Molecular genetic diversity and differentiation of Nile tilapia (Oreochromis niloticus, L. 1758) in East African natural and stocked populations.

BACKGROUND: The need for enhancing the productivity of fisheries in Africa triggered the introduction of non-native fish, causing dramatic changes to local species. In East Africa, the extensive translocation of Nile tilapia (Oreochromis niloticus) is one of the major factors in this respect. Using 40 microsatellite loci with SSR-GBS techniques, we amplified a total of 664 individuals to investigate the genetic structure of O. niloticus from East Africa in comparison to Ethiopian and Burkina Faso populations. RESULTS: All three African regions were characterized by independent gene-pools, however, the Ethiopian population from Lake Tana was genetically more divergent (Fst = 2.1) than expected suggesting that it might be a different sub-species. In East Africa, the genetic structure was congruent with both geographical location and anthropogenic activities (Isolation By Distance for East Africa, R2 = 0.67 and Uganda, R2 = 0.24). O. niloticus from Lake Turkana (Kenya) was isolated, while in Uganda, despite populations being rather similar to each other, two main natural catchments were able to be defined. We show that these two groups contributed to the gene-pool of different non-native populations. Moreover, admixture and possible hybridization with other tilapiine species may have contributed to the genetic divergence found in some populations such as Lake Victoria. We detected other factors that might be affecting Nile tilapia genetic variation. For example, most of the populations have gone through a reduction in genetic diversity, which can be a consequence of bottleneck (G-W, < 0.5) caused by overfishing, genetic erosion due to fragmentation or founder effect resulting from stocking activities. CONCLUSIONS: The anthropogenic activities particularly in the East African O. niloticus translocations, promoted artificial admixture among Nile Tilapia populations. Translocations may also have triggered hybridization with the native congenerics, which needs to be further studied. These events may contribute to outbreeding depression and hence compromising the sustainability of the species in the region.

Exploring the morphological dynamics of Nile tilapia (Oreochromis niloticus Linn. 1758) in Victoria Nile as depicted from geometric morphometrics.

BACKGROUND: Various anthropogenic activities continue to threaten the fish biodiversity of the East African water bodies such as the Victoria Nile. Although the Victoria Nile is a significant source of livelihood for human populations, the biology and ecology of Nile tilapia in this ecosystem remain understudied with little or no information on the morphology of the fish given varying and immense anthropogenic activities. Here, we use geometric morphometrics to examine the morphology/shape variations of Nile tilapia populations in Victoria Nile to gain insights into their current ecological state. RESULTS: Our results indicate unexpectedly smaller Nile tilapia body weights in Victoria Nile than in L. Victoria. Despite this, nearly all the populations displayed a relative condition factor (Kn) of greater ≥1 suggesting a healthy stock. However, two populations, LMF and VN_Bukeeka demonstrated Kn values of less than one (< 1). We also report that some Upper and Lower Victoria Nile populations display morphological similarities. Apart from L. Albert, Nile tilapia populations from Lakes Victoria and Kyoga are morphologically divergent from the riverine ones. We note that Nile tilapia from Nalubale Dam Reservoir is morphologically distinct from the close neighbouring Victoria Nile populations which are likely allied to the influence of the Nalubale Hydroelectric power dam as a barrier. CONCLUSION: Nile tilapia's morphological variation appears to be influenced by various anthropogenic disturbances notably, overfishing, hydroelectric power dams, and fish translocational history in Uganda. Management should enforce regulatory frameworks to avert human-mediated activities as these are likely to compromise the sustainability of the fisheries. Further studies are required to follow these populations with molecular genetics and environmental data to gain a deeper understanding of the fish species for informed sustainable management and conservation options.

Identifying geographically differentiated features of Ethopian Nile tilapia (Oreochromis niloticus) morphology with machine learning.

