Faroese whole genomes provide insight into ancestry and recent selection

Our DNA contains a wealth of information about our ancestors. By examining the DNA of present-day populations, researchers can infer aspects of their history, including migration patterns, interactions with other groups, changes in population size, and adaptation to local environments.

When a small group of “founders” settles a new location, they carry only a subset of the larger population’s genetic diversity. As a result, their descendants often exhibit reduced genetic diversity and elevated frequencies of certain genetic variants, some of which may influence health, disease, or adaptation.

The Faroe Islands, a remote North Atlantic archipelago, were settled around the 9th century CE, primarily by people from Scandinavia and the British Isles. Today’s population of approximately 54,000 Faroese descends from this relatively small founding group. This distinctive demographic history – characterized by mixed ancestry, geographic isolation, and a limited number of founders – is likely reflected in the genomes of present-day Faroese individuals.

To investigate the genetic diversity, ancestry, and evolutionary history of the Faroese population, Hamid et al. conducted whole-genome sequencing on 40 individuals selected to represent the geographic diversity of the islands. Previous studies of the Faroese population were limited either to small sample sizes (fewer than 10 individuals) or to specific regions of the genome, leaving substantial gaps in our understanding of the population’s full genetic landscape. The Faroe Islands also have elevated rates of several diseases, including inflammatory bowel disease and type 2 diabetes, compared with other European populations. Understanding the unique genetic architecture and demographic history of the Faroese population may therefore provide important insight into the genetic basis of these health disparities.

The analyses revealed that Faroese individuals carry numerous rare and potentially disease-associated genetic variants that are absent from mainland European populations, including variants predicted to disrupt gene function. Compared with other European groups –including Finns, another well-known founder population – Faroese genomes contain longer runs of homozygosity (long, identical DNA segments), reflecting extensive segments of identical DNA inherited from common ancestors. This pattern suggests a stronger or more recent population bottleneck in the Faroese population.

Hamid et al. also identified signatures of natural selection in genes involved in vitamin D metabolism and dietary fat absorption (SLC10A1), as well as DNA repair (POLQ), which may reflect adaptation to the Faroese environment and traditional diet. Comparisons with ancient European genomes indicated that the Faroese derive approximately equal ancestry from Iron Age “West European” (Celtic-related) and “North European” (Viking-related) populations. Importantly, the data suggest that this genetic mixing likely occurred before the settlement of the islands rather than afterwards.

These findings have direct relevance for the Faroese population because they identify genetic variants enriched in the islands that may contribute to conditions such as glycogen storage disease, ankylosing spondylitis, and other disorders. In the future, this knowledge could help inform disease prevention strategies and clinical care in the Faroe Islands. However, the study of Hamid et al. represents only a pilot phase. A greater ongoing effort, the FarGen project, aims to integrate genomic data with detailed health records to better understand the relationship between genetics and disease in the Faroese population. More broadly, the Faroe Islands provide an important model for studying how historical isolation and founder effects shape genetic diversity and disease risk in human populations worldwide.

The Faroe Islands, nestled in the North Atlantic Ocean between Iceland and Norway, are home to the descendants of a North Atlantic founder population with a rich cultural heritage and a unique history shaped by both migration and periods of relative isolation. The exact settlement history of the islands is unclear, though historical records and analysis of Y-chromosome microsatellite markers point to a few founders most likely having arrived primarily from Scandinavia and the British Isles starting around the ninth century CE (Johnston, 1975; Jorgensen et al., 2004; Young, 1979). However, archeological evidence supports a possible earlier settlement of the island around the fourth to sixth centuries CE (Church et al., 2013). Studies of mtDNA reveal an excess of maternal ancestry from the British Isles, while Y chromosome studies reveal an excess of paternal ancestry from Scandinavia, suggesting sex-biased admixture between these ancestral groups during the founding of the population (Jorgensen et al., 2004; Als et al., 2006). Since settlement and early waves of migration, the Faroe Islands have been mostly isolated and have experienced minimal immigration and population growth until recent years, with a census size of about 4000 people in the 1700s (West, 1972) increasing to over 54,000 as of August 2023 (https://hagstova.fo/en/population/population/population). Patterns of genetic diversity and linkage disequilibrium from a few genetic markers suggest a founder event, followed by a historically small population size and subsequent rapid expansion (Jorgensen et al., 2002).

