Midas Cichlid Research Articles

Fish community structure in Sermo Reservoir, Yogyakarta, Indonesia: Initial study on invasive fish species

Invasive species are becoming issues in freshwater ecosystems throughout the world including Indonesia. Sermo Reservoir is located in Yogyakarta, Centra Java, was indicated to have invasive species identified as Cichlidae family. The study aimed to assess fish communities’ structure and identified invasive fish in Sermo Reservoir. The research was conducted in Sermo Reservoirs, Yogyakarta, Indonesia on March-October 2019. In total, about 3,084 individuals of 10 fish species belonging to 3 families and 8 genera were captured using a experimental gillnets (mesh size 0.75; 1; 1.5; 2; 2.5; 3 inch) at five stations. The fish community in Sermo Reservoir was dominated by Cichlid fish (98.66%). Red devil (Amphilophus labiatus) and Midas cichlid (A. citrinellus) were dominant species founded in Sermo Reservoir (58.82% and 37.00%, respectively). Another species of cichlid that caught consist of nile tilapia (Oreochromis niloticus), mozambique tilapia (O. mossambicus), and jaguar cichlid (Parachromis managuensis). The study showed that Amphilophus spp. have high dispersal (One-way ANOSIM revealed Amphilophus spp. was not significantly different for spatio-temporal (p>0.05)). SIMPER analysis (p < 0.05) showed that A. citrinellus and A. labiatus had spread throughout the waters and were concentrated in Tegiri station which had more littoral zones.

The comparative genomic landscape of adaptive radiation in crater lake cichlid fishes.

Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where species numbers and phenotypic divergence in two closely related lineages are notably different. We investigated one such natural experiment using two de novo assembled and 40 resequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; nonradiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole‐genome inferred demography suggests that priority effects are not likely to be the cause of the dissimilarities. Also, genome‐wide levels of selection, transposable element dynamics, gene family expansion, major chromosomal rearrangements and the number of genes under positive selection were not markedly different between the two lineages. To more finely investigate particular subsets of the genome that have undergone adaptive divergence in Midas cichlids, we also examined if there was evidence for ‘molecular pre‐adaptation’ in regions identified by QTL mapping of repeatedly diverging adaptive traits. Although most of our analyses failed to pinpoint substantial genomic differences, we did identify functional categories containing many genes under positive selection that provide candidates for future studies on the propensity of Midas cichlids to radiate. Our results point to a disproportionate role of local, rather than genome‐wide factors underlying the propensity for these cichlid fishes to adaptively radiate.

Potential benefit of I-Tiao-Gung (Glycine tomentella) extract to enhance ornamental fish welfare during live transport

Multiple stressors associated with live fish transport, such as shaking, packing, hyper‑oxygenation, and cold stress, present a growing concern for fish welfare. The current study was designed to evaluate the fish welfare promoting effects of I-Tiao-Gung extract (Glycine tomentella, GTE), an extract derived from a Chinese herb, during live transport of blood parrot cichlid (Amphilophus citrinellus x Cichlasoma synspilum) and koi (Cyprinus carpio). The study analyzed plasma electrolytes, glucose, lactate, and cortisol levels from blood of both fishes during simulated transport. Results showed that adding GTE in water significantly decreased cortisol levels in blood parrot cichlid after 2–6 h and in koi after 4–6 h of simulated transport, respectively. Levels of glucose, lactate, and K+ in blood parrot cichlid began to elevate significantly between 2 and 6 h under stress. While levels of blood Na+, Ca2+ and lactate of koi significantly increased after simulated transport. Interestingly, Cl− levels were depressed significantly upon stress in both fishes. An indirect approach using ventilation frequency (VF) to gauge metabolism was taken to assess the physiological effects. VF was significantly slower in blood parrot cichlid after GTE addition comparing to that of the control group, but the effect was not significant in koi. Therefore, addition of GTE mitigated transport stress responses in both ornamental fishes through down-regulation of cortisol; thereby, promoting fish welfare during live transport.

Acusicola margulisae n. sp. (Copepoda: Ergasilidae) from freshwater fishes in a Nicaraguan crater lake based on morphological and molecular evidence.

