The rise of Astyanax cavefish

Extraordinary model systems for regeneration

Regeneration is the remarkable phenomenon through which an organism can regrow lost or damaged parts with fully functional replacements, including complex anatomical structures, such as limbs. In 2019, Development launched its 'Model systems for regeneration' collection, a series of articles introducing some of the most popular model organisms for studying regeneration in vivo. To expand this topic further, this Perspective conveys the voices of five expert biologists from the field of regenerative biology, each of whom showcases some less well-known, but equally extraordinary, species for studying regeneration.

Gross morphology of the brain and some sense organs of subterranean pencil catfishes of the genus Ituglanis Costa and Bockmann, 1993 (Siluriformes, Trichomycteridae), with a discussion on sensory compensation versus preadaptation in subterranean fishes

Subterranean organisms provide excellent opportunities to investigate morphological evolution, especially of sensory organs and structures and their processing areas in the central nervous system. We describe the gross morphology of the brain and some cephalic sensory organs (olfactory organ, eye, semicircular canals of the inner ear) and the swim bladder (a non-sensory accessory structure) of subterranean species of pencil catfishes of the genus Ituglanis Costa and Bockmann, 1993 (Siluriformes, Trichomycteridae) and compare them with an epigean species of the genus, Ituglanis goya Datovo, Aquino and Langeani, 2016. We compared qualitatively the size of the different brain regions and sense organs of the subterranean species with those of the epigean one, searching for modifications possibly associated with living in the subterranean environment. Our findings suggest that species of Ituglanis exhibit sensory characteristics that are preadaptive for the subterranean life, as only slight modifications were observed in the brains and sense organs of the subterranean species of the genus when compared with the epigean one. Because most subterranean fish species belong to lineages putatively preadapted for subterranean life, our results, discussed in the context of available information on the brain and sense organs of other subterranean species, help identify general trends for the evolution of the brain and sensory organs of subterranean fishes in general.

Discovery of putative long non-coding RNAs expressed in the eyes of Astyanax mexicanus (Actinopterygii: Characidae)

Astyanax mexicanus is a well-known model species, that has two morphotypes, cavefish, from subterranean rivers and surface fish, from surface rivers. They are morphologically distinct due to many troglomorphic traits in the cavefish, such as the absence of eyes. Most studies on A. mexicanus are focused on eye development and protein-coding genes involved in the process. However, lncRNAs did not get the same attention and very little is known about them. This study aimed to fill this knowledge gap, identifying, describing, classifying, and annotating lncRNAs expressed in the embryo's eye tissue of cavefish and surface fish. To do so, we constructed a concise workflow to assemble and evaluate transcriptomes, annotate protein-coding genes, ncRNAs families, predict the coding potential, identify putative lncRNAs, map them and predict interactions. This approach resulted in the identification of 33,069 and 19,493 putative lncRNAs respectively mapped in cavefish and surface fish. Thousands of these lncRNAs were annotated and identified as conserved in human and several species of fish. Hundreds of them were validated in silico, through ESTs. We identified lncRNAs associated with genes related to eye development. This is the case of a few lncRNAs associated with sox2, which we suggest being isomorphs of the SOX2-OT, a lncRNA that can regulate the expression of sox2. This work is one of the first studies to focus on the description of lncRNAs in A. mexicanus, highlighting several lncRNA targets and opening an important precedent for future studies focusing on lncRNAs expressed in A. mexicanus.

Oogenesis and in vitro reproduction of the twospot astyanax Astyanax bimaculatus (Linnaeus, 1758) exposed to conspecific alarm substance

Stress situations can be essential to trigger reproduction in fish; however, it may also inhibit it. One of those situations involves the release of the conspecific alarm substance (CAS), a natural stressor, into the water by specific fish epidermal cells after a predator attack. Little is known about the effects of that substance on fish reproduction. This study aimed to evaluate the effects of CAS exposure on the oogenesis and reproduction of the twospot astyanax Astyanax bimaculatus before the hormonal induction for artificial reproduction. No macroscopic or cellular changes in the ovaries were observed for the females exposed to CAS, and the oocyte stages show all females in the same phase of maturation (Spawning Capable). Females exposed to CAS spawned 20 min before the females without exposure. On the other hand, they ovulated only once, whereas the females from the control group ovulated multiple times for approximately two hours after hormonal induction. Moreover, the precocious ovulation of the females submitted to CAS did not generate offspring, since all generated zygotes did not develop. In contrast, the control group females produced more than 11 thousand healthy larvae. Exposing the female fish to CAS during their reproductive management in captivity may reduce breeding success.