Overall, despite the small size and remote location of the Faroe Islands, the above evidence suggests that the genetic makeup of Faroese people may have been influenced by waves of early migration and admixture from various northwest European and Scandinavian populations. However, no population genomic studies have yet been carried out on whole–genome sequencing data to date, with the exception of one study investigating relatedness and autozygosity for a limited sample size of eight individuals (Gislason, 2023). An in-depth analysis of the genomic architecture of the Faroese may reveal how the islands’ demographic history has contributed to present-day health and disease in this population. This is of particular interest as the Faroese have a high burden of certain diseases relative to global and other European populations, such as inflammatory bowel disease and type 2 diabetes, among others (Leblond et al., 2019; Rasmussen et al., 2014; Passa, 2002; Veyhe et al., 2018; Burisch et al., 2014; Dean et al., 2014; Schwartz et al., 1995; Joensen, 2011; Hammer et al., 2016; Gregersen et al., 2016). The Faroe Genome (FarGen) Project set out to understand how the genetic diversity of the Faroese contributes to health (Gregersen et al., 2021).

Moreover, studying the genetic diversity of the Faroese provides potential insight into human migration, adaptation, and population structure in the North Atlantic region. Recently developed haplotype-based methods can provide fine resolution for inferring shared ancestry among individuals and the detection of population-specific haplotypes, but they require panels of whole-genome sequencing data (Meisner and Albrechtsen, 2022). These methods serve to better account for recent patterns of population structure and cryptic relatedness in population-based genetic studies, particularly in populations like the Faroe Islands with strong founder effects.

In this study, we present the first whole genomes sequenced as part of the FarGen Project. A set of 40 individuals were selected to optimally represent the genetic diversity of the broader Faroese population, with the aid of genealogical data reaching back to approximately 1650 CE. Whole genome sequencing (WGS) data was generated and used to identify putatively functional alleles enriched in the Faroese population, assess ancestry patterns within contemporary genomes, map signals of recent positive selection, and analyze local ancestry in a combined dataset of ancient and contemporary genomes of European descent spanning a period of 3000 years.

This study provides insight into the genetic variation, demographic history, and selection landscape of the Faroese population. These first whole genomes from FarGen may serve as a useful reference for studies on the broad implications of various evolutionary genetic processes, including bottlenecks, ancient admixture, and positive selection. More in-depth studies may expand this current study by further investigating the genetic architecture of the Faroese to unravel the demographic and evolutionary history of the population and its impact on complex traits and diseases in the islands.

Here, we have presented the first whole-genome sequence data from 40 minimally related individuals from across the Faroe Islands, a North Atlantic founder population. The Faroese have a high prevalence of several diseases in comparison to other European or global populations, several of which have been of particular interest in epidemiological studies of the region (e.g. inflammatory bowel disease, type 2 diabetes, multiple sclerosis) (Leblond et al., 2019; Rasmussen et al., 2014; Passa, 2002; Veyhe et al., 2018; Burisch et al., 2014; Dean et al., 2014; Schwartz et al., 1995; Joensen, 2011; Hammer et al., 2016; Gregersen et al., 2016). Additionally, observational evidence from the FarGen project recruitment data suggest a higher prevalence of ankylosing spondylitis, although follow-up epidemiological studies are required. We investigated the frequency of HLA-B*27 in the Faroe Islands, an allele which has been previously associated with ankylosing spondylitis (AS). We found that despite the observed high prevalence of AS in the Faroe Islands, there was no evidence of increased HLA-B*27 allele frequency compared to other European populations. However, a stop gain variant in SERPINB10 was among those enriched in the Faroese cohort, and it may contribute to increased AS risk (rs138084090, AF = 2.5%). Rare variant analysis of this gene in the UK Biobank found that an independent stop gain variant in the same gene is nominally associated with increased AS risk (rs145346731, p=2.5e-4), which was the most significant phenotypic association for the gene (Karczewski et al., 2022). SERPINB10 is most highly expressed in neutrophilic metamyelocytes, (George et al., 2024) a cell type with disease relevance to AS (Coletto et al., 2023). CCDC168, another gene with a Faroese enriched stop gain variant had highly significant rare variant associations in the UK Biobank with corneal hysteresis and intraocular pressure (rs1361247423, p=1.79e-57, p=5.21e-13, respectively). Finally, a Faroese enriched stop gain variant in AGL identified in this study (rs113994128) has been previously reported as causing glycogen storage disease type IIIA in the Faroe Islands, which is estimated to have the highest prevalence of the disease worldwide (Santer et al., 2001). These findings emphasize the importance of further research into the role that unique genetic variation in the Faroe Islands may play in the incidence of diseases that, while common in the Faroes, have a global burden as well.