The ergasilid copepod Acusicola margulisae n. sp. is described based on material from three species of cichlid, Amphilophus citrinellus (Günther), Parachromis managuensis (Günther), and Oreochromis sp., and from the poecilid Poecilia mexicana (Steindachner), in the crater Lake Asososca León, Nicaragua. This constitutes the 15th species described in the genus Acusicola Cressey, 1970. The new species differs from all its congeners by the relatively longer first endopodal segment of leg 1, and the size and number of setae on second endopodal segment of leg 1. We provide the first gene sequence for a species of Acusicola. To examine the intraspecific genetic variation of the new species collected from different host species, sequences of the mitochondrial barcode region cox1 were generated. In addition, partial regions of the 18S and 28S ribosomal RNA genes were sequenced and used to infer the phylogenetic relationships of the genus Acusicola within the family Ergasilidae Burmeister, 1835. The phylogenetic trees yielded the isolates of Acusicola margulisae n. sp. as a reciprocally monophyletic lineage, and as the sister taxa of five genera of ergasilid copepods. The genus Ergasilus von Nordmann, 1832 was recovered as a paraphyletic group. These analyses indicate that phylogenetic relationships are not yet well resolved and more representative species and genera of the family are required to provide a robust classification of this highly diverse group of copepods.

Implementing Large Genomic Single Nucleotide Polymorphism Data Sets in Phylogenetic Network Reconstructions: A Case Study of Particularly Rapid Radiations of Cichlid Fish.

The Midas cichlids of the Amphilophus citrinellus spp. species complex from Nicaragua (13 species) are an extraordinary example of adaptive and rapid radiation ($<$24,000 years old). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of incomplete lineage sorting (ILS), as well as past and current gene flow. Assuming solely a vertical transfer of genetic material from an ancestral lineage to new lineages is not appropriate in many cases of genes transferred horizontally in nature. Recently developed methods to infer phylogenetic networks under such circumstances might be able to circumvent these problems. These models accommodate not just ILS, but also gene flow, under the multispecies network coalescent (MSNC) model, processes that are at work in young, hybridizing, and/or rapidly diversifying lineages. There are currently only a few programs available that implement MSNC for estimating phylogenetic networks. Here, we present a novel way to incorporate single nucleotide polymorphism (SNP) data into the currently available PhyloNetworks program. Based on simulations, we demonstrate that SNPs can provide enough power to recover the true phylogenetic network. We also show that it can accurately infer the true network more often than other similar SNP-based programs (PhyloNet and HyDe). Moreover, our approach results in a faster algorithm compared to the original pipeline in PhyloNetworks, without losing power. We also applied our new approach to infer the phylogenetic network of Midas cichlid radiation. We implemented the most comprehensive genomic data set to date (RADseq data set of 679 individuals and $>$37K SNPs from 19 ingroup lineages) and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. [Genomics; multispecies network coalescent; phylogenetic networks; phylogenomics; RADseq; SNPs.].

Phylogeography and Ecological Niche Shape the Cichlid Fish Gut Microbiota in Central American and African Lakes.

Cichlid fishes, with their repeated colonization of lakes and subsequent radiations at different scales of phylogenetic and ecological diversification, offer an excellent model system to understand the factors shaping the host-gut microbiota association in nature. Here, we characterized the gut microbiota of the Amphilophus species complex from Central America (known as the Midas cichlid complex), encompassing 158 wild specimens (13 species) collected from seven Nicaraguan lakes, and combined these data with previously published data from two African lakes (spanning 29 species). Our aim was to comprehensively explore trends in microbiota variation and persistence along the large spatial and temporal scales of cichlid diversification (from the oldest radiation in L. Tanganyika, 9–12 My old, to young ones in Nicaraguan crater lakes, <0.5 My old), in allopatry and sympatry (within and across lakes), and across the range of dietary niches (from highly specialized to generalist feeders). Despite their extraordinary diversity, cichlids shared a remarkably conserved microbial taxonomic profile, which argues for a primary role of the host genetics in the assembly and maintenance of these microbial communities. Within this partly constrained microbiota profile, geographic isolation (continent and lake) represented the first level of discrimination. For the Midas cichlid, a partial congruency was found between host microbiota and genetic distances, suggesting that microbial communities have partly diversified along their cichlid phylogeographic history of crater lake colonization. In sympatry (within lakes), the young and poorly ecologically diversified cichlid assemblages of Central American lakes display largely unresolved gut microbiotas (in terms of both alpha and beta diversities), whereas the phylogenetically and ecologically diverse species found in African lakes showed greater microbial interspecific diversity. This pattern largely points to the level of habitat segregation, trophic niche overlap, and reproductive barriers as major modulators of the gut microbiota connectivity among sympatric species.

