Cavefish Research Articles

Genetics and hybridization in surface and caveAstyanax(Teleostei): a comparison of regressive and constructive traits

Change in ecological conditions, as seen in surface and cave populations of Astyanax (Teleostei), has caused the divergent evolution of a large number of traits like eyes, coloration, taste, lateral line, and different kinds of behaviour like schooling, sleep or feeding posture. Because of the interfertility of surface and cave forms these fish are an exceptional object to study the morphological and genetic basis of the evolution of such complex regressive and constructive traits. Classical crossing analyses and genomic studies are contributing to growing understanding. Both kinds of traits mostly rely on multiple genetic bases and the phenotypic manifestation in the various crosses is similar. The gene effect underlying the phenotypic manifestation may exhibit an exponential increase at differing amounts in the various traits and crosses. Missing or presence of such genetic interaction helps determine whether the variability of eyes or pigmentation exhibited by Astyanax cave fish populations like Micos, is due to a more recent origin or to secondary hybridization with the surface fish. Neither crossing analysis nor QTL mapping revealed that eye reduction is pleiotropically antagonistically related to the increase of taste buds or lateral line sense. Independent inheritance of traits suggests that Astyanax cave fish are subjected to mosaic evolution.

Tetrapod V1R-like ora genes in an early-diverging ray-finned fish species: the canonical six ora gene repertoire of teleost fish resulted from gene loss in a larger ancestral repertoire.

BackgroundChemical senses serve a multitude of essential functions across the animal kingdom. Vertebrates employ four GPCR families to detect odors, among them the v1r/ora gene family. The V1R family is known to evolve rapidly in the lobe-finned lineage giving rise to tetrapods, but the homologous ORA family consists of just six highly conserved genes in teleost fish, with direct orthologs in the lobe-finned fish coelacanth. Thus, the teleost repertoire of six canonical ora genes was assumed to be the ancestral feature before the divergence of ray-finned and lobe-finned fish. So far, this hypothesis has not been tested with earlier diverging ray-finned fish.ResultsWe have newly identified the complete ora gene repertoires of five teleost species, and of spotted gar, a basal ray-finned fish, using thorough data mining and extensive phylogenetic analysis. The genomes of eight further teleost species were re-analyzed for their ORA repertoires. We report that direct orthologs of the six canonical ora genes (ora1-6) were present in all newly analyzed species, with faithfully preserved exon/intron structure and mostly preserved genomic arrangement in symmetric pairs for ora1-4. In four teleost species including medaka and cave fish we observe species-specific gene duplication events. Thus, the ora gene repertoire in teleost fish is not quite as strictly conserved as previously assumed. In fact, the examination of non-synonymous vs. synonymous substitution rates (dN/dS) shows pronounced negative selection in five of the six ora genes, but also rare occurrence of positive selection in ora3 and ora6. Surprisingly, spotted gar possesses beyond the six canonical genes three additional genes, ora7-8b, orthologous to coelacanth genes v1r07-10. No orthologs for these genes were found in teleosts and cartilaginous fish.ConclusionsEarly diverging ray-finned fish such as the spotted gar possess several v1r-like genes previously assumed to be restricted to the lobe-finned lineage, but now found to be already present in the most recent common ancestor of lobe- and ray-finned fish. Thus, the presence of just six canonical ora genes in many teleost species is not the ancestral feature of the ray-finned lineage, but caused by loss of two ancestral genes in teleosts.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2399-6) contains supplementary material, which is available to authorized users.

Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes.

