Population genomics of Nigerian goat breeds and neighbouring populations in the West Africa–Cameroon transboundary livestock corridor

Indigenous goats in Nigeria and neighbouring countries support livelihoods across forest–savanna–Sahel environments, yet genomic structure, connectivity history, and adaptive signals are rarely investigated in a single corridor-scale transboundary framework. We analysed three Nigerian populations (Sahel, Red Sokoto/Maradi, and West African Dwarf; WAD) and seven neighbouring populations from Burkina Faso, Mali, and Cameroon using 46,431 autosomal markers from 209 unrelated animals (with a South Asian outgroup where needed). We tested whether recurrent vernacular labels map onto shared genomic backgrounds across borders, reconstructed time-layered connectivity, quantified demographic contraction and inbreeding, and prioritised candidate adaptive regions using a structure-aware approach. Model-based ancestry and principal component analysis supported three transboundary genomic backgrounds: (i) a Sahel–Sudan background spanning Nigeria, Burkina Faso, and Mali; (ii) a southern Djallonké/WAD background spanning Nigeria, Burkina Faso, and Mali; and (iii) a distinct Cameroon dwarf lineage, with Guéra representing a drifted subgroup within the Sahel–Sudan background. Admixture-timing analysis, interpreted as approximate dates inferred from linkage-disequilibrium decay, suggested very recent cross-border involving Nigerian Sahel goats (~30–40 years under the assumed generation interval), superimposed on older Sahelian–dwarf exchange (~160–1,000 years). Effective population size declined from ~1,400–2,700 at ~960 generations ago to ~40–111 at 13 generations ago. Runs of homozygosity indicated low-to-moderate genomic inbreeding (0.004–0.040), with long segments (>8 Mb) most pronounced in Guéra and Red Sokoto/Maradi. A multi-statistic composite selection scan identified 53 candidate windows. Enrichment highlighted adhesion and translation quality-control themes in the Djallonké/WAD background background, neuronal/neuroendocrine terms in Guéra, and olfactory transduction in the Sahel–Sudan background. These results define transboundary genomic backgrounds rather than country-bounded “breeds” and provide background-specific hypotheses that can be validated in resilience-oriented breeding under ongoing mobility.