ABSTRACT Lake Malombe has been under severe fishing pressure despite its continued provision of significant ecosystem services to the surrounding communities. Despite several research interests, there is limited updated knowledge on the status of fish stocks; hence, a study was conducted to address that. The study specifically determined catch rates, density, fish species diversity and biomass. It hypothesised that fish catch rates, densities, fish species diversity and biomass were the same between the 2017 and 2025 surveys. Multiple data analysis tools were used in conducting statistical analyses for both 2017 and 2025 data. The current survey results registered a significant decline in fish catches ( p = 0.048), catch rates ( p = 0.0007) and densities ( p = 0.008) between the 2017 and 2025 surveys. Fish catch rates and density significantly varied across the blocks ( p = 0.022) and ( p = 0.0323), respectively. There was a significant decline in fish biomass of key fish species between the survey periods and across blocks. Both surveys revealed relatively low fish diversity and evenness with no differences between the periods ( p = 0.085) and across the blocks ( p = 0.066). Across the two surveys, the 54 identified fish species belonged to various conservation statuses. Changes in fish populations, including the decline of historically dominant species and the rise of smaller haplochromines, may reflect the impacts of overfishing and habitat damage to the ecosystem. Interventions that promote resource users are strongly recommended, such as better regulation enforcement, a community‐based co‐management approach and habitat rehabilitation, so that the long‐term restoration and conservation of fisheries resources in Lake Malombe can be achieved.

Lake Chilwa in southern Malawi undergoes periodic drying that severely impacts fisheries, aquatic biodiversity, and the livelihoods of millions. Recovery of the lake fishery depends largely on deep pools in influent rivers, which serve as critical fish refugia during lake recession. These pools are increasingly threatened by environmental degradation, unsustainable irrigation, and poor fishing practices. This study examined the role of deep pools in tributary rivers in maintaining fish biodiversity and supporting fisheries recovery during and after lake drying. Deep pools in the Likangala and Domasi rivers were mapped and assessed for productivity and species diversity between December 2018 and 2019. Baseline water quality data from 2015/16, covering dry and wet seasons at 16 sites, were analysed using standard methods, together with Environmental Water Flow assessments based on a desktop reserve model. Water quality varies by river, season, and channel type, with significantly higher concentrations of most parameters during the dry season. Hydrochemical analysis showed bicarbonate dominance, suggesting mineral denudation driven by CO2-charged runoff as the main controlling process. Clear hydrochemical gradients distinguish deep pools from open channels, confirming deep pools as chemically and biologically distinct habitats. Desktop Reserve Model results indicated that the Domasi River is in better ecological condition, while the Likangala River shows over-commitment of water resources. In both rivers, deep pools maintained fish biodiversity and acted as key refugia and breeding habitats during lake recession through maintenance of water volume at a quality amenable for fish production. However, fish biomass, productivity, and species diversity were significantly higher in Likangala River pools, reflecting their larger size and depth, higher water volumes, and better community-based fisheries management. This shows that favourable ecological conditions alone are insufficient without effective governance. Fish production rose from about 5 000 tonnes before the 2017 recession to a record 42 000 tonnes in 2024. Recovery followed flood-pulse dynamics, enhanced by cyclone-driven nutrient inputs and an extended closed fishing season. Despite this, unregulated water abstraction, catchment degradation, agricultural runoff, weak governance, and invasive species threaten sustainability. Strengthening local management, community awareness, multi-sectoral coordination, and long-term monitoring is essential to sustain fishery resilience under increasing climate variability.

This study investigated the ecological significance of community-managed spawning sites in Lakes Chilwa and Chiuta catchments in Malawi. The study was conducted to generate usable information that guides fisheries conservation and management efforts by determining fish species diversity, population structure and conservation status. Five spawning sites (Chitundu, Nambala, Nansato, Bowo and Zakwere) were monitored, and fish were sampled using open seine nets. Several techniques and statistical tools were deployed in the sampling, data entry and analyses. A total of nine species were recorded, with cyprinids dominating the catch (79.3%). Enteromius paludinosus was the most abundant species (57.8%) among the fish species sampled. Fish diversity was generally low, with Shannon-Weiner diversity indices ranging from 0.14 to 0.87. Most of the dominating E. paludinosus were not sexually mature by the time of sampling. Among the species recorded, Oreochromis mossambicus was the only species classified as vulnerable (VU) on the IUCN Red List. The study demonstrated that the identified spawning sites were indeed the spawning sites of fish species, particularly the E. paludinosus. These findings emphasize the need for enhanced regulatory measures through the development of ecosystem-based management plans that include stricter enforcement of no-fishing policies and the use of sustainable fishing gears to protect juvenile fish and ensure the long-term sustainability of fisheries. This study revealed the potential of community-based fisheries management (CBFM) in conserving vital spawning grounds and promoting ecosystem resilience.

