Lake Tanganyika Research Articles

Phylogenomic and Population Genomic Analyses of Ultraconserved Elements Reveal Deep Coalescence and Introgression Shaped Diversification Patterns in Lamprologine Cichlids of the Congo River.

Understanding the drivers of diversification is a central goal in evolutionary biology but can be challenging when lineages radiate quickly and/or hybridize frequently. Cichlids in the tribe Lamprologini, an exceptionally diverse clade found in the Congo basin, exemplify these issues: their evolutionary history has been difficult to untangle with previous datasets, particularly with regard to river-dwelling lineages in the genus Lamprologus. This clade notably includes the only known blind and depigmented cichlid, L. lethops. Here, we reconstructed the evolutionary, population, and biogeographic history of a Lamprologus clade from the Congo River by leveraging genomic data and sampling over 50 lamprologine species from the entire Lake Tanganyika radiation. This study provides the most comprehensive species-level coverage to date of the riverine taxa within this lacustrine-origin clade. We found that in the mid-late Pliocene, two lineages of Lake Tanganyika lamprologines independently colonized the Congo River, where they subsequently hybridized and diversified, forming the current monophyletic group of riverine Lamprologus. Our estimates for divergence time and introgression align with the region's geological history and suggest rapid speciation in Lamprologus species from the Congo River marked by rapids-driven vicariance and water level fluctuations, and repeated episodes of secondary contact and reticulation. As a result of our analyses, we propose the taxonomic restriction of the genus Lamprologus to Congo River taxa only. The complex evolutionary history of this group-characterized by introgressive hybridization followed by a rapid series of isolation and reconnection-illustrates the multifaceted dynamics of speciation that have shaped the rich biodiversity of this region. [African cichlids; Congo River; diversification; hybridization; Lamprologini; phylogenomics; UCEs; ultraconserved elements].

Metagenomic Insights Into the Dietary Diversity of the Adaptive Radiation of Cichlid Fishes in Lake Tanganyika.

Diet specialisation is a main driver of diversification in many adaptive radiations. Therefore, identifying diet items is essential to characterise trophic specialisations and to understand the dynamics of dietary adaptations. In this study, we explored the trophic niches of 56 species from the adaptive radiation of cichlid fishes in Lake Tanganyika, encompassing all major phylogenetic lineages and feeding specialisations. We employed a metagenomic sequencing approach to identify the food sources of the investigated species at high taxonomic resolution, sequencing over 400 digestive content samples from wild-caught individuals at around 50 million paired-end read depth per sample. Our analyses revealed Arthropoda, Chordata (fishes), Bacillariophyta and Streptophyta as the primary diet phyla of the Tanganyikan cichlids. Moreover, we confirmed the presence of other food sources and identified taxa not previously documented to be part of the cichlids' diet. Based on their dietary compositions, the Tanganyikan cichlids can be grouped into herbivores, invertivores, piscivores and mixed feeders. Further, we showed that trophic disparity in the radiation is shaped by rapid divergence and documented cases of dietary niche convergence. Diet composition correlated with carbon and nitrogen stable isotope values, gut length, and body morphology. Differences in diet-such as the consumption of diatoms, streptophytes and chlorophytes versus fish and arthropods-were associated with changes in body, upper oral jaw and lower pharyngeal jaw shape. Collectively, this study presents a comprehensive and detailed diet classification of the Tanganyikan cichlids, highlighting the power of metagenomic approaches in delineating dietary adaptations.

Two new species of the genera Pseudocandona and Cytherissa (Ostracoda, Podocopida) from the coastal zone of Lake Baikal.

Most freshwater ostracods are endemic at either the local or regional level, and ancient lakes, such as Lakes Baikal and Tanganyika, are biodiversity hotspots for this group of organisms. Here we describe and name two new species of endemic ostracods from Lake Baikal in honor of Professors Stephanie Guildford and Robert Hecky who served as editors for the Journal of Great Lakes Research for 13 years. Illustrated descriptions of females and males of these two ostracod species of the genera Pseudocandona Kaufmann, 1900 and Cytherissa Sars, 1925-Pseudocandona guildfordae Alekseeva, Krivorotkin & Timoshkin sp. nov. and Cytherissa heckyi Alekseeva, Krivorotkin & Timoshkin sp. nov.-are presented and their habitats briefly described. These species were discovered when examining the ostracod collections of the famous Russian freshwater biologist, Prof. G.F. Mazepova.

