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The Finnish population is a unique example of a genetic isolate affected by a recent founder event. Previous studies have suggested that 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 between Finns and Estonians directly, we first assessed the efficacy of imputation of low-coverage ancient genomes by sequencing a medieval Estonian genome to high depth (23×) and evaluated the performance of its down-sampled replicas. We find that ancient genomes imputed from >0.1× coverage can be reliably used in principal-component analyses without projection. By searching for long shared allele intervals (LSAIs; 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 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 centuries 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. [ABSTRACT FROM AUTHOR]

The contemporary European genetic makeup formed in the last 8,000 years when local Western Hunter-Gatherers (WHGs) mixed with incoming Anatolian Neolithic farmers and Pontic Steppe pastoralists. 1–3 This encounter combined genetic variants with distinct evolutionary histories and, together with new environmental challenges faced by the post-Neolithic Europeans, unlocked novel adaptations. 4 Previous studies inferred phenotypes in these source populations, using either a few single loci 5–7 or polygenic scores based on genome-wide association studies, 8–10 and investigated the strength and timing of natural selection on lactase persistence or height, among others. 6,11,12 However, how ancient populations contributed to present-day phenotypic variation is poorly understood. Here, we investigate how the unique tiling of genetic variants inherited from different ancestral components drives the complex traits landscape of contemporary Europeans and quantify selection patterns associated with these components. Using matching individual-level genotype and phenotype data for 27 traits in the Estonian biobank 13 and genotype data directly from the ancient source populations, we quantify the contributions from each ancestry to present-day phenotypic variation in each complex trait. We find substantial differences in ancestry for eye and hair color, body mass index, waist/hip circumferences, and their ratio, height, cholesterol levels, caffeine intake, heart rate, and age at menarche. Furthermore, we find evidence for recent positive selection linked to four of these traits and, in addition, sleep patterns and blood pressure. Our results show that these ancient components were differentiated enough to contribute ancestry-specific signatures to the complex trait variability displayed by contemporary Europeans. • Ancient groups differentially contributed to complex traits in contemporary Europeans • In contemporary Estonians 11 out of 27 traits show association with some ancestry • Hunter-Gatherer and Yamnaya ancestries divergently influence cholesterol levels • Post-admixture selection is not necessary to have trait-ancestry associations Marnetto e al. quantitatively analyze how ancient populations differentially contributed to the complex trait variability in contemporary Europeans. Using the Estonian biobank as case study, they find that 11 out of 27 traits show association with some ancestral European group, including anthropometric, pigmentation, and metabolic traits. [ABSTRACT FROM AUTHOR]

The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden., (© 2021. The Author(s), under exclusive licence to European Society of Human Genetics.)

Several recent studies detected fine-scale genetic structure in human populations. Hence, groups conventionally treated as single populations harbour significant variation in terms of allele frequencies and patterns of haplotype sharing. It has been shown that these findings should be considered when performing studies of genetic associations and natural selection, especially when dealing with polygenic phenotypes. However, there is little understanding of the practical effects of such genetic structure on demography reconstructions and selection scans when focusing on recent population history. Here we tested the impact of population structure on such inferences using high-coverage (~30×) genome sequences of 2305 Estonians. We show that different regions of Estonia differ in both effective population size dynamics and signatures of natural selection. By analyzing identity-by-descent segments we also reveal that some Estonian regions exhibit evidence of a bottleneck 10-15 generations ago reflecting sequential episodes of wars, plague and famine, although this signal is virtually undetected when treating Estonia as a single population. Besides that, we provide a framework for relating effective population size estimated from genetic data to actual census size and validate it on the Estonian population. This approach may be widely used both to cross-check estimates based on historical sources as well as to get insight into times and/or regions with no other information available. Our results suggest that the history of human populations within the last few millennia can be highly region specific and cannot be properly studied without taking local genetic structure into account.

High-coverage whole-genome sequence studies have so far focused on a limited number of geographically restricted populations, or been targeted at specific diseases, such as cancer. Nevertheless, the availability of high-resolution genomic data has led to the development of new methodologies for inferring population history and refuelled the debate on the mutation rate in humans. Here we present the Estonian Biocentre Human Genome Diversity Panel (EGDP), a dataset of 483 high-coverage human genomes from 148 populations worldwide, including 379 new genomes from 125 populations, which we group into diversity and selection sets. We analyse this dataset to refine estimates of continent-wide patterns of heterozygosity, long- and short-distance gene flow, archaic admixture, and changes in effective population size through time as well as for signals of positive or balancing selection. We find a genetic signature in present-day Papuans that suggests that at least 2% of their genome originates from an early and largely extinct expansion of anatomically modern humans (AMHs) out of Africa. Together with evidence from the western Asian fossil record, and admixture between AMHs and Neanderthals predating the main Eurasian expansion, our results contribute to the mounting evidence for the presence of AMHs out of Africa earlier than 75,000 years ago., Competing Interests: The authors declare no competing financial interests.