Genetics studies of cichlid Oreochromis shiranus towards sustainable aquaculture and fisheries management in Malawi

Thesis (PhDAgric)--Stellenbosch University, 2020.ENGLISH ABSTRACT: Oreochromis shiranus is an economically important fish species in Malawi, but levels of harvest from the wild have declined due to overexploitation and habitat degradation. There is an urgent need to devise strategies for sustainable utilization of this species. The aim of this study was to understand the reproductive behaviour, geographic distribution, genetic diversity, population structure, past demographic fluctuations and association of quantitative trait loci (QTL) with traits of economic importance which are prerequisites for the design and implementation of these strategies. A random sample of 306 live fish, collected across the main water bodies in Malawi, were reared in one pond to reproduce an F1 generation in random families. This study observed that mate selection and competition among the females for males and mating sites resulted in only a few females (42%) and males (27%) contributing to the F1 generation. However, there was no statistically significant variation in genetic diversity between the broodstock and the F1 generation, because of the large genetic base and participation of broodstock from all the sampled locations. The study concluded that due to limited gene flow, O. shiranus populations in the wild in Malawi were structured according to and within water basins. There was evidence of population bottlenecks in the wild, which corresponded to small effective population sizes (Ne = 104). The population bottlenecks did not result in low genetic diversity and inbreeding depression due to isolate breaking. Finally, the association of some QTLs for body weight in Oreochromis spp. suggest considerable evolutionary conservation and synteny within the genus. The observed levels of genetic diversity and Ne across the main water bodies in Malawi are adequate to increase Ne and mitigate against future bottlenecks if closed fishing seasons and fishing net mesh size are enforced. Restocking programmes may not be necessary at the moment unless in the event of complete desiccation. During restocking, it is therefore recommended that, to ensure genetic diversity, broodstock for stock enhancement should be randomly sampled from the different populations within the water body. In aquaculture, where interest is to increase production of large fish, these findings will greatly inform management and breeding programmes to ensure genetic diversity and increase selection efficiency by using QTLs. Although it was not possible to determine the ideal number of individuals that should be included as founder population for selective breeding programmes, this study recommends that a wide genetic base is required to ensure genetic diversity. The results of this study are useful in conservation management of the species in the wild and the establishment of genetic improvement programs in aquaculture.AFRIKAANSE OPSOMMING: Oreochromis shiranus is 'n ekonomies belangrike visspesie in Malawi, maar die oesvlakke in die natuur het afgeneem as gevolg van oorbenutting en agteruitgang van die habitat. Dit is dringend nodig om strategieë vir die volhoubare benutting van hierdie spesie te ontwerp. Die doel van hierdie studie was om die voortplantingsgedrag, geografiese verspreiding, genetiese diversiteit, populasiestruktuur, historiese demografiese skommelinge en assosiasie van kwantitatiewe eienskap loci (KEL) met eienskappe van ekonomiese belang te verstaan, wat voorvereistes is vir die ontwerp en implementering van hierdie strategieë. 'n Ewekansige monster van 306 lewende visse wat oor die belangrikste waterliggame in Malawi versamel is, is in een dam grootgemaak om ‘n F1-generasie in ewekansige families weer te gee. In hierdie studie is opgemerk dat maatkeuse en kompetisie tussen vroulike diere vir mannetjies en paringsgebiede tot gevolg gehad het dat slegs enkele wyfies (42%) en mannetjies (27%) tot die F1-generasie bygedra het. Daar was egter geen statisties beduidende variasie in genetiese diversiteit tussen die broeidiere en die F1-generasie nie, as gevolg van die groot genetiese basis en deelname van die broeidiere van die al versamelde lokatiteite. Die studie het tot die gevolgtrekking gekom dat O. shiranus bevolkings in die natuur in Malawi as gevolg van beperkte geenvloei volgens en binne waterliggame gestruktureer is. Daar was bewyse van populasie bottelnekke in die natuur, wat ooreenstem met klein effektiewe populasiegroottes (Ne = 104). Die populasie bottelnekke het nie gelei tot lae genetiese diversiteit en inteling verval as gevolg van isolasiebreuk nie. Laastens, die assosiasie van sommige KEL's vir liggaamsgewig in Oreochromis spp. dui op aansienlike evolusionêre bewaring en sintenie binne die genus. Die waargenome vlakke van genetiese diversiteit en Ne in die belangrikste waterliggame in Malawi is voldoende om Ne te verhoog en die populasies te beskerm teen toekomstige bottelnekke as geslote visvangseisoene en die visnet groottes toegepas word. Aanvullings programme is op die oomblik miskien nie nodig nie, tensy in die geval van volledige uitdroging. Tydens die aanvulling word dus aanbeveel dat om genetiese diversiteit te verseker, broeidiere vir broeidier verbetering lukraak uit die verskillende populasies in die waterliggaam geneem moet word. In akwakultuur, waar belangstelling is om die produksie van groot visse te verhoog, sal hierdie bevindings die bestuur- en teelprogramme baie inlig om genetiese diversiteit te verseker en seleksiedoeltreffendheid te verhoog deur gebruik te maak van KEL's. Alhoewel dit nie moontlik was om die ideale aantal individue te bepaal wat opgeneem moet word as stigterpopulasie vir selektiewe teelprogramme nie, beveel hierdie studie aan dat 'n wye genetiese basis benodig word om genetiese diversiteit te verseker. Die resultate van hierdie studie is nuttig vir die bewaring van die spesies in die natuur en vir die opstel van genetiese verbeteringsprogramme in akwakultuur.Doctora

