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107 results for “cavefish”
Datasets: Population genomics and mitochondrial DNA reveal cryptic diversity in North American Spring Cavefishes (Amblyopsidae, Forbesichthys)
<p>Forbesichthys_allsites.vcf: Dataset in VCF format used to perform Effective Population Size estimation.</p> <p>Forbesichthys_SNPs_NoLD.vcf: Dataset in VCF format used to perform PCA, fastStrucuture, and phylogenetic analyses.</p> <p>Files with extension .sfs contain site spectrum frequencies generated with the program easySFS.py.</p>
FIGURE 7 in Revision of the Endemic Malagasy Cavefish Genus Typhleotris (Teleostei: Gobiiformes: Milyeringidae), with Discussion of its Phylogenetic Placement and Description of a New Species
FIGURE 7. Dorsal view of the anterior portion of the head in the three described species of Typhleotris: A. T. madagascariensis, AMNH 245603; B. T. pauliani, AMNH 245651; C. T. mararybe, AMNH 245601, holotype.
Evolution of a central dopamine circuit underlies adaptation of light-evoked sensorimotor response in the blind cavefish, <em>Astyanax mexicanus</em>
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Social-like responses are inducible in the asocial and blind Mexican cavefish despite the continued exhibition of strong repetitive behavior
<p>Demo code and demo video files for the manuscript of "Social-like responses are inducible in the asocial and blind Mexican cavefish despite the continued exhibition of strong repetitive behavior." This zip file contains three folders, representing (1) ImageJ script for background subtraction; (2) python script to adjust swapped IDs in the result of idTracker analysis; and (3) MatLab script for detecting the social interactions</p>
Genetic differentiation and phenotypic plasticity drive troglomorphic character development in European cavefish
<p>The Aach cave loach (<em>Barbatula barbatula</em>), a recently discovered member of the Nemacheilidae family, offers a unique opportunity to understand the mechanisms underlying evolutionary change. In a common garden experiment, we reared groups of laboratory-bred cave, surface, and hybrid loach under different light conditions. Troglomorphic characters varied significantly among the fish, influenced to a different extent by parental origin and light conditions. Cavefish progeny consistently exhibited smaller eyes, lighter pigmentation, longer barbels, and larger olfactory epithelia than surface fish, while hybrids displayed intermediate characteristics. Surface and hybrid fish raised in complete darkness resembled the cavefish phenotype, while cavefish raised under a natural photoperiod approached the surface form. Characters associated with eye degeneration were found to be primarily heritable. Conversely, traits related to chemo- and mechano-reception were enhanced in the surface and hybrid groups reared in complete darkness, suggesting phenotypic plasticity. Our findings offer valuable insights into the interplay between genetic differentiation and phenotypic plasticity to troglomorphic adaption. This contributes to the broader understanding of the early stages of adaptation, where phenotypic plasticity, drift, and selection shape phenotypes. Relatively recently established cavefish, such as the Aach cave loach, are promising candidates for comparative research investigating evolutionary mechanisms.</p>
Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
<p><span><span><span>Cave-dwelling animals evolve distinct troglomorphic traits, such as loss of eyes, skin pigmentation, and augmentation of senses following long-term adaptation to the perpetual darkness. However, the molecular genetic mechanisms underlying these phenotypic variations remain unclear. In this study, we conducted comparative histology and comparative transcriptomics study of the skin of eight <i>Sinocyclocheilus</i> species (Cypriniformes: Cyprinidae) that included surface and cave-dwelling species. We analyzed four surface and four cavefish species by using next-generation sequencing, and a total of 802,798,907 clean reads were generated and assembled into 505,495,009 transcripts, which contributed to 1,037,334 unigenes. Bioinformatics comparisons of four different surface-cave fish groups revealed between 10,629 and 6442 significantly differentially expressed unigenes. Further, tens of differentially expressed genes (DEGs) potentially related to skin pigmentation were identified. Most of these DEGs (including <i>GNAQ</i>, <i>PKA</i>, <i>NRAS</i>, and <i>p38</i>) are downregulated in cavefish species. They are involved in key signaling pathways of pigment synthesis, such as the melanogenesis, Wnt, and MAPK pathways. This trend of downregulation was confirmed through qPCR experiments. This study will deepen our understanding of the formation of troglomorphic traits in cavefishes.</span></span></span></p>