Impact of a multi-pronged cholera intervention in an endemic setting.

Cholera is a bacterial water-borne diarrheal disease transmitted via the fecal-oral route that causes high morbidity in sub-Saharan Africa and Asia. It is preventable with vaccination, and Water, Sanitation, and Hygiene (WASH) improvements. However, the impact of vaccination in endemic settings remains unclear. Cholera is endemic in the city of Kalemie, on the shore of Lake Tanganyika, in the Democratic Republic of Congo, where both seasonal mobility and the lake, a potential environmental reservoir, may promote transmission. Kalemie received a vaccination campaign and WASH improvements in 2013-2016. We assessed the impact of this intervention to inform future control strategies in endemic settings. We fit compartmental models considering seasonal mobility and environmentally-based transmission. We estimated the number of cases the intervention avoided, and the relative contributions of the elements promoting local cholera transmission. We estimated the intervention avoided 5,259 cases (95% credible interval: 1,576.6-11,337.8) over 118 weeks. Transmission did not rely on seasonal mobility and was primarily environmentally-driven. Removing environmental exposure or contamination could control local transmission. Repeated environmental exposure could maintain high population immunity and decrease the impact of vaccination in similar endemic areas. Addressing environmental exposure and contamination should be the primary target of interventions in such settings.

Mixed Parentage Broods Indicate Group Spawning in the Brood Parasitic Cuckoo Catfish.

Obligate brood parasites delegate the workload of costly parental care to their hosts. Theory predicts that release from demanding parental care increases the importance of other factors to shape mating patterns. However, behavioural observations and parentage estimates are notoriously difficult to obtain in species with covert reproductive strategies, such as brood parasites, and evidence for their mating strategies are scarce. Molecular genetic methods provide a powerful tool to identify concealed mating patterns. Here, we reconstruct the parentage of cuckoo catfish (Synodontis multipunctatus) clutches collected in the wild using a combination of newly developed microsatellite markers, mitochondrial markers, and maximum likelihood estimates of pairwise relatedness. Cuckoo catfish parasitise mouthbrooding cichlids in Lake Tanganyika, but a natural spawning of the brood parasite has never been observed. We examined 429 females of confirmed host cichlid species (parasitism prevalence 6%; 24 parasitised clutches with 1-14 embryos) and found that 46% of clutches with three or more offspring (i.e., 6 out of 13) were parented by more than two catfish individuals. We demonstrated variable mating patterns including polyandrous and polygynous mating, and host sharing by separate, genetically monogamous, catfish pairs. This indicates that cuckoo catfish parasitism involves groups of catfish with reduced capability to monopolise mating opportunities. In general, our results demonstrate how reproductive strategy and mating patterns in a species with concealed breeding behaviour can be investigated and provide valuable insights into the mating system of a brood parasitic species other than hitherto studied avian brood parasites.

Investigation of sex determination in African cichlids reveals lack of fixed sex chromosomes in wild populations.

