Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region

Abstract

Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.

Keywords: Baltic; ancient DNA; breeds; domestication; sheep.

Fig. 1.

Map showing the Baltic Sea with some of the neighboring countries. Samples are marked by the square and the diamond. The inset map in the lower right corner shows the extent of the main map on a map of Europe. Map created using ggspatial (Dunnington 2022) using geographic data from the rnaturalearth packages (Massicotte and South 2022).

Fig. 2.

PCA biplot of the ancient Baltic sheep projected over the WGS dataset for PCs 2 and 3. PC2 matches the geographical distribution of modern sheep, while PC3 polarizes some of the NEST breeds from other European sheep. The inner square represents a zoom-in on the ancient samples.

Fig. 3.

Outgroup f₃ biplot measuring the shared drift of the ancient Baltic sheep from both sites/time periods versus modern breeds. Error bars show two block-jackknife standard errors. a) WGS dataset and b) SNPCHP dataset.

Fig. 4.

Maximum likelihood tree (using OrientAGraph; Molloy et al. 2021) based on the covariances of allele frequencies in the SNPCHP data restricted to NEST and Russian breeds. The tree was estimated with OrientAGraph not allowing any migration edges.

Fig. 5.

Genetic diversity results. Pairwise mismatch rate between randomly sampled individuals from the same group are shown in a) for the WGS dataset and b) for the SNPCHP dataset. Error bars indicate two block-jackknife standard errors (for most groups, the error bars disappear behind the symbols). This analysis is based on transversions only to avoid postmortem damage driving the differences between ancient and modern populations. ROH comparison of ASTF002 and modern breeds is shown in c) for the WGS dataset and d) for the SNPCHP dataset.