MicroRNA Gene Regulation in Extremely Young and Parallel Adaptive Radiations of Crater Lake Cichlid Fish.

Cichlid fishes provide textbook examples of explosive phenotypic diversification and sympatric speciation, thereby making them ideal systems for studying the molecular mechanisms underlying rapid lineage divergence. Despite the fact that gene regulation provides a critical link between diversification in gene function and speciation, many genomic regulatory mechanisms such as microRNAs (miRNAs) have received little attention in these rapidly diversifying groups. Therefore, we investigated the posttranscriptional regulatory role of miRNAs in the repeated sympatric divergence of Midas cichlids (Amphilophus spp.) from Nicaraguan crater lakes. Using miRNA and mRNA sequencing of embryos from five Midas species, we first identified miRNA binding sites in mRNAs and highlighted the presences of a surprising number of novel miRNAs in these adaptively radiating species. Then, through analyses of expression levels, we identified putative miRNA/gene target pairs with negatively correlated expression level that were consistent with the role of miRNA in downregulating mRNA. Furthermore, we determined that several miRNA/gene pairs show convergent expression patterns associated with the repeated benthic/limnetic sympatric species divergence implicating these miRNAs as potential molecular mechanisms underlying replicated sympatric divergence. Finally, as these candidate miRNA/gene pairs may play a central role in phenotypic diversification in these cichlids, we characterized the expression domains of selected miRNAs and their target genes via in situ hybridization, providing further evidence that miRNA regulation likely plays a role in the Midas cichlid adaptive radiation. These results provide support for the hypothesis that extremely quickly evolving miRNA regulation can contribute to rapid evolutionary divergence even in the presence of gene flow.

Divergent Allometric Trajectories in Gene Expression and Coexpression Produce Species Differences in Sympatrically Speciating Midas Cichlid Fish.

The mechanisms of speciation without geographic isolation (i.e., sympatric speciation) remain debated. This is due in part to the fact that the genomic landscape that could promote or hinder species divergence in the presence of gene flow is still largely unknown. However, intensive research is now centered on understanding the genetic architecture of adaptive traits associated with this process as well as how gene expression might affect these traits. Here, using RNA-Seq data, we investigated gene expression of sympatrically speciating benthic and limnetic Neotropical cichlid fishes at two developmental stages. First, we identified groups of coexpressed genes (modules) at each stage. Although there are a few large and well-preserved modules, most of the other modules are not preserved across life stages. Second, we show that later in development more and larger coexpression modules are associated with divergence between benthic and limnetic fish compared with the earlier life stage. This divergence between benthic and limnetic fish in coexpression mirrors divergence in overall expression between benthic and limnetic fish, which is more pronounced later in life. Our results reveal that already at 1-day posthatch benthic and limnetic fish diverge in (co)expression, and that this divergence becomes more substantial when fish are free-swimming but still unlikely to have divergent swimming and feeding habits. More importantly, our study describes how the coexpression of several genes through development, as opposed to individual genes, is associated with benthic–limnetic species differences, and how two morphogenetic trajectories diverge as fish grow older.

First report of the Non-native Midas Cichlid, Amphilophus citrinellus (Gunther, 1864), in Laguna de Bay, Philippines

First report of the Non-native Midas Cichlid, Amphilophus citrinellus (Gunther, 1864), in Laguna de Bay, Philippines

Lessons from a natural experiment: Allopatric morphological divergence and sympatric diversification in the Midas cichlid species complex are largely influenced by ecology in a deterministic way.