Triplophysa fishes are the primary component of the fish fauna on the Tibetan Plateau and are well adapted to the high-altitude environment. Despite the importance of Triplophysa fishes on the plateau, the genetic mechanisms of the adaptations of these fishes to this high-altitude environment remain poorly understood. In this study, we generated the transcriptome sequences for three Triplophysa fishes, that is, Triplophysa siluroides, Triplophysa scleroptera, and Triplophysa dalaica, and used these and the previously available transcriptome and genome sequences from fishes living at low altitudes to identify potential genetic mechanisms for the high-altitude adaptations in Triplophysa fishes. An analysis of 2,269 orthologous genes among cave fish (Astyanax mexicanus), zebrafish (Danio rerio), large-scale loach (Paramisgurnus dabryanus), and Triplophysa fishes revealed that each of the terminal branches of the Triplophysa fishes had a significantly higher ratio of nonsynonymous to synonymous substitutions than that of the branches of the fishes from low altitudes, which provided consistent evidence for genome-wide rapid evolution in the Triplophysa genus. Many of the GO (Gene Ontology) categories associated with energy metabolism and hypoxia response exhibited accelerated evolution in the Triplophysa fishes compared with the large-scale loach. The genes that exhibited signs of positive selection and rapid evolution in the Triplophysa fishes were also significantly enriched in energy metabolism and hypoxia response categories. Our analysis identified widespread Triplophysa-specific nonsynonymous mutations in the fast evolving genes and positively selected genes. Moreover, we detected significant evidence of positive selection in the HIF (hypoxia-inducible factor)-1A and HIF-2B genes in Triplophysa fishes and found that the Triplophysa-specific nonsynonymous mutations in the HIF-1A and HIF-2B genes were associated with functional changes. Overall, our study provides new insights into the adaptations and evolution of fishes in the high-altitude environment of the Tibetan Plateau and complements previous findings on the adaptations of mammals and birds to high altitudes.

Neural Evolution: Costing the Benefits of Eye Loss

What selective forces contribute to eye loss in cave animals? A new study shows the eye and optic tectum of a cave fish consumes ∼5-17% of the total energy consumption, emphasising that selection to reduce energy consumption may drive eye loss.

Tempo and Mode in Astyanax mexicanus cavefish evolution: a population genomic reappraisal

Tempo and Mode in Astyanax mexicanus cavefish evolution: a population genomic reappraisal

Spontaneous behavior of basal Copionodontinae cave catfishes from Brazil (Teleostei, Siluriformes, Trichomycteridae)

Cave animals are particularly interesting due to their behavioral specializations, resultant from evolution in isolation. We present data from a spontaneous behavior study (spatial distribution and preference for microhabitats) of two troglobitic catfish from Brazil: Glaphyropoma spinosum and a new species of Copionodon. We compared the data with those obtained of a sympatric epigean species, Copionodon pecten. These Trichomycteridae species belong to a basal and apparently monophyletic subfamily – Copiono dontinae, endemic to Chapada Diamantina, central Bahia state, eastern Brazil. We observed the fishes in natural and laboratory conditions through ad libitum and focal animal methods. Each spatial behavioral category (hidden, bottom, midwater, surface and wall swimming and stationary in the bottom) was timed individually, with a sample of 12 specimens per species. Unlike most troglobitic fishes, cave copionodon tines tested herein did not extend exploratory behavior to midwater, with benthonic and thigmotacticrelated exploratory behavior. This behavior is possibly related to its feeding behavior specializations, strong territorialism and photophobic behavior. The epigean Copionodon species is also benthonic. The spatial behavior of the cave Copionodontinae could be interpreted as a retained and plesiomorphic characterstate in relation to other trichomycterid catfishes.

Study of the digestive tract of a rare species of Iranian blind cave fish (Iranocypris typhlops)

Ebrahimi A. 2015. Study of the digestive tract of a rare species of Iranian blind cave fish (Iranocypris typhlops). Biodiversitas 16: 173-178. The Iranian blind cave fish (Iranocypris typhlops) is a unique taxon which only lives within a cave in Lorestan Province insouthwest of Iran. Regardless of its enormous genetic interest, this species faces an imminent risk of extinction as no conservationefforts have been done for its protection. This study aimed to analyze the morphology of the digestive tract of this interesting fish using ahistological approach. Detailed examinations of the fishes showed that the mouth is horseshoe-shaped and located in an inferior situation(ventral side) of the head. In it, there are three rows of pharyngeal teeth including inner, middle and outer rows, which bear 5, 3 and 3 teethrespectively. The esophagus is very short and lined with an epithelium containing numerous mucous folds. The stomach is not present.The anterior segment of the intestine is S-shaped which comprises about one half the gut. In this part, there are mucosal folds which showdifferent sizes and mucous layer is thicker than other layers (submucosa, muscle layer and serosa). The distal portion of the intestine isstraight (rectal) and terminates to the anal region. In general, the ratio of intestine length is 1.2, as compared to the body length. Thisstudy showed that the liver in this taxon is composed of two lobes, the right lobe being two-parts and bigger than the left one. The gallbladder is clear and spherical in appearance. The pancreas is red or orange and observed as scattered masses of cells on the mesentery of thedigestive system. To our best knowledge, this is the first study to analyze the morphological characteristics of the digestive tract of theIranian blind cave fish, and its unique characteristics here found confirmed its singularity and so, the urgent need for its conservation.

