Shifting genomes, changing flocks: recent dynamics of Italian sheep biodiversity

Understanding how livestock biodiversity is changing over short timeframes is essential to support effective conservation. Italian sheep provide an excellent case study, combining high breed diversity with a wide range of environments, farming systems and breeding histories. Here, we integrated demographic records and genomic data to investigate recent dynamics of Italian sheep breeds. Demographic data from the national herd book (2010–2024) indicate that most breeds are experiencing contraction in population size and/or number of farms, while only a minority show stable or positive trends; accordingly, the majority of populations are currently classified as at risk under FAO criteria. This heterogeneity points to multiple underlying drivers, including management, economic and policy factors, rather than a single common pattern. To investigate how these trends are reflected at the genomic level, we analysed SNP data from 816 individuals belonging to 34 Italian populations and compared them with 8 foreign breeds. Despite a clear geographic structuring consistent with historical differentiation, breeds show marked differences in genetic diversity, inbreeding levels, and effective population size, with several populations displaying signals of genetic erosion. A temporal comparison with populations sampled about 20 years ago (Biovita project [1]) reveals that, although breed identity is largely maintained, many populations have undergone detectable genomic changes. These include increased inbreeding and/or shifts in ancestry composition, often associated with recent admixture. In particular, the current genomic background of Nera di Arbus and Gentile di Puglia shows substantial contributions from Sarda and Merinizzata Italiana, respectively. Local ancestry inference in these breeds indicated that introgression often affects genomic regions associated with breed-specific traits, suggesting that it may alter breed typicality while introducing advantageous alleles. To further investigate temporal changes, we performed Fstbased comparisons between past and present populations, identifying genomic regions showing the highest differentiation over time. These include candidate genes and QTLs related to production, fitness, and morphological traits, suggesting that both management and selection have contributed to recent genomic shifts. At the same time, environmental changes appear to play a role in shaping recent genomic patterns. Associations between genomic differentiation and variation in climatic variables across breeding ranges - particularly precipitationsupport the presence of ongoing adaptive processes acting over relatively short timescales. Overall, these results indicate that Italian sheep biodiversity is currently undergoing rapid and heterogeneous change. Rather than representing static genetic resources, these breeds should be viewed as dynamic populations, whose future will depend on the balance between demographic trends, management decisions, introgression, and environmental pressures [2]. Acknowledgements: Associazione Nazionale della Pastorizia (CHEESR and SHEEP&GOAT projects), especially Alessio Negro and Silverio Grande; Viviana Floridia (Messina University); Francesca Maria Sarti (Perugia University). [1] Ciani et al. Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds, Animal Genetics, 45(2):256–266, 2014 [2] Bionda et al. Genomic insights into the recent evolution and biodiversity of Italian sheep breeds, Mammalian Genome, 37(1):5, 2026