The effect of engaging unpaid informal providers on case detection and treatment initiation rates for TB and HIV in rural Malawi (Triage Plus): A cluster randomised health system intervention trial

Background The poor face barriers in accessing services for tuberculosis (TB) and Human Immuno-deficiency Virus (HIV) disease. A cluster randomised trial was conducted to investigate the effectiveness of engaging unpaid informal providers (IPs) to promote access in a rural district. The intervention consisted of training unpaid IPs in TB and HIV disease recognition, sputum specimen collection, appropriate referrals, and raising community awareness. Methods In total, six clusters were defined in the study areas. Through a pair-matched cluster randomization process, three clusters (average cluster population = 200,714) were allocated to receive the intervention in the Early arm. Eleven months later the intervention was rolled out to the remaining three clusters (average cluster population = 209,564)—the Delayed arm. Treatment initiation rates for TB and Anti-Retroviral Therapy (ART) were the primary outcome measures. Secondary outcome measures included testing rates for TB and HIV. We report the results of the comparisons between the Early and Delayed arms over the 23 month trial period. Data were obtained from patient registers. Poisson regression models with robust standard errors were used to express the effectiveness of the intervention as incidence rate ratios (IRR). Results The Early and Delayed clusters were well matched in terms of baseline monthly mean counts and incidence rate ratios for TB and ART treatment initiation. However there were fewer testing and treatment initiation facilities in the Early clusters (TB treatment n = 2, TB testing n = 7, ART initiation n = 3, HIV testing n = 20) than in the Delayed clusters (TB treatment n = 4, TB testing n = 9, ART initiation n = 6, HIV testing n = 18). Overall there were more HIV testing and treatment centres than TB testing and treatment centres. The IRR was 1.18 (95% CI: 0.903–1.533; p = 0.112) for TB treatment initiation and 1.347 (CI:1.00–1.694; p = 0.049) for ART initiation in the first 12 months and the IRR were 0.552 (95% CI:0.397–0.767; p<0.001) and 0.924 (95% CI: 0.369–2.309, p = 0.863) for TB and ART treatment initiations respectively for the last 11 months. The IRR were 1.152 (95% CI:1.009–1.359, p = 0.003) and 1.61 (95% CI:1.385–1.869, p<0.001) for TB and HIV testing uptake respectively in the first 12 months. The IRR was 0.659 (95% CI:0.441–0.983; p = 0.023) for TB testing uptake for the last 11 months. Conclusions We conclude that engagement of unpaid IPs increased TB and HIV testing rates and also increased ART initiation. However, for these providers to be effective in promoting TB treatment initiation, numbers of sites offering TB testing and treatment initiation in rural areas should be increased. Trial registration ClinicalTrials.gov NCT02127983

Systematic review and chemoinformatics analysis of anti-allergic medicinal plants used in Malawi

