African Suid Genomes Provide Insights into the Local Adaptation to Diverse African Environments.

African wild suids consist of several endemic species that represent ancient members of the family Suidae and have colonized diverse habitats on the African continent. However, limited genomic resources for African wild suids hinder our understanding of their evolution and genetic diversity. In this study, we assembled high-quality genomes of a common warthog (Phacochoerus africanus), a red river hog (Potamochoerus porcus), as well as an East Asian Diannan small-ear pig (Sus scrofa). Phylogenetic analysis showed that common warthog and red river hog diverged from their common ancestor around the Miocene/Pliocene boundary, putatively predating their entry into Africa. We detected species-specific selective signals associated with sensory perception and interferon signaling pathways in common warthog and red river hog, respectively, which contributed to their local adaptation to savannah and tropical rainforest environments, respectively. The structural variation and evolving signals in genes involved in T-cell immunity, viral infection, and lymphoid development were identified in their ancestral lineage. Our results provide new insights into the evolutionary histories and divergent genetic adaptations of African suids.

Analysis of the genetic variation in mitochondrial DNA, Y-chromosome sequences, and MC1R sheds light on the ancestry of Nigerian indigenous pigs.

BACKGROUND: The history of pig populations in Africa remains controversial due to insufficient evidence from archaeological and genetic data. Previously, a Western ancestry for West African pigs was reported based on loci that are involved in the determination of coat color. We investigated the genetic diversity of Nigerian indigenous pigs (NIP) by simultaneously analyzing variation in mitochondrial DNA (mtDNA), Y-chromosome sequence and the melanocortin receptor 1 (MC1R) gene. RESULTS: Median-joining network analysis of mtDNA D-loop sequences from 201 NIP and previously characterized loci clustered NIP with populations from the West (Europe/North Africa) and East/Southeast Asia. Analysis of partial sequences of the Y-chromosome in 57 Nigerian boars clustered NIP into lineage HY1. Finally, analysis of MC1R in 90 NIP resulted in seven haplotypes, among which the European wild boar haplotype was carried by one individual and the European dominant black by most of the other individuals (93%). The five remaining unique haplotypes differed by a single synonymous substitution from European wild type, European dominant black and Asian dominant black haplotypes. CONCLUSIONS: Our results demonstrate a European and East/Southeast Asian ancestry for NIP. Analyses of MC1R provide further evidence. Additional genetic analyses and archaeological studies may provide further insights into the history of African pig breeds. Our findings provide a valuable resource for future studies on whole-genome analyses of African pigs.

Comparison of proximate composition and sensory attributes of Clariid catfish species of Clarias gariepinus, Heterobranchus bidorsalis, and their hybrids.

Clariid catfish are favorite food fish especially in African and Asian continents. Recently there has been preference for particular species or hybrids of these species based on quality assurance and value addition. Consequently, this study aimed to evaluate the possible effect of different catfish species and their hybrids on proximate composition and sensory attributes. Catfish species, Clarias gariepinus (CC), Heterobranchus bidorsalis (HH), with their hybrid (CH), and reciprocal hybrid (HC) were evaluated for sensory variables - cognitive (sweet, salty, sour, bitter, and recent characteristic taste 'umami') and qualitative (texture, aroma, flavor, and color) tests; and nutritional variables - proximate composition (moisture, protein, ether/fat, and ash). A 5-point hedonic scale from 'neutral/neither like nor dislike' to 'excellent/like extremely' was employed in sensory testing. The results showed similar (P > 0.05) high moisture contents (>70%) in all species and high but different (P < 0.05) ash contents (11-14%) that suggested good sources of mineral elements. The parent species CC and HH had higher ash contents than CH or HC. The crude protein contents were high and similar (P > 0.05) across species (>57%). Fat or ether extract was different (P < 0.05) and tended to be higher for species with Clarias as the female parent than Heterobranchus. Sensory analysis showed the parent species, CC and HH, more favorably rated for sweet and umami than the hybrids, CH and HC. However, CH was less sour and bitter than all other species and HC better than CH for salty but similar to CC and HH. All fish species were very well liked for texture, but the parent species were superior in flavor than the hybrids. All species were very well liked for aroma, color, and overall acceptability except HC, which was moderately liked. HC rated inferior to the other species overall in sensory attributes. All the fish species did not rate 'excellent/like extremely' for any attribute. It can be concluded that the parent catfish species possess better sensory qualities than hybrids, but all species need exogenous enhancement to their natural sensory components.