ABSTRACT It can be challenging to determine the identity of tilapia species in aquaculture using morphological characteristics alone. In central Tanzania, there is ongoing expansion of small‐scale inland aquaculture, mainly focused on the large‐bodied non‐native Nile tilapia (Oreochromis niloticus) and the native Wami tilapia (Oreochromis urolepis). The spread of Nile tilapia has been accompanied by blue‐spotted tilapia (Oreochromis leucostictus), a small‐bodied non‐native species that has the potential to compromise fisheries production. Given the phenotypic similarity of the three species, particularly at the juvenile stage, we developed an environmental DNA (eDNA)‐based assay to determine the distribution and relative abundance of the three Oreochromis species within aquaculture and natural settings in Tanzania. In a field test of the assay in 15 water bodies—comparing eDNA results with genotyping of sampled fish—we found that the confirmed presence of a species, as inferred from their mitochondrial DNA (mtDNA) ND1 haplotypes, led to an on average one‐thousand‐fold increase in eDNA copies relative to water bodies where the species was not confirmed. In a more expansive eDNA field survey across 52 water bodies from 32 locations, we found that the vast majority of water bodies were dominated by O. niloticus or O. urolepis, with O. leucostictus widespread but typically present in low relative abundance. Collectively, our results indicate that O. leucostictus is currently unlikely to compromise the productive capacity of aquaculture of the region. However, caution should be exercised to reduce the influence of the species on yield. We conclude that eDNA‐based methods can be a valuable source of information for the identification of fish in mixed cultured stocks and may, in the future, have a role in optimising regional aquaculture.

Lake Malawi/Nyasa/Niassa (LMNN) contains exceptional fish diversity with more than 800 species recognised, yet the rivers flowing into LMNN also contain a rich variety of fish species. Here, we report a study, using a combination of morphological and genetic evidence, that shows that the Malagarasi sardine Engraulicypris spinifer Bailey and Matthes, 1971 is present in the northern sector of the LMNN catchment. Previously, the species was only known from the Lake Rukwa, Rufiji River and Malagarasi River catchments. We found that individuals from the LMNN catchment possess the same mitochondrial COI haplotype as those in the Malagarasi River catchment, and that both groups share key diagnostic morphological traits of the species. These findings support theories of past hydrological connectivity between LMNN and the neighbouring Rukwa and Rufiji catchments. They also indicate potential for further discoveries of novel fish diversity in riverine habitats of the LMNN catchment.

Evolutionary divergence in body size is common in animal adaptive radiations and is often associated with differences in key ecological traits, including habitat use and prey consumption. Here we characterize a notable case of body size-associated adaptive radiation in a group of predatory open water cichlid fish species from the Lake Malawi catchment. Using whole-genome sequences, we show that body size differences have evolved multiple times in the focal genus, Rhamphochromis, and that the group possesses well-defined signals of ancient interspecific hybridization. We identify genetic variants strongly associated with body size and show that these variants are connected to genes enriched for functions in vertebrate skeletal and nervous system development. We focus our analyses on two species of Rhamphochromis endemic to Lake Kingiri, a small (600 m diameter) crater lake geographically isolated from the main body of Lake Malawi but within the catchment. We show that these two ecomorphologically divergent sympatric species-one small-bodied, the other larger-bodied-share a unique common ancestor and diverged from one another ∼2000 years ago. We demonstrate strong directional selection focused on the larger-bodied Kingiri species, specifically on genetic variants connected to genes with anatomical development and nervous system function. Collectively, these results are supportive of body size-associated speciation taking place rapidly in the Lake Malawi cichlid fish superradiation. We conclude that body size-associated genetic variants have been important targets of selection during large-scale cichlid fish diversification, including in a crater lake sympatric speciation context.

