Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
328
datasets available to search
ShareScore release 0.9.0
Dataset results
328 results for “cichlid fish”
Data from: Metagenomic insights into the dietary diversity of the adaptive radiation of cichlid fishes in Lake Tanganyika
Open the record for dataset details and reuse information.
Data from: Inbreeding and competitor’s genetic relatedness affect dynamic male color-ornament expression in a cichlid fish
Open the record for dataset details and reuse information.
Widespread temporal niche partitioning in an adaptive radiation of cichlid fishes
Open the record for dataset details and reuse information.
Data from: Ancient and recent hybridization in the Oreochromis cichlid fishes
Open the record for dataset details and reuse information.
Data from: Signatures of convergence in Neotropical cichlid fish
Open the record for dataset details and reuse information.
Visual opsin gene expression evolution in the adaptive radiation of cichlid fishes of Lake Tanganyika
Open the record for dataset details and reuse information.
Drivers and dynamics of a massive adaptive radiation in cichlid fishes
<p>Adaptive radiation is the likely source of much of the ecological and morphological diversity of life. How adaptive radiations proceed and what determines their extent remains elusive in most cases. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on 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 virtually all ~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 morphospace expansion. We provide empirical support for two theoretical predictions on how adaptive radiations proceed, the 'early-burst' scenario (for body shape) and the stages model (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.</p>
Gene expression remodelling and immune response during adaptive divergence in an African cichlid fish
<p><span>Variation in gene expression contributes to ecological speciation by facilitating population persistence in novel environments. Likewise, immune response can be a relevant factor in speciation driven by adaptation to different environments. Previous studies examining gene expression differences between recently diverged ecotypes often relied on only one pair of populations, targeted the expression of only a subset of genes, or used wild caught-individuals. Here, we investigated the contribution of habitat-specific parasites and symbionts and the underlying immunological capabilities of ecotype hosts to adaptive divergence in lake-river population pairs of the cichlid fish <i>Astatotilapia burtoni</i>. To shed light on the role of phenotypic plasticity in adaptive divergence, we compared parasite and microbiota communities, immune response, and gene expression patterns of fish from natural habitats and a lake-like pond setup. In all investigated population pairs, lake fish were more heavily parasitized than river fish, both in terms of parasite taxa composition and infection abundance. Innate immune response in the wild was higher in lake than in river populations and elevated in a river population exposed to lake parasites in the pond setup. Environmental differences between lake and river habitat and their distinct parasite communities shaped differential gene expression, involving genes functioning in osmoregulation and immune response. Most changes in gene expression between lake and river samples in the wild and in the pond setup were based on a plastic response. Finally, gene expression and bacterial communities of wild-caught individuals and individuals acclimated to lake-like pond conditions showed shifts underlying adaptive phenotypic plasticity.</span></p>
Data from: Effect of craniofacial genotype on the relationship between morphology and feeding performance in cichlid fishes
The relationship between morphology and performance is complex, but important for understanding the adaptive nature of morphological variation. Recent studies have sought to better understand this system by illuminating the interconnectedness of different functional systems; however, the role of genetics is often overlooked. In this study, we attempt to gain insights into this relationship by examining the effect of genotypic variation at putative craniofacial loci on the relationship between morphology and feeding performance in cichlids. We studied two morphologically disparate species, as well as a morphologically intermediate hybrid population. We assessed feeding performance, jaw protrusion, and general facial morphology for each fish. We also genotyped hybrid animals at six previously identified craniofacial loci. Cichlid species were found to differ in facial geometry, kinematic morphology, and performance. Significant correlations were also noted between these variables; however, the explanatory power of facial geometry in predicting performance was relatively poor. Notably, when hybrids were grouped by genotype, the relationship between shape and performance improved. This relationship was especially robust in animals with the specialist allele at sox9b, a well-characterized regulator of craniofacial development. These data suggest a novel role for genotype in influencing complex relationships between form and function.