Fish assemblages of Mediterranean marine caves.

Fish assemblages associated with 14 marine caves and adjacent external rocky reefs were investigated at four Marine Protected Areas (MPAs) along the coasts of Italy. Within the caves sampling was carried out in different sub-habitats: walls, ceilings, bottoms and ends of caves. On the whole, 38 species were recorded inside the 14 caves investigated. Eighteen species were exclusively found inside the caves: they were mainly represented by speleophilic (i.e. species preferentially or exclusively inhabiting caves) gobids (e.g. Didogobius splechtnai) and nocturnal species (e.g. Conger conger). Forty-one species were censused outside, 20 of which were shared with cave habitats. Apogon imberbis was the most common fish found in all 14 caves investigated, followed by Thorogobius ephippiatus (recorded in 13 caves), and Diplodus vulgaris and Scorpaena notata (both censused in 12 caves). Distinct fish assemblages were found between external rocky reefs and the different cave sub-habitats. New data on the distribution of some speleophilic gobids were collected, showing the existence of a pool of species shared by marine caves on a large scale (i.e. hundreds of km). Considering the uniqueness of cave fishes (18 exclusive species and different assemblage structures), the inclusion of marine caves among the habitats routinely investigated for fish biodiversity monitoring could facilitate the achievement of more comprehensive inventories. Due to their contribution to local species diversity and the shelter they provide to species valuable for conservation, marine caves should be prioritized for their inclusion not only within future MPAs through the Mediterranean Sea, but also into larger management spatial planning.

Reduction of Energetic Demands through Modification of Body Size and Routine Metabolic Rates in Extremophile Fish.

Variation in energy availability or maintenance costs in extreme environments can exert selection for efficient energy use, and reductions in organismal energy demand can be achieved in two ways: reducing body mass or metabolic suppression. Whether long-term exposure to extreme environmental conditions drives adaptive shifts in body mass or metabolic rates remains an open question. We studied body size variation and variation in routine metabolic rates in locally adapted populations of extremophile fish (Poecilia mexicana) living in toxic, hydrogen sulfide-rich springs and caves. We quantified size distributions and routine metabolic rates in wild-caught individuals from four habitat types. Compared with ancestral populations in nonsulfidic surface habitats, extremophile populations were characterized by significant reductions in body size. Despite elevated metabolic rates in cave fish, the body size reduction precipitated in significantly reduced energy demands in all extremophile populations. Laboratory experiments on common garden-raised fish indicated that elevated routine metabolic rates in cave fish likely have a genetic basis. The results of this study indicate that adaptation to extreme environments directly impacts energy metabolism, with fish living in cave and sulfide spring environments expending less energy overall during routine metabolism.

Population density and habitat of an endangered cave fish Eigenmannia vicentespelaea Triques, 1996 (Ostariophysi: Gymnotiformes) from a karst area in central Brazil

The troglobitic electric fish Eigenmannia vicentespelaea, endemic to a single cave-system and included in the Brazilian Red List of Threatened Fauna, was studied in relation to population densities and habitat. For comparison, we used the epigean species, E. trilineata. We verify if the population densities recorded for E. vicentespelaea follow the pattern observed for other subterranean fishes; if there are seasonal fluctuations in these densities and which environmental variables explain the densities variation. We estimated abundances and population densities during three consecutive dry seasons concomitant with habitat description and physicochemical variables measurements. For E. vicentespelaea: in six stream reaches in the São Vicente II cave. For E. trilineata: from counts of active fish in rio da Lapa. The mean population density recorded for E. vicentespelaea is considered low (0.17 ind.m-2), similar to those of E. trilineata (0.13 ind.m-2), without significant differences between the years, but with marked fluctuations during dry seasons within each year, suggesting seasonality. Estimated population size of E. vicentespelaea is considered low (270 individuals in average). Depth, water current and substrate, allied to plant debris explain better the variation of densities. Urgent actions for E. vicentespelaea conservation include protection of headsprings in Terra Ronca State Park.

