Demographic history and management practices shape the genomic landscape of New Zealand’s feral Kaimanawa Horses

Abstract Background New Zealand’s feral Kaimanawa Horses provide a unique opportunity to investigate how founder history, demographic processes, and human management influence genetic diversity and inbreeding in a free-ranging horse population. Here, we generate genome-wide SNP data and integrate these with previously generated mitochondrial and Y-chromosome markers from Kaimanawa Horses to compare them with 22 domestic breeds and characterize their genetic composition, population structure, genetic diversity, and demographic history, including changes in effective population size. Results Kaimanawa Horses exhibit a complex genetic composition, with shared genetic components mainly associated with British pony, Thoroughbred, Arabian, and draft horse lineages, consistent with historical records of multiple breed contributions. The population shows reduced heterozygosity, elevated inbreeding, and an effective population size below 50, reflecting isolation, and recent demographic contraction. Population structure analyses identify two genetic subgroups, while Y-chromosome analysis reveals private paternal haplotypes absent from modern breed reference panels, indicating the retention of unique paternal diversity. Conclusion Together, these findings provide the first genomic framework for understanding the genetic composition, diversity, and demographic history of the Kaimanawa horse population. These results demonstrate the value of genomic approaches for guiding conservation and management strategies, preserving genetic diversity, and supporting future research on feral horse populations.