Molecular phylogeny of Oreochromis (Cichlidae: Oreochromini) reveals mito-nuclear discordance and multiple colonisation of adverse aquatic environments.

Although the majority of cichlid diversity occurs in the African Great Lakes, these fish have also diversified across the African continent. Such continental radiations, occurring in both rivers and lakes have received far less attention than lacustrine radiations despite some members, such as the oreochromine cichlids (commonly referred to as 'tilapia'), having significant scientific and socio-economic importance both within and beyond their native range. Unique among cichlids, several species of the genus Oreochromis exhibit adaptation to soda conditions (including tolerance to elevated temperatures and salinity), which are of interest from evolutionary biology research and aquaculture perspectives. Questions remain regarding the factors facilitating the diversification of this group, which to date have not been addressed within a phylogenetic framework. Here we present the first comprehensive (32/37 described species) multi-marker molecular phylogeny of Oreochromis and closely related Alcolapia, based on mitochondrial (1583 bp) and nuclear (3092 bp) sequence data. We show widespread discordance between nuclear DNA and mitochondrial DNA trees. This could be the result of incomplete lineage sorting and/or introgression in mitochondrial loci, although we did not find a strong signal for the latter. Based on our nuclear phylogeny we demonstrate that adaptation to adverse conditions (elevated salinity, temperature, or alkalinity) has occurred multiple times within Oreochromis, but that adaptation to extreme (soda) conditions (high salinity, temperature, and alkalinity) has likely arisen once in the lineage leading to O. amphimelas and Alcolapia. We also show Alcolapia is nested within Oreochromis, which is in agreement with previous studies, and here revise the taxonomy to synonymise the genus in Oreochromis, retaining the designation as subgenus Oreochromis (Alcolapia).

Genomics of Adaptation to Multiple Concurrent Stresses: Insights from Comparative Transcriptomics of a Cichlid Fish from One of Earth's Most Extreme Environments, the Hypersaline Soda Lake Magadi in Kenya, East Africa.

The Magadi tilapia (Alcolapia grahami) is a cichlid fish that inhabits one of the Earth's most extreme aquatic environments, with high pH (~10), salinity (~60% of seawater), high temperatures (~40 °C), and fluctuating oxygen regimes. The Magadi tilapia evolved several unique behavioral, physiological, and anatomical adaptations, some of which are constituent and thus retained in freshwater conditions. We conducted a transcriptomic analysis on A. grahami to study the evolutionary basis of tolerance to multiple stressors. To identify the adaptive regulatory changes associated with stress responses, we massively sequenced gill transcriptomes (RNAseq) from wild and freshwater-acclimated specimens of A. grahami. As a control, corresponding transcriptome data from Oreochromis leucostictus, a closely related freshwater species, were generated. We found expression differences in a large number of genes with known functions related to osmoregulation, energy metabolism, ion transport, and chemical detoxification. Over-representation of metabolism-related gene ontology terms in wild individuals compared to laboratory-acclimated specimens suggested that freshwater conditions greatly decrease the metabolic requirements of this species. Twenty-five genes with diverse physiological functions related to responses to water stress showed signs of divergent natural selection between the Magadi tilapia and its freshwater relative, which shared a most recent common ancestor only about four million years ago. The complete set of genes responsible for urea excretion was identified in the gill transcriptome of A. grahami, making it the only fish species to have a functional ornithine-urea cycle pathway in the gills--a major innovation for increasing nitrogenous waste efficiency.

High levels of interspecific gene flow in an endemic cichlid fish adaptive radiation from an extreme lake environment.

Studying recent adaptive radiations in isolated insular systems avoids complicating causal events and thus may offer clearer insight into mechanisms generating biological diversity. Here, we investigate evolutionary relationships and genomic differentiation within the recent radiation of Alcolapia cichlid fish that exhibit extensive phenotypic diversification, and which are confined to the extreme soda lakes Magadi and Natron in East Africa. We generated an extensive RAD data set of 96 individuals from multiple sampling sites and found evidence for genetic admixture between species within Lake Natron, with the highest levels of admixture between sympatric populations of the most recently diverged species. Despite considerable environmental separation, populations within Lake Natron do not exhibit isolation by distance, indicating panmixia within the lake, although individuals within lineages clustered by population in phylogenomic analysis. Our results indicate exceptionally low genetic differentiation across the radiation despite considerable phenotypic trophic variation, supporting previous findings from smaller data sets; however, with the increased power of densely sampled SNPs, we identify genomic peaks of differentiation (FST outliers) between Alcolapia species. While evidence of ongoing gene flow and interspecies hybridization in certain populations suggests that Alcolapia species are incompletely reproductively isolated, the identification of outlier SNPs under diversifying selection indicates the radiation is undergoing adaptive divergence.