Explaining why some lineages diversify while others do not and how are key objectives in evolutionary biology. Young radiations of closely related species derived from the same source population provide an excellent opportunity to disentangle the relative contributions of possible drivers of diversification. In these settings, lineage‐specific effects are shared and can be ruled out. Moreover, the relevant demographic and ecological parameters can be estimated accurately. Midas cichlid fish in Nicaragua have repeatedly colonized several crater lakes, diverged from the same source populations, and, interestingly, diversified in some of them but not others. Here, using the most comprehensive molecular and geometric morphometric data set on Midas cichlids to date (∼20,000 SNPs, 12 landmarks, ∼700 individuals), we aim to understand why and how crater lake populations diverge and why some of them are more prone to diversify in sympatry than others. Taking ancestor‐descendant relationships into account, we find that Midas cichlids diverged in parallel from their source population mostly—but not exclusively—by evolving more slender body shapes in all six investigated crater lakes. Admixture among crater lakes has possibly facilitated this process in one case, but overall, admixture and secondary waves of colonization cannot predict morphological divergence and intralacustrine diversification. Instead, morphological divergence is larger the more dissimilar a crater lake is compared to the source lake and happens rapidly after colonization followed by a slow‐down with time. Our data also provide some evidence that founder effects may positively contribute to divergence. The depth of a crater lake is positively associated with variation in body shapes (and number of species), presumably by providing more ecological opportunities. In conclusion, we find that parallel morphological divergence in allopatry and the propensity for diversification in sympatry across the entire Midas cichlid fish radiation is partly predictable and mostly driven by ecology.

Evolution in caves: selection from darkness causes spinal deformities in teleost fishes.

Only few fish species have successfully colonized subterranean habitats, but the underlying biological constraints associated with this are still poorly understood. Here, we investigated the influence of permanent darkness on spinal-column development in one species (Midas cichlid, Amphilophus citrinellus) with no known cave form, and one (Atlantic molly, Poecilia mexicana) with two phylogenetically young cave forms. Specifically, fish were reared under a normal light : dark cycle or in permanent darkness (both species). We also surveyed wild-caught cave and surface ecotypes of P. mexicana In both species, permanent darkness was associated with significantly higher rates of spinal deformities (especially in A. citrinellus). This suggests strong developmental (intrinsic) constraints on the successful colonization of subterranean environments in teleost fishes and might help explain the relative paucity of cave-adapted lineages. Our results add depth to our understanding of the aspects of selection driving trait divergence and maintaining reproductive isolation in cave faunas.

Heterochronic opsin expression due to early light deprivation results in drastically shifted visual sensitivity in a cichlid fish: Possible role of thyroid hormone signaling.

During early ontogeny, visual opsin gene expression in cichlids is influenced by prevailing light regimen. Red light, for example, leads to an early switch from the expression of short-wavelength sensitive to long-wavelength sensitive opsins. Here, we address the influence of light deprivation on opsin expression. Individuals reared in constant darkness during the first 14 days post-hatching (dph) showed a general developmental delay compared with fish reared under a 12:12hr light-dark cycle (control group). Several characters including pigmentation patterns and eye development, appeared later in dark-reared individuals. Quantitative real-time PCR and fluorescent in situ hybridization at six time points during the 14 days period revealed that fish from the control group expressed opsin genes from 5dph on and maintained a short-wavelength sensitive phenotype (sws1, rh2b, and rh2a). Onset of opsin expression in dark-reared Midas cichlids was delayed by 4 days and visual sensitivity rapidly progressed toward a long-wavelength sensitive phenotype (sws2b, rh2a, and lws). Shifts in visual sensitivities toward longer wavelengths are mediated by thyroid hormone (TH) in many vertebrates. Compared to control fish, dark-reared individuals showed elevated dio3 expression levels - a validated proxy for TH concentration - suggesting higher circulating TH levels. Despite decelerated overall development, ontogeny of opsin gene expression was accelerated, resulting in retinae with long-wavelength shifted predicted sensitivities compared to light-reared individuals. Indirect evidence suggests that this was due to altered TH metabolism.