Divergent tooth development mechanisms of Mexican tetra fish (Astyanax mexicanus) of Pachón cave origin

The Mexican tetra (Astyanax mexicanus) is one of the fresh water teleost fish models in evolutionary developmental biology. The existence of two morphs: eyed, pigmented surface fish and blind depigmented cavefish from multiple cave populations, provides a unique system to study adaptive radiation. Compared to the adult surface fish, cavefish have large oral jaws with an increased number of structurally-complex teeth. Early tooth development has not been studied in detail in cavefish populations. In this study, bone-stained growth series and vital dye staining was used to trace the development and replacement of dentitions in Pachón cavefish. Our results show that first tooth eruption was delayed in cavefish compared to the surface fish. In particular, the first tooth eruption cycle persisted until 35 days post fertilization (dpf). Unlike surface fish, there are multicuspid teeth in cavefish first generation dentition. In addition to the teeth in the marginal oral jaw bones, Pachón cavefish have teeth in the ectopterygoid bone of the palatine roof. Next, we characterised the expression of ectodysplasin signalling pathway genes in tooth-forming regions of surface and cavefish. Interestingly, higher expression of Eda and Edar was found in cavefish compared to the surface fish. The altered ectodysplasin expression needs further investigation to confirm the different molecular mechanisms for tooth development in the oral and pharyngeal regions of surface fish and cavefish.

Discordant Genome Assemblies Drastically Alter the Interpretation of Single-Cell RNA Sequencing Data Which Can Be Mitigated by a Novel Integration Method

Advances in sequencing and assembly technology have led to the creation of genome assemblies for a wide variety of non-model organisms. The rapid production and proliferation of updated, novel assembly versions can create vexing problems for researchers when multiple-genome assembly versions are available at once, requiring researchers to work with more than one reference genome. Multiple-genome assemblies are especially problematic for researchers studying the genetic makeup of individual cells, as single-cell RNA sequencing (scRNAseq) requires sequenced reads to be mapped and aligned to a single reference genome. Using the Astyanax mexicanus, this study highlights how the interpretation of a single-cell dataset from the same sample changes when aligned to its two different available genome assemblies. We found that the number of cells and expressed genes detected were drastically different when aligning to the different assemblies. When the genome assemblies were used in isolation with their respective annotations, cell-type identification was confounded, as some classic cell-type markers were assembly-specific, whilst other genes showed differential patterns of expression between the two assemblies. To overcome the problems posed by multiple-genome assemblies, we propose that researchers align to each available assembly and then integrate the resultant datasets to produce a final dataset in which all genome alignments can be used simultaneously. We found that this approach increased the accuracy of cell-type identification and maximised the amount of data that could be extracted from our single-cell sample by capturing all possible cells and transcripts. As scRNAseq becomes more widely available, it is imperative that the single-cell community is aware of how genome assembly alignment can alter single-cell data and their interpretation, especially when reviewing studies on non-model organisms.

Innate Mechanisms of Heart Regeneration

Heart regeneration is a remarkable process whereby regrowth of damaged cardiac tissue rehabilitates organ anatomy and function. Unfortunately, the human heart is highly resistant to regeneration, which creates a shortage of cardiomyocytes in the wake of ischemic injury, and explains, in part, why coronary artery disease remains a leading cause of death worldwide. Luckily, a detailed blueprint for achieving therapeutic heart regeneration already exists in nature because several lower vertebrate species successfully regenerate amputated or damaged heart muscle through robust cardiomyocyte proliferation. A growing number of species are being interrogated for cardiac regenerative potential, and several commonalities have emerged between those animals showing high or low innate capabilities. In this review, we provide a historical perspective on the field, discuss how regenerative potential is influenced by cardiomyocyte properties, mitogenic signals, and chromatin accessibility, and highlight unanswered questions under active investigation. Ultimately, delineating why heart regeneration occurs preferentially in some organisms, but not in others, will uncover novel therapeutic inroads for achieving cardiac restoration in humans.

