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The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700 meters in diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet, and trophic morphology. With whole-genome sequences of 146 fish, we identified 98 clearly demarcated genomic \"islands\" of high differentiation and demonstrated the association of genotypes across these islands with divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight-vision–associated genes), hormone signaling, and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi.

The adaptive radiation of East African cichlids has led to more than 1200 species across a number of lakes. Across these species, many convergent traits have emerged, including the presence or absence of horizontal stripes. Kratochwil et al. show that the appearance or loss of stripes is related to changes in the agouti-related peptide 2 gene, which acts as a kind of on-off switch for stripe generation (see the Perspective by Gante). This action has enabled rapid and repeated evolution of stripes across this speciose radiation. Science , this issue p. 457 ; see also p. 396 A genetic switch that can turn horizontal stripe production on or off in East African cichlids is dissected. The color patterns of African cichlid fishes provide notable examples of phenotypic convergence. Across the more than 1200 East African rift lake species, melanic horizontal stripes have evolved numerous times. We discovered that regulatory changes of the gene agouti-related peptide 2 ( agrp2 ) act as molecular switches controlling this evolutionarily labile phenotype. Reduced agrp2 expression is convergently associated with the presence of stripe patterns across species flocks. However, cis-regulatory mutations are not predictive of stripes across radiations, suggesting independent regulatory mechanisms. Genetic mapping confirms the link between the agrp2 locus and stripe patterns. The crucial role of agrp2 is further supported by a CRISPR-Cas9 knockout that reconstitutes stripes in a nonstriped cichlid. Thus, we unveil how a single gene affects the convergent evolution of a complex color pattern.

The light environment exerts a profound selection pressure on the visual system, driving morphological and molecular adaptations that may also contribute to species diversification. Here, we investigate the evolution and genetic basis of visual system diversification in deepwater cichlid fishes of the genus Diplotaxodon. We find that Diplotaxodon exhibit the greatest eye size variation among Lake Malawi cichlids and that this variation is largely uncoupled from phylogeny, with various nonsister species sharing similar eye sizes. Using a combination of genome-wide association analysis across nine Diplotaxodon species, haplotype-based selection scans, and transcriptome analysis, we uncover consistent and widespread signatures of evolution in visual pathways, centered on green-sensitive opsins and throughout the phototransduction cascade, suggesting coordinated evolution of eye size and visual molecular pathways. Our findings underscore the role of visual system diversification in niche specialization within deepwater habitats and offer new insights into visual system evolution within this extraordinary cichlid radiation.

Adaptive radiation is the likely source of much of the ecological and morphological diversity of life 1 – 4 . How adaptive radiations proceed and what determines their extent remains unclear in most cases 1 , 4 . Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in Lake Tanganyika. On the basis of whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology and lower pharyngeal jaw shape), scoring of pigmentation patterns and approximations of the ecology of nearly all of the approximately 240 cichlid species endemic to Lake Tanganyika, we show that the radiation occurred within the confines of the lake and that morphological diversification proceeded in consecutive trait-specific pulses of rapid morphospace expansion. We provide empirical support for two theoretical predictions of how adaptive radiations proceed, the ‘early-burst’ scenario 1 , 5 (for body shape) and the stages model 1 , 6 , 7 (for all traits investigated). Through the analysis of two genomes per species and by taking advantage of the uneven distribution of species in subclades of the radiation, we further show that species richness scales positively with per-individual heterozygosity, but is not correlated with transposable element content, number of gene duplications or genome-wide levels of selection in coding sequences. Analyses of molecular, anatomical, pigmentation and ecological characteristics of nearly all of the approximately 240 species of cichlid fishes in Lake Tanganyika show that the massive adaptive radiation occurred within the confines of the lake through trait-specific pulses of accelerated evolution.

This research aimed to explore the effect of Phyllanthus emblica powder on the growth performance, blood hematology, body composition, serum biochemistry, organ histology, gene expression and resistance of Nile Tilapia ( Oreochromis niloticus ) against Aspergillus flavus . A total of 240 fish (30.5 ± 2.0 g) were distributed in 12 ponds with 20 fish per pond and fed a basal diet supplemented with 0, 1%, 2% and 3% of P. emblica powder for 60 days. A challenge experiment was performed at the end of the trial. All supplemented groups showed better growth performance (final body weight, weight gain, and specific growth rates) ( P  < 0.05), while feed intake did not affect ( P  > 0.05). The feed conversion ratio enhanced by the inclusion of dietary P. emblica ( P  < 0.05). In terms of body composition, crude lipids decreased, while ash percentages increased after fish were fed with P. emblica ( P  < 0.05). Liver function decreased significantly, while protein fraction, blood hematology and digestive enzymatic profile (amylase, and lipase) were significantly increased in all treated groups. Fish fed with P. emblica exhibited a higher survival rate and increased resistance to A. flavus compared to the control diet. Diets containing P. emblica improved the histoarchitecture of hepatopancreatic and intestine of Nile Tilapia. The inclusion of P. emblica significantly upregulated the expression of CC chemokine , IL-1β , IL-8 , SOD , and GPx genes, with a gradual increase in P. emblica levels in the diet ( P  < 0.05). In conclusion, dietary supplementation with P. emblica powder may serve as an effective strategy for promoting growth and acting as an immunostimulant in Nile Tilapia aquaculture.