Small size today, aquarium dumping tomorrow: sales of juvenile non-native large fish as an important threat in Brazil

ABSTRACT Informal sales of large-bodied non-native aquarium fishes (known as “tankbusters”) is increasing among Brazilian hobbyists. In this study, we surveyed this non-regulated trade on Facebook® from May 2012 to September 2016, systematically collecting information about the fishes available for trading: species, family, common/scientific names, native range, juvenile length, behavior, number of specimens available in five geographical regions from Brazil. We also assessed the invasion risk of the most frequently sold species using the Fish Invasiveness Screening Test (FIST). We found 93 taxa belonging to 35 families. Cichlidae was the dominant family, and most species were native to South America. All species are sold at very small sizes (&lt; 10.0 cm), and most display aggressive behavior. The hybrid Amphilophus trimaculatus × Amphilophus citrinellus, Astronotus ocellatus, Uaru amphiacanthoides, Osteoglossum bicirrhosum, Cichla piquiti, Pangasianodon hypophthalmus, Datnioides microlepis and Cichla kelberi were the main species available. The southeast region showed the greatest trading activity. Based on biological traits, the FIST indicated that Arapaima gigas, C. kelberi and C. temensis are high-risk species in terms of biological invasions via aquarium dumping. We suggest management strategies such as trade regulations, monitoring, euthanasia and educational programs to prevent further introductions via aquarium dumping.

Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus) \u2014 towards understanding gene function and regulatory evolution in an ecological model system for rapid phenotypic diversification

BackgroundThe Midas cichlid species complex (Amphilophus spp.) is widely known among evolutionary biologists as a model system for sympatric speciation and adaptive phenotypic divergence within extremely short periods of time (a few hundred generations). The repeated parallel evolution of adaptive phenotypes in this radiation, combined with their near genetic identity, makes them an excellent model for studying phenotypic diversification. While many ecological and evolutionary studies have been performed on Midas cichlids, the molecular basis of specific phenotypes, particularly adaptations, and their underlying coding and cis-regulatory changes have not yet been studied thoroughly.ResultsFor the first time in any New World cichlid, we use Tol2 transposon-mediated transgenesis in the Midas cichlid (Amphilophus citrinellus). By adapting existing microinjection protocols, we established an effective protocol for transgenesis in Midas cichlids. Embryos were injected with a Tol2 plasmid construct that drives enhanced green fluorescent protein (eGFP) expression under the control of the ubiquitin promoter. The transgene was successfully integrated into the germline, driving strong ubiquitous expression of eGFP in the first transgenic Midas cichlid line. Additionally, we show transient expression of two further transgenic constructs, ubiquitin::tdTomato and mitfa::eGFP. Transgenesis in Midas cichlids will facilitate further investigation of the genetic basis of species-specific traits, many of which are adaptations.ConclusionTransgenesis is a versatile tool not only for studying regulatory elements such as promoters and enhancers, but also for testing gene function through overexpression of allelic gene variants. As such, it is an important first step in establishing the Midas cichlid as a powerful model for studying adaptive coding and non-coding changes in an ecological and evolutionary context.

Rapid adaptation to a novel light environment: The importance of ontogeny and phenotypic plasticity in shaping the visual system of Nicaraguan Midas cichlid fish (Amphilophus citrinellus spp.).

Colonization of novel habitats is typically challenging to organisms. In the initial stage after colonization, approximation to fitness optima in the new environment can occur by selection acting on standing genetic variation, modification of developmental patterns or phenotypic plasticity. Midas cichlids have recently colonized crater Lake Apoyo from great Lake Nicaragua. The photic environment of crater Lake Apoyo is shifted towards shorter wavelengths compared to great Lake Nicaragua and Midas cichlids from both lakes differ in visual sensitivity. We investigated the contribution of ontogeny and phenotypic plasticity in shaping the visual system of Midas cichlids after colonizing this novel photic environment. To this end, we measured cone opsin expression both during development and after experimental exposure to different light treatments. Midas cichlids from both lakes undergo ontogenetic changes in cone opsin expression, but visual sensitivity is consistently shifted towards shorter wavelengths in crater lake fish, which leads to a paedomorphic retention of their visual phenotype. This shift might be mediated by lower levels of thyroid hormone in crater lake Midas cichlids (measured indirectly as dio2 and dio3 gene expression). Exposing fish to different light treatments revealed that cone opsin expression is phenotypically plastic in both species during early development, with short and long wavelength light slowing or accelerating ontogenetic changes, respectively. Notably, this plastic response was maintained into adulthood only in the derived crater lake Midas cichlids. We conclude that the rapid evolution of Midas cichlids' visual system after colonizing crater Lake Apoyo was mediated by a shift in visual sensitivity during ontogeny and was further aided by phenotypic plasticity during development.