Sensory adaptation is widely hypothesized to drive ecological speciation, yet empirical evidence from natural populations undergoing early stage divergence remains limited. In Lake Masoko, a young crater lake in East Africa, the haplochromine cichlid Astatotilapia calliptera is undergoing early stage sympatric speciation into shallow-water littoral and deep-water benthic ecotypes that experience contrasting light environments. Here, we integrate retinal transcriptomics, phenotypic analyses, and visual modeling to uncover rapid sensory divergence associated with this ecological transition. We find striking shifts in cone opsin expression, with the benthic ecotype exhibiting a switch from short-wavelength sensitive SWS2B to SWS2A and an overall narrowing of cone sensitivity toward the center of the light spectrum, consistent with changes in deep-water light environment. In contrast, coding sequence variation in opsin genes was limited and no significant differences in allele frequencies were detected across nine polymorphic sites, pointing to expression regulation as the primary axis of early divergence in visual systems. In parallel, we observed divergence in male signaling traits, with benthic males displaying deeper red egg-spots, aligning with predictions from visual modeling of signal efficiency in different light environments. These results demonstrate rapid transcriptomic and phenotypic divergence in associated signaling traits—within ∼1,000 years—supporting a potential role for regulatory evolution in sensory adaptation during early ecological speciation.

ABSTRACTManagement and conservation of species‐rich tropical freshwater systems require reliable information on the diversity and distribution of species present. Here, we used environmental DNA metabarcoding to reveal the diversity of the fishes in the Rufiji River catchment of central Tanzania. Across 174 samples from 49 sites, and using a newly developed reference library, we mapped the presence of 66 fish species from an estimated 91 that we are confident are present in the system. We found clear evidence of community structuring of the assemblage linked to key environmental gradients—elevation, temperature, and turbidity. We also identified core distributions of rare or threatened taxa, including migratory species such as the anguillid eels. With a focused analysis of 50 samples collected over a small spatial scale (<2 km) from the Kilombero River, we showed that each single sample can capture an average of 23.1 species, while three samples can capture 39.4 species, from a total of 56 species encountered in the 50 samples. Collectively the results help to identify species vulnerable to ongoing change in the catchment, including dam construction and agricultural intensification. The results clearly demonstrate how eDNA‐based metabarcoding can reliably describe the diversity and distributions of riverine fish species across a catchment, providing standardized information that will be valuable for environmental management.

Abstract Geological, climate, and ecosystem changes in Africa probably influenced speciation of Afrotropical freshwater crabs. In total, the subfamily Potamonautinae comprises over 120 species, and this diversity provides a valuable opportunity to explore speciation processes. Here we study diversification of potamonautid crabs in the Lake Malawi catchment, and investigate whether speciation has taken place across a lake–river boundary. Specifically, we reconstruct evolutionary relationships of the Malawi blue crab, Arcopotamonautes orbitospinus (Cunnington, 1907), an endemic of Lake Malawi, and of A. montivagus (Chace, 1953) from rivers and streams draining into Lake Malawi, and smaller lakes within this catchment. Our phylogenetic analysis of over 28 000 single nucleotide polymorphisms shows a monophyletic A. orbitospinus nested within a clade otherwise comprising A. montivagus from across the Lake Malawi catchment (A. montivagus Group I). We also identified a second allopatric clade of A. montivagus from the Rungwe mountains of Tanzania, and neighbouring Zambia (A. montivagus Group II). Morphological differences were apparent between all three groups. Collectively these results show A. montivagus is a paraphyletic riverine taxon that has diversified in allopatry, and that this species entered Lake Malawi and seeded the specialized heavily armoured lacustrine species, A. orbitospinus. We hypothesize that formation of deep-water conditions within Lake Malawi, together with differences in predation pressures between the rivers and lake, provided ecological opportunities for natural selection to drive speciation across the lake–river boundary. We conclude that geographical separation and ecological adaptation are potentially important drivers of evolutionary diversification in these enigmatic freshwater crabs.