The adaptive radiation of cichlid fishes in East African Lake Malawi encompasses over 500 species that are believed to have evolved within the last 800,000 years from a common founder population. It has been proposed that hybridization between ancestral lineages can provide the genetic raw material to fuel such exceptionally high diversification rates, and evidence for this has recently been presented for the Lake Victoria region cichlid superflock. Here, we report that Lake Malawi cichlid genomes also show evidence of hybridization between two lineages that split 3–4 Ma, today represented by Lake Victoria cichlids and the riverine Astatotilapia sp. “ruaha blue.” The two ancestries in Malawi cichlid genomes are present in large blocks of several kilobases, but there is little variation in this pattern between Malawi cichlid species, suggesting that the large-scale mosaic structure of the genomes was largely established prior to the radiation. Nevertheless, tens of thousands of polymorphic variants apparently derived from the hybridization are interspersed in the genomes. These loci show a striking excess of differentiation across ecological subgroups in the Lake Malawi cichlid assemblage, and parental alleles sort differentially into benthic and pelagic Malawi cichlid lineages, consistent with strong differential selection on these loci during species divergence. Furthermore, these loci are enriched for genes involved in immune response and vision, including opsin genes previously identified as important for speciation. Our results reinforce the role of ancestral hybridization in explosive diversification by demonstrating its significance in one of the largest recent vertebrate adaptive radiations.

Probiotic administration can be a nutritional strategy to improve the immune response and growth performance of fish. The current study aimed to evaluate the effects of a probiotic blend (Bacillus sp., Pediococcus sp., Enterococcus sp., Lactobacillus sp.) as a dietary supplement on growth performance, feed utilization, innate immune and oxidative stress responses and intestinal morphology in juvenile Nile tilapia (Oreochromis niloticus). The probiotic was incorporated into a basal diet at three concentrations: 0 g/kg (A0: control), 3 g/kg (A1: 1.0×106 colony forming unit (CFU)/g) and 6 g/kg (A2: 2.3×106 CFU/g diet). After 8 weeks of probiotic feeding, weight and specific growth rate where significantly higher in fish-fed A1 diet than in fish-fed A0. Alternative complement in plasma was significantly enhanced in fish-fed A2 when compared with A0. The hepatic antioxidant indicators were not affected by probiotic supplementation. Villi height and goblet cell counts increased significantly in the intestine of fish-fed A1 and A2 diets compared with A0. The dietary probiotic supplementation was maintained until 20 weeks of feeding. Then the selected immune parameters, digestive enzymes and apparent digestibility of diets were studied. No effect of probiotic feeding was observed after that longer period supplementation. The dietary supplementation of mixed species probiotic may constitute a valuable nutritional approach towards a sustainable tilapia aquaculture. The improvement of the immune responses and intestinal morphology play an important role in increasing growth performance, nutrient absorption and disease resistance in fish, important outcomes in such a competitive and developing aquaculture sector.

Rates of lineage diversification vary considerably across the tree of life, often as a result of evolutionary innovations 1 , 2 , 3 , 4 – 5 . Although the ability to produce new traits can vary between clades and may drive ecological transitions 6 , 7 , 8 – 9 , the impact of differences in the pace at which innovations evolve at macroevolutionary scales has been overlooked. Complex teeth are one innovation that contributed to the evolutionary success of major vertebrate lineages 10 , 11 – 12 . Here we show that evolutionary lability of tooth complexity, but not complexity itself, spurs rapid diversification across ray-finned fishes. Speciation rates are five times higher when transitions between simple and complex teeth occur rapidly. We find that African cichlids are unique among all fishes; they are dominated by lineages that transition between simple and complex teeth at unparalleled rates. This innovation interacted with the ecological versatility of complex teeth to spur rapid adaptive radiations in lakes Malawi, Victoria and Barombi Mbo. The marked effect on diversification stems from the tight association of tooth complexity with microhabitat and diet. Our results show that phylogenetic variation in how innovations evolve can have a stronger effect on patterns of diversification than the innovation itself. Investigating the impact of innovations from this new perspective will probably implicate more traits in causing heterogeneous diversification rates across the tree of life. A study shows that the rapid diversification of cichlids in African lakes is driven by their ability to evolve between having simple or complex teeth.

The transition from ‘well-marked varieties’ of a single species into ‘well-defined species’—especially in the absence of geographic barriers to gene flow (sympatric speciation)—has puzzled evolutionary biologists ever since Darwin 1 , 2 . Gene flow counteracts the buildup of genome-wide differentiation, which is a hallmark of speciation and increases the likelihood of the evolution of irreversible reproductive barriers (incompatibilities) that complete the speciation process 3 . Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs 4 , but empirical tests of this theory are scant because comprehensive data are difficult to collect and synthesize across species, owing to their unique biologies and evolutionary histories 5 . Here, within a young species complex of neotropical cichlid fishes ( Amphilophus spp.), we analysed genomic divergence among populations and species. By generating a new genome assembly and re-sequencing 453 genomes, we uncovered the genetic architecture of traits that have been suggested to be important for divergence. Species that differ in monogenic or oligogenic traits that affect ecological performance and/or mate choice show remarkably localized genomic differentiation. By contrast, differentiation among species that have diverged in polygenic traits is genomically widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation with gene flow as previously suggested, whereas polygenic architectures can promote rapid and stable speciation in sympatry. Population genomic analyses of Midas cichlid fishes in young Nicaraguan crater lakes suggest that sympatric speciation is promoted by polygenic architectures.