The role of rare morph advantage and conspicuousness in the stable gold-dark colour polymorphism of a crater lake Midas cichlid fish.

Genetically based stable colour polymorphisms provide a unique opportunity to study the evolutionary processes that preserve genetic variability in the wild. Different mechanisms are proposed to promote the stability of polymorphisms, but only few empirical examples have been documented, resulting in an incomplete understanding of these mechanisms. A remarkable genetically determined stable colour polymorphism is found in the Nicaraguan Midas cichlid species complex (Amphilophus cf. citrinellus). All Midas cichlids start their life with a dark-grey coloration (dark morph), but individuals carrying the dominant "gold" allele (c. 10%) lose their melanophores later in life, revealing the underlying orange coloration (gold morph). How this polymorphism is maintained remains unclear. Two main hypotheses have been proposed, both suggesting differential predation upon colour morphs as the proximate mechanism. One predicts that the conspicuous gold morph is more likely to be preyed upon, but this disadvantage is balanced by their competitive dominance over the dark morph. The second hypothesis suggests a rare morph advantage where the rarer gold morph experiences less predation. Empirical evidence for either of these mechanisms is still circumstantial and inconclusive. We conducted two field experiments in a Nicaraguan crater lake using wax models simulating both morphs to determine predation pressure upon Midas cichlid colour morphs. First, we tested the interaction of coloration and depth on attack rate. Second, we tested the interaction of fish size and coloration. We contrasted the pattern of attacks from these experiments to the predicted predation patterns from the hypotheses proposed to explain the colour polymorphism's stability. Large models imitating colour morphs were attacked at similar rates irrespectively of their position in the water column. Yet, attacks upon small models resembling juveniles were directed mainly towards dark models. This resulted in a significant size-by-colour interaction. We suggest that gold Midas cichlids experience a rare morph advantage as juveniles when individuals of this morph are extremely uncommon. But this effect is reduced or disappears among adults, where gold individuals are relatively more common. Thus, the interaction of rare morph advantage and conspicuousness, rather than either of those factors alone, is a likely mechanism resulting in the stability of the colour polymorphism in Midas cichlids.

Rapid and Parallel Adaptive Evolution of the Visual System of Neotropical Midas Cichlid Fishes.

Midas cichlid fish are a Central American species flock containing 13 described species that has been dated to only a few thousand years old, a historical timescale infrequently associated with speciation. Their radiation involved the colonization of several clear water crater lakes from two turbid great lakes. Therefore, Midas cichlids have been subjected to widely varying photic conditions during their radiation. Being a primary signal relay for information from the environment to the organism, the visual system is under continuing selective pressure and a prime organ system for accumulating adaptive changes during speciation, particularly in the case of dramatic shifts in photic conditions. Here, we characterize the full visual system of Midas cichlids at organismal and genetic levels, to determine what types of adaptive changes evolved within the short time span of their radiation. We show that Midas cichlids have a diverse visual system with unexpectedly high intra- and interspecific variation in color vision sensitivity and lens transmittance. Midas cichlid populations in the clear crater lakes have convergently evolved visual sensitivities shifted toward shorter wavelengths compared with the ancestral populations from the turbid great lakes. This divergence in sensitivity is driven by changes in chromophore usage, differential opsin expression, opsin coexpression, and to a lesser degree by opsin coding sequence variation. The visual system of Midas cichlids has the evolutionary capacity to rapidly integrate multiple adaptations to changing light environments. Our data may indicate that, in early stages of divergence, changes in opsin regulation could precede changes in opsin coding sequence evolution.

