provides a computationally tractable way to detect fine scale structure in large cohorts.