Sensory evolution in a cavefish radiation: Patterns of neuromast distribution and associated behaviour in Sinocyclocheilus (Cypriniformes: Cyprinidae)
<p><em>Sinocyclocheilus</em>, a large radiation of freshwater cavefish, are well-known for their presence of regressive features (e.g., variable eye reduction). Fewer constructive features are known, such as the expansion of the lateral line system (LLS) involved in detecting water movements. The precise relationship between LLS expansion and cave adaptation is not well understood. Here we examine morphological and behavioural features of the LLS in <em>Sinocyclocheilus</em> characterized by broad variation in eye size, habitat and geographic distribution. Using live-staining techniques and automated behavioural analyses, we examined 26 <em>Sinocyclocheilus</em> species and quantified neuromast organ numbers, positions, and laterality within a phylogenetic context. We then examined how these morphological features may relate to wall-following, an established cave-associated behaviour mediated by the lateral line. We show that most species demonstrated laterality (i.e., asymmetry) in neuromast organs on the head, often biased to the right. We also found that wall-following behaviour was distinctive within cavefish, particularly among eyeless species. These diverse patterns of LLS expansion appear to correlate with the degree of eye loss, as well as geographic distribution. This work reveals that constructive LLS evolution is convergent across distant cavefish taxa, and may mediate asymmetric behavioural features that enable survival in stark subterranean microenvironments.</p>
Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish
<p>The development of animal model systems is dependent on the standardization of husbandry protocols that increase fecundity and reduce generation time. The blind Mexican tetra, <em>Astyanax mexicanus</em>, is an emerging genetic vertebrate model for evolution and biomedical research. Surface and cave populations of <em>A. mexicanus</em> have independently evolved, providing a model system for studying the genetic basis of divergent biological traits. While a rapid increase in the use of <em>A. mexicanus</em> has led to the generation of genetic tools including gene-editing and transgenesis, a slow and inconsistent growth rate remains a major limitation to the expanded application of <em>A. mexicanus</em>. The optimization of husbandry protocols that maximize high-nutrient feed, smaller tank densities, and larger tank sizes across development, would facilitate faster growth and expand the use of this model. Here, we describe standardized husbandry practices that optimize growth through a high-protein diet, increased feeding, growth sorting of larvae and juveniles, and tank size transitions based on standard length. These changes to husbandry had a significant effect on growth rates and decreased the age of sexual maturity in comparison to our previous protocols. To determine whether our nutritional change and increased feeding impacted behavior, we tested fish in exploration and schooling assays. We found that a change in diet had no effect on the behaviors we tested, suggesting that increased feeding and rapid growth will not impact the natural variation in behavioral traits. Taken together, this standardized husbandry protocol will accelerate the development of <em>A. mexicanus</em> as a genetic model.</p>
Astyanax cavefish body shape coordinates from: Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Fillipi 1853) (Actinopterygii, Characidae)
<p>The <em>Astyanax mexicanus</em> complex includes two different morphs, a surface and a cave-adapted ecotype, found at three mountain ranges in Northeastern Mexico: Sierra de El Abra, Sierra de Guatemala, and Sierra de la Colmena (Micos). Since their discovery, multiple studies have attempted to characterize the timing and the number of events that gave rise to the evolution of these cave-adapted ecotypes. Here, using RAD-seq and genome-wide sequencing, we assessed the phylogenetic relationships, genetic structure, and gene flow events between the cave and surface <em>Astyanax</em> <em>mexicanus</em> populations, to estimate the time and mode of evolution of the cave-adapted ecotypes. We also evaluated the body shape evolution across different cave lineages using geometric morphometrics to examine the role of phylogenetic signal vs. environmental pressures. We found strong evidence of parallel evolution of cave-adapted ecotypes derived from two separate lineages of surface fish and hypothesize that there may be up to four independent invasions of caves from surface fish. Moreover, a strong congruence between the genetic structure and geographic distribution was observed across the cave populations, with the Sierra de Guatemala the region exhibiting most genetic drift among the cave populations analyzed. Interestingly, we found no evidence of phylogenetic signal in body shape evolution, but we found support for parallel evolution in body shape across independent cave lineages, with cavefish from the Sierra de El Abra reflecting the most divergent morphology relative to surface and other cavefish populations.</p>
