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Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats.

ABSTRACT: Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.

SUBMITTER: Tarekegn GM

PROVIDER: S-EPMC8287980 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description: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.

Project description:BackgroundMore than 75% of neonatal deaths occurred in the first weeks of life as a result of adverse birth outcomes. Low birth weight, preterm births are associated with a variety of acute and long-term complications. In Sub-Saharan Africa, there is insufficient evidence of adverse birth outcomes. Hence, this study aimed to determine the pooled prevalence and determinants of adverse birth outcomes in Sub-Saharan Africa.MethodData of this study were obtained from a cross-sectional survey of the most recent Demographic and Health Surveys (DHS) of ten Sub-African (SSA) countries. A total of 76,853 children born five years preceding the survey were included in the final analysis. A Generalized Linear Mixed Models (GLMM) were fitted and an adjusted odds ratio (AOR) with a 95% Confidence Interval (CI) was computed to declare statistically significant determinants of adverse birth outcomes.ResultThe pooled prevalence of adverse birth outcomes were 29.7% (95% CI: 29.4 to 30.03). Female child (AOR = 0.94, 95%CI: 0.91 0.97), women attended secondary level of education (AOR = 0.87, 95%CI: 0.82 0.92), middle (AOR = 0.94,95%CI: 0.90 0.98) and rich socioeconomic status (AOR = 0.94, 95%CI: 0.90 0.99), intimate-partner physical violence (beating) (AOR = 1.18, 95%CI: 1.14 1.22), big problems of long-distance travel (AOR = 1.08, 95%CI: 1.04 1.11), antenatal care follow-ups (AOR = 0.86, 95%CI: 0.83 0.86), multiparty (AOR = 0.88, 95%CI: 0.84 0.91), twin births (AOR = 2.89, 95%CI: 2.67 3.14), and lack of women involvement in healthcare decision-making process (AOR = 1.10, 95%CI: 1.06 1.13) were determinants of adverse birth outcomes.ConclusionThis study showed that the magnitude of adverse birth outcomes was high, abnormal baby size and preterm births were the most common adverse birth outcomes. This finding suggests that encouraging antenatal care follow-ups and socio-economic conditions of women are essential. Moreover, special attention should be given to multiple pregnancies, improving healthcare accessibilities to rural areas, and women's involvement in healthcare decision-making.

Project description:The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.

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Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats.

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