Decoupled jaws promote trophic diversity in Cichlid fishes
Functional decoupling of oral and pharyngeal jaws is widely considered to have expanded the ecological repertoire of cichlid fishes. But, the degree to which the evolution of these jaw systems is decoupled and whether decoupling has impacted trophic diversification remains unknown. Focusing on the large Neotropical radiation of cichlids, we ask whether oral and pharyngeal jaw evolution is correlated and how their evolutionary rates respond to feeding ecology. In support of decoupling, we find relaxed evolutionary integration between the two jaw systems, resulting in novel trait combinations that potentially facilitate feeding mode diversification. These outcomes are made possible by escaping the mechanical trade-off between force transmission and mobility, which characterizes a single jaw system that functions in isolation. In spite of the structural independence of the two jaw systems, results using a Bayesian, state-dependent, relaxed-clock model of multivariate Brownian motion indicate strongly aligned evolutionary responses to feeding ecology. So, while decoupling of prey capture and processing functions released constraints on jaw evolution and promoted trophic diversity in cichlids, the natural diversity of consumed prey has also induced a moderate degree of evolutionary integration between the jaw systems, reminiscent of the original mechanical trade-off between force and mobility.
Evolutionary dynamics of structural variation at a key locus for color pattern diversification in cichlid fishes
<p>Color patterns in African cichlid fishes vary spectacularly. Although phylogenetic analysis showed already 30 years ago that many color patterns evolved repeatedly in these adaptive radiations, only recently have we begun to understand the genomic basis of color variation. Horizontal stripe patterns evolved and were lost several times independently across the adaptive radiations of Lake Victoria, Malawi, and Tanganyika and regulatory evolution of agouti-related peptide 2 (agrp2/asip2b) has been linked to this phenotypically labile trait. Here, we asked whether the agrp2 locus exhibits particular characteristics that facilitate divergence in color patterns. Based on comparative genomic analyses, we discovered several recent duplications, insertions, and deletions. Interestingly, one of these events resulted in a tandem duplication of the last exon of agrp2. The duplication likely precedes the East African radiations that started 8–12 Ma, is not fixed within any of the radiations, and is found to vary even within some species. Moreover, we also observed variation in copy number (two to five copies) and secondary loss of the duplication, illustrating a surprising dynamic at this locus that possibly promoted functional divergence of agrp2. Our work suggests that such instances of exon duplications are a neglected mechanism potentially involved in the repeated evolution and diversification that deserves more attention.</p>
Implementing large genomic SNP datasets in phylogenetic network reconstructions: a case study of particularly rapid radiations of cichlid fish
<p><span><span><span><span><span><span><span><span><span><span><span>The Midas cichlids of the <i>Amphilophus</i> <i>citrinellus </i>spp<i>.</i> species complex from Nicaragua, are an extraordinary adaptive rapid radiation (<24,000 years old; 13 described species). These cichlids are a very challenging group to infer its evolutionary history in phylogenetic analyses, due to the apparent prevalence of 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 incomplete lineage sorting, but also gene flow, under the multispecies network coalescent model (MSNC), 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. 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 dataset to date (RADseq dataset of 679 individuals and >37K SNPs from 19 ingroup lineages) <span><span>and present estimated phylogenetic networks for this extremely young and fast-evolving radiation of cichlid fish. </span></span>We demonstrate that the MSNC is more appropriate than the multispecies coalescent alone for the analysis of this rapid radiation. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Repeated divergence in opsin genes expression mirrors photic habitat changes in rapidly evolving crater lake cichlid fishes
<div> <div> <div class="msocomtxt"> <p class="MsoNormal"><span>Selection pressures differ along environmental gradients and organisms' phenotypes. Traits tightly linked to fitness (e.g., the visual system) are expected to closely track environmental variation along gradients. Within such gradients, adaptation to local conditions might be due to heritable and non-heritable, environmentally induced variation. Disentangling these sources of phenotypic variation requires studying, in nature and the laboratory, closely related populations experiencing different environments. The Nicaraguan great and crater lakes show an environmental gradient in photic conditions extending from clear crater lakes to very turbid great lakes. From two old, turbid great lakes, Midas cichlid fish (<em>Amphilophus </em>cf.<em> citrinellus</em>) independently colonized seven isolated crater lakes of varying light conditions, resulting in a small adaptive radiation. We estimated the variation in visual sensitivities along this photic gradient by measuring differential cone opsin gene expression among populations from different lakes. The visual sensitivities observed in all seven derived crater lake populations have not changed randomly but shifted predictably in direction and magnitude, repeatedly mirroring changes in photic conditions. Intrapopulation phenotypic variation decreases as environments become spectrally narrower suggesting different selective landscapes within the gradient. Comparing wild-caught and lab-reared fish revealed that 48% of this phenotypic variation is genetically determined and evolved rapidly. Our results demonstrate deterministic, rapid phenotypic evolution that fine-tunes visual sensitivity to fine-scale environmental variation.</span></p> <p class="MsoCommentText"><span> </span></p> </div> </div> </div>