Repeated colonization of caves leads to phenotypic convergence in catfishes (Siluriformes: Trichomycterus) at a small geographical scale

Across various animal groups, adaptation to the challenging conditions of cave environments has resulted in convergent evolution. We document a Neotropical cavefish system with ample potential to study questions related to convergent adaptation to cave environments at the population level. In the karstic region of the Andes of Santander, Colombia, cave-dwelling catfish in the genus Trichomycterus exhibit variable levels of reduction of eyes and body pigmentation relative to surface congeners. We tested whether cave-dwelling, eye-reduced, depigmented Trichomycterus from separate caves in Santander were the result of a single event of cave colonization and subsequent dispersal, or of multiple colonizations to caves by surface ancestors followed by phenotypic convergence. Using mitochondrial DNA sequences to reconstruct phylogenetic relationships, we found that caves in this region have been colonized independently by two separate clades. Additional events of cave colonization – and possibly recolonization of surface streams – may have occurred in one of the clades, where surface and cave-dwelling populations exhibit shallow differentiation, suggesting recent divergence or divergence with gene flow. We also identify potentially undescribed species and likely problems with the circumscription of named taxa. The system appears promising for studies on a wide range of ecological and evolutionary questions.

Unlocking the Secrets of the Regenerating Fish Heart: Comparing Regenerative Models to Shed Light on Successful Regeneration

The adult human heart cannot repair itself after injury and, instead, forms a permanent fibrotic scar that impairs cardiac function and can lead to incurable heart failure. The zebrafish, amongst other organisms, has been extensively studied for its innate capacity to repair its heart after injury. Understanding the signals that govern successful regeneration in models such as the zebrafish will lead to the development of effective therapies that can stimulate endogenous repair in humans. To date, many studies have investigated cardiac regeneration using a reverse genetics candidate gene approach. However, this approach is limited in its ability to unbiasedly identify novel genes and signalling pathways that are essential to successful regeneration. In contrast, drawing comparisons between different models of regeneration enables unbiased screens to be performed, identifying signals that have not previously been linked to regeneration. Here, we will review in detail what has been learnt from the comparative approach, highlighting the techniques used and how these studies have influenced the field. We will also discuss what further comparisons would enhance our knowledge of successful regeneration and scarring. Finally, we focus on the Astyanax mexicanus, an intraspecies comparative fish model that holds great promise for revealing the secrets of the regenerating heart.

Reduced Oxygen as an Environmental Pressure in the Evolution of the Blind Mexican Cavefish

Extreme environmental features can drive the evolution of extreme phenotypes. Over the course of evolution, certain environmental changes may be so drastic that they lead to extinction. Conversely, if an organism adapts to harsh environmental changes, the adaptations may permit expansion of a novel niche. The interaction between environmental stressors and adaptive changes is well-illustrated by the blind Mexican cavefish, Astyanaxmexicanus, which has recurrently adapted to the stark subterranean environment. The transition from terrestrial rivers and streams (occupied by extant surface morphs of the same species) to the cave has been accompanied by the resorption of eyes, diminished pigmentation and reduced metabolism in cave-dwelling morphs. The principal features of caves most often associated with evolution of these common cave features are the absence of light and limited nutrition. However, a putatively essential cave feature that has received less attention is the frequently low concentration of oxygen within natural karst environments. Here, we review the potential role of limited oxygen as a critical environmental feature of caves in the Sierra de El Abra. Additionally, we review evidence that Astyanax cavefish may have evolved adaptive features enabling them to thrive in lower oxygen compared to their surface-dwelling counterparts.

Subterranean life: Behavior, metabolic, and some other adaptations of Astyanax cavefish

The ability of fishes to adapt to any aquatic environment seems limitless. It is enthralling how new species keep appearing at the deep sea or in subterranean environments. There are close to 230 known species of cavefishes, still today the best-known cavefish is Astyanax mexicanus, a Characid that has become a model organism, and has been studied and scrutinized since 1936. There are two morphotypes for A. mexicanus, a surface fish and a cavefish. The surface fish lives in central and northeastern Mexico and south of the United States, while the cavefish is endemic to the "Sierra del Abra-Tanchipa region" in northeast Mexico. The extensive genetic and genomic analysis depicts a complex origin for Astyanax cavefish, with multiple cave invasions and persistent gene flow among cave populations. The surface founder population prevails in the same region where the caves are. In this review, we focus on both morphotype's main morphological and physiological differences, but mainly in recent discoveries about behavioral and metabolic adaptations for subterranean life. These traits may not be as obvious as the troglomorphic characteristics, but are key to understand how Astyanax cavefish thrives in this environment of perpetual darkness.