Comparative studies of whole genomes have increasingly shown that genetic introgression between closely related species is surprisingly common across the tree of life, making the description of biodiversity and understanding the process of speciation complex and challenging. The adaptive radiation of cichlid fishes in Lake Malawi, that is characterised by hybrid origins and cases of recent introgression, provides a valuable model system to study the evolutionary implications of introgression. However, many potential sources of introgression into the radiation have not yet been investigated. Here we use whole genome data from 239 species from Lake Malawi and 76 species from surrounding African river and lake systems to identify previously unknown introgression events involving the Malawi radiation. Computing genome-wide excess allele sharing (ABBA-BABA statistics) and window-based statistics, we find that three independent riverine cichlid lineages show significantly higher allele sharing with the Malawi radiation than expected, suggesting historical genetic exchange. Introgressed haplotypes are distributed relatively uniformly across the Malawi radiation, indicating that most hybrid-derived polymorphism was acquired and sorted before the formation of the contemporary Malawi radiation. Our results point towards several previously unknown contributors to the Malawi cichlid hybrid swarm and show that the history of one of the largest vertebrate radiations is more complex than previously thought.

The SAR11-IIIb genus Fontibacterium within the order 'Ca. Pelagibacterales' is recognized for its ubiquitous presence in freshwater environments. However, cultivation limitations have hampered deeper ecophysiological understanding of this genus, with most data limited to lakes in the Northern Hemisphere. Here we present seven isolates representing two previously undescribed species, along with 93 high-quality metagenome-assembled genomes (MAGs) derived from a global survey across five continents. Phylogenomic analysis revealed 16 species forming nine distinct biogeographic clusters, indicating speciation patterns linked to water temperature and latitude. We observed endemic species restricted to African lakes, and quasi-endemic species confined to the Northern or Southern Hemisphere, which co-exist alongside cosmopolitan species. Metabolic profiling and growth experiments uncovered species- and strain-specific adaptations for nutrient uptake, along with unique pathways for sulfur metabolism. These findings provide a global-scale genomic and ecological overview for this underexplored lineage of freshwater SAR11.

Chromosomal inversions contribute to adaptive speciation by linking co-adapted alleles. Querying 1,375 genomes of the species-rich Malawi cichlid fish radiation, we discovered five large inversions segregating in the benthic subradiation that each suppress recombination over more than half a chromosome. Two inversions were transferred from deepwater pelagic Diplotaxodon via admixture, while the others established early in the deep benthics. Introgression of haplotypes from lineages inside and outside the Malawi radiation coincided with bursts of species diversification. Inversions show evidence for transient sex linkage and a striking excess of protein changing substitutions pointing towards selection on sensory, behavioural and reproductive genes. We conclude that repeated interplay between depth adaptation and sex-specific selection on large inversions has been central to the evolution of this iconic system. ### Competing Interest Statement The authors have declared no competing interest.

Telonemia are one of the oldest identified marine protists that for most part of their history have been recognized as a distinct incertae sedis lineage. Today, their evolutionary proximity to the SAR supergroup (Stramenopiles, Alveolates, and Rhizaria) is firmly established. However, their ecological distribution and importance as a natural predatory flagellate, especially in freshwater food webs, still remain unclear. To unravel the distribution and diversity of the phylum Telonemia in freshwater habitats, we examined over a thousand freshwater metagenomes from all over the world. In addition, to directly quantify absolute abundances, we analyzed 407 samples from 97 lakes and reservoirs using Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). We recovered Telonemia 18S rRNA gene sequences from hundreds of metagenomic samples from a wide variety of habitats, indicating a global distribution of this phylum. However, even after this extensive sampling, our phylogenetic analysis did not reveal any new major clades, suggesting current molecular surveys are near to capturing the full diversity within this group. We observed excellent concordance between CARD-FISH analyses and estimates of abundances from metagenomes. Both approaches suggest that Telonemia are largely absent from shallow lakes and prefer to inhabit the colder hypolimnion of lakes and reservoirs in the Northern Hemisphere, where they frequently bloom, reaching 10%-20% of the total heterotrophic flagellate population, making them important predatory flagellates in the freshwater food web.