Effect of dietary lipid on growth, expression of canthaxanthin-based coloration, digestive enzymes activities and immunity in blood parrot cichlidAmphilophus citrinellus × Paraneetroplus synspilus

A 42-day experiment was carried out to evaluate the effects of four different lipid containing diets (lipid 74.0, 105.3, 135.0, 168.1 g/kg diet) on growth, digestive enzymes activities, immunology and expression of canthaxanthin-based coloration in parrot cichlid (Amphilophus citrinellus × Paraneetroplus synspilus). Each diet contained canthaxanthin 0.05 g/kg diet. Two hundred and eighty-eight fish were randomly stocked into 12 glass aquaria to form four triplicate groups. Fish were fed one of four diets daily at 20 g/kg of their total body weight. Growth, digestive enzymes activities, immunology and body colour parameters were measured at the end of experiment. Based on the polynomial regression of dietary lipid level and specific growth rate, the dietary lipid level inclusion was calculated as 117.2 g/kg for the highest specific growth rate of these animals. The polynomial regression of skin colour parameters and dietary lipid levels indicated the critical threshold lipid inclusions in diet: 113.7 g/kg for the best expression of lightness, 112.1 g/kg for redness, 127.5 g/kg for yellowness and 125.3 g/kg for chroma of fish's skin. Considering redness, lightness and specific growth rate are most important variables, a diet containing lipid 115.0 g/kg can be recommended for blood parrot cichlid.

QuaddRAD: a new high-multiplexing and PCR duplicate removal ddRAD protocol produces novel evolutionary insights in a nonradiating cichlid lineage.

The identification of thousands of variants across the genomes and their accurate genotyping are crucial for estimating the genetic parameters needed to address a host of molecular ecological and evolutionary questions. With rapid advances of massively parallel high-throughput sequencing technologies, several methods have recently been developed to access genomewide data on population variation. One of the most successful and widely used techniques relies on the combination of restriction enzymes and sequencing-by-synthesis: restriction-site-associated DNA sequencing (RADSeq). We developed a new, more time- and cost-efficient double-digest RAD paired-end protocol (quaddRAD) that simplifies and speeds up the identification of PCR duplicates and permits large-scale multiplexing. Assessing its performance on a technical data set, we also applied the quaddRAD method on population samples of a Neotropical cichlid fish lineage (Archocentrus centrarchus) to assess its genetic structure and demographic history. While we identified allopatric interlake genetic divergence, most likely driven by drift, no signature of sympatric divergence was detected. This differs from what has been observed in the clade of Midas cichlids (Amphilophus citrinellus spp.), another cichlid lineage that inhabits the same lakes and shares a similar demographic history, but has evolved into small-scale adaptive radiations via sympatric speciation. We demonstrate that quaddRAD is a robust and efficient method for genotyping a massive number and widely overlapping set of loci with high accuracy. Furthermore, the results on A.centrarchus open new research avenues providing an ideal system to investigate genome-level mechanisms that could alter the speciation potential of different but closely related cichlid lineages.

Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

BackgroundThe Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes.ResultsHere, we characterized the genes of MHC class IIB chain of the Midas cichlid species complex (Amphilophus cf. citrinellus) including fish from five lakes in Nicaragua. We designed 19 new specific primers anchored in a stepwise fashion in order to detect all alleles present. We obtained 866 genomic DNA (gDNA) sequences from thirteen individuals and 756 additional sequences from complementary DNA (cDNA) of seven of those individuals. We identified 69 distinct alleles with up to 25 alleles per individual. We also found considerable intron length variation and mismatches of alleles detected in cDNA and gDNA suggesting that some loci have undergone pseudogenization. Lastly, we created a model of protein structure homology for each allele and identified their key structural components.ConclusionsOverall, the Midas cichlid has one of the most diverse repertoires of MHC class IIB genes known, which could serve as a powerful tool to elucidate the process of divergent radiations, colonization and speciation in sympatry.