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Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably

Understanding the origins of phenotypic diversity among closely related species remains an important largely unsolved question in evolutionary biology. With over 800 species, Lake Malawi haplochromine cichlid fishes are a prominent example of extremely fast evolution of diversity including variation in coloration. Previously, a single major effect gene, agrp2 (asip2b), has been linked to evolutionary losses and gains of horizontal stripe patterns in cichlids, but it remains unknown what causes more fine-scale variation in the number and continuity of the stripes. Also, the genetic basis of the most common color pattern in African cichlids, vertical bars, and potential interactions between the two color patterns remain unknown. Based on a hybrid cross of the horizontally striped Lake Malawi cichlid Pseudotropheus cyaneorhabdos and the vertically barred species Chindongo demasoni we investigated the genetic basis of both color patterns. The distribution of phenotypes in the F2 generation of the cross indicates that horizontal stripes and vertical bars are independently inherited patterns that are caused by two sets of genetic modules. While horizontal stripes are largely controlled by few major effect loci, vertical bars are a highly polygenic trait. Horizontal stripes show substantial variation in the F2 generation that, interestingly, resemble naturally occurring phenotypes found in other Lake Malawi cichlid species. Quantitative trait loci (QTL) mapping of this cross reveals known (agrp2) and unknown loci underlying horizontal stripe patterns. These findings provide novel insights into the incremental fine-tuning of an adaptive trait that diversified through the evolution of additional modifier loci.

Funder: The Branco Weiss Fellowship – Society in Science; doi: http://dx.doi.org/10.13039/501100001710, UNLABELLED: Sex determination systems are highly conserved among most vertebrates with genetic sex determination, but can be variable and evolve rapidly in some. Here, we study sex determination in a clade with exceptionally high sex chromosome turnover rates. We identify the sex determining chromosomes in three interspecific crosses of haplochromine cichlid fishes from Lakes Victoria and Malawi. We find evidence for different sex determiners in each cross. In the Malawi cross and one Victoria cross the same chromosome is sex-linked but while females are the heterogametic sex in the Malawi species, males are the heterogametic sex in the Victoria species. This chromosome has not previously been reported to be sex determining in cichlids, increasing the number of different chromosomes shown to be sex determining in cichlids to 12. All Lake Victoria species of our crosses are less than 15,000 years divergent, and we identified different sex determiners among them. Our study provides further evidence for the diversity and evolutionary flexibility of sex determination in cichlids, factors which might contribute to their rapid adaptive radiations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10750-021-04560-7.

Tooth shape is used to differentiate between morphologically similar species of vertebrates, including fish. This study aimed to quantify tooth shape of three sympatric species: Haplochromis kamiranzovu, H. insidiae, and H. astatodon endemic to Lake Kivu, whose existing identification criteria are currently only qualitative. A quantitative tooth shape analysis was performed based on digitized tooth outline data with a subsequent elliptic Fourier analysis to test for differences among the three species. We looked at crown shape and size differences within H. kamiranzovu and H. insidiae at geographical, habitat, and gender levels. No comparison at habitat level was done for H. astatodon because it is found only in littoral zone. The analysis revealed significant tooth shape differences among the three species. Haplochromis astatodon had a significantly longer major cusp height and a longer and larger minor cusp than that of H. insidiae. It had also a longer major cusp height and a longer and larger minor cusp than that of H. kamiranzovu. Tooth shape differences of H. kamiranzovu and H. insidiae species were not significantly different between littoral and pelagic fish (p > .05) while differences were significant between southern and northern Lake Kivu populations (p .05). Tooth shape was also significantly different with sharp teeth for males compared with females of southern populations versus northern ones. These shape‐ and size‐related differences between sexes suggest differences in the foraging strategies toward available food resources in the lake habitat. Further research should explain the genetic basis of the observed pattern., We quantified tooth shape trait to distinguish the three morphological similar Haplochromis kamiranzovu, H. insidiae, and H. astatodon) endemic to Lake Kivu.

Studying phenotypic and genetic differentiation between very young species can be very informative with regard to learning about processes of speciation. Identifying and characterizing genetic species structure and distinguishing it from spatial genetic structure within a species is a prerequisite for this and is often not given sufficient attention. Young radiations of cichlid fish are classical speciation study systems. However, it is only during the past decade that population genomics based on next-generation sequencing has begun to provide the power to resolve species and distinguish speciation from spatial population structure for the youngest of these radiations. The Lake Victoria haplochromine cichlids constitute the youngest large cichlid fish radiation, probably

BackgroundElasmoid scales are one of the most common dermal appendages and can be found in almost all species of bony fish differing greatly in their shape. Whilst the genetic underpinnings behind elasmoid scale development have been investigated, not much is known about the mechanisms involved in the shaping of scales. To investigate the links between gene expression differences and morphological divergence, we inferred shape variation of scales from two different areas of the body (anterior and posterior) stemming from ten haplochromine cichlid species from different origins (Lake Tanganyika, Lake Malawi, Lake Victoria and riverine). Additionally, we investigated transcriptional differences of a set of genes known to be involved in scale development and morphogenesis in fish.ResultsWe found that scales from the anterior and posterior part of the body strongly differ in their overall shape, and a separate look on scales from each body part revealed similar trajectories of shape differences considering the lake origin of single investigated species. Above all, nine as well as 11 out of 16 target genes showed expression differences between the lakes for the anterior and posterior dataset, respectively. Whereas in posterior scales four genes (dlx5, eda, rankl and shh) revealed significant correlations between expression and morphological differentiation, in anterior scales only one gene (eda) showed such a correlation. Furthermore, eda displayed the most significant expression difference between species of Lake Tanganyika and species of the other two younger lakes. Finally, we found genetic differences in downstream regions of eda gene (e.g. in the eda-tnfsf13b inter-genic region) that are associated with observed expression differences. This is reminiscent of a genetic difference in the eda-tnfsf13b inter-genic region which leads to gain or loss of armour plates in stickleback.ConclusionThese findings provide evidence for cross-species transcriptional differences of an important morphogenetic factor, eda, which is involved in formation of ectodermal appendages. These expression differences appeared to be associated with morphological differences observed in the scales of haplochromine cichlids indicating potential role of eda mediated signal in divergent scale morphogenesis in fish.