AbstractOctopus cyanea (Gray, 1849), abundant in the South‐West Indian Ocean (SWIO), constitutes a vital resource for both subsistence and commercial fisheries. However, despite this socioeconomic importance, and recent indications of overfishing, little is known about the population structure of O. cyanea in the region. To inform sustainable management strategies, this study assessed the spatio‐temporal population structure and genetic variability of O. cyanea at 20 sites in the SWIO (Kenya, Tanzania, Mozambique, Madagascar, Mauritius, Rodrigues, and the Seychelle Islands) by complementary analysis of mitochondrial DNA (mtDNA) noncoding region (NCR) sequences and microsatellite markers. MtDNA analysis revealed a shallow phylogeny across the region, with demographic tests suggesting historic population fluctuations that could be linked to glacial cycles. Contrary to expectations, NCR variation was comparable to other mtDNA regions, indicating that the NCR is not a hypervariable region. Both nuclear and mtDNA marker types revealed a lack of genetic structure compatible with high gene flow throughout the region. As adults are sedentary, this gene flow likely reflects connectivity by paralarval dispersal. All samples reported heterozygote deficits, which, given the overall absence of structure, likely reflect ephemeral larval recruitment variability. Levels of mtDNA and nuclear variability were similar at all locations and congruent with those previously reported for harvested Octopodidae, implying resilience to genetic erosion by drift, providing current stock sizes are maintained. However, as O. cyanea stocks in the SWIO represent a single, highly connected population, fisheries may benefit from additional management measures, such as rotational closures aligned with paralarval ecology and spanning geopolitical boundaries.

The introduction of non-native species can lead to competition with native species for key resources, driving the decline and extinction of endemic biodiversity. Recently, a newly discovered and evolutionarily distinct lineage of Korogwe tilapia (Oreochromis korogwe) was reported from small lakes in southern Tanzania. This small-bodied lineage is potentially threatened by introduced Nile tilapia (Oreochromis niloticus), an invasive large-bodied congeneric with a pan-tropical non-native distribution. Nile tilapia is known to dominate ecologically-similar native tilapia in competitive interactions, preventing access to resources such as food and shelter. We therefore hypothesised that competition between Nile tilapia and Korogwe tilapia could limit access to resources by the native species and hence reduce their growth rate, a key determinant of fitness. In this study, tilapia were collected from Lake Rutamba in two field seasons, and individuals were classified using microsatellite DNA genotypes as O. niloticus, O. korogwe or interspecific hybrids. Recent growth rate of these individuals was determined by measuring the distance between scale circuli. In contrast to expectations, we found that native O. korogwe overall had a faster growth rate than the invasive O. niloticus, with hybrids showing growth rates more similar to O. korogwe. We propose that in Lake Rutamba the persistence of O. korogwe could be partially enabled by a faster growth rate than the large-bodied invasive O. niloticus. Based on these results, we suggest that predictions of the effects of invasive species on native biodiversity may benefit from information on relative fitness, in addition to ecological niche overlap.

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.

Seascape configuration is known to influence fish distribution and abundance in coastal waters. However, there is little information regarding how the shape of the coastal seascape influences catches of landed fisheries species, particularly so in the understudied western Indian Ocean (WIO). With focus on big blue octopus (Octopus cyanea), which is a widely found cephalopod species in the WIO, we compared landed catches (biomass, catch rate, and density) in submerged and exposed reefs, and explored the influence of proximity to fishing villages and reef habitat size on octopus landings. We used fishery-dependent data collected between 2018 and 2020 from eight landing sites spread across the Tanzanian coast. We found a strong relationship between biomass of octopus catch and distance from fished reefs to fishing villages, with higher fished biomass on reefs farther away. Octopus densities were higher, while catch rates were lower, on reefs very close to (within one km distance from) fishing villages compared to more distant reefs. In general, submerged reefs provided higher catches than exposed reefs. The low octopus catches on the exposed reefs were attributed to high fishing pressure, while submerged reefs that are only accessible through diving provide optimal areas for octopuses to grow. Octopus catches were, however, not significantly affected by reef size. The findings suggest that management policies should propor-tionate fishing efforts to ensure sustainable exploitation of reefs and associated fishery resources.