Data from: An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes
<p><span><span><span><span><span><span><span><span><span><span><span>Polymorphisms have fascinated biologists for a long time, but their genetic underpinnings often remained elusive. Here, we aimed to uncover the genetic basis of the gold/dark polymorphism that is eponymous of Midas cichlid fish (<i>Amphilophus </i>spp.) adaptive radiations in Nicaraguan crater lakes. While most Midas cichlids are of the melanic "dark morph", about 10% of individuals lose their melanic pigmentation during their ontogeny and transition into a conspicuous "gold morph". Using a new haplotype-resolved long-read assembly we discovered an 8.2kb, transposon-derived inverted repeat in an intron of an undescribed gene, which we term <i>goldentouch</i> in reference to the Greek myth of King Midas. The gene <i>goldentouch</i> is differentially expressed between morphs, likely due to structural implications of inverted repeats in both DNA and RNA (cruciform and hairpin formation). The near-perfect association with the phenotype across several independent populations suggests that this insertion likely underlies this trans-specific, stable polymorphism.</span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Thyroid hormone tinkering elicits integrated phenotypic changes potentially explaining rapid adaptation of color vision in cichlid fish
Vision is critical for most vertebrates, including fish. One challenge that aquatic habitats pose is the high variability in spectral properties depending on depth, turbidity and composition of the water body. By altering opsin gene expression and chromophore usage, cichlid fish modulate visual sensitivities to maximize sensory input from the available light in their respective habitat. Thyroid hormone (TH) has been proposed to play a role in governing adaptive diversification in visual sensitivity in Nicaraguan Midas cichlids, which evolved in less than ~3,100 generations. As suggested by indirect measurements of TH levels (i.e., expression of deiodinases), populations adapted to short wavelength light in clear lakes have lower TH levels than ones inhabiting turbid lakes enriched in long-wavelength light. We experimentally manipulated TH levels by exposing two-week-old Midas cichlids to exogenous TH or a TH-inhibitor and measured opsin gene expression and chromophore usage (via cyp27c1 expression). Whereas exogenous TH induces long-wavelength sensitivity by changing opsin gene expression and chromophore usage in a concerted manner, TH-inhibited fish exhibit a visual phenotype with sensitivities shifted to shorter-wavelengths. Tinkering with TH levels in eyes results in concerted phenotypic changes that can provide a rapid mechanism of adaptation to novel light environments. --
Molecular evolution and depth-related adaptations of rhodopsin in the adaptive radiation of cichlid fishes in Lake Tanganyika
<p><span>The visual sensory system is essential for animals to perceive their environment and is thus under strong selection. In aquatic environments, light intensity and spectrum differ primarily along a depth gradient. Rhodopsin (RH1) is the only opsin responsible for dim-light vision in vertebrates and has been shown to evolve in response to the respective light conditions, including along a water depth gradient in fishes. In this study, we examined the diversity and sequence evolution of RH1 in the virtually entire adaptive radiation of cichlid fishes in Lake Tanganyika, focusing on adaptations to the achromatic environment with respect to depth. We show that Tanganyikan cichlid genomes contain a single copy of RH1. The 76 variable amino acid sites detected in RH1 across the radiation were not uniformly distributed along the protein sequence, and 31 of these variable sites show signals of positive selection. Moreover, the amino acid substitutions at 15 positively selected sites appeared to be depth-related, including three key tuning sites that directly mediate shifts in the peak spectral sensitivity, one site involved in protein stability, and 11 sites that may be functionally important on the basis of their </span><span>physicochemical properties. Among the strongest candidate sites for deep-water adaptations are two known key tuning sites (positions 292 and 299) and three newly identified variable sites (37, 104 and 290). Our study, which is th first compralehensive analysis of RH1 evolution in a massive adaptive radiation of cichlid fishes, provides novel insights into the evolution of RH1 in a freshwater environment.</span></p>