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.

Adaptation to heterogeneous sensory environments has been implicated as a key parameter in speciation. Cichlid fish are a textbook example of divergent visual adaptation, mediated by variation in the sequences and expression levels of cone opsin genes (encoding the protein component of visual pigments). In some vertebrates including fish, visual sensitivity is also tuned by the ratio of Vitamin A1/A2-derived chromophores (i.e. the light-sensitive component of the visual pigment, bound to the opsin protein), where higher proportions of A2 cause a more red-shifted wavelength absorbance. Here, we explore variation in chromophore ratios across multiple cichlid populations in Lake Victoria, using as a proxy the enzyme CYP27C1 that catalyses the conversion of Vitamin A1-into A2. We focus on sympatric Pundamilia cichlids, where species with blue or red male coloration co-occur at multiple islands, but occupy different depths and consequently different visual habitats. In the red species, we found higher cyp27c1 expression in populations from turbid-water than from clear-water locations, but there was no such pattern in the blue species. Across populations, differences between the sympatric species in cyp27c1 expression had a consistent relationship with species differences in opsin expression patterns, but the red/blue identity reversed between clear- and turbid-water locations. To assess the contribution of heritable versus environmental causes of variation, we tested whether light manipulations induce a change in cyp27c1 expression in the laboratory. We found that cyp27c1 expression was not influenced by experimental light conditions, suggesting that the observed variation in the wild is due to genetic differences. Establishing the biological importance of this variation requires testing the link between cyp27c1 expression and A1/A2 ratios in the eye, as well as its consequences for visual performance.

Understanding the interplay between ecological and population genetic processes through space and time is a central goal of landscape genetics. However, most studies that place diversification dynamics in an ecological context have focused on vertebrates, leaving a significant gap in our understanding of the effects of ecosystem change on community composition and demography of invertebrates. In the East African Rift System, cichlid fishes have emerged as a powerful model system for understanding adaptive radiation (Kornfield & Smith, 2000), but few studies have examined diversification of other taxa. In this issue of Molecular Ecology, Van Bocxlaer et al. (2020) use landscape genetic approaches to model historical demography and diversification of viviparid gastropods in the Lake Victoria ecoregion. They show that while phylogeographic patterns are similar between the two, viviparids and cichlids have responded in very different ways to the climatic upheavals of the Pleistocene and that their responses have been at least partially asynchronous. Viviparids have experienced population collapse 30- to 50-fold more severe than that seen in haplochromine cichlids from the region, and population declines began 100K years earlier, prior to the last glacial maximum (~15,000-18,000 years ago). Their results reveal a new facet to the profound and lasting impacts of Pleistocene climate change on the modern fauna of the Lake Victoria ecoregion and its ability to respond to current human-mediated stressors.

Lake Edward, East Africa, harbours a largely understudied assemblage of haplochromine cichlids that displays a range of adaptions to various specialised trophic niches. In this system, we discovered specimens of Haplochromis with morphologies similar to those of oral-mollusc shellers from Lake Victoria. These morphologies are characterised by short oral jaws with stout teeth that are used either to crush molluscs or to grab the soft bodies of snails and wrench them out of their shells. A morphometric study on 47 specimens from Lake Edward revealed the presence of three new species with an oral-shelling morphology: Haplochromis concilians sp. nov., H. erutus sp. nov. and H. planus sp. nov. All three species are formally described. Stomach-content observations confirmed an opportunistic oral-shelling ecology for H. concilians sp. nov. and H. erutus sp. nov. Within H. planus sp. nov., only large specimens displayed a specialised oral-shelling morphology, but their stomachs were nearly empty, while small specimens consumed mainly Ostracoda and Hydrachnidia. Remarkably, the three species differed considerably in morphology from each other, but they each resembled oral-sheller species from Lake Victoria.

Background Understanding how variation in gene expression contributes to morphological diversity is a major goal in evolutionary biology. Cichlid fishes from the East African Great lakes exhibit striking diversity in trophic adaptations predicated on the functional modularity of their two sets of jaws (oral and pharyngeal). However, the transcriptional basis of this modularity is not so well understood, as no studies thus far have directly compared the expression of genes in the oral and pharyngeal jaws. Nor is it well understood how gene expression may have contributed to the parallel evolution of trophic morphologies across the replicate cichlid adaptive radiations in Lake Tanganyika, Malawi and Victoria. Results We set out to investigate the role of gene expression divergence in cichlid fishes from these three lakes adapted to herbivorous and carnivorous trophic niches. We focused on the development stage prior to the onset of exogenous feeding that is critical for understanding patterns of gene expression after oral and pharyngeal jaw skeletogenesis, anticipating environmental cues. This framework permitted us for the first time to test for signatures of gene expression underlying jaw modularity in convergent eco-morphologies across three independent adaptive radiations. We validated a set of reference genes, with stable expression between the two jaw types and across species, which can be important for future studies of gene expression in cichlid jaws. Next we found evidence of modular and non-modular gene expression between the two jaws, across different trophic niches and lakes. For instance, prdm1a, a skeletogenic gene with modular anterior-posterior expression, displayed higher pharyngeal jaw expression and modular expression pattern only in carnivorous species. Furthermore, we found the expression of genes in cichlids jaws from the youngest Lake Victoria to exhibit low modularity compared to the older lakes. Conclusion Overall, our results provide cross-species transcriptional comparisons of modularly-regulated skeletogenic genes in the two jaw types, implicating expression differences which might contribute to the formation of divergent trophic morphologies at the stage of larval independence prior to foraging. Electronic supplementary material The online version of this article (10.1186/s12862-019-1483-3) contains supplementary material, which is available to authorized users.