We found elevated amounts of the genome contained in long runs of homozygosity (ROHs) compared to other European reference cohorts, including another founder population from Finland. The higher proportion of the Faroese genome contained in these long ROHs suggests a stronger or more recent bottleneck in the Faroese population history. With the second phase of the FarGen study, a larger sample size will facilitate investigation into the timing and severity of the bottleneck(s). Additionally, founder populations, such as the Finnish, have been a common focus for studies of founder events, genetic isolation, and the effects of haplotype sharing on aspects of human health and disease (Norio, 2003; Kerminen et al., 2017; Peltonen et al., 1999; Sabatti et al., 2009). As such, the Faroese population may serve as another useful global reference for studying the influence of demographic history on genetic variation and trait architecture. Long ROHs, in particular, can be enriched for deleterious variation or be of interest in understanding the genetic architecture of health-related traits in human populations (Ceballos et al., 2018; Szpiech et al., 2013). Studying these long ROHs may be relevant for future studies of health outcomes or other traits of interest in the Faroese population.

We also detected several regions under recent positive selection in the population. It is likely that iHS measures selection older than the settlement of the Faroe Islands. Indeed, we found that many of the top selection signals were shared between the Faroese and British cohorts, which is unsurprising given the recent divergence between these two populations and likely reflecting selection that began prior to this divergence. We did find differences in the strength of these signals; for example, there is more diversity on the Faroese LCT/MCM6 lactase persistence haplotypes. The lactase persistence allele rs4988235 (chr2_135851076_G_A) has been inferred to be under strong selection at least until the medieval period in northwestern European groups (Patterson et al., 2022; Burger et al., 2020). Patterson et al., 2022 found that the rate of increase in allele frequency may have slowed in recent periods; however, this does not exclude the possibility of continued or fluctuating selective pressure, as this is consistent with the expected sigmoidal trajectory for an allele under ongoing selection (Haldane, 1927). While the increased diversity on the Faroese lactase persistence haplotypes may be simply explained by population-specific drift, this result could also indicate relaxed selection for lactase persistence alleles after settlement of the Faroe Islands, possibly due to changes in dietary habits in the new environment. The traditional diet of the Faroe Islands consisted of a higher reliance on animal and marine fats, such as sheep tallow, whale blubber, and liver from codfishes, while dairy products, such as milk and cheese, and particularly that from cattle, were more limited in availability (Svanberg, 2021). The selected variant at rs4988235 is at 74% frequency in the modern Faroese cohort, and based on the ancient genomes for which we have available data, we can attest that the allele was present in the Faroe Islands at high frequencies already in the 17^th/18^th centuries (~82%), and imputation further suggests the haplotype containing the allele to at least have been present in the islands 800 years ago. We caveat that the sample size of the historical Faroese (11 individuals) is small and coverage of ancient samples is low, leading to potential errors in imputation. In the absence of selection or drift, we can calculate the expected frequency of an allele in an admixed population as the linear combination of allele frequencies and average ancestry contributions from the sources. Based on the frequency of the rs4988235 variant in proxy sources from the ancient panel, the expected allele frequency in the ancestral population at the time of admixture is approximately 47%. The difference in observed and expected allele frequencies may be due to drift, demography, changes in selection pressure, or a combination of these and other factors. We note limitations in this calculation as the proxy samples may not be good representatives for the true sources at the time of admixture, and there may have been multiple admixture events rather than a single pulse.

We detected selection targets that were specific to the Faroese population using the XPEHH statistic with the British cohort as the comparison population. As XPEHH has the best power to identify alleles that are fixed or approaching fixation in one population but not others, it is unlikely to detect older selection events or incomplete sweeps from shared ancestral populations. One top selection signal is in POLQ, which plays a role in DNA repair and various cancers. Without collecting relevant phenotypes or environmental factors, it is difficult to hypothesize what selection pressure may be driving the strong signal in POLQ, so this will be an important area of follow-up for future studies. In another top signal, we find SLC10A1 which plays a role in fat and vitamin D absorption. Positive selection related to differences in dietary fat intake has been hypothesized in many human populations, such as the Inuit population in Greenland (Buckley et al., 2017; Fumagalli et al., 2015). Also situated in a far northern latitude, the Faroese diet is similar to that of the Inuit population, relying on animal and marine fats (Svanberg, 2021; Andersen and Hansen, 2018). The relationship between SLC10A1 and vitamin D levels may also be relevant, as the northern latitudes of the Faroe Islands and minimal UV exposure can lead to vitamin D deficiency, which has been hypothesized to be a strong selection pressure in populations in extreme latitudes (Hlusko et al., 2018; Nielsen et al., 2017).