Sex chromosomes are theorised to stop recombining and become fixed, yet many taxa show ambiguous genomic signals of sex consistent with either continuous recombination or sex chromosome turnover. Elucidating the basis of sex chromosome conservation or alternatively, turnover, requires comparative studies among natural populations with shared evolutionary histories. The African Great Lake radiations of cichlid fishes display an outstanding propensity to rapidly evolve novel sex-linked regions, yet older cichlid lineages external to these radiations seem to show conservation of a few sex chromosomes. Here, we studied sex-determining regions of species uniquely representing two older lineages within Lake Tanganyika; Oreochromis tanganicae (Oreochromini) and Tylochromis polylepis (Tylochromini). Using a combined SNP- and kmer-based approach, we confirm a ZW system on linkage group (LG) 3 in O. tanganicae, but not the previously proposed sex-determining gene. However, in T. polylepis, no clear region of sex-association could be identified, although kmer-based analyses point towards LG12 as a candidate sex chromosome. Additionally, we investigated four other species from older, non-East African radiation lineages and confirm LG3 to be frequently associated with sex, but also find stronger signals of sex association on different chromosomes not previously discovered. Combined, these results suggest that homomorphic sex chromosomes are a feature of African cichlids at large. LG3 frequently harbours regions of sex-linkage, but is often polygenic with more strongly sex-linked regions on other chromosomes, possibly denoting its ancestral function as sex-determining across African cichlids, that leaves traces as novel sex-determining regions emerge. Our investigation captures this in a phylogenetic context, from emergence, to fixation, or turnover to a new sex chromosome.

Intrinsic timing of brood care in shell-dwelling cichlids.

Intrinsic timing of brood care in shell-dwelling cichlids.

Behavioral sequences during courtship and territorial defense of male Benthochromis horii in Lake Tanganyika

Behavioral sequences during courtship and territorial defense of male Benthochromis horii in Lake Tanganyika

Admixture and environmental fluctuations shape the evolutionary history of a predator radiation in East Africa's Lake Tanganyika.

When introduced to novel ecosystems, top predators can cause major alterations to biodiversity and food webs. Species introductions to novel habitats can also provide invading taxa with ecological opportunities that facilitate evolutionary diversification. Here, we find evidence that the radiation of endemic top predators in East Africa's Lake Tanganyika originated surprisingly recently, and that these species have experienced periods of hybridization with a widespread riverine relative throughout their history. These findings have major implications for the history of the lake and suggest that the introduction of Nile perch into Lake Victoria, which caused dramatic ecosystem and food web changes, may be a contemporary analog to the historical events in Lake Tanganyika.

THE RISING WATERS OF LAKE TANGANYIKA AND THEIR IMPACT ON SOCIOECONOMIC DEVELOPMENT: THE CASE OF THE TOWN OF KALEMIE, TANGANYIKA PROVINCE, DEMOCRATIC REPUBLIC OF THE CONGO

Lake Tanganyika is one of the lakes in the African Great Lakes region. It stretches over 4 countries: the Democratic Republic of Congo (DRC), Burundi, Tanzania and Zambia. Goods and people move through these 4 countries via ports, the most important of which are: Kalemie in the DRC, Bujumbura in Burundi, Kigoma in Tanzania and Mpulungu in Zambia. In terms of surface area, Lake Tanganyika is the second largest lake in Africa after Lake Victoria; in terms of depth, it is the second deepest in the world after Lake Baikal in Russia; and in terms of length, it is the longest freshwater lake in the world at 677 km. From March 2024 to October 2024, the waters of Lake Tanganyika began to rise to alarming levels, becoming very harmful to the population. Many houses, beaches, nightclubs, schools, churches and businesses were swallowed up by the waters of the lake, a real natural calamity, a complex phenomenon with serious consequences for the lives of the people living along its shores. The causes of this rise are multiple, including climate change (39%), persistent heavy rains (20%) followed by human activities (19%), waste dumped in the lake (9%), and others even speak of God's wrath (13%). All these factors combined are gradually raising the waters of Lake Tanganyika to alarming and dangerous levels. The extent of the socio-economic and humanitarian damage caused by the rising waters of Lake Tanganyika is clear for all to see. Among the many consequences are: destruction of infrastructure (67%), massive population displacement (16%), housing problems (7%), slowdown of economic activities (6%) and job losses (4%).

Morphological diversity of the genus Telmatochromis from the Lake Tanganyika drainage with the description of a new riverine species and the generic reassignment of the Malagarasi River lamprologine.