Visual characteristics are among the most important features for characterizing the phenotype of biological organisms. Color and geometric properties define population phenotype and allow assessing diversity and adaptation to environmental conditions. To analyze geometric properties classical morphometrics relies on biologically relevant landmarks which are manually assigned to digital images. Assigning landmarks is tedious and error prone. Predefined landmarks may in addition miss out on information which is not obvious to the human eye. The machine learning (ML) community has recently proposed new data analysis methods which by uncovering subtle features in images obtain excellent predictive accuracy. Scientific credibility demands however that results are interpretable and hence to mitigate the black-box nature of ML methods. To overcome the black-box nature of ML we apply complementary methods and investigate internal representations with saliency maps to reliably identify location specific characteristics in images of Nile tilapia populations. Analyzing fish images which were sampled from six Ethiopian lakes reveals that deep learning improves on a conventional morphometric analysis in predictive performance. A critical assessment of established saliency maps with a novel significance test reveals however that the improvement is aided by artifacts which have no biological interpretation. More interpretable results are obtained by a Bayesian approach which allows us to identify genuine Nile tilapia body features which differ in dependence of the animals habitat. We find that automatically inferred Nile tilapia body features corroborate and expand the results of a landmark based analysis that the anterior dorsum, the fish belly, the posterior dorsal region and the caudal fin show signs of adaptation to the fish habitat. We may thus conclude that Nile tilapia show habitat specific morphotypes and that a ML analysis allows inferring novel biological knowledge in a reproducible manner.

Genetic diversity of Nile tilapia (Oreochromis niloticus) populations in Ethiopia: insights from nuclear DNA microsatellites and implications for conservation.

BACKGROUND: Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) is among the economically most important freshwater fish species in East Africa, and a major source of protein for local consumption. Human induced translocations of non-native stocks for aquaculture and fisheries have been found as a potential threat to the genetic diversity and integrity of local populations. In the present study, we investigate the genetic structure of O. niloticus from 16 waterbodies across Ethiopia using 37 microsatellite loci with SSR-GBAS techniques. RESULTS: The samples are structured into three main clusters shaped either by biogeographic factors or stocking activities. High FST values (Global FST = 0.438) between populations indicate a high level of genetic differentiation and may suggest long term isolation even within the same drainage systems. Natural populations of the Omo-Turkana system and the lakes in the Southern Main Ethiopian Rift showed the highest genetic variability while low variability was found in stocked populations of lakes Hora, Hashenge and Hayq. CONCLUSIONS: The results presented herein, may provide an essential basis for the management and conservation of the unique genetic resources in northern East Africa, and advance our understanding of biodiversity, phylogeny, evolution and development towards phylogenetically more accurate taxonomic classifications.

Characteristics of municipal fresh solid wastes from the selected large urban centres in Uganda: Implication for re-use and soil amendment strategies.

In Uganda, the municipal solid wastes are generally a menace to the environment, ranging from indiscriminate dumping, open burning, and landfills, which would be utilized to augment agricultural fields through organic manure. The National Environment Management Authority (NEMA) of Uganda, however from 2009 to 2012 initiated and implemented a Clean Development Mechanism project. This project was established and conducted in nine urban centers with the key objective of reducing methane and other environmental nuisances while generating compost manure. The in-coming fresh municipal wastes at composting facilities were sorted into six categories; i) wood and wood products, ii) food and food wastes, iii) textiles, iv) garden, yard and park wastes, v) paper and pulp, and vi) glass, plastics, and metals. These were laboratory analyzed based on standard procedures, characterized and investigated for the pH, total organic carbon (TOC), total nitrogen (TN), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) (g kg-1). Statistical analyses were performed based on One-Way ANOVA, implemented in the SPSS program. The results indicate that the municipal fresh solid wastes were mainly dominated by biodegradable organic matter; garden, yard, and park wastes (49%), food and food wastes (43.2%), and the other wastes falling below 5.4%. Overall, the pH was 7.7 ± 0.02, TOC 318.2 ± 2.90, TN 12.1 ± 0.10, C/N 26.7 ± 0.20, P 4.4 ± 0.04, K 35.0 ± 0.49, Ca 38.9 ± 0.51, and Mg 5.8 ± 0.09. The concentration of the fresh wastes and macro-nutrients varied per municipality and were congruent with the economic activities and population lifestyles. We detected the effect of season/month on the concentration of wastes which corresponded with the various agronomical activities. The results from this study suggest that the notion of composting is potentially a viable organic waste management strategy in the country which can ultimately generate sufficient organic manure for agricultural input and thus enhanced carbon sequestration.Implications: In this study, we characterized the in-coming fresh municipal solid wastes and investigated the pH, total organic carbon (TOC), total nitrogen (TN), phosphorus (P), potassium (K), calcium (Ca), and magnesium (Mg) (g kg-1). We found that the municipal fresh solid wastes were mainly dominated by biodegradable organic matter (>90%). The results from this study suggest the notion of composting to be potentially a viable organic waste management strategy in Uganda which can ultimately generate sufficient organic manure for agricultural input. This is typically vital for enhancing carbon sequestration towards minimizing greenhouse gas emissions.