Parallel molecular mechanisms underlie convergent evolution of the exaggerated snout phenotype in East African cichlids

Studying instances of convergent evolution of novel phenotypes can shed light on the evolutionary constraints that shape morphological diversity. Cichlid fishes from the East African Great Lakes are a prime model to investigate convergent adaptations. However, most studies on cichlid craniofacial morphologies have primarily considered bony structures, while soft tissue adaptations have been less intensely scrutinised. A rare example of an exaggerated soft tissue phenotype is the formation of a snout flap. This tissue flap develops from the upper lip and has evolved in only one cichlid genus from Lake Malawi and one genus from Lake Tanganyika. To investigate the molecular basis of snout flap convergence, we used mRNA sequencing to compare two species with snout flap (Labeotropheus trewavasae and Ophthalmotilapia nasuta) to their close relatives without snout flaps (Tropheops tropheops and Ophthalmotilapia ventralis) from Lake Tanganyika and Malawi. Our analysis revealed a greater complexity of differential gene expression patterns underlying the snout flap in the younger adaptive radiation of Lake Malawi than in the older Lake Tanganyika radiation. We identified 201 genes that were repeatedly differentially expressed between species with and without the snout flap in both lakes, suggesting that the pathway that gives rise to snout flaps is evolutionarily constrained, even though the flaps play very different functions in each species. The convergently expressed genes are involved in proline and hydroxyproline metabolism, which have been linked to human skin and facial deformities. Additionally, we also found enrichment for transcription factor binding sites upstream of differentially expressed genes such as members of the FOX transcription factor family, especially foxf1 and foxa2, which also showed an increased expression in the flapped snout and are linked to nose morphogenesis in mammals, as well as ap4 (tfap4), a transcription factor showing reduced expression in the flapped snout with an unknown role in the development of craniofacial soft tissues. As genes involved in cichlids snout flap development are associated with many human mid-line facial dysmorphologies, our findings imply a conservation of genes involved in mid-line patterning across vastly distant evolutionary lineages of vertebrates.

oca2 targeting using CRISPR/Cas9 in the Malawi cichlid Astatotilapia calliptera

Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterising the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in Astatotilapia calliptera, a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene oca2 required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, likely a result of non-homologous end joining, and a large deletion in the 3′ UTR due to homology-directed repair. We find that oca2 knock-out A. calliptera lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As A. calliptera resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation.

Descriptions of two new shell-dwelling species of Metriaclima (Cichlidae) from Lake Malaŵi, Africa

Metriaclima is the most speciose genus of rock-dwelling fishes (mbuna) found in Lake Malaŵi with 32 described species and with about 40 recognized forms that still await formal description. The genus is comprised of many geographically narrow populations restricted to specific habitat landmarks, such as reefs or islands. A few species have taken to the open sandy habitat where empty gastropod shells provide shelter. Two species of such shell-dwellers are here described as new. A combination of a black submarginal band in the dorsal and anal fins and five or fewer bars on the flank distinguishes Metriaclima ngarae sp. n. and M. gallireyae sp. n. from all other species of Metriaclima. Metriaclima ngarae sp. n. differs from M. gallireyae by a greater interorbital width and by a greater ratio of the snout length in the distance between snout tip and pelvic fin origin. Adult males of M. gallireyae have a blue-brown overall coloration obscuring the bar pattern on the flank while males of M. ngarae and those of the closely related M. lanisticola retain the bar pattern and have a coloration very similar to that of females.

