Abstract
<jats:p>Pakistan's Punjab province harbours seven documented indigenous goat breeds Beetal, Barbari, Daira Din Panah, Nachi, Pahari, Local Pothwari and Teddi that together underpin smallholder meat and milk production across the province. Despite their economic and genetic importance, the historical demography of these breeds has not previously been reconstructed from genome-wide marker data. Using Illumina Caprine 50 K SNP Bead Chip genotypes from 827 unrelated animals, we applied a linkage-disequilibrium (LD)–based method to reconstruct effective population size (Ne) trajectories spanning approximately 11 to 5,000 generations ago for each breed. All seven breeds showed an ancestral Ne of 2,700–4,500 that increased to a mid-history peak of 3,400–8,300 individuals roughly 1,400–2,300 generations ago, followed by a pronounced and accelerating decline toward the present. At the most recent distance class examined (~11 generations ago), estimated Ne ranged from 63 (Barbari) to 968 (Beetal), representing declines of 78.4% to 97.7% relative to ancestral levels. Five of the seven breeds (Barbari, Daira Din Panah, Nachi, Pahari and Teddi) presently show a recent Ne below 150, and six of seven fall below the FAO threshold of 100 associated with elevated risk of inbreeding depression and loss of adaptive genetic variation over the short term. These results indicate that recent demographic and breeding-management pressures, rather than ancient bottlenecks, are the dominant driver of contemporary genetic erosion in Punjab goat breeds, and they provide a quantitative, breed-specific evidence base for prioritising in situ and ex situ conservation and structured breeding programmes.</jats:p>