Background Cichlids are a prime model system in evolutionary research and several of the most prominent examples of adaptive radiations are found in the East African Lakes Tanganyika, Malawi and Victoria, all part of the East African cichlid radiation (EAR). In the past, great effort has been invested in reconstructing the evolutionary and biogeographic history of cichlids (Teleostei: Cichlidae). In this study, we present new divergence age estimates for the major cichlid lineages with the main focus on the EAR based on a dataset encompassing representative taxa of almost all recognized cichlid tribes and ten mitochondrial protein genes. We have thoroughly re-evaluated both fossil and geological calibration points, and we included the recently described fossil †Tugenchromis pickfordi in the cichlid divergence age estimates. Results Our results estimate the origin of the EAR to Late Eocene/Early Oligocene (28.71 Ma; 95% HPD: 24.43–33.15 Ma). More importantly divergence ages of the most recent common ancestor (MRCA) of several Tanganyika cichlid tribes were estimated to be substantially older than the oldest estimated maximum age of the Lake Tanganyika: Trematocarini (16.13 Ma, 95% HPD: 11.89–20.46 Ma), Bathybatini (20.62 Ma, 95% HPD: 16.88–25.34 Ma), Lamprologini (15.27 Ma; 95% HPD: 12.23–18.49 Ma). The divergence age of the crown haplochromine H-lineage is estimated to 22.8 Ma (95% HPD: 14.40–26.32 Ma) and of the Lake Malawi radiation to 4.07 Ma (95% HDP: 2.93–5.26 Ma). In addition, we recovered a novel lineage within the Lamprologini tribe encompassing only Lamprologus of the lower and central Congo drainage with its divergence estimated to the Late Miocene or early Pliocene. Furthermore we recovered two novel mitochondrial haplotype lineages within the Haplochromini tribe: ‘Orthochromis’ indermauri and ‘Haplochormis’ vanheusdeni. Conclusions Divergence time estimates of the MRCA of several Tanganyika cichlid tribes predate the age of the extant Lake Tanganyika basin, and hence are in line with the recently formulated “Melting-Pot Tanganyika” hypothesis. The radiation of the ‘Lower Congo Lamprologus clade’ might be linked with the Pliocene origin of the modern lower Congo rapids as has been shown for other Lower Congo cichlid assemblages. Finally, the age of origin of the Lake Malawi cichlid flock agrees well with the oldest age estimate for lacustrine conditions in Lake Malawi. Electronic supplementary material The online version of this article (10.1186/s12862-019-1417-0) contains supplementary material, which is available to authorized users.

Why sex chromosomes turn over and remain undifferentiated in some taxa, whereas they degenerate in others, is still an area of ongoing research. The recurrent occurrence of homologous and homomorphic sex chromosomes in distantly related taxa suggests their independent evolution or continued recombination since their first emergence. Fishes display a great diversity of sex-determining systems. Here, we focus on sex chromosome evolution in haplochromines, the most species-rich lineage of cichlid fishes. We investigate sex-specific signatures in the Pseudocrenilabrus philander species complex, which belongs to a haplochromine genus found in many river systems and ichthyogeographic regions in northern, eastern, central, and southern Africa. Using whole-genome sequencing and population genetic, phylogenetic, and read-coverage analyses, we show that one population of P. philander has an XX–XY sex-determining system on LG7 with a large region of suppressed recombination. However, in a second bottlenecked population, we did not find any sign of a sex chromosome. Interestingly, LG7 also carries an XX–XY system in the phylogenetically more derived Lake Malawi haplochromine cichlids. Although the genomic regions determining sex are the same in Lake Malawi cichlids and P. philander, we did not find evidence for shared ancestry, suggesting that LG7 evolved as sex chromosome at least twice in haplochromine cichlids. Hence, our work provides further evidence for the labile nature of sex determination in fishes and supports the hypothesis that the same genomic regions can repeatedly and rapidly be recruited as sex chromosomes in more distantly related lineages.