In Malawi, ethnobotanical surveys have been carried out on the plants used to treat or manage allergies and their symptoms. However, studies focusing on information analysis such as systematic reviews of anti-allergic plants and natural products are not yet published. This review highlighted and analysed data of potential anti-allergic medicinal plants used in Malawi in order to discover potential treatments for allergies through various approaches and improve well-being of people. Literature search strategy was used to collect data of medicinal plants. Chemoinformatics analysis was applied to compile associated natural products and to profile the physicochemical properties (drug-likeness and fingerprint diversity) with references to 60 antihistamine 1 drugs (H1R drugs) and 277 anti-H1 receptor inhibitors. Sixty (60) medicinal plants from 36 families out of 645 reported plant species had information of diseases or symptoms of allergies. The Malawian Natural Products (MNP) data set composed of 1757 unique compounds was compiled for the first time from 39 of 60 medicinal plants and approximately 48.9 % and 45.3 % of the compounds did not violate Lipinski and Veber drug-like rules respectively. Chemical space mapping revealed that compounds from Malawian medicinal plants are structurally diverse and share a small space with antihistamine compounds and drugs. This information is useful in exploring other anti-allergy biological mechanisms for natural products. Similarity screening identified usambarine (CID442121), which is structurally similar to 2,8-Dimethyl-5-(2-pyrazine-2-ylethyl)-gamma-carboline (CHEMBL1783970) and 29 other antihistamine compounds. The results will be used as a baseline for further studies which may eventually lead to the discovery of potential allergy treatments through various approaches. This could improve health and well-being of people which is in line with goal number 3 of Sustainable Development Goals, Africa's Union's Agenda 2063 and National Research Agenda for the Malawi 2063

Monthly and cumulative HIV testing rates per 1,000 adults: Results in individuals aged 12 years and above over the first 11 months of the study before the scale up of the Delayed intervention arm are shown.

<p>The line graphs represent the cumulative HIV testing rates. The green triangle line graph indicates the Early Intervention arm and the purple cubed line graph indicates the Delayed Intervention arm. The solid bar graphs represent the monthly HIV testing rates per 1,000 adults for every month over the 11 months of the study. The blue bars represent the Early Intervention Arm while the grey bars represent the Delayed Intervention Arm.</p

Monthly and cumulative TB testing rates per 10,000 adults: Results in individuals aged 12 years and above over the 23 months of the study are shown.

<p>The line graphs represent the cumulative TB testing rates. The green triangle line graph indicates the Early Intervention arm and the purple cubed line graph indicates the Delayed Intervention arm. The solid bar graphs represent the monthly TB testing rates per 1,000 adults for each month over the 23 months of the study. The blue bars represent the Early Intervention Arm while the grey bars represent the Delayed Intervention Arm.</p

Adjusted incidence rate ratios for intervention effects in access rates to HIV testing and treatment services over the 23 months of the intervention.

<p>Adjusted incidence rate ratios for intervention effects in access rates to HIV testing and treatment services over the 23 months of the intervention.</p

Incidence rate ratios for intervention effects in access rates to TB diagnostic and treatment services over the 23 months of the intervention.

<p>Incidence rate ratios for intervention effects in access rates to TB diagnostic and treatment services over the 23 months of the intervention.</p

Monthly and cumulative ART treatment initiations rates per 10,000 adults: Results in individuals aged 12 years and above over the 23 months of the study before the scale up of the Delayed intervention arm are shown.

<p>The line graphs represent the cumulative ART initiation rates. The green triangle line graph indicates the Early Intervention arm and the purple cubed line graph indicates the Delayed Intervention arm. The solid bar graphs represent the monthly ART initiation rates per 1,000 adults for every month over the 23 months of the study. The blue bars represent the Early Intervention Arm while the grey bars represent the Delayed Intervention Arm.</p

Triage Plus study design: Phased, pair-matched, parallel cluster design used to randomise study clusters to Early and Delayed arms.

<p>The blue colour represents the baseline period and the dark pink represents when the intervention package was implemented in the respective arms and the light pink represents study period when no intervention was implemented in the Delayed arm.</p

Map of Lilongwe District showing the distinction between urban and rural areas and the rural clusters allocated to the Early (pink) and Delayed (brown) arms of the trial.

<p>Map of Lilongwe District showing the distinction between urban and rural areas and the rural clusters allocated to the Early (pink) and Delayed (brown) arms of the trial.</p