The lamprologine cichlid genus Telmatochromis was long considered primarily lacustrine and endemic to Lake Tanganyika until an undescribed Telmatochromis species was reported from the Lufubu River (Lake Tanganyika drainage, Zambia). A phylogenomic study in 2021 confirmed the association of Telmatochromis sp. "lufubu" with Telmatochromis along with another riverine species, Neolamprologus devosi (Malagarasi drainage, Tanzania). Here, we quantify the morphological diversity of the genus Telmatochromis and the two associated riverine species using a multivariate dataset combining geometric and classical morphometrics, as well as meristics. We identify three distinct morphological clusters: the "Telmatochromis vittatus complex" with highly elongated bodies and short heads, the "Telmatochromis temporalis complex" with deeper bodies, and the two riverine species with intermediate body elongation and large heads. Further, we formally describe the species endemic to the lower Lufubu River as Telmatochromis salzburgeri sp. nov. and reassign N. devosi to Telmatochromis. Telmatochromis devosi comb. nov. differs from all congeners by the absence of bi- and tricuspid teeth in the inner tooth rows of the oral dentition. T. salzburgeri sp. nov. can be distinguished from all other Telmatochromis species by a prominent orange stripe along the base of the dorsal fin and from T. devosi comb. nov. by the relatively smaller size of the lower pharyngeal jaw. Both riverine species differ from all lacustrine Telmatochromis by a lower number of dorsal-fin spines. Additionally, the riverine species can be distinguished from the T. vittatus complex by having larger heads and longer oral jaws, and from the T. temporalis complex by their lower relative body depth. With the inclusion of new riverine members, the genus Telmatochromis is revealed to be more morphologically and ecologically diverse than previously recognized.

Catfishes from the North-Western Part of Lake Tanganyika: Contribution to a Reference Library of DNA Barcodes

In spite of the global barcoding effort, there is still a lack of genetic data on African freshwater fishes. We aimed to contribute to bridging this gap by providing molecular data on commercially important catfish species from the north-western part of Lake Tanganyika. We collected 215 catfish specimens and sequenced the standard vertebrate barcoding gene (COI) for 41 specimens. Additionally, we sequenced 20 specimens for the mitochondrial Cyt-b gene to make the link to previously published datasets. We identified 11 species using morphology, compared DNA sequences with those available on GenBank, and employed Automatic Barcode Gap Discovery (ABGD) and phylogenetic approaches. The dataset includes the first molecular data (COI and Cyt-b) for Chrysichthys acsiorum, as well as the first-ever COI sequences for Dinotopterus cunningtoni and Malapterurus tanganyikaensis. Our findings extend the known distribution of C. acsiorum by approximately 100 km. Additionally, we demonstrated the difficulty in delineating species of Chrysichthys and Synodontis from Lake Tanganyika with molecular tools. For Chrysichthys, automated methods, such as ABGD, failed to delineate species. However, barcoding does seem promising as all the individual species are resolved as clades. Within Synodontis, the study found a strong similarity between S. grandiops and S. multipunctatus, highlighting a need for revision. Our findings emphasize the necessity for integrative taxonomy in the study of catfishes from Lake Tanganyika.

Population Genetics and Gene Flow in Cyphotilapia frontosa and Cyphotilapia gibberosa Along the East Coast of Lake Tanganyika

The radiation of cichlid species in the East African Great Lakes is remarkable and rapid. The population genetics of two deep-water Cyphotilapia species along the east coast of Lake Tanganyika from Burundi to southern Tanzania was determined using ddRAD-seq. A combination of ADMIXTURE, PCA, genome polarization, and 2D site frequency spectrum analyses confirmed the presence of two species, C. frontosa in the north and C. gibberosa in the south, as documented in other studies. We also found evidence of a potential hybrid zone connecting the two species at a sharp genetic cline centered in the middle of the lake and apparent introgression in both directions, but predominantly from ‘gibberosa’ into ‘frontosa’. The highest proportion of introgressed ‘gibberosa’ ancestry was present in the southernmost populations of C. frontosa collected near Karilani Island and Cape Kabogo. At the intra-specific level, there was support for between 1 and 3 populations of C. frontosa, whereas the results indicated only a single homogeneous population of C. gibberosa. The presence of different morphs in the lake despite the low levels of heterozygosity suggests that a small number of loci may be involved in the morphological variation and/or that there is a more complex interplay between genetics and the environment in different locations.