African cichlids are model systems for evolutionary studies and for host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Here, we sampled five locations in southern Lake Victoria, the youngest of the African Great Lakes. We surveyed gillinfecting monogeneans from 18 cichlid species belonging to the Lake Victoria radiation superflock and two cichlid species representing two older and distantly related lineages. We found one species of Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Cichlidogyrus (Dactylogyridae, Monogenea). Four species are herein described: Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Another species is reported but not formally described (because of few specimens and morphological similarity with C. furu n. sp.). Two other species are redescribed: Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the other hooks, highlighting the need to re-evaluate the current classification system of haptoral configurations that considers hook pairs III-VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis and C. nyanza n. sp. suggest that these are closely related to other congeners that infect haplochromines. We also found morphological indications that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonized by two cichlid tribes (Haplochromini and Oreochromini).DisclaimerThis preprint is disclaimed for purposes of Zoological Nomenclature in accordance with the International Code of Zoological Nomenclature, Fourth Edition Articles 8.2 and 8.3 (ICZN 1999). No new names or nomenclatural changes are available from statements in this preprint.Résumé - Quatre espèces nouvelles de Cichlidogyrus (Platyhelminthes, Monogenea, Dactylogyridae) parasites d’haplochrominé (Cichlidae) du lac Victoria, avec la redescription de C. bifurcatus and C. longipenisA cause des radiations adaptatives qu’ils ont subies, les cichlidés africain sont des systèmes modèles pour étudier l’évolution, mais aussi les relations hôtes/parasites, car ils hébergent de nombreuses espèces de Monogènes parasites qui présentent une spécificité étroite vis-à-vis de leurs hôtes. Dans ce travail, nous avons échantillonné cinq localités dans le Sud du lac Victoria, le plus jeune des grands lacs d’Afrique de l’Est. Nous avons examiné les Monogènes présents sur les branchies de 18 espèces de Cichlidés appartenant à la radiation adaptative « superflock » du lac Victoria et de deux espèces représentant deux lignées anciennes et non étroitement apparentées. Nous avons trouvé une espèce de Gyrodactylus (Gyrodactylidae, Monogenea), Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011 et sept espèces de Cichlidogyrus (Dactylogyridae, Monogenea). Quatre espèces nouvelles sont décrites dans le présent travail : Cichlidogyrus pseudodossoui n. sp., C. nyanza n. sp., C. furu n. sp., C. vetusmolendarius n. sp.. Une est signalée mais non décrite formellement (trop peux d’individus recueillis, morphologiquement proche de C. furu n. sp.). Deux autres sont redécrites : Cichlidogyrus bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Nos résultats confirment que la faune des Monogènes des Cichlidés du lac Victoria fait preuve d’une richesse spécifique et d’une spécificité moins importante que celle du lac Tanganyika. Chez C. furu n. sp. la paire de crochet V étant nettement plus longue que les autres, il faudra reconsidérer le système de classification actuel des types de hapteurs chez les Cichlidogyrus, qui considère que tous les crochets (III à VII) ont la même taille. Quelques caractéristiques morphologiques de C. bifurcatus, C. longipenis et C. nyanza n. sp. pourraient être la preuve d’une ascendance commune avec des congénères présents chez d’autres Haplochrominés. De même, certains caractères indiqueraient que des représentants des Cichlidogyrus ont colonisé les Haplochrominés du lac Victoria, ou leurs ancêtres, au moins à deux reprises, ce qui est cohérent avec une colonisation du lac par deux lignées de cichlidés distinctes (Haplochromini and Oreochromini).

A species of haplochromine cichlid fish of the genus Diplotaxodon Trewavas, endemic to Lake Malaŵi is described: Diplotaxodon dentatus, new species. All eight type specimens were trawled together off Thumbi East Island in the Southeastern arm of the lake at 73 meters in 1985. They were initially identified as D. argenteus because the teeth on the oral jaws were fully exposed with a closed mouth. The shorter snout length of D. dentatus (26.6–29.2 % HL) clearly separates it from D. argenteus (31.7–34.2 % HL). A plot of a principal components analysis further supports the separation of D. dentatus from D. argenteus.

The haplochromine cichlids of Lake Victoria exhibit the fastest adaptive radiation of vertebrates known. Species identification of these lacustrine cichlids has been subject of debate for many years. Over the past 35 years, environmental perturbations have resulted in phenotypic change and possibly in hybridization, making species delimitation even more problematic. In this chapter, we document the effects of a changed environment on the ecomorphology of the zooplanktivore Haplochromis (Yssichromis) pyrrhocephalus over a 20-year period. We found that this species has extended its habitat to shallower waters and adjusted its diet to larger and more robust prey. Adaptive morphological responses to predation, to larger and tougher prey and to a hypoxic environment were found. Whether these morphological changes are the result of hybridization, phenotypic plasticity or evolutionary adaptation remains unclear. The morphological responses are sometimes so large that they transcend morphological species boundaries and even one of the limits of the genus Yssichromis. The extent of the morphological responses makes clear that nuptial colouration is indispensable for species distinction and the assessment of species richness. We review advanced molecular techniques that might make it possible to distinguish species genetically. These techniques may also reveal how adaptive responses might have played a role in the remarkable resurgence of these rapidly adapting cichlids.

Lakes Victoria, Kyoga, and Nabugabo (���the Lake Victoria region���) are remarkable for hosting one of the largest assemblages of cichlid fishes among the African inland lakes. Here, we review the role and severity of anthropogenic and environmental stressors on the cichlid communities in the Lake Victoria region to understand the mechanisms leading to the persistence and resurgence of some of the cichlid fishes. Our review suggests that (1) the native Oreochromis species populations primarily collapsed due to overfishing and that the introduced species and habitat change suppressed their ability to recover; (2) without primary triggers associated with change in the environment and habitat conditions, particularly eutrophication and associated anoxia and reduced water transparency, Nile perch (Lates niloticus) predation alone may not have caused the massive loss of species diversity; and (3) the resurgence of haplochromine cichlids is due to a combination of general improvement in the environment and reduction in L. niloticus abundance, with additionally possibly some rapid ecological adaptations. We conclude that environmental stressors will likely continue to shape the ecosystems in which the remaining endemic cichlid fish diversity continue to evolve, clearly involving genetic exchange between species. If water clarity can be improved again, it is possible to maintain a diverse assemblage of endemic species.

In an effort to contribute to resilient food and nutritional security in urban slums, a food system approach was applied to understand the key socio-economic factors driving fish species consumption in Kibera, the largest informal settlement in Africa located in Nairobi, Kenya. Data were collected from 385 randomly selected households using a structured questionnaire. A multivariate probit model was applied to estimate the relationship between the variables in order to determine the socio-economic drivers of preferences for different fish species. The results indicated that Lake Victoria sardine (Rastrineobola argentea) had the highest preference (73%) among the respondents, followed by Nile tilapia (Oreochromis niloticus) (70%) and Nile perch (Lates niloticus) (23%), respectively, with other fish species at 12%, including African catfish, marbled lungfish, common carp, fulu and tuna (Clarias gariepinus, Protopterus aethiopicus, Cyprinus carpio, Haplochromine cichlids and Thunnus sp., respectively). Large household size showed an increase in preference for the Lake Victoria sardine, while higher income influenced preference for Nile tilapia and Nile perch positively, implying that when more income is available, Nile tilapia is the preferred fish over other fish species. Increased fish prices positively influenced preference for Nile tilapia, which is explained by the willingness to pay extra for quality and origin, for instance, to avoid the cheaply cultivated Chinese fish. In the case of the Lake Victoria sardine, lower prices positively affected the preferences. Religious and cultural practices and beliefs influenced preference for species and consumption of fish. Residents who migrated from western Kenya had a higher preference for the Lake Victoria sardine, while residents born and raised in Kibera had a higher preference for Nile tilapia. Neighbourhood effects reduced the preference for consuming Nile perch. These findings provide insights into future market opportunities for specific target groups. For instance, given that small-sized fish like the Lake Victoria sardine is highly demanded, in order to increase resiliency in food and nutrition security, small-sized cheap Nile tilapia will have a large potential in the future, with ever higher demand specifically from the residents born and raised in Kibera.