Fish is an important source of animal protein for many people living around Lake Malawi. The evaluation of population structure and genetic diversity can yield useful information for management and conservation of fish species but is complicated in Lake Malawi by the close genetic relatedness of species of the recent cichlid adaptive radiation. In this study, we analyzed whole-genome sequencing data of "true utaka," a group of cichlids previously common in fisheries, but that has faced strong decline due to overfishing. Our analysis of 224 individuals collected from fishermen's catches along the western shoreline of Lake Malawi confirmed that Copadichromis mloto (that has been referred to as Copadichromis sp. "virginalis kajose") is the true utaka most targeted by fisheries. Genetic principal component analysis, phylogenetic inference, and admixture analysis revealed complex patterns of population structure. The presence of at least three geographically widespread genetic clades that have remained separate despite gene flow and partial sympatry hints at the presence of currently undescribed, cryptic species diversity in C. mloto. This result leads us to suggest that, despite the lack of obvious habitat barriers, pelagic species of Malawi cichlids might harbor unidentified species diversity and calls for further genetic and taxonomic research to define appropriate conservation units.

To ensure the long-term sustainable use of African Great Lakes (AGL), and to better understand the functioning of these ecosystems, authorities, managers and scientists need regularly collected scientific data and information of key environmental indicators over multi-years to make informed decisions. Monitoring is regularly conducted at some sites across AGL; while at others sites, it is rare or conducted irregularly in response to sporadic funding or short-term projects/studies. Managers and scientists working on the AGL thus often lack critical long-term data to evaluate and gauge ongoing changes. Hence, we propose a multi-lake approach to harmonize data collection modalities for better understanding of regional and global environmental impacts on AGL. Climate variability has had strong impacts on all AGL in the recent past. Although these lakes have specific characteristics, their limnological cycles show many similarities. Because different anthropogenic pressures take place at the different AGL, harmonized multi-lake monitoring will provide comparable data to address the main drivers of concern (climate versus regional anthropogenic impact). To realize harmonized long-term multi-lake monitoring, the approach will need: (1) support of a wide community of researchers and managers; (2) political goodwill towards a common goal for such monitoring; and (3) sufficient capacity (e.g., institutional, financial, human and logistic resources) for its implementation. This paper presents an assessment of the state of monitoring the AGL and possible approaches to realize a long-term, multi-lake harmonized monitoring strategy. Key parameters are proposed. The support of national and regional authorities is necessary as each AGL crosses international boundaries.

Lake Malawi/Niassa/Nyasa (LMNN) is one of the most important and third-largest African Great Lakes. It has the largest number of freshwater fish species in the world, most of which are endemic. Current estimates put the number of fish species in the range of 800-1000. The riparian countries of Malawi, Mozambique and Tanzania enjoy enormous benefits that accrue from the ecosystem services that the lake provides. However, LMNN is experiencing severe adverse impacts resulting from anthropogenic and climatic stressors, leading to increased sediment and nutrient loading. This observation motivated this study to identify existing research gaps to enhance the lake's sustainable management. Specifically, the assessment focused on three key issues identified and prioritised by the LMNN Basin Fisheries and Aquaculture Network (LMNNBFAN), namely: fishery health, invasive species, and climate change. Data collection involved stakeholder consultations, field surveys, and desk reviews. Recommendations from study findings, that would create a conducive environment for the sustainable management of the lake, have been grouped into four main categories: research needs, infrastructure development, human capacity building and funding.

