Ancient and Recent Hybridization in the Oreochromis Cichlid Fishes.

Cichlid fishes of the genus Oreochromis (tilapia) are among the most important fish for inland capture fisheries and global aquaculture. Deliberate introductions of non-native species for fisheries improvement and accidental escapees from farms have resulted in admixture with indigenous species. Such hybridization may be detrimental to native biodiversity, potentially leading to genomic homogenization of populations and the loss of important genetic material associated with local adaptation. By contrast, introgression may fuel diversification when combined with ecological opportunity, by supplying novel genetic combinations. To date, the role of introgression in the evolutionary history of tilapia has not been explored. Here we studied both ancient and recent hybridization in tilapia, using whole genome resequencing of 575 individuals from 23 species. We focused on Tanzania, a natural hotspot of tilapia diversity, and a country where hybridization between exotic and native species in the natural environment has been previously reported. We reconstruct the first genome-scale phylogeny of the genus and reveal prevalent ancient gene flow across the Oreochromis phylogeny. This has likely resulted in the hybrid speciation of one species, O. chungruruensis. We identify multiple cases of recent hybridization between native and introduced species in the wild, linked to the use of non-native species in both capture fisheries improvement and aquaculture. This has potential implications for both conservation of wild populations and the development of the global tilapia aquaculture industry.

Whole genome resequencing data enables a targeted SNP panel for conservation and aquaculture of Oreochromis cichlid fishes.

Cichlid fish of the genus Oreochromis form the basis of the global tilapia aquaculture and fisheries industries. Broodstocks for aquaculture are often collected from wild populations, which in Africa may be from locations containing multiple Oreochromis species. However, many species are difficult to distinguish morphologically, hampering efforts to maintain good quality farmed strains. Additionally, non-native farmed tilapia populations are known to be widely distributed across Africa and to hybridize with native Oreochromis species, which themselves are important for capture fisheries. The morphological identification of these hybrids is particularly unreliable. Here, we describe the development of a single nucleotide polymorphism (SNP) genotyping panel from whole-genome resequencing data that enables targeted species identification in Tanzania. We demonstrate that an optimized panel of 96 genome-wide SNPs based on FST outliers performs comparably to whole genome resequencing in distinguishing species and identifying hybrids. We also show this panel outperforms microsatellite-based and phenotype-based classification methods. Case studies indicate several locations where introduced aquaculture species have become established in the wild, threatening native Oreochromis species. The novel SNP markers identified here represent an important resource for assessing broodstock purity in hatcheries and helping to conserve unique endemic biodiversity.

Metabarcoding Analysis of Bacterial Communities Associated with Media Grow Bed Zones in an Aquaponic System.

The development of environmentally sustainable plant and fish production in aquaponic systems requires a complete understanding of the systems' biological components. In order to better understand the role of microorganisms in this association, we studied the bacterial communities in the dry, root, and mineralized zones of a flood-and-drain media bed aquaponic system. Bacterial communities were characterized using metabarcoding of the V3-V4 16S rRNA regions obtained from paired-end Illumina MiSeq reads. Proteobacteria, Actinobacteria, and Bacteroidetes accounted for more than 90% of the total community in the dry zone and the effluent water. These phyla also accounted for more than 68% of the total community in the root and mineralized zones. The genera Massilia, Mucilaginibacter, Mizugakiibacter, and Rhodoluna were most dominant in the dry, root, and mineralized zones and in the effluent water, respectively. The number of shared operational taxonomic units (OTUs) for the three zones was 241, representing 7.15% of the total observed OTUs. The number of unique OTUs in samples from dry zone, root zone, mineralized zone, and effluent water was 485, 638, 445, and 383, respectively. The samples from the root zone harbored more diverse communities than either the dry or mineralized zones. This study is the first to report on the bacterial community within the zones of a flood-and-drain media bed. Thus, this information will potentially accelerate studies on other microbial communities involved in the bioconversion of nitrogen compounds and mineralization within these types of aquaponic systems.

Nutrient composition of fish protein powder developed from Brycinus nurse (Rüppell, 1832).

A new product in the form of edible fish powder was developed from small pelagic fish (Brycinus nurse) which constitutes one of the major commercial fisheries in Lake Albert, Uganda. The objective of the study was to determine the proximate and mineral composition of the newly developed fish powder and also to compare it with Nile tilapia powder already on market. Results indicated that the changes in the amount of protein and ash were found to be significantly higher (p < 0.05) in fish powder than in fried samples. The increase in fat content of fried fish samples was found to be significant compared to other fish samples. No significant changes (p > 0.05) were observed in carbohydrate content for raw, fried, and powdered samples. Vitamin A decreased significantly in powdered samples. Comparing the B. nurse powder and tilapia powder (made from juvenile tilapia as raw material), the results indicated that B. nurse had higher levels of iron and manganese. Extracting proteins from B. nurse provides an opportunity to increase the utilization of harvested catch.

Histomorphological Description of the Digestive System of Pebbly Fish, Alestes baremoze (Joannis, 1835).

Histomorphological studies of the digestive system of Alestes baremoze captured from Lake Albert, Uganda, were done using standard procedures. These revealed that A. baremoze has a fleshy-lipped terminal small mouth, large molar, short oesophagus, a three-lobed liver, pouch-like stomach, a nine-fingered caeca, and a long tubular intestine. A stratified squamous epithelium with numerous mucus-secreting cells lined the lips with no taste buds. Stratified squamous epithelia lined the oesophagus in the anterior portion which turned into a columnar epithelium towards the stomach. The lamina propria had numerous tubular glands throughout the entire oesophageal length. The stomach consisted of three distinct regions (cardiac, fundic, and pyloric) with distinguished lamina propria glands. The intestinal mucosa was thrown into villi of varying heights, with the tallest in the anterior part, lined with a simple columnar epithelium with numerous lymphocytes-like infiltrations. Numerous goblet cells appeared in the intestinal lamina epithelialis; these increased uniformly towards the anal opening. The liver was divided into lobules, with a central vein. Hepatocytes were visibly arranged closely, forming irregular cords, and the scattered tubular acinar glands formed the exocrine pancreas (hepatopancreas). Stomach content analysis indicated that the fish eats plankton, mollusks, crustaceans, and insects as the main proportion of its diet.