Rh proteins and NH4(+)-activated Na+-ATPase in the Magadi tilapia (Alcolapia grahami), a 100% ureotelic teleost fish.

The small cichlid fish Alcolapia grahami lives in Lake Magadi, Kenya, one of the most extreme aquatic environments on Earth (pH ~10, carbonate alkalinity ~300 mequiv l(-1)). The Magadi tilapia is the only 100% ureotelic teleost; it normally excretes no ammonia. This is interpreted as an evolutionary adaptation to overcome the near impossibility of sustaining an NH3 diffusion gradient across the gills against the high external pH. In standard ammoniotelic teleosts, branchial ammonia excretion is facilitated by Rh glycoproteins, and cortisol plays a role in upregulating these carriers, together with other components of a transport metabolon, so as to actively excrete ammonia during high environmental ammonia (HEA) exposure. In Magadi tilapia, we show that at least three Rh proteins (Rhag, Rhbg and Rhcg2) are expressed at the mRNA level in various tissues, and are recognized in the gills by specific antibodies. During HEA exposure, plasma ammonia levels and urea excretion rates increase markedly, and mRNA expression for the branchial urea transporter mtUT is elevated. Plasma cortisol increases and branchial mRNAs for Rhbg, Rhcg2 and Na(+),K(+)-ATPase are all upregulated. Enzymatic activity of the latter is activated preferentially by NH4(+) (versus K(+)), suggesting it can function as an NH4(+)-transporter. Model calculations suggest that active ammonia excretion against the gradient may become possible through a combination of Rh protein and NH4(+)-activated Na(+)-ATPase function.

Adaptation of the carbamoyl-phosphate synthetase enzyme in an extremophile fish.

Tetrapods and fish have adapted distinct carbamoyl-phosphate synthase (CPS) enzymes to initiate the ornithine urea cycle during the detoxification of nitrogenous wastes. We report evidence that in the ureotelic subgenus of extremophile fish Oreochromis Alcolapia, CPS III has undergone convergent evolution and adapted its substrate affinity to ammonia, which is typical of terrestrial vertebrate CPS I. Unusually, unlike in other vertebrates, the expression of CPS III in Alcolapia is localized to the skeletal muscle and is activated in the myogenic lineage during early embryonic development with expression remaining in mature fish. We propose that adaptation in Alcolapia included both convergent evolution of CPS function to that of terrestrial vertebrates, as well as changes in development mechanisms redirecting CPS III gene expression to the skeletal muscle.

Gyrodactylus magadiensis n. sp. (Monogenea, Gyrodactylidae) parasitising the gills of Alcolapia grahami (Perciformes, Cichlidae), a fish inhabiting the extreme environment of Lake Magadi, Kenya.

A new species of Gyrodactylus von Nordmann, 1832 is described from the gills of Alcolapia grahami, a tilapian fish endemic to Lake Magadi. This alkaline soda lake in the Rift Valley in Kenya is an extreme environment with pH as high as 11, temperatures up to 42 °C, and diurnal fluctuation between hyperoxia and virtual anoxia. Nevertheless, gyrodactylid monogeneans able to survive these hostile conditions were detected from the gills the Magadi tilapia. The worms were studied using light microscopy, isolated sclerites observed using scanning electron microscopy, and molecular techniques used to genetically characterize the specimens. The gyrodactylid was described as Gyrodactylus magadiensis n. sp. and could be distinguished from other Gyrodactylus species infecting African cichlid fish based on the comparatively long and narrow hamuli, a ventral bar with small rounded anterolateral processes and a tongue-shaped posterior membrane, and marginal hooks with slender sickles which are angled forward, a trapezoid to square toe, rounded heel, a long bridge prior to reaching marginal sickle shaft, and a long lateral edge of the toe. The species is also distinct from all other Gyrodactylus taxa based on the ITS region of rDNA (ITS1-5.8s-ITS2), strongly supporting the designation of a new species. These findings represent the second record of Gyrodactylus from Kenya, with the description of G. magadiensis bringing the total number of Gyrodactylus species described from African cichlids to 18.

