Data from: Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Indigenous goats make significant contributions to Cameroon’s national and
local economy, but little effort has been devoted to identifying the
populations. Here, we assessed the genetic diversity and demographic
dynamics of Cameroon goat populations using mitochondrial DNA (two
populations) and autosomal markers (four populations) generated with the
Caprine 50K SNP chip. To infer genetic relationships at continental and
global level, genotype data on six goat populations from Ethiopia and one
population each from Egypt, Morocco, Iran, and China were included in the
analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to
haplogroup A, in Cameroon goats. Four haplotypes were shared between goats
found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia.
Analysis of autosomal SNPs in Cameroon goats revealed the lowest HO
(0.335±0.13) and HE (0.352±0.15) in the North-west Highland and Central
Highland populations, respectively. Overall, the highest HO (0.401±0.12)
and HE (0.422±0.12) were found for Barki and Iranian goats, respectively.
Barki goats had the highest average MAF, while Central Highland Cameroon
goats had the lowest. Overall, Cameroon goats demonstrated high FIS. AMOVA
revealed that 13.29% of the variation was explained by genetic differences
between the six population groups. Low average FST (0.01) suggests
intermixing among Cameroon goats. All measures indicated that Cameroon
goats are closer to Moroccan goats than to other goat populations. PCA and
STRUCTURE analyses poorly differentiated the Cameroon goats, as did
genetic distance, Neighbor-Net network, and neighbor-joining tree
analyses. The haplotype analysis of mtDNA showed the initial dispersion of
goats to Cameroon and central Africa from north-east Africa following the
Nile Delta. Whereas, the approximate Bayesian computation indicated
Cameroon goats were separated from Moroccan goats after 506 generations in
later times (~1518 YA), as supported by the phylogenetic net-work and
admixture outputs. Overall, indigenous goats in Cameroon show weak
phylogenetic structure, suggesting either extensive intermixing.