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.