Wall-following – phylogenetic context of an enhanced behaviour in stygomorphic <em>Sinocyclocheilus</em> (Cypriniformes: Cyprinidae) cavefishes
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Data from: Ancient climate changes and relaxed selection shape cave colonization in North American cavefishes
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Novel husbandry practices result in rapid rates of growth and sexual maturation without impacting adult behavior in the blind Mexican cavefish
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Comparative transcriptomics reveals the molecular genetic basis of pigmentation loss in Sinocyclocheilus cavefishes
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Genetic differentiation and phenotypic plasticity drive troglomorphic character development in European cavefish
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Astyanax cavefish body shape coordinates from: Phylogeographic relationships and morphological evolution between cave and surface Astyanax mexicanus populations (De Fillipi 1853) (Actinopterygii, Characidae)
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Cavefish genomes resolve the ages of North American subterranean ecosystems
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Sensory evolution in a cavefish radiation: Patterns of neuromast distribution and associated behaviour in Sinocyclocheilus (Cypriniformes: Cyprinidae)
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Data from: Sporadic feeding regulates robust food entrainable circadian clocks in blind cavefish
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Data from: Evidence for hearing loss in amblyopsid cavefishes
The constant darkness of caves and other subterranean habitats imposes sensory constraints that offer a unique opportunity to examine evolution of sensory modalities. Hearing in cavefishes has not been well explored, and here we show that cavefishes in the family Amblyopsidae are not only blind but have also lost a significant portion of their hearing range. Our results showed that cave and surface amblyopsids shared the same audiogram profile at low frequencies but only surface amblyopsids were able to hear frequencies higher than 800 Hz and up to 2 kHz. We measured ambient noise in aquatic cave and surface habitats and found high intensity peaks near 1 kHz for streams underground, suggesting no adaptive advantage in hearing in those frequencies. In addition, cave amblyopsids had lower hair cell densities compared with their surface relative. These traits may have evolved in response to the loud high-frequency background noise found in subterranean pools and streams. This study represents the first report of auditory regression in a subterranean organism.
Data from: Evidence for repeated loss of selective constraint in rhodopsin of amblyopsid cavefishes (Teleostei: Amblyopsidae)
The genetic mechanisms underlying regressive evolution—the degeneration or loss of a derived trait—are largely unknown, particularly for complex structures such as eyes in cave organisms. In several eyeless animals, the visual photoreceptor rhodopsin appeared to retain functional amino-acid sequences. Hypotheses to explain apparent maintenance of function include weak selection for retention of light-sensing abilities and its pleiotropic roles in circadian rhythms and thermotaxis. In contrast, we show that there has been repeated loss of functional constraint of rhodopsin in amblyopsid cavefishes, as at least three cave lineages have independently accumulated unique loss-of-function mutations over the last 10.3 My. While several cave lineages still possess functional rhodopsin, they exhibit increased rates of nonsynonymous mutations that have greater effect on the structure and function of rhodopsin compared to those in surface lineages. These results indicate that functionality of rhodopsin has been repeatedly lost in amblyopsid cavefishes. The presence of a functional copy of rhodopsin in some cave lineages is likely explained by stochastic accumulation of mutations following recent subterranean colonization.
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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.