Revised taxonomy of Synodontis catfishes (Siluriformes: Mochokidae) from the Lake Tanganyika basin reveals lower species diversity than expected

Abstract Synodontis Cuvier, 1816 is a species-rich group of African catfishes. Prior to this analysis, 13 species of Synodontis were recognized from Lake Tanganyika and its tributaries, composing the only extant lacustrine radiation of the genus, with a unique origin of obligate brood parasitism among all fishes. Species differentiation and phylogenetic relationships of this group remained largely unresolved. Herein, the taxonomy of Synodontis in the Lake Tanganyika basin is revised, including redescriptions of all species and an updated identification key. Genetic (mitochondrial and nuclear genomic markers) and morphological data suggest a lower species diversity than previously recognized, supporting the distinction of 10 Synodontis species in the lake basin. Based on our findings, we recognize Synodontis grandiops, Synodontis ilebrevis, and Synodontis lucipinnis as junior synonyms of Synodontis multipunctatus, Synodontis polli, and Synodontis petricola, respectively. No recent material of Synodontis dhonti and Synodontis tanganyicae (with Synodontis lacustricolus as a synonym) was available. Morphometric/meristic data suggest their close relationship to Synodontis granulosus. Sequencing of historical specimens inferred S. tanganyicae as sister to S. granulosus but with a 1.7% divergence based on mitochondrial data. In contrast to previous studies, phylogenomic data support the lacustrine assemblage of Synodontis in Lake Tanganyika as monophyletic.

Process evaluation of an urban piped water supply infrastructure improvement programme in Uvira, Democratic Republic of the Congo

Major investments in water supply infrastructure will be required to achieve Sustainable Development Goal (SDG) 6. Safely managed water services are also central to global cholera and diarrhoeal diseases prevention strategies. However, evidence remains scarce on how to efficiently improve piped water services in complex settings where infrastructure investments are most needed. We conducted a process evaluation of a large-scale water supply infrastructure improvement programme in Uvira, Democratic Republic of the Congo, in parallel to a pragmatic trial. Considering three evaluation domains–context, implementation, and population response–, we assessed the validity of the programme’s theory of change and underlying assumptions. Information sources included construction works documentation, operational and billing records from the water utility, and household surveys. The evaluation covers the period 2014–2021. Trial results are not within the scope of this manuscript. The programme did not achieve expected improvements in the water supply service during the evaluation period. Out of 16 assumptions underlying the theory of change, six remained valid, seven partially valid, and three turned out to be invalid. Contextual challenges included extreme flooding in 2020 and the Covid-19 pandemic, which disrupted construction works. Issues related to electricity supply and the rise of Lake Tanganyika emphasise the need for cross-sectoral approaches and consideration of climate change in the planning of water supply infrastructure. Implementation challenges underlined the importance of capacity strengthening alongside infrastructure improvements. Population response elements suggest that affordability and informal practices such as tap sharing should be taken into account. The programme was a good example of early engagement with researchers and provides unique insights into the implementation of large-scale infrastructure improvements in a complex, low-income setting. Pragmatic evaluation approaches should be adopted for the generation of scientific evidence from complex programmes in order to optimise future infrastructure investments contributing to progress towards SDG6.

Just keep exploring: Genetics of fish niche adaptation.

Although the diversification of species has fascinated researchers for centuries, we know remarkably little about how behavior influences niche adaptation and the genetic mechanisms through which behavior evolves. In their recent study, Sommer-Trembo et al. (Science, 384, 470-475, 2024) demonstrate a critical role for the regulatory gene cacng5b in modulating phenotypic variation in exploratory behavior in one of the most exceptional adaptive radiations: the African cichlid fishes of Lake Tanganyika.