The timing of Timezyme diversification in vertebrates.

All biological functions in vertebrates are synchronized with daily and seasonal changes in the environment by the time keeping hormone melatonin. Its nocturnal surge is primarily due to the rhythmic activity of the arylalkylamine N-acetyl transferase AANAT, which thus became the focus of many investigations regarding its evolution and function. Various vertebrate isoforms have been reported from cartilaginous fish to mammals but their origin has not been clearly established. Using phylogeny and synteny, we took advantage of the increasing number of available genomes in order to test whether the various rounds of vertebrate whole genome duplications were responsible for the diversification of AANAT. We highlight a gene secondary loss of the AANAT2 in the Sarcopterygii, revealing for the first time that the AAANAT1/2 duplication occurred before the divergence between Actinopterygii (bony fish) and Sarcopterygii (tetrapods, lobe-finned fish, and lungfish). We hypothesize the teleost-specific whole genome duplication (WDG) generated the appearance of the AANAT1a/1b and the AANAT2/2′paralogs, the 2′ isoform being rapidly lost in the teleost common ancestor (ray-finned fish). We also demonstrate the secondary loss of the AANAT1a in a Paracantopterygii (Atlantic cod) and of the 1b in some Ostariophysi (zebrafish and cave fish). Salmonids present an even more diverse set of AANATs that may be due to their specific WGD followed by secondary losses. We propose that vertebrate AANAT diversity resulted from 3 rounds of WGD followed by previously uncharacterized secondary losses. Extant isoforms show subfunctionalized localizations, enzyme activities and affinities that have increased with time since their emergence.

Lens defects in Astyanax mexicanus Cavefish: evolution of crystallins and a role for alphaA-crystallin.

The fish Astyanax mexicanus presents, within the same species, populations of river-dwelling surface fish (SF) and blind cave-living fish. In cavefish (CF), the eyes develop almost normally during embryogenesis. But 40 h after fertilization, the lens enters apoptosis, triggering the progressive degeneration of the entire eye. Before apoptosis, the CF lens expresses early differentiation factors correctly. Here, we searched for possible late differentiation defects that would be causal in CF lens degeneration. We reasoned that crystallins, the major lens structural proteins, could be defective or misregulated. We surveyed the CF and SF transcriptomes and uncovered 14 Astyanax crystallins from the beta, gamma, lambda, mu, and zeta families. These proteins are less polymorphic and accumulate more fixed mutations, some at highly conserved positions, in CF than in SF, suggesting relaxed selection at these loci in CF. In situ hybridizations and qPCR show that crybb1c, crybgx, crygm5 are expressed at much lower levels or are not expressed in the CF lens. For the best crystallin candidates, we tested a potential causal role in CF lens apoptosis. Crybgx, crybb1c (not expressed in CF from very early on), and cryaa (previously shown to be faintly expressed in CF) failed to induce any defect when knocked-down in zebrafish embryos. However, the anti-apoptotic cryaa protected lens cells from apoptosis when reexpressed by transgenesis in CF, suggesting a cell-autonomous effect of cryaa on lens cell survival. Altogether, these data suggest that crystallin sequence evolution and expression defects may contribute to the loss of eyes in CF.

Eyeless Mexican cavefish save energy by eliminating the circadian rhythm in metabolism.