Developmental Transcriptomic Analysis of the Cave-Dwelling Crustacean, Asellus aquaticus

Cave animals are a fascinating group of species often demonstrating characteristics including reduced eyes and pigmentation, metabolic efficiency, and enhanced sensory systems. Asellus aquaticus, an isopod crustacean, is an emerging model for cave biology. Cave and surface forms of this species differ in many characteristics, including eye size, pigmentation, and antennal length. Existing resources for this species include a linkage map, mapped regions responsible for eye and pigmentation traits, sequenced adult transcriptomes, and comparative embryological descriptions of the surface and cave forms. Our ultimate goal is to identify genes and mutations responsible for the differences between the cave and surface forms. To advance this goal, we decided to use a transcriptomic approach. Because many of these changes first appear during embryonic development, we sequenced embryonic transcriptomes of cave, surface, and hybrid individuals at the stage when eyes and pigment become evident in the surface form. We generated a cave, a surface, a hybrid, and an integrated transcriptome to identify differentially expressed genes in the cave and surface forms. Additionally, we identified genes with allele-specific expression in hybrid individuals. These embryonic transcriptomes are an important resource to assist in our ultimate goal of determining the genetic underpinnings of the divergence between the cave and surface forms.

Sensory ecology of the fish lateral-line system: Morphological and physiological adaptations for the perception of hydrodynamic stimuli

Fishes are able to detect and perceive the hydrodynamic and physical environment they inhabit and process this sensory information to guide the resultant behaviour through their mechanosensory lateral-line system. This sensory system consists of up to several thousand neuromasts distributed across the entire body of the animal. Using the lateral-line system, fishes perceive water movements of both biotic and abiotic origin. The anatomy of the lateral-line system varies greatly between and within species. It is still a matter of debate as to how different lateral-line anatomies reflect adaptations to the hydrodynamic conditions to which fishes are exposed. While there are many accounts of lateral-line system adaptations for the detection of hydrodynamic signals in distinct behavioural contexts and environments for specific fish species, there is only limited knowledge on how the environment influences intra and interspecific variations in lateral-line morphology. Fishes live in a wide range of habitats with highly diverse hydrodynamic conditions, from pools and lakes and slowly moving deep-sea currents to turbulent and fast running rivers and rough coastal surf regions. Perhaps surprisingly, detailed characterisations of the hydrodynamic properties of natural water bodies are rare. In particular, little is known about the spatio-temporal patterns of the small-scale water motions that are most relevant for many fish behaviours, making it difficult to relate environmental stimuli to sensory system morphology and function. Humans use bodies of water extensively for recreational, industrial and domestic purposes and in doing so often alter the aquatic environment, such as through the release of toxicants, the blocking of rivers by dams and acoustic noise emerging from boats and construction sites. Although the effects of anthropogenic interferences are often not well understood or quantified, it seems obvious that they change not only water quality and appearance but also, they alter hydrodynamic conditions and thus the types of hydrodynamic stimuli acting on fishes. To date, little is known about how anthropogenic influences on the aquatic environment affect the morphology and function of sensory systems in general and the lateral-line system in particular. This review starts out by briefly describing naturally occurring hydrodynamic stimuli and the morphology and neurobiology of the fish lateral-line system. In the main part, adaptations of the fish lateral-line system for the detection and analysis of water movements during various behaviours are presented. Finally, anthropogenic influences on the aquatic environment and potential effects on the fish lateral-line system are discussed.

Behavioural changes controlled by catecholaminergic systems explain recurrent loss of pigmentation in cavefish

Multiple cave populations of the teleost Astyanax mexicanus have repeatedly reduced or lost eye and body pigmentation during adaptation to dark caves. Albinism, the complete