Although we hypothesize that these results suggest possible adaptations to environmental pressures of diet or UV exposure in northern latitudes, we cannot draw definitive conclusions based on this current study. It is certainly possible that variants that have risen to high frequencies due to past or ongoing positive selection now play a role in health outcomes in modern populations. For example, the gene TBC1D4, which was shown to be under positive selection in the Greenlandic Inuit population likely due to a historical diet low in carbohydrates, has been associated with type 2 diabetes and insulin resistance in the same population (Andersen and Hansen, 2018; Moltke et al., 2014). The prevalences of some diseases enriched in the Faroese population may be related to genomic regions under positive selection. For example, the results of several studies have suggested a role of vitamin D deficiency in the development of multiple sclerosis (Salzer et al., 2012; Sintzel et al., 2018; Laursen et al., 2015). Future studies could involve collection of relevant phenotypes and focus on characterizing selective pressures and fine-mapping targets of selection as have been done in studies that more thoroughly characterized selection signals related to dietary adaptation and UV exposure and their functional consequences in other northern latitude populations (Fumagalli et al., 2015; Andersen and Hansen, 2018; Hlusko et al., 2018; Moltke et al., 2014).

We have inferred ancestry tracts in the present day Faroese genomes that were inherited from ancient populations throughout Europe. We found that present-day Faroese individuals have similar relative ancestry contributions from past ‘North’ and ‘West Europe’ Iron Age populations. The most ancient genome available from the Faroe Islands matches ancestry patterns found in Iron Age West Europe. Admixture could have occurred either via a mixture of the original ‘West Europe’ ancestry with individuals of predominantly ‘North Europe’ ancestry, or by replacement with individuals that were already of mixed ancestry at the time of arrival in the islands (the latter are not uncommon in Viking Age mainland Europe). Our analysis also suggests a bottleneck or a more progressive differentiation process in the islands relative to the mainland, which may postdate the most ancient Faroese genome currently available (approximately 800 years old). The most ancient Faroese sample from Margaryan et al. - composed almost entirely of ‘West Europe’ ancestry - is a male individual found in a chapel-site in Suðuroy. Consistent with this, a local legend suggests this site may have been occupied by Irish monks (Arge, 2015). We note that it is difficult to draw conclusions based on a single individual. It is possible that this particular individual moved to the Faroe Islands within their lifetime. More ancient and present-day samples from the islands could shed further light on the history of the Faroese population.

The average admixture timing between ‘North Europe’ and ‘West Europe’ sources (as estimated by DATES) pre-dates the settlement of the Faroe Islands (137 BCE - 980 BCE). This is consistent with the low variance in ancestry proportion within the Faroese individuals (both historical and modern), indicating enough time for recombination to break up long ancestry tracts and for global ancestry proportions to reach an equilibrium in the population. That is, these ancestry patterns, combined with the DATES estimates, suggest that the present-day Faroese population is most likely descended from already admixed founders who arrived on the islands. Importantly, estimates of admixture timing had high statistical noise, possibly due to several confounding factors including drift, demography, and low differentiation between sources. In particular, it is unclear how the bottleneck history of the Faroese population may affect the performance of DATES. In future studies, it will be informative to estimate and simulate the bottleneck size in the Faroese population, and then test the performance of DATES on those simulations to confirm whether bottleneck history has affected the empirical estimates of admixture timing. Additionally, it will be important to model single-pulse versus multiple pulses of admixture to determine whether this has resulted in the different estimates for admixture timing in modern and ancient Faroese.

This study focused on population genomic analyses, such as selection scans, population structure, kinship, and ancestry. Given the unique settlement history and genetic architecture of the Faroe Islands, future studies which combine genomic data with relevant phenotype data could provide useful insight into the underlying genetic mechanisms of those traits. In particular, larger-scale genomic studies in the Faroese could investigate genetic risk factors which contribute to the high prevalence of autoimmune and metabolic disease on the islands. This is a focus of the second phase of the FarGen study, which is currently ongoing.

Custom scripts for analyses described in this manuscript can be found on GitHub (https://github.com/olavurmortensen/wgs_selection, Mortensen, 2020). Additional analyses in this study utilized publicly available software and pipelines as described and cited in the Methods. Variant-level summary statistics and genome-wide selection scan results for iHS and XPEHH are available for research via Zenodo (https://doi.org/10.5281/zenodo.19475278). Individual-level genetic and associated metadata are not publicly available due to participant consent restrictions. These data carry a risk of re-identification, particularly in a small population, and are therefore accessible only for approved research under controlled access conditions. Genetic and meta data from this study is stored at the Faroese Health Authority. Researchers will be granted access to de-identified genetic data and metadata, provided that a research proposal describing the intended use of the data is submitted and the project protocol has been approved by the Faroese Scientific Ethical Committee and a template material/data transfer agreement has been signed with the Faroese Health Authority in compliance with GDPR (see Gregersen et al., 2021). Depending on the scope of the proposed research, additional participant re-consent may be required. Requests should be made to Noomi O. Gregersen (noomi@fargen.fo). All data are available for non-commercial use only.