Deciphering why some lineages produce spectacular radiations while others do not provides important insights into biodiversity, but the molecular basis underlying this process remains largely unknown. Here, we identified a lineage-restricted gene, which we namedlg. Combined omics analyses showed thatlgis under positive selection in the most species-rich lineage of cichlid fishes, the modern haplochromine (MH) lineage, indicating its evolutionary advantage. Using transgenic zebrafish, we functionally showed that a cichlid fish-specific upstream insertion oflgcan drive new and strong eGFP expression in tissues noted for adaptation in the MH lineage, but not in other lineages. Furthermore, the deletion of three MH-specific SNPs within this region can reconstitute weak and limited expression patterns similar to those in non-MH lineages. We thus demonstrated that a series ofcis-regulatory changes in an advantageous gene are linked with a gain of expression that is related to an astonishingly adaptive radiative lineage.

International audience; Ecosystems of Lake Victoria and riparian communities have been strongly disrupted by the introduction of the invasive Nile perch and its fishing industry. Beyond this invasion and other recent anthropogenic stressors, the Lake Victoria ecoregion also underwent phases of pronounced aridity over the Late Pleistocene, lastly during the Last Glacial Maximum (LGM). The consequences of recent and historic environmental change have been canvassed for the adaptive radiation of haplochromine cichlids occupying the ecoregion, but their effect on freshwater invertebrate diversity remains largely unknown. Here we use 15 microsatellite loci and approximate Bayesian computation to test whether viviparid gastropods experienced a population bottleneck during the LGM, as did cichlids. Clustering analyses support three viviparid gene pools in the Lake Victoria ecoregion, gathering specimens from 1) Lake Albert and the White Nile, 2) the Victoria Nile and Lake Kyoga and 3) Lake Victoria and tributaries. The last group contains the highest genetic diversity, but all groups have a considerable number of private alleles and are inferred to predate the LGM. Examinations of demographic history reveal a 190-to 500-fold population decline that started ~125-150 ka ago, thus substantially before the LGM bottleneck documented in haplochromine cichlids. Population collapses in viviparids are an order of magnitude more severe than declines in cichlids and have not been halted by the re-establishment of freshwater ecosystems since the LGM. Recent anthropogenic ecosystem deterioration is causing homogenization of previously diversified microhabitats, which may contribute to (local) extinction and enhanced gene flow among species within gene pools.

Local adaptation to the littoral and pelagic zones in two cichlid haplochromine fish species from Lake Kivu was investigated using morphometrics. Cranial variation and inferred jaw mechanics in both sexes of the two species across the two habitat types were quantified and compared. Comparisons of littoral versus pelagic populations revealed habitat‐specific differences in the shape of the feeding apparatus. Also, kinematic transmission of the anterior jaw four‐bar linkage that promotes greater jaw protrusion was higher in the pelagic zone than in the littoral zone for both species. Inferred bite force was likewise higher in pelagic zone fish. There were also sex‐specific differences in craniofacial morphology as males exhibited longer heads than females in both habitats. As has been described for other cichlids in the East African Great Lakes, local adaptation to trophic resources in the littoral and pelagic habitats characterizes these two Lake Kivu cichlids. Similar studies involving other types of the Lake Kivu fishes are recommended to test the evidence of the observed trophic patterns and their genetic basis of divergences., Comparisons of littoral versus pelagic Lake Kivu haplochromine species revealed habitat‐specific differences in the shape of the feeding apparatus.

Two monotypic haplochromine cichlid genera (Teleostei: Cichlidae) of the Pseudocrenilabrus group are described from northern Zambia. One new genus is Palaeoplex gen. nov., with Pa. palimpsest sp. nov. as the type species, from the Luongo and Kalungwishi Rivers (Upper Congo drainage, Luapula subdrainage). It is diagnosed by a unique combination of morphological characters: (1) a fully developed infraorbital series without a distinct gap between the lachrymal and second infraorbital bone, (2) fused hypuralia 1+2 and hypuralia 3+4, (3) molariform teeth on the sagittal series of the lower pharyngeal jaw, and (4) a large maximum size. The second new genus, Lufubuchromis gen. nov., with L. relictus sp. nov. as the type species, is restricted to the upper Lufubu River catchment (Upper Congo drainage, Lake Tanganyika subdrainage). It is diagnosed by a unique combination of morphological characters: (1) a fully developed infraorbital series without a distinct gap between the lachrymal and second infraorbital bone, (2) fused hypuralia 1+2 (rarely with a visible suture) and fused hypuralia 3+4, (3) a unique male coloration pattern, i.e. deep crimson red colored areas on the anterior ventral flank parts, chest and belly and on the lower head; remaining parts of flanks and caudal peduncle bluish), and (4) a Pseudocrenilabrus blotch present in both sexes. Both new genera are compared with all remaining taxa of the Pseudocrenilabrus group and with all representatives of all other major haplotilapiine lineages.