Quantitative trait loci mapping in cichlid fishes: Aulonocara koningsi x Metriaclima mbenjii and Labidochromis caeruleus x Labeotropheus trewavasae
<p>Since the time of Darwin, biologists have sought to understand the evolution and origins of phenotypic variation. To understand the genetic and molecular sources of morphological differences, we capitalize on the cichlid fish system. Cichlids of the East African Rift Lakes have undergone an extensive adaptive radiation, including variation in body shape, head shape, and pigmentation. These morphological differences are often intimately linked to the ecology and behavior of these animals. Here, we investigate the genetic basis of these phenotypes using quantitative trait loci (QTL) mapping using four genera of Lake Malawi cichlids and two F<sub>2</sub> hybrid populations. The first hybrid cross is between <em>Aulonocara koningsi</em>, which lives in the open sandy region and feeds insects from the open sand, and <em>Metriaclima mbenjii</em>, an omnivore rock-dwelling fish. The second cross is between <em>Labidochromis caeruleus</em>, a suction-feeding insectivore that swims continuously searching for prey, and <em>Labeotropheus trewavasae</em>, which feeds by biting or scraping attached algae from the rocks in its benthic habitat. Such work can provide insights into the molecular basis of phenotypic adaptation, the genetic architecture of morphology, and the evolution of cichlid fishes.</p>
Supplementary material 1 from: Venere P, Valente G, Vitorino C, Cabral-de-Mello D, Oliveira C, Souza I, Martins C (2012) Comparative cytogenetics of ten species of cichlid fishes (Teleostei, Cichlidae) from the Araguaia River system, Brazil, by conventional cytogenetic methods. Comparative Cytogenetics 6(2): 163-181. https://doi.org/10.3897/compcytogen.v6i2.1739
Table with synthesis of karyotypic traits of cichlids.
Data for: Multiple behavioral mechanisms shape development in a highly social cichlid fish
<p>Early-life social experiences shape adult phenotype, yet the underlying behavioral mechanisms remain poorly understood. We manipulated early-life social experience in the highly social African cichlid fish Astatotilapia burtoni to investigate the effects on behavior and stress axis function in juveniles. Juveniles experienced different numbers of social partners in stable pairs (1 partner), stable groups (6 fish; 5 partners), and socialized pairs (a novel fish was exchanged every 5 days; 5 partners). Treatments also differed in group size (groups vs. pairs) and stability (stable vs. socialized). We then measured individual behavior and water-borne cortisol to identify effects of early-life experience. We found treatment differences in behavior across all assays: open field exploration, social cue investigation, dominant behavior, and subordinate behavior. Treatment did not affect cortisol. Principal components (PC) analysis revealed robust co-variation of behavior across contexts, including with cortisol, to form behavioral syndromes sensitive to early-life social experience. PC1 (25.1 %) differed by social partner number: juveniles with more partners (groups and socialized pairs) were more exploratory during the social cue investigation, spent less time in the territory, and were more interactive as dominants. PC5 (8.5 %) differed by stability: socialized pairs were more dominant, spent less time in and around the territory, were more socially investigative, and had lower cortisol than stable groups or pairs. Observations of the home tanks provided insights into the social experiences that may underlie these effects. These results contribute to our understanding of how early-life social experiences are accrued and exert strong, lasting effects on phenotype.</p>
Data from: Genetic and developmental basis for fin shape variation in African cichlid fishes
Adaptive radiations are often characterized by the rapid evolution of traits associated with divergent feeding modes. For example, the evolutionary history of African cichlids is marked by repeated and coordinated shifts in skull, trophic, fin and body shape. Here, we seek to explore the molecular basis for fin shape variation in Lake Malawi cichlids. We first described variation within an F2 mapping population derived by crossing two cichlid species with divergent morphologies including fin shape. We then used this population to genetically map loci that influence variation in this trait. We found that the genotype–phenotype map for fin shape is largely distinct from other morphological characters including body and craniofacial shape. These data suggest that key aspects of fin, body and jaw shape are genetically modular and that the coordinated evolution of these traits in cichlids is more likely due to common selective pressures than to pleiotropy or linkage. We next combined genetic mapping data with population-level genome scans to identify wnt7aa and col1a1 as candidate genes underlying variation in the number of pectoral fin ray elements. Gene expression patterns across species with different fin morphologies and small molecule manipulation of the Wnt pathway during fin development further support the hypothesis that variation at these loci underlies divergence in fin shape between cichlid species. In all, our data provide additional insights into the genetic and molecular mechanisms associated with morphological divergence in this important adaptive radiation.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.