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

Genetic basis of body shape variation along the benthic-pelagic axis in cichlid fishes

Divergence along the benthic-pelagic axis is one of the most widespread and repeated patterns of morphological variation in fishes, producing body shape diversity associated with ecology and swimming mechanics. This ecological shift is also the first stage of the explosive adaptive radiation of cichlid fishes in the East African Rift Lakes. We use two hybrid crosses of cichlids (Metriaclima sp. x Aulonocara sp. and Labidochromis sp. x Labeotropheus sp., >975 animals total) along the benthic-pelagic ecomorphological axis to determine the genetic basis of body shape diversification. Using a series of both linear and geometric shape measurements, we identify 55 quantitative trait loci (QTL) that underlie various aspects of body shape variation associated with benthic-pelagic divergence. These QTL are spread throughout the genome, each explain 3.0-7.2% of phenotypic variation, and are largely modular. Further, QTL are distinct both between these two crosses of Lake Malawi cichlids and compared to previously identified QTL for body shape in fishes such as sticklebacks. We find that body shape is controlled by many genes of small effects. In all, we find that convergent benthic and pelagic body phenotypes commonly observed across fish clades are most likely due to distinct genetic and molecular mechanisms.

Geographic and occupational mobility of small-scale fishers of Lake Malawi: an exploratory study of water, sanitation, and hygiene access, Malawi

The livelihood of small-scale fishers on the world's freshwater lakes cuts across the Sustainable Development Goal (SDG) 6, which covers water and sanitation, and SDG 8 on economic growth. The aim of this study was to examine the nature and extent of fishers' mobility patterns and access to improved sanitation facilities, safe drinking water, and handwashing practices while at work and home for two fishing camps in Malawi. The study used key informant interviews, questionnaires, water quality testing, and an observational checklist, followed by interviews on fishers' occupational migration. Many fishers (85%; 51/60) live and work in fishing camps with their families. Most fishers only went on day trips, but 8% of their working days were away from the fishing camps. Only eight fishers had safe (0 cfu/100 ml) drinking water at home. Most fishers reported drinking from and going to the toilet in the lake during fishing. Historical trends in cholera cases did not correlate with higher periods of migratory behavior of fishers observed in this study. Improving the livelihoods of small-scale fishers requires attention to their culture, the economics of the industry, and geographic criteria while at work and within fishing communities along the shores of Lake Malawi.

Male Genital Schistosomiasis Along the Shoreline of Lake Malawi: Baseline Prevalence and Associated Knowledge, Attitudes and Practices Among Local Fishermen in Mangochi District, Malawi

Male genital schistosomiasis (MGS) is an often-overlooked chronic consequence of urogenital schistosomiasis (UGS) associated with Schistosoma haematobium eggs and associated pathologies in the genital system of afflicted men. Despite the first formal description of MGS in 1911 by Madden, its epidemiology, diagnostic testing and case management of today are not well-described. However, since several interactions between MGS and the Human Immunodeficiency Virus (HIV) are known, there is renewed public health interest in MGS across sub-Saharan Africa (SSA). To shed new light upon MGS in Malawi, a longitudinal cohort study was set up among fishermen along the southern shoreline of Lake Malawi in Mangochi District, Malawi, to document its prevalence and assess mens' knowledge, attitudes and practices (KAP). After providing informed written consent, fishermen (n = 376) aged 18+ years (median age: 30 years, range: 18–70 years) were recruited and submitted urine and semen for point-of-care (POC) field and laboratory diagnostic parasitological tests. Individual questionnaires were administered to assess their KAP, with praziquantel (PZQ) treatment provided to all participants. Baseline prevalence of MGS (S. haematobium eggs in semen) was 10.4% (n = 114, median: 5.0 eggs per ml, range: 0.1–30.0) while for UGS (S. haematobium eggs in urine) was 17.1% (n = 210, median: 2.3 eggs per 10 ml, range: 0.1–186.0) and 3.8% were positive by POC circulating cathodic antigen (POC-CCA), indicative of a Schistosoma mansoni infection. Just under 10% of participants reported having experienced symptoms associated with MGS, namely genital or coital pain, or haemospermia. A total of 61.7% reported previous difficulties in accessing PZQ therapy, with 34.8% having received PZQ therapy before. There was a significant correlation between MGS infection and the frequency of fishing in a week (rho = −0.25, n = 100, p = 0.01). In conclusion, MGS is prevalent among local fishermen yet knowledge of the disease is poor. We therefore call for improved availability and accessibility to MGS diagnostics, PZQ treatment within ongoing control interventions. This will improve the lives and reproductive health of men, their partners and communities in this shoreline environment of Lake Malawi.