Nile perch (Lates niloticus), a main target for Lake Victoria's fisheries, shifts its diet from invertebrates to fish during its ontogeny. We combined stomach contents with stable isotopes to study these diet shifts in Mwanza Gulf, southern Lake Victoria. During four seasons between 2009 and 2011 we collected and analysed 6697 stomachs and 516 stable isotope samples of Nile perch. Caridina shrimp and haplochromine cichlids were the major food items in Nile perch of 5–40 cm. Based on stomach contents, the shift of dominance of Caridina towards haplochromines in the diet varied from 6.7 cm length in the southern part of the gulf, to >20 cm in the northern part, possibly related to the higher abundance of Caridina in the north. In general isotope-based and stomach-content-based estimates of Nile perch diets agreed. We observed only two discrepancies: in Nile perch >20 cm, the isotope-based estimates of the contribution of haplochromines to the diet were much lower than based on stomach contents and the contribution of juvenile Nile perch to the diet were much higher in the isotope-based estimates than in the stomach based-based estimates. This discrepancy may be explained by e.g. different timespan-coverages between isotopes and stomach contents, by movements of Nile perch between the Gulf and the rest of Lake Victoria, or by the overlapping isotopic profiles of haplochromines and juvenile Nile perch. With the recent recovery of haplochromines in Lake Victoria, Nile perch appears to rely more on this prey again, as it did in the 1980s.

In many haplochromine cichlids, body coloration is an important communication cue during social interactions. In some cichlids, individuals can change color, but we have little information about the underlying physiological mechanisms. We examined the regulation of coloration in the color polymorphic cichlid fish Astatotilapia burtoni where males are either blue or yellow. Previous studies implicated the melanocortin system, a neuroendocrine center that regulates pigmentation and the stress response, in regulating the color polymorphism in this species. We found that both blue and yellow males express a high density of yellow xanthophores. Dispersal of xanthophore pigments in both yellow and blue morphs occurred within minutes in a dose-dependent manner. Similarly, exogenous α-melanocyte stimulating hormone (α-MSH, a melanocortin hormone) increased yellowness of the body in a dose-independent fashion. We observed many color changes in males housed in social communities with the proportion of yellow males increasing over the 2-week experimental period. However, color phenotype or color change was not influenced by experimental alteration of the stability of the social hierarchy. The effects of α-MSH suggest that the melanocortin system contributes to the polymorphism in coloration in A. burtoni but the role of social interactions and social stress in regulating color remains unclear.

The Lake Edward system in Eastern Central Africa, including Lakes Edward and George and their associated rivers, is home to a species assemblage of endemic haplochromine cichlids. Currently, 36 of these species have been formally described, while it is estimated that the system may harbour a total of 60 species. Species flocks of haplochromine cichlids are morphologically and ecologically very diverse and have radiated into many specialised trophic niches. Paedophagy is the feeding on eggs and larvae. In Haplochromis, most paedophages steal fry and eggs from the buccal cavities of mouthbrooding female cichlids. Hitherto, one formally described species with this diet is known from the Lake Edward system: Haplochromis taurinus. We performed a morphometrical revision of all species of Haplochromis from this system with a morphology that suggests a paedophagous diet: long oral jaws set with small teeth. Sixty-eight specimens were studied by taking 28 measurements and 20 counts and by performing stomach content observations. We discovered that H. paradoxus also had a paedophagous diet. Our analyses further revealed the presence of three new species: H. gracilifur sp. nov., H. molossus sp. nov., and H. relictidens sp. nov. All five of these species were described or redescribed.

Debate on the contribution of Nile perch (Lates niloticus) to the demise of Lake Victoria’s 500+ endemic haplochromine cichlids centers around the “top-down” and “bottom-up” hypotheses. The former suggests Nile perch destroyed the haplochromines, causing the disruption of food chains and nutrient cycling and so initiating the accelerated eutrophication of the lake. The latter proposes that haplochromines suppressed Nile perch by preying on its eggs and fry or competing with juveniles for food. A recent paper argued that accelerated eutrophication caused by a climatic event led to their collapse, allowing Nile perch to explode. However, the Nile perch population grew before haplochromines decreased, and they only collapsed once Nile perch biomass exceeded theirs. The chronology indicates that accelerated eutrophication of the lake followed rather than preceded the haplochromine collapse, suggesting that eutrophication was not its cause. A size-selective predation model developed to support the bottom-up hypothesis is discussed in light of existing data, but does not support the bottom-up hypothesis. It was concluded that the top-down model better fits the data and conforms to the law of parsimony.

The past subsistence of the Lake Victoria fishery was dominated by rich, diverse haplochromine cichlids. This multispecies fishery has undergone a decline over the past four decades, evolving into a commercial fishery consisting mainly of Nile perch (Lates niloticus), Nile tilapia (Oreochromis niloticus) and cyprinid (Rastrineobola argentea species). To better understand Lake Victoria fisheries, studies dating as far back as the 1920s have been carried out to assess the status of the fish stocks. These past studies indicated the lake fisheries were declining because of numerous major challenges, including intense fishing, invasive species, loss of biodiversity, ecological alterations, climate change, inadequate information to inform management and unharmonized policies. Numerous policies and regulations have been developed and implemented over the years to address these issues and manage the fisheries sustainably. Most of the interventions have been sectorial, disjointed and unharmonized and have not reduced the declining fish catch rates. With reestablishment of the East Africa Community (EAC) with several institutions in 1994, the Lake Victoria riparian states initiated an ecosystem approach to manage the Lake Victoria fishery resources in a sustainable manner. This study reviews the development of the Lake Victoria fisheries, outlines major past and present management challenges and provides a set of new strategies to manage the lake's fisheries resources, with emphasis on an ecosystem approach.

