Goats (Capra hircus) support livelihoods across the West Africa–Cameroon region, spanning forest–savanna–Sahel gradients with diverse climatic, disease and feed challenges. In this production context, vernacular labels such as “Sahel,” “Red Sokoto/Maradi,” and “West African Dwarf (Djallonké)” are commonly used in national statistics and management. However, those labels may not correspond to discrete, countrybound genetic units because long-standing trade, transhumance and cross-border exchange link production zones. This study frames genetic variation in terms of transboundary genomic backgrounds, aiming to assess whether recurrent breed names map onto shared genomic affinities across Nigeria and neighbouring countries and to integrate structure, connectivity chronology, demography, and adaptive signatures within a corridor-scale sampling design.
The analysis used publicly available AdaptMap genotype data comprising 209 unrelated animals sampled from three Nigerian populations (Sahel, Red Sokoto/Maradi, and West African Dwarf/Djallonké) and seven neighbouring populations from Burkina Faso, Mali, and Cameroon. A South Asian outgroup was included where needed. After quality control, 46,431 autosomal single-nucleotide polymorphism (SNP) markers were analysed. The study did not generate new genotype data; all genotype files and analysis scripts are publicly available via the Dryad AdaptMap resource and Zenodo as stated by the authors.
Principal component analysis and model-based ancestry inference supported three principal transboundary genomic backgrounds rather than strict country-bounded breeds. These were: a Sahel–Sudan background spanning Nigeria, Burkina Faso and Mali; a southern Djallonké/West African Dwarf (WAD) background also spanning Nigeria, Burkina Faso and Mali; and a genetically distinct Cameroon dwarf lineage. Within this scheme, Guéra (a Cameroonian sampling group) appeared as a drifted subgroup nested within the Sahel–Sudan background.
Admixture-timing analyses based on linkage-disequilibrium decay provided layered temporal context for connectivity. The authors interpreted inferred dates as approximate under their assumed generation interval. Results suggested very recent cross-border gene flow involving Nigerian Sahel goats—on the order of decades (~30–40 years under the study assumptions)—superimposed on older Sahelian–dwarf exchange events estimated in a broader window (~160–1,000 years). These results are consistent with ongoing mobility and episodic historical contact across the corridor.
Effective population size (Ne) reconstruction showed a marked long-term contraction. Estimated Ne declined from approximately 1,400–2,700 at around 960 generations ago to about 40–111 at 13 generations ago. This trajectory indicates substantial reduction in historical effective numbers by recent generations across the sampled populations.
Runs of homozygosity (ROH) analyses indicated overall low-to-moderate genomic inbreeding, with FROH values reported in the range of 0.004–0.040. Long ROH segments (>8 Mb) were most pronounced in Guéra and Red Sokoto/Maradi, consistent with recent drift or recent consanguinity in those sampling groups.
A multi-statistic composite selection scan combining several signals detected 53 candidate genomic windows putatively under selection. The scan was applied in a structure-aware framework, meaning candidate signals were prioritised with consideration of the transboundary genomic backgrounds identified by the authors.
Enrichment analysis of the candidate windows revealed different functional themes across genomic backgrounds. In the Djallonké/WAD background, terms related to adhesion and translation quality-control were highlighted. Guéra showed enrichment for neuronal and neuroendocrine terms. The Sahel–Sudan background exhibited enrichment for olfactory transduction-related terms. These background-specific hypotheses point to different candidate pathways potentially relevant to resilience or local adaptation in each genomic background.
The analyses support interpreting common vernacular labels not as closed national breeds but as transboundary genomic backgrounds shaped by historical and ongoing mobility, admixture and drift. For breeding and conservation, the authors argue that corridor-scale, background-aware strategies are more realistic than assuming country-limited genetic units. Background-specific candidate regions and functional hypotheses can inform resilience-oriented breeding and validation work, but the authors present these as testable hypotheses rather than definitive causal discoveries.
This corridor-scale population genomic study of Nigerian goats and neighbouring populations defines three major transboundary genomic backgrounds—Sahel–Sudan, Djallonké/WAD, and a distinct Cameroon dwarf lineage—documents a history of recent and older admixture, quantifies demographic contraction and inbreeding patterns, and nominates candidate adaptive regions with background-specific enrichments. The results emphasise that vernacular breed names often reflect phenotypic and management categories embedded in mobile exchange systems; genetic conservation and improvement planning should therefore be informed by transboundary genomic context and validated adaptive hypotheses.