The Impact on People who Trade on the Fish Species ‘Limnothrissa miodon’ - Kapenta for their Livelihood: Practical Perceptions of Traders of Siavonga

Lake Kariba is the world’s largest man-made lake and reservoir by volume. It lies 1300km upstream from the Indian Ocean, along the border between Zambia and Zimbabwe. Lake Kariba was filled between 1958 and 1963 following the completion of the Kariba dam at its north eastern end flooding the Kariba Gorge on the Zambezi River. Culturally controversial, the local people believed that the construction of the dam would anger the Zambezi river god Nyami-nyami, who rise up and cause the dam would wall to collapse destroying the bridge as well as resulting in floods of catastrophic proportions. It is believed that the Nyami-nyami lives under a rock close to the Kariba dam wall. The rock is called ‘Kariwa’ meaning trap as the local people believed if you canoed past its location you would be sucked down in whirlpool never to be seen again. This where the name Kariba originates from, laced with the local mythology. In the late 1960s a type of fish Limnothrissa miodon locally known as Kapenta was introduced in Lake Kariba from lake Tanganyika. Kapenta is a small sardine fish which supports a large and viable fishery for Zimbabwe and Zambia. Kapenta, a type of fish also known as fresh water sardine has several chemical compositions that help reduce the risk of various diseases including prostate cancer. A recent chemical composition analysis of Kapenta by the National Food and Nutrition Commission (NFNC) shows a great variation in the nutrient composition for the dry and fresh Kapenta. NFNC principal nutritionist Mr. Musonda Mofu says dry Kapenta contains 209 calories of food energy compared with 85 calories of food energy in fresh Kapenta. In addition dry Kapenta contains 63 grammes of protein and only 16 grams of protein in fresh Kapenta. The paper reflects on the declining population of this small nutrient rich fish due to over-harvesting, climatic changes with increasing temperatures and with the decreasing levels of water storage. A cumulative study on the pattern of nurturing the fish for economic and social flexibility is the main concern of this paper.

Evolution and morphological diversity of the genus Diploneis (Bacillariophyta) in Lake Malawi, with description of six new species

ABSTRACT Lake Malawi, one of the world’s oldest and most important freshwater systems, harbours a remarkable biotic diversity partly due to variable fluctuations in climate and lake level. Over time, these fluctuations have contributed to the emergence and development of different ecological niches and microhabitats that have facilitated diversification within the lake. Despite our extensive knowledge of different animal groups, the evolutionary history of species-rich diatom groups in Africa and, particularly, in Lake Malawi has yet to be studied. Here, we used a combination of morphological, molecular, and paleontological data to assess the species richness and evolutionary processes of the diatom genus Diploneis in this lake. The comprehensive dataset revealed four putative new endemic species from modern and two apparently extinct Diploneis species from the fossil record of the lake, described here as new to science. Morphological analyses showed that all these new species exhibit remarkable differences and unique morphological patterns that were recently discovered in Diploneis species from nearby Lake Tanganyika. Molecular phylogenetic analyses revealed that the four new species now living in Lake Malawi are nested within a clade of Lake Tanganyika Diploneis species but do not form a monophyletic group. This suggests that the new Lake Malawi Diploneis species are derived from one or more Tanganyikan ancestors and that more than one colonization event probably occurred. However, further analyses are needed to elucidate their origin.

Preliminary survey on the origin and analysis of distribution channels for fish processed and sold at the Maendeleo market in Uvira, Democratic Republic of the Congo: The case of economically important fish communities in Lake Tanganyika

Preliminary survey on the origin and analysis of distribution channels for fish processed and sold at the Maendeleo market in Uvira, Democratic Republic of the Congo: The case of economically important fish communities in Lake Tanganyika

Three small species of shrews (Soricidae) from the Salonga National Park, Democratic Republic of the Congo, representing two new taxa and a new record

Abstract We report on a small collection of shrews from the central part of the Democratic Republic of Congo. Three taxa are recognized, of which a long-tailed and a middle-sized species of Crocidura are described as C. salonga sp. nov. and C. binco sp. nov. Crocidura lwiroensis is recorded for the first time since its description from near Lake Tanganyika in 2013.