There is considerable potential for nuclear genomic material in environmental DNA (eDNA) to inform us of population genetic structure within aquatic species. We tested if nuclear allelic composition data sourced from eDNA can resolve fine scale spatial genetic structure of the cichlid fish Astatotilapia calliptera in Lake Masoko, Tanzania. In this ∼35 m deep crater lake the species is diverging into two genetically distinguishable ecomorphs, separated by a thermo-oxycline at ∼15 m that divides biologically distinct water masses. We quantified population genetic structure along a depth transect using single nucleotide polymorphisms (SNPs) derived from genome sequencing of 530 individuals. This population genetic structure was reflected in a focal set of SNPs that were also reliably amplified from eDNA - with allele frequencies derived from eDNA reflecting those of fish within each depth zone. Thus, by targeting known genetic variation between populations within aquatic eDNA, we measured genetic structure within the focal species.

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.

Hybridization may enable adaptive diversification by generating unique genetic combinations when hybrid lineages are faced with ecological opportunity. Conversely, hybridization with exotic species may be detrimental to native biodiversity, by leading to homogenisation and the loss of important genetic material associated with local adaptation. Here we studied both ancient and contemporary hybridization in cichlid fishes of the genus Oreochromis (tilapia), which are among the most important fish for global aquaculture. We use whole genome resequencing of 575 individuals from 23 species, focussing 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 introgression has not led to large-scale adaptive radiation as seen in other cichlid lineages. We identify multiple cases of contemporary hybridization between native and introduced species in the wild, linked to the use of non-native species in aquaculture improvement and stocking for capture fisheries. Our study shows how ancient hybridization contributed to modern tilapia diversity, but is now a threat to both the genetic integrity of wild populations and the long-term prospects of the global tilapia aquaculture industry.

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.

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.

Epigenetic variation can alter transcription and promote phenotypic divergence between populations facing different environmental challenges. Here, we assess the epigenetic basis of diversification during the early stages of speciation. Specifically, we focus on the extent and functional relevance of DNA methylome divergence in the very young radiation of Astatotilapia calliptera in crater Lake Masoko, southern Tanzania. Our study focuses on two lake ecomorphs that diverged approximately 1,000 years ago and a population in the nearby river from which they separated approximately 10,000 years ago. The two lake ecomorphs show no fixed genetic differentiation, yet are characterized by different morphologies, depth preferences and diets. We report extensive genome-wide methylome divergence between the two lake ecomorphs, and between the lake and river populations, linked to key biological processes and associated with altered transcriptional activity of ecologically relevant genes. Such genes differing between lake ecomorphs include those involved in steroid metabolism, hemoglobin composition and erythropoiesis, consistent with their divergent habitat occupancy. Using a common-garden experiment, we found that global methylation profiles are often rapidly remodeled across generations but ecomorph-specific differences can be inherited. Collectively, our study suggests an epigenetic contribution to the early stages of vertebrate speciation.

Molecular phylogenetic evidence clearly resolves the African cichlid fish genus Ctenochromis, as defined by Greenwood (1979), as paraphyletic. Here, we redefine the genus Ctenochromis and assign Ctenochromis horei, a member of the Tropheini from Lake Tanganyika, to a new genus Shuja gen. nov. We restrict Ctenochromis to Ctenochromis pectoralis and Ctenochromis scatebra sp. nov., both of which are endemic to the Pangani River catchment in northern Tanzania, and are resolved as sister taxa in a phylogenetic analysis using genome-wide data. Ctenochromis pectoralis is the type species of the genus and described from specimens collected near Korogwe, Tanzania. The species was declared extinct in a 2016 IUCN Red List Assessment. We confirm the continued presence of a population of C. pectoralis within the Ruvu tributary linking Lake Jipe to Nyumba ya Mungu Reservoir. The new taxon Ctenochromis scatebra sp. nov. is described from Chemka Springs, and recognised on the basis of differences from C. pectoralis in tooth and jaw morphology.

