Conservation & local programs

Ancient lineages in modern landscapes: genomic evidence from native northern European goats

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Abstract

Native goat breeds have adapted to diverse environments, developing unique traits and genomic patterns compared with breeds shaped by intensive artificial selection. However, their lower productivity has led to long-term neglect, placing many of these breeds at risk of extinction. Northern European local breeds, in particular, remain understudied, resulting in an underestimation of their contribution to global caprine genetic diversity. As most of them are currently classified as endangered, improved genomic and cultural characterisation is urgently required to support their sustainable management. To address this gap, we generated a comprehensive SNP dataset by combining newly generated data from primitive goats of the Irish and British Isles (Old Irish Goat, Bagot, Cheviot) and three Swedish native breeds (Göingeget, Jämtget, Lappget) with publicly available data from Scandinavia and Ireland. We further included three high-performing Swiss dairy breeds (Alpine, Saanen, Toggenburg), widely used in breeding programmes, as well as the bezoar as an outgroup. Population-genomic analyses - principal component analysis (PCA, PLINK v1.4), model-based clustering (ADMIXTURE v1.3), and demographic modeling (qpGraph, ADMIXTOOLS2) - were performed on a pruned dataset of 20 breeds, including 358 individuals (8-30 per population; BITE v1) and 45,150 SNPs. ROH-based inbreeding estimates (FROH) were obtained from an LD-filtered dataset of 46,925 markers (DetectRUNS v0.9). Except for the three dairy breeds, all endangered populations displayed variable levels of genomic inbreeding, with the Icelandic landrace (FROH = 0.60), Cheviot (0.40), and Bagot (0.37) showing the highest values. Irish breeds showed low to moderate inbreeding, although Aran goats exhibited the highest values within this group, and Bilberry goats displayed the largest proportion of long ROH ( >16 Mb). Short ROH (2-8 Mb) were frequent in Swedish native and Icelandic goats (~40%), suggesting long-term isolation, and were also abundant in dairy breeds (~50%), consistent with strong directional selection. PCA and ADMIXTURE analyses revealed a clear separation between Northern European native breeds and improved dairy populations. Jämtget, Lappget, and Norwegian coastal goats clustered together near the Icelandic landrace, indicating shared ancestry, whereas Göingeget grouped with Norwegian dairy and Finnish goats. Icelandic goats derive predominantly from Norwegian ancestry (consistent with Viking colonization ca. 870-930 CE) but retain Eastern Scandinavian components shared with Finnish populations, indicating a pan-Scandinavian origin. British-Irish breeds form a distinct Atlantic cluster, while elevated inbreeding in isolated populations (Iceland, Lapland, British Isles) reflects prolonged geographic isolation shaped by human-mediated movements and variable introgression. Overall, our study provides new insights into the genetic structure, diversity, and gene flow dynamics of Northern European goat breeds, emphasising their importance as reservoirs of unique genetic resources. Further investigation incorporating ancient DNA will be essential to reconstruct their demographic history more comprehensively.

Keywords: 2026

How to Cite:

Manunza, A., Cozzi, P., Lenstra, J., Carolan, S., Johansson, A., Grøva, L., Berg, P., Gidlund, A., Ryder, J. & Stella, A., (2026) “Ancient lineages in modern landscapes: genomic evidence from native northern European goats”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2287107. doi: https://doi.org/10.31274/wcgalp.24213

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