The eyed surface form and eyeless cave form of the Mexican tetra Astyanax mexicanus experience stark differences in the daily periodicities of light, food and predation, factors which are likely to have a profound influence on metabolism. We measured the metabolic rate of Pachón cave and surface fish at a fixed swimming speed under light/dark and constant dark photoperiods. In constant darkness surface forms exhibited a circadian rhythm in metabolism with an increase in oxygen demand during the subjective daytime, whereas cave forms did not. The lack of circadian rhythm in metabolism leads to a 27% energy savings for Pachón cave fish compared to surface fish when comparing both forms in their natural photoperiods. When surface forms were tested under constant dark conditions they expended 38% more energy than cave forms under equivalent conditions. Elimination of the circadian rhythm in metabolism may be a general feature of animals that live in perpetually dark food-limited environments such as caves or the deep sea.

Quantitative food web analysis supports the energy-limitation hypothesis in cave stream ecosystems.

Energy limitation has long been the primary assumption underlying conceptual models of evolutionary and ecological processes in cave ecosystems. However, the prediction that cave communities are actually energy-limited in the sense that constituent populations are consuming all or most of their resource supply is untested. We assessed the energy-limitation hypothesis in three cave streams in northeastern Alabama (USA) by combining measurements of animal production, demand, and resource supplies (detritus, primarily decomposing wood particles). Comparisons of animal consumption and detritus supply rates in each cave showed that all, or nearly all, available detritus was required to support macroinvertebrate production. Furthermore, only a small amount of macroinvertebrate prey production remained to support other predatory taxa (i.e., cave fish and salamanders) after accounting for crayfish consumption. Placing the energy demands of a cave community within the context of resource supply rates provided quantitative support for the energy-limitation hypothesis, confirming the mechanism (limited energy surpluses) that likely influences the evolutionary processes and population dynamics that shape cave communities. Detritus-based surface ecosystems often have large detrital surpluses. Thus, cave ecosystems, which show minimal surpluses, occupy the extreme oligotrophic end of the spectrum of detritus-based food webs.

Population ecology and seasonal demography of the endangered grotto sculpin (Cottus specus)

AbstractSubterranean fishes are understudied worldwide and often at risk before their populations are discovered and described. The nature of karst systems limits the applicability of ecological paradigms and hinders our ability to identify and preserve endemic fauna. Aquatic karst taxa in particular are subject to environmental threats that increase in severity over time. Once a population or species is recognised as distinct, it is imperative we gain understanding of its biology to inform effective resource management and mitigate risk factors. The grotto sculpin (Cottus specus) is endemic to Perry County, Missouri, U.S. caves and was formally described and listed as endangered under the U.S. Endangered Species Act in 2013. We used mark–recapture methods to quantify population densities and estimate population sizes in two caves and two corresponding spring branches. Size structure varied among habitats and seasons. Spring branches were dominated by juveniles year‐round with peak young‐of‐year (YOY) densities in May. Adult densities in both macrohabitats decreased in winter, possibly due to recruitment or seasonal stress, and were lower at spring branches compared to caves and declined further during late winter which may be indicative of cave spawning. YOY were captured variably underground with peak densities in summer. The ecology of grotto sculpin appears to be more complex than has been reported previously for subterranean fishes. Variable patterns of demography requiring multiple contiguous habitats are unique for cave species and support the recently substantiated suggestion that subterranean systems are not as simple or disconnected as once thought.

An assay for lateral line regeneration in adult zebrafish.

Due to the clinical importance of hearing and balance disorders in man, model organisms such as the zebrafish have been used to study lateral line development and regeneration. The zebrafish is particularly attractive for such studies because of its rapid development time and its high regenerative capacity. To date, zebrafish studies of lateral line regeneration have mainly utilized fish of the embryonic and larval stages because of the lower number of neuromasts at these stages. This has made quantitative analysis of lateral line regeneration/and or development easier in the earlier developmental stages. Because many zebrafish models of neurological and non-neurological diseases are studied in the adult fish and not in the embryo/larvae, we focused on developing a quantitative lateral line regenerative assay in adult zebrafish so that an assay was available that could be applied to current adult zebrafish disease models. Building on previous studies by Van Trump et al. that described procedures for ablation of hair cells in adult Mexican blind cave fish and zebrafish (Danio rerio), our assay was designed to allow quantitative comparison between control and experimental groups. This was accomplished by developing a regenerative neuromast standard curve based on the percent of neuromast reappearance over a 24 hr time period following gentamicin-induced necrosis of hair cells in a defined region of the lateral line. The assay was also designed to allow extension of the analysis to the individual hair cell level when a higher level of resolution is required.