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Author details

1. Iman Hamid

   Variant Bio Inc., Seattle, United States

   Contribution

   Formal analysis, Investigation, Visualization, Writing – original draft, Writing – review and editing, Conducted kinship, ROH, and selection scan analyses and interpreted results

   Contributed equally with

   Ólavur Mortensen and Alba Refoyo-Martínez

   Competing interests

   is an employee and options or shareholder of Variant Bio Inc. The author has no other competing interests to declare

   "This ORCID iD identifies the author of this article:" 0000-0003-2168-9727

2. Ólavur Mortensen

   1. FarGen, Department of Research, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
   2. Centre of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands

   Contribution

   Formal analysis, Investigation, Methodology, Writing – review and editing, Performed relatedness pruning and sample selection for WGS

   Contributed equally with

   Iman Hamid and Alba Refoyo-Martínez

   Competing interests

   No competing interests declared

3. Alba Refoyo-Martínez

   Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark

   Contribution

   Formal analysis, Investigation, Visualization, Writing – original draft, Writing – review and editing, Carried out ancient admixture and local ancestry analysis and interpreted results

   Contributed equally with

   Iman Hamid and Ólavur Mortensen

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0002-3674-4007

4. Leivur N Lydersen

   FarGen, Department of Research, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands

   Contribution

   Data curation, Formal analysis, Writing – review and editing, Prepared samples for WGS, Performed the WGS analyses

   Competing interests

   No competing interests declared

5. Anne-Katrin Emde

   Variant Bio Inc., Seattle, United States

   Contribution

   Formal analysis, Validation, Visualization, Writing – review and editing, Processed sequencing data, Performed imputation, Carried out quality control

   Competing interests

   is an employee and options or shareholder of Variant Bio Inc. The author has no other competing interests to declare

6. Melissa Hendershott

   Variant Bio Inc., Seattle, United States

   Contribution

   Project administration, Writing – review and editing

   Competing interests

   is an employee and options or shareholder of Variant Bio Inc. The author has no other competing interests to declare

7. Katrin D Apol

   FarGen, Department of Research, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands

   Contribution

   Project administration, Writing – review and editing, Secured ethical permissions, Facilitated the inclusion of participants, Oversaw the compliance with ethical standards and protocols

   Competing interests

   No competing interests declared

   "This ORCID iD identifies the author of this article:" 0000-0001-5488-2334

8. Guðrið Andorsdóttir

   FarGen, Department of Research, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands

   Contribution

   Data curation, Writing – review and editing, Prepared the data for the genealogy analysis

   Competing interests

   No competing interests declared

9. Jonas Meisner

   1. Mental Health Centre Copenhagen, Copenhagen University Hospital, Copenhagen, Denmark
   2. Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark

   Contribution

   Software, Writing – review and editing, Added functionalities to Haplonet software for semi-supervised admixture and fine-structure analysis

   Competing interests

   No competing interests declared

10. Kaja A Wasik

    Variant Bio Inc., Seattle, United States

    Contribution

    Conceptualization, Project administration, Writing – review and editing

    Competing interests

    is an employee and options or shareholder of Variant Bio Inc. The author has no other competing interests to declare

11. Fernando Racimo

    Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark

    Contribution

    Conceptualization, Supervision, Funding acquisition, Project administration, Writing – review and editing

    For correspondence

    fracimo@sund.ku.dk

    Competing interests

    No competing interests declared

    "This ORCID iD identifies the author of this article:" 0000-0002-5025-2607

12. Stephane E Castel

    Variant Bio Inc., Seattle, United States

    Contribution

    Conceptualization, Supervision, Writing – original draft, Project administration, Writing – review and editing

    For correspondence

    stephane@variantbio.com

    Competing interests

    is an employee and options or shareholder of Variant Bio Inc. The author has no other competing interests to declare

    "This ORCID iD identifies the author of this article:" 0000-0002-0707-2133

13. Noomi O Gregersen

    1. FarGen, Department of Research, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
    2. Centre of Health Science, University of the Faroe Islands, Tórshavn, Faroe Islands

    Contribution

    Conceptualization, Supervision, Project administration, Writing – review and editing, Secured ethical permissions, Facilitated the inclusion of participants, Oversaw the compliance with ethical standards and protocols

    For correspondence

    noomi@fargen.fo

    Competing interests

    No competing interests declared

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