The electric yellow cichlid Labidochromis caeruleus is a mouth-brooding haplochromine cichlid from Lake Malawi and one of the most popular cichlids in the ornamental fish industry. To investigate the early development of L. caeruleus from hatching until the juvenile stage, we studied its morphological development and allometric growth patterns. In newly-hatched larvae, most organs and body parts were not yet differentiated and continued to develop until 15 days post hatching (dph). The yolk sac was depleted at 13 dph. There was allometric growth, primarily in the anterior and posterior regions of the body, and inflection points when trajectories of allometric growth changed. Head and tail growth was prioritized, suggesting that body parts linked to feeding and swimming behaviour mature earlier than the rest of the body. Additionally, growth patterns revealed that development of organs related to vital functions such as branchial respiration, sensation, exogenous feeding and swimming was prioritized. Comparisons with other African and Neotropical cichlids revealed differences in ontogenetic processes and allometric growth along the anterior-posterior axis as well as variation in developmental timing. These results indicate how early morphological development and ontogenic processes might respond to the distinctive parental care observed in mouth-brooding cichlids.

Two species of haplochromine cichlid fishes of the genus Diplotaxodon Trewavas, endemic to Lake Malaŵi are described: Diplotaxodon longimaxilla, new species, and Diplotaxodon altus, new species. Diplotaxodon altus is diagnosed from other species in the genus based on body depth (35.1–37.8% SL), number of gill rakers (21–26), and a smaller cheek depth (18.2–20.0% HL). Diplotaxodon longimaxilla is delimited from other Diplotaxodon spp. based on body depth (28.9–32.4% SL), horizontal eye diameter (HED 27.1–32.1% HL), smaller cheek depth (15.2–19.4% HL), and number of lateral-line scales (35–38). Other authors have indicated that several other Diplotaxodon spp. occur, but too few specimens were available to permit detailed comparisons. The two new species occur sympatrically at depths of between 40–130 m. Specimens of Diplotaxodon altus were sampled from nets deployed at night using light attraction, while specimens of D. longimaxilla were sampled from nets operated both at night and day. We further ...

Labeotropheus is a genus of haplochromine cichlids endemic to Lake Malaŵi, Africa. Since its original description, surprisingly few additional species have been described, largely due to a misinterpretation of the historical taxonomic treatment of allopatric populations of Labeotropheus. Previously published evidence of genetic and morphological divergence among southern populations of Labeotropheus suggests that species diversity is underestimated. Morphometric, meristic, and color characteristics are employed to describe a new species of Labeotgropheus endemic to Mumbo Island and Thumbi West Island near the Nankumba Peninsula in southern Lake Malaŵi. The new species is distinguished from congeners by a wider body, longer pectoral fins, a shorter snout, and male nuptial coloration.

Male secondary sexual traits are targets of inter- and/or intrasexual selection, but can vary due to a correlation with life-history traits or as by-product of adaptation to distinct environments. Trade-offs contributing to this variation may comprise conspicuousness towards conspecifics versus inconspicuousness towards predators, or between allocating resources into coloration versus the immune system. Here, we examine variation in expression of a carotenoid-based visual signal, anal-fin egg-spots, along a replicate environmental gradient in the haplochromine cichlid fish Astatotilapia burtoni. We quantified egg-spot number, area, and coloration; applied visual models to estimate the trait's conspicuousness when perceived against the surrounding tissue under natural conditions; and used the lymphocyte ratio as a measure for immune activity. We find that (i) males possess larger and more conspicuous egg-spots than females, which is likely explained by their function in sexual selection; (ii) riverine fish generally feature fewer but larger and/or more intensively colored egg-spots, which is probably to maintain signal efficiency in intraspecific interactions in long-wavelength shifted riverine light conditions; and (iii) egg-spot number and relative area correlate with immune defense, suggesting a trade-off in the allocation of carotenoids. Taken together, haplochromine egg-spots feature the potential to adapt to the respective underwater light environment, and are traded-off with investment into the immune system

Feeding is a complex behaviour comprised of satiety control, foraging, ingestion and subsequent digestion. Cichlids from the East African Great Lakes are renowned for their diverse trophic specializations, largely predicated on highly variable jaw morphologies. Thus, most research has focused on dissecting the genetic, morphological and regulatory basis of jaw and teeth development in these species. Here for the first time we explore another aspect of feeding, the regulation of appetite related genes that are expressed in the brain and control satiety in cichlid fishes. Using qPCR analysis, we first validate stably expressed reference genes in the brain of six haplochromine cichlid species at the end of larval development prior to foraging. We next evaluate the expression of 16 appetite related genes in herbivorous and carnivorous species from the parallel radiations of Lake Tanganyika, Malawi and Victoria. Interestingly, we find increased expression of two anorexigenic genes, cart and npy2r, in the brain of carnivorous species in all the lakes. This supports the notion that herbivory compared to carnivory requires stronger appetite stimulation in order to feed larger quantity of food and to compensate for the relatively poorer nutritional quality of a plant- and algae-based diet. Our study contributes to the limited body of knowledge on the neurological circuitry that controls feeding transitions and adaptations and in cichlids and other teleosts.

Ecological speciation is facilitated when divergent adaptation has direct effects on selective mating. Divergent sensory adaptation could generate such direct effects, by mediating both ecological performance and mate selection. In aquatic environments, light attenuation creates distinct photic environments, generating divergent selection on visual systems. Consequently, divergent sensory drive has been implicated in the diversification of several fish species. Here, we experimentally test whether divergent visual adaptation explains the divergence of mate preferences in Haplochromine cichlids. Blue and red Pundamilia co‐occur across south‐eastern Lake Victoria. They inhabit different photic conditions and have distinct visual system properties. Previously, we documented that rearing fish under different light conditions influences female preference for blue versus red males. Here, we examine to what extent variation in female mate preference can be explained by variation in visual system properties, testing the causal link between visual perception and preference. We find that our experimental light manipulations influence opsin expression, suggesting a potential role for phenotypic plasticity in optimizing visual performance. However, variation in opsin expression does not explain species differences in female preference. Instead, female preference covaries with allelic variation in the long‐wavelength‐sensitive opsin gene (LWS), when assessed under broad‐spectrum light. Taken together, our study presents evidence for environmental plasticity in opsin expression and confirms the important role of colour perception in shaping female mate preferences in Pundamilia. However, it does not constitute unequivocal evidence for the direct effects of visual adaptation on assortative mating., Pundamilia cichlids exhibit light‐induced opsin expression plasticity, which correlates with female mate preference, but does not explain species differences in preference. Instead, female preference covaries with allelic variation in the LWS opsin in broad‐spectrum light, confirming the important role of colour perception in shaping Pundamilia mate preferences.