TITLE: Gyrodactylus magadiensis n. sp. (Monogenea, Gyrodactylidae), parasite des branchies d'Alcolapia grahami (Perciformes, Cichlidae), un poisson habitant l'environnement extrême du lac Magadi au Kenya. ABSTRACT: Une nouvelle espèce de Gyrodactylus von Nordmann, 1832 est décrite à partir des branchies d'Alcolapia grahami, un tilapia endémique du lac Magadi. Ce lac de soude alcaline dans la vallée du Rift au Kenya est un environnement extrême avec un pH allant jusqu'à 11, des températures allant jusqu'à 42 °C et des fluctuations diurnes entre l'hyperoxie et l'anoxie virtuelle. Néanmoins, des Monogènes Gyrodactylidae capables de survivre dans ces conditions hostiles ont été détectés sur les branchies du tilapia de Magadi. Les vers ont été étudiés par microscopie optique, les sclérites isolés ont été observés au microscope électronique à balayage et des techniques moléculaires ont été utilisées pour caractériser génétiquement les spécimens. Le gyrodactylidé est décrit comme étant Gyrodactylus magadiensis n. sp. et se distingue des autres espèces de Gyrodactylus infectant les cichlidés d'Afrique grâce à ses hamuli relativement longs et étroits, à une barre ventrale avec de petits processus antérolatéraux arrondis et à une membrane postérieure en forme de langue, ainsi qu'à des crochets marginaux à faucilles minces inclinées vers l'avant, un trapèze à bout carré, un talon arrondi, un long pont avant d'atteindre la faucille marginale et un long bord latéral de l'extrémité. L'espèce est également distincte de tous les autres taxons de Gyrodactylus sur la base sur la région ITS de l'ADNr (ITS1­5.8s­ITS2), ce qui soutient fortement la désignation d'une nouvelle espèce. Ces découvertes représentent la seconde mention d'un Gyrodactylus au Kenya, et la description de G. magadiensis amène à 18 le nombre total d'espèces de Gyrodactylus décrites parmi les cichlidés d'Afrique.

Niche divergence facilitated by fine-scale ecological partitioning in a recent cichlid fish adaptive radiation.

Ecomorphological differentiation is a key feature of adaptive radiations, with a general trend for specialization and niche expansion following divergence. Ecological opportunity afforded by invasion of a new habitat is thought to act as an ecological release, facilitating divergence, and speciation. Here, we investigate trophic adaptive morphology and ecology of an endemic clade of oreochromine cichlid fishes (Alcolapia) that radiated along a herbivorous trophic axis following colonization of an isolated lacustrine environment, and demonstrate phenotype-environment correlation. Ecological and morphological divergence of the Alcolapia species flock are examined in a phylogenomic context, to infer ecological niche occupation within the radiation. Species divergence is observed in both ecology and morphology, supporting the importance of ecological speciation within the radiation. Comparison with an outgroup taxon reveals large-scale ecomorphological divergence but shallow genomic differentiation within the Alcolapia adaptive radiation. Ancestral morphological reconstruction suggests lake colonization by a generalist oreochromine phenotype that diverged in Lake Natron to varied herbivorous morphologies akin to specialist herbivores in Lakes Tanganyika and Malawi.

Morphological evaluation of spermatogenesis in Lake Magadi tilapia (Alcolapia grahami): a fish living on the edge.

Spermatogenesis in Lake Magadi tilapia (Alcolapia grahami), a cichlid fish endemic to the highly alkaline and saline Lake Magadi in Kenya, was evaluated using light and transmission electron microscopy. Spermatogenesis, typified by its three major phases (spermatocytogenesis, meiosis and spermiogenesis), was demonstrated by the presence of maturational spermatogenic cells namely spermatogonia, spermatocytes, spermatids and spermatozoa. Primary spermatogonia, the largest of all the germ cells, underwent a series of mitotic divisions producing primary spermatocytes, which then entered two consecutive meiotic divisions to produce secondary spermatocytes and spermatids. Spermatids, in turn, passed through three structurally distinct developmental stages typical of type-I spermiogenesis to yield typical primitive anacrosomal spermatozoa of the externally fertilizing type (aquasperm). The spermatozoon of this fish exhibited a spheroidal head with the nucleus containing highly electron-dense chromatin globules, a midpiece containing ten ovoid mitochondria arranged in two rows and a flagellum formed by the typical 9 + 2 microtubule axoneme. In addition, the midpiece, with no cytoplasmic sheath, appeared to end blindly distally in a lobe-like pattern around the flagellum; a feature that was unique and considered adaptive for the spermatozoon of this species to the harsh external environment. These observations show that the testis of A. grahami often undergoes active spermatogenesis despite the harsh environmental conditions to which it is exposed on a daily basis within the lake. Further, the spermiogenic features and spermatozoal ultrastructure appear to be characteristic of Cichlidae and, therefore, may be of phylogenetic significance.