Abstract There is overwhelming evidence that the shallow water stocks of Lake Malawi have been noticeably overexploited by both the artisanal and commercial trawl fishers. However, there have been some recent initiatives to restore these areas such as enhancing monitoring, control and surveillance, revamping local fisheries management authorities and establishments of community managed fish protected areas. Yet, information evaluating the impacts of such interventions on the fish stocks is limited. This information is critical for fisheries management and planning. Therefore, a study to reveal the current status of Chambo (Oreochromisspecies) and other shallow water fish stocks of the southwest arm (SWA) and southeast arm (SEA) of Lake Malawi was conducted. The study compared the status of fish stocks in the two arms using stock abundance and biodiversity indicators. Results indicated similar fish species diversity in the two arms. Overall, Chambo (Oreochromis spp.) was among the top ten fish that contributed a significant amount of weight to the total sampled catch. The SWA and SEA reported average catch rates of 77.4±22.6Kg/0.5hr and 177.7±18.4Kg/0.5hr, respectively whereas Chambo registered mean catch rates of 61.0±8.1Kg/0.5hr and 68.0±13.7Kg/0.5hr, respectively. Overall fish densities for all fish species in the SWA and SEA were estimated at 2.9tons/km2and 3.5tons/km2, respectively. Chambo density estimates for both SWA and SEA were calculated as 1.1tons/km2 and 1.2tons/km2, respectively. A total biomass of 10, 722 tons was estimated in both regions with the SEA contributing 57% while the biomass estimates of Chambo was 3,964 tons of which 54% was registered in the SEA. A decline in fish stocks in the shallow waters was observed and masks the efforts that the Government is doing to ensure the restoration and sustainability of fish stocks in the areas. It is therefore strongly believed thatregulating mesh sizes, limiting fishing effort and protecting critical breeding habitats are critical in reversing the observed trends.

A comparative analysis of solar tent drying (Samva Nyengo) and open sun drying were evaluated for their effectiveness on quality of Copadichromis virginalis on nutritional content, microbial load and sensory quality. Solar tent dried and open sun dried Copadichromis virginalis contained 62.89±0.05% and 62.73±0.096% of crude protein, 23.24±0.66% and 23.41±0.59% of fat, 7.22±0.021% and 16.31±0.36% of moisture 14.48±1.08% and 21.97±0.36% of ash respectively. Moisture and ash were significant difference (p = 0.001), crude protein and crude fat showed a non-significant difference (p = 0.05). Open sun dried had significantly higher bacteria load (4.1×10 5 CFU/g) (0.001) than solar tent dried fish (2.2×10 2 CFU/g). Isolated bacteria from solar tent dried and open sun dried fish were 1.2×10 1 and 5.0 ×10 3 for Total coliform, 0 and 1.0 × 10 4 for Escherishia coli , 0 and 6.1 × 10 3 for Salmonella , 0 and 3.8 ×10 3 for Shigella , 5.9×10 2 and 5.1×10 4 for Psuedomonas . Panellist had high preference for solar tent dried than open sun dried fish confirmed by scores for overall acceptability which were high at 3.8 and 2.2 respectively. The results reveal a possible application of solar tent drying as a SMART proven and emerging technology for fish processing in Malawi. It has proved that use of solar tent drying would support fish processors to produce quality dried fish with good nutritive value, reduced microbial contamination, and consumer acceptability that will be central to food security of the country.

Fish parasites have diverse ecological impacts on fish populations and are presently becoming useful as bio-indicators of fish migration and feeding. Studies of fish parasite in Lake Malawi severely lag behind the strides made in eco-evolutionary studies of its ichthyofauna. Over a period of eleven months from April 2003, we examined more than 1300 Engraulicypris sardella from Lake Malawi for cestode parasites. About 54 % of the fish had infections of between one and eight Ligula intestinalis plerocercoids. The infection occurred throughout the study period (mean prevalence 59 ±13%) but was most prevalent in December and June and was least prevalent in April. The majority of the hosts (78%) had a light parasite burden (one or two). Parasite prevalence increased with age of the fish. Prevalence and infection intensity oscillated closely with periods of peak abundance of zooplankton, the main food of E. sardella and intermediate hosts (copepods) of L. intestinalis . Increased exposure to the parasite with age aggravated by an ontogenetic diet shift from phytoplanktivory to zooplanktivory may be interacting with fluctuations in zooplankton production in driving the trophic transmission patterns of L. intestinalis in this ecosystem. Keywords : Engraulicypris sardella; Ligula intestinalis ; trophic transmission; Lake Malawi