BackgroundAfrican cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to understand the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages.ResultsWe re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We developed a newde novogenome assembly of the Lake Malawi cichlid,Metriaclima zebra, using high-coverage PacBio sequencing, and anchored contigs to linkage groups (LGs) using four different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes.Large intra-chromosomal structural differences (~2-28Mbp) among species are common, while inter-chromosomal differences are rare (< 10Mbp total). Placement of the centromeres within chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11 and LG20 are associated with reductions in recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids.M. zebrahas a larger number of recent transposable element (TE) insertions compared toO. niloticus, suggesting that several TE families have a higher rate of insertion in the haplochromine cichlid lineage.ConclusionThis study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.

A brief historical (1956-2014) review of the Lake Victoria ecological development is presented. The Lake Victoria ecosystem structure was thoroughly modified after the invasion of the predator fish Lates niloticus (Nile perch). The relative capacity and functional activity of the food-web compartments was quantitative and qualitative altered. The trophic status of Lake Victoria ecosystem was shifted toward eutrophication : phytoplankton species composition and densities were modified, fish assemblages were converted from about 400 Haplochromine species diversity to large body predator , Nile perch dominance. Consequently , the fishery was changed accompanied by Socio-Economic consequences. The thermal structure trait shifted towards enhancement of anoxia and Hypolimnetic volume extension.

Sensory adaptation to the local environment can contribute to speciation. Aquatic environments are well suited for studying this process: The natural attenuation of light through water results in heterogeneous light environments, to which vision-dependent species must adapt for communication and survival. Here, we study visual adaptation in sympatric Pundamilia cichlids from southeastern Lake Victoria. Species with blue or red male nuptial coloration co-occur at many rocky islands but tend to be depth-differentiated, entailing different visual habitats, more strongly at some islands than others. Divergent visual adaptation to these environments has been implicated as a major factor in the divergence of P. pundamilia and P. nyererei, as they show consistent differentiation in the long-wavelength-sensitive visual pigment gene sequence (LWS opsin). In addition to sequence variation, variation in the opsin gene expression levels may contribute to visual adaptation. We characterized opsin gene expression and LWS genotype across Pundamilia populations inhabiting turbid and clear waters, to examine how different mechanisms of visual tuning contribute to visual adaptation. As predicted, the short-wavelength-sensitive opsin (SWS2b) was expressed exclusively in a population from clear water. Contrary to prediction however, expression levels of the other opsins were species- and island-dependent and did not align with species differences in LWS genotype. Specifically, in two locations with turbid water, the shallow-water dwelling blue species expressed more LWS and less RH2A than the deeper-dwelling red species, while the opposite pattern occurred in the two locations with clear water. Visual modeling suggests that the observed distribution of opsin expression profiles and LWS genotypes does not maximize visual performance, implying the involvement of additional visual tuning mechanisms and/or incomplete adaptation.OPEN RESEARCH BADGE: This article has earned an Open Data Badge for making publicly available the digitally-shareable data necessary to reproduce the reported results. The data is available at https://hdl.handle.net/10411/I1IUUQ.

Even though the idea that modes of speciation other than allopatric speciation are possible in nature is now widespread, compelling examples of ecological speciation in sympatry remain rare. We studied an undescribed radiation of haplochromine cichlids in a young crater lake in western Uganda, and in the small river that is nearby but has currently no known surface connection to the lake. We describe two different modes of speciation that occurred in this cichlid lineage within the past 1,500–10,000 years. Not constrained by gene flow, allopatric divergence between river and lake cichlids affects many different morphological traits as well as nuptial colouration—muted in the river, but intensified and polymorphic in lake cichlids—and neutral genetic differentiation. More surprisingly, we demonstrate a case for sympatric speciation within the small lake that is associated with dramatic differences in male breeding colouration (yellow with bright red-chest versus bright blue) and subtle differences in microhabitat, feeding regime and morphology. Reproductive isolation by assortative mating is suggested by significant differentiation between yellow and blue males in neutral markers of gene flow despite complete sympatry. We hypothesize speciation is mediated by divergent selection on sexual signalling between microhabitats., The genetic lab work was supported by Swiss National Science Foundation Grants 3100A0-118293/1 and 31003A_163338 to OS. Field work conducted by LJC was supported by Funding for this research was provided from the National Science Foundation and the Wildlife Conservation Society.

The haplochromine cichlid genus Labeotropheus is endemic to Lake Malaŵi, Africa. This genus presently contains two recognized species, Labeotropheus fuelleborni and L. trewavasae. As currently recognized, both species consist of geographically isolated populations scattered throughout the lake, each distinguished by a unique male nuptial color pattern. While other such allopatric populations of Lake Malaŵi cichlids have been described as different species, those of Labeotropheus have not, largely due to misunderstandings or misinterpretations of criteria applied to other Malaŵian endemics. Taking a refined approach to the recognition of putative species of Labeotropheus, I used morphometric, meristic, and color characteristics to describe two new, very similarly colored, species of Labeotropheus, both of which are found near Katale Island alongside the Luromo Peninsula in northwestern Lake Malaŵi.