Genomic signatures of historical pastoralism in Iberian livestock dogs

Livestock working dogs provide a powerful system for understanding how human cultural practices shape domestic animal genomes. Across Iberia, centuries of pastoralism and transhumance brought together dogs selected for distinct tasks, including livestock guarding and herding, yet their evolutionary history remains poorly understood. We combined Y-linked and autosomal microsatellite markers with genome-wide SNP data from 445 Iberian livestock dogs to investigate genetic diversity, population structure and gene flow. Iberian livestock dogs retain high genetic diversity and generally low inbreeding. Despite clear behavioural and morphological differences between guarding and herding dogs, we found little evidence of genome-wide differentiation. Instead, genetic structure was more strongly associated with breed identity and geography. We also detected widespread signatures of historical gene flow among breeds, including across working types. These patterns are consistent with traditional pastoral practices, particularly transhumance, promoting long-term genetic connectivity while allowing more recent breed differentiation to emerge. Specialization for distinct working roles does not necessarily produce strong genome-wide divergence when population connectivity is maintained. In Iberian livestock dogs, historical pastoral mobility appears to have preserved diversity and blurred boundaries between working roles, leaving genomic signatures that persist despite the decline of traditional pastoralism. More broadly, our findings illustrate how human cultural practices can leave lasting imprints on domestic animal genomes.