Dinâmica populacional do bagre cego de Iporanga, Pimelodella kronei: 70 anos de estudo

The Iporanga blind catfish, Pimelodella kronei, from the Alto Ribeira karst area, was the first troglobite discovered and described in Brazil, and it is still one of the most intensively studied. These catfish were collected during the 1970´s, causing a population decline recorded by E.Trajano ten years later. We present data on the population dynamics in the Areias de Cima Cave gathered two decades after, focusing on distribution of length and condition factor, movements and individual growth, based on a mark-recapture program carried out from October 2008 to May 2010. These data are compared to those by Pavan (1945) and Trajano (1987). This is the first long-term monitoring for Brazilian cave fishes. Keywords. Cave fish; Population ecology; Monitoring; Pimelodella kronei; Brazil. *Contato do autor: analuizaguil@gmail.com

Life: Some cave fish partially deaf: Loss may be adaptation to distracting background noise

Science NewsVolume 183, Issue 9 p. 9-9 In the News Life: Some cave fish partially deaf: Loss may be adaptation to distracting background noise Puneet Kollipara, Puneet KolliparaSearch for more papers by this author Puneet Kollipara, Puneet KolliparaSearch for more papers by this author First published: 24 April 2013 https://doi.org/10.1002/scin.5591830906Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat No abstract is available for this article. Volume183, Issue94 May 2013Pages 9-9 RelatedInformation

Albinism in phylogenetically and geographically distinct populations of Astyanax cavefish arises through the same loss-of-function Oca2 allele

The Mexican tetra, Astyanax mexicanus, comprises 29 populations of cave-adapted fish distributed across a vast karst region in northeastern Mexico. These populations have a complex evolutionary history, having descended from 'old' and 'young' ancestral surface-dwelling stocks that invaded the region ∼6.7 and ∼2.8 MYa, respectively. This study investigates a set of captive, pigmented Astyanax cavefish collected from the Micos cave locality in 1970, in which albinism appeared over the past two decades. We combined novel coloration analyses, coding sequence comparisons and mRNA expression level studies to investigate the origin of albinism in captive-bred Micos cavefish. We discovered that albino Micos cavefish harbor two copies of a loss-of-function ocular and cutaneous albinism type II (Oca2) allele previously identified in the geographically distant Pachón cave population. This result suggests that phylogenetically young Micos cavefish and phylogenetically old Pachón cave fish inherited this Oca2 allele from the ancestral surface-dwelling taxon. This likely resulted from the presence of the loss-of-function Oca2 haplotype in the 'young' ancestral surface-dwelling stock that colonized the Micos cave and also introgressed into the ancient Pachón cave population. The appearance of albinism in captive Micos cavefish, caused by the same loss-of-function allele present in Pachón cavefish, implies that geographically and phylogenetically distinct cave populations can evolve the same troglomorphic phenotype from standing genetic variation present in the ancestral taxon.

The Second Northernmost Cave-Adapted Fish in the World? Groundwork on the Tytoona Cave Sculpin Population

A new cave population of sculpin fish from Central Pennsylvania is described that, if confirmed to be cave adapted, would become the second northernmost cave-adapted fish in the world. The Tytoona Cave fish lack the suite of modifications typical of troglomorphic populations. Their eyes, pectoral fins, and mouths appear to be as large as those of their surface counterparts, they have the same number of cephalic lateralis pores, and their pigmentation levels do not appear to be much lower. Nonetheless, they are considered to be cave adapted due to the presence of ovigerous females, a lack of evidence for starvation, and primarily because the cephalic lateralis pores (part of the lateral line system) are significantly larger than those of similar-sized surface fish. It may be that the Tytoona Cave population only has some emergent cave adaptations because in high latitudes the extent of polar ice sheet migration during the Pleistocene era restricted colonization by fish at least until 12 ka ago, when the ice age ended.