The Horn of Africa forms one of the two main historical entry points of domestics into the continent and Ethiopia is particularly important in this regard. Through the analysis of mitochondrial DNA (mtDNA) d‐loop region in 309 individuals from 13 populations, we reveal the maternal genetic variation and demographic dynamics of Ethiopian indigenous goats. A total of 174 variable sites that generated 231 haplotypes were observed. They defined two haplogroups that were present in all the 13 study populations. Reference haplotypes from the six globally defined goat mtDNA haplogroups show the two haplogroups present in Ethiopia to be A and G, the former being the most predominant. Although both haplogroups are characterized by an increase in effective population sizes (N_e) predating domestication, they also have experienced a decline in N_e at different time periods, suggesting different demographic histories. We observed seven haplotypes, six were directly linked to the central haplotypes of the two haplogroups and one was central to haplogroup G. The seven haplotypes were common between Ethiopia, Kenya, Egypt, and Saudi Arabia populations, suggesting common maternal history and the introduction of goats into East Africa via Egypt and the Arabian Peninsula, respectively. While providing new mtDNA data from a historically important region, our results suggest extensive intermixing of goats mediated by human socio‐cultural and economic interactions. These have led to the coexistence of the two haplogroups in different geographic regions in Ethiopia resulting in a large caprine genetic diversity that can be exploited for genetic improvement.

Macrobrachium (Bate, 1868) is a large and cosmopolitan crustacean genus of high economic importance worldwide. We investigated the morphological and molecular identification of freshwater prawns of the genus Macrobrachium in South, South West, and Littoral regions of Cameroon. A total of 1,566 specimens were examined morphologically using a key described by Konan (Diversité morphologique et génétique des crevettes des genres Atya Leach, 1816 et Macrobrachium Bate, 1868 de Côte d'Ivoire, 2009, Université d'Abobo Adjamé, Côte d'Ivoire), leading to the identification of seven species of Macrobrachium: M. vollenhovenii (Herklots, 1857); M. macrobrachion (Herklots, 1851); M. sollaudii (De Man, 1912); M. dux (Lenz, 1910); M. chevalieri (Roux, 1935); M. felicinum (Holthuis, 1949); and an undescribed Macrobrachium species M. sp. To validate the genetic basis of the identified species, 94 individuals representing the species were selected and subjected to genetic characterization using 1,814 DArT markers. The admixture analysis revealed four groups: M. vollenhovenii and M. macrobrachion; M. chevalieri; M. felicinum and M. sp; and M. dux and M. sollaudii. But, the principal component analysis (PCA) separated M. sp and M. felicinum to create additional group (i.e., five groups). Based on these findings, M. vollenhovenii and M. macrobrachion may be conspecific, as well as M. dux and M. sollaudii, while M. felicinum and M. sp seems to be different species, suggesting a potential conflict between the morphological identification key and the genetic basis underlying speciation and species allocation for Macrobrachium. These results are valuable in informing breeding design and genetic resource conservation programs for Macrobrachium in Africa.

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.

Domestic goats are distributed worldwide, with approximately 35% of the one billion world goat population occurring in Africa. Ethiopia has 52.5 million goats, ~99.9% of which are considered indigenous landraces deriving from animals introduced to the Horn of Africa in the distant past by nomadic herders. They have continued to be managed by smallholder farmers and semi-mobile pastoralists throughout the region. We report here 57 goat genomes from 12 Ethiopian goat populations sampled from different agro-climates. The data were generated through sequencing DNA samples on the Illumina NovaSeq 6000 platform at a mean depth of 9.71x and 150 bp pair-end reads. In total, ~2 terabytes of raw data were generated, and 99.8% of the clean reads mapped successfully against the goat reference genome assembly at a coverage of 99.6%. About 24.76 million SNPs were generated. These SNPs can be used to study the population structure and genome dynamics of goats at the country, regional, and global levels to shed light on the species’ evolutionary trajectory.

Objective: This study was carried out to assess the haplotype diversity and population dynamics in cattle populations of Ethiopia. Methods: We sequenced the complete mitochondrial cytochrome b gene of 76 animals from five indigenous and one Holstein FriesianxBarka cross bred cattle populations. Results: In the sequence analysis, 18 haplotypes were generated from 18 segregating sites and the average haplotype and nucleotide diversities were 0.7540 +/- 0.043 and 0.0010 +/- 0.000, respectively. The population differentiation analysis shows a weak population structure (4.55%) among the populations studied. Majority of the variation (95.45%) is observed by within populations. The overall average pair-wise distance (F-ST) was 0.049539 with the highest (F-ST = 0.1245) and the lowest (F-ST = 0.011) F-ST distances observed between Boran and Abigar, and Sheko and Abigar from the indigenous cattle, respectively. The phylogenetic network analysis revealed that all the haplotypes detected clustered together with the Bos taurus cattle and converged to a haplogroup. No haplotype in Ethiopian cattle was observed clustered with the reference Bos indicus group. The mismatch distribution analysis indicates a single population expansion event among the cattle populations. Conclusion: Overall, high haplotype variability was observed among Ethiopian cattle populations and they share a common ancestor with Bos taurus.

Background: Ethiopian sheep living in different climatic zones and having contrasting morphologies are a most promising subject of molecular-genetic research. Elucidating their genetic diversity and genetic structure is critical for designing appropriate breeding and conservation strategies.Objective: The study was aimed to investigate genome-wide genetic diversity and population structure of eight Ethiopian sheep populations.Methods: A total of 115 blood samples were collected from four Ethiopian sheep populations that include Washera, Farta and Wollo (short fat-tailed) and Horro (long fat-tailed). DNA was extracted using Quick-DNA™ Miniprep plus kit. All DNA samples were genotyped using Ovine 50 K SNP BeadChip. To infer genetic relationships of Ethiopian sheep at national, continental and global levels, genotype data on four Ethiopian sheep (Adilo, Arsi-Bale, Menz and Black Head Somali) and sheep from east, north, and south Africa, Middle East and Asia were included in the study as reference.Results: Mean genetic diversity of Ethiopian sheep populations ranged from 0.352 ± 0.14 for Horro to 0.379 ± 0.14 for Arsi-Bale sheep. Population structure and principal component analyses of the eight Ethiopian indigenous sheep revealed four distinct genetic cluster groups according to their tail phenotype and geographical distribution. The short fat-tailed sheep did not represent one genetic cluster group. Ethiopian fat-rump sheep share a common genetic background with the Kenyan fat-tailed sheep.Conclusion: The results of the present study revealed the principal component and population structure follows a clear pattern of tail morphology and phylogeography. There is clear signature of admixture among the study Ethiopian sheep populations