• The periodic, temporary closure has positive economic benefits to coastal fishing villages. • The timing of octopus temporal closure requires scientific evidence for an effective outcome. • Improving the management of octopus fisheries can deliver endless benefits throughout the octopus supply chain while rebuilding the stocks.

African cichlid fishes not only exhibit remarkably high rates of speciation but also have some of the fastest evolving sex determination systems in vertebrates. However, little is known empirically in cichlids about the genetic mechanisms generating new sex-determining variants, what forces dictate their fate, the demographic scales at which they evolve, and whether they are related to speciation. To address these questions, we looked for sex-associated loci in full genome data from 647 individuals of Astatotilapia calliptera from Lake Masoko, a small isolated crater lake in Tanzania, which contains two distinct ecomorphs of the species. We identified three separate XY systems on recombining chromosomes. Two Y alleles derive from mutations that increase expression of the gonadal soma-derived factor gene ( gsdf ) on chromosome 7; the first is a tandem duplication of the entire gene observed throughout much of the Lake Malawi haplochromine cichlid radiation to which A. calliptera belongs, and the second is a 5 kb insertion directly upstream of gsdf . Both the latter variant and another 700 bp insertion on chromosome 19 responsible for the third Y allele arose from transposable element insertions. Males belonging to the Masoko deep-water benthic ecomorph are determined exclusively by the gsdf duplication, whereas all three Y alleles are used in the Masoko littoral ecomorph, in which they appear to act antagonistically among males with different amounts of benthic admixture. This antagonism in the face of ongoing admixture may be important for sustaining multifactorial sex determination in Lake Masoko. In addition to identifying the molecular basis of three coexisting sex determining alleles, these results demonstrate that genetic interactions between Y alleles and genetic background can potentially affect fitness and adaptive evolution.

The haplochromine cichlid fauna of the rivers and smaller lakes of Tanzania and SE Africa are of key importance in understanding the origins and inter-relationships of the great lake cichlid radiations of Malawi, Tanganyika and Victoria. Prior to formal taxonomic investigations, here we present the results of investigations of the type specimens, identification of type localities and superficial characterisation of freshly-collected material. The type locality of Astatotilapia bloyeti (Sauvage, 1883) is identified as the Mkondowa River, near Kilosa. This species appears to be the only haplochromine found in the Wami system. It is concluded that junior synonyms of A. bloyeti include A. strigigena (Pfeffer, 1893), A. kilossana (Steindachner, 1915) and A. paludinosa Greenwood, 1980. Astatotilapia sparsidens (Hilgendorf, 1905) is closely related and may constitute a junior synonym or a sister taxon. The range of A. bloyeti includes the Pangani system. The type locality for Astatotilapia gigliolii (Pfeffer, 1896) is identified as the Kingani River, or southern Ruvu, where it appears to be the only haplochromine in the river system. Junior synonyms include Astatotilapia vollmeringi (Steindachner, 1915) from the Great Ruaha River at Kidatu and Astatotilapia tweddlei Jackson, 1985 from Lakes Chilwa and Chiuta. The species is also reported from the lower part of the Rufiji system, the Ruvuma system and from other lakes and rivers in between. A few specimens were also collected in and around a fish farm at Songea, in the upper reaches of the Ruhuhu system (Lake Malawi catchment). Apart from this record, the only Astatotilapia species in the Lake Malawi catchment is A. calliptera. Four undescribed Astatotilapia species are identified from the Rufiji system, while other possibly undescribed taxa from the basins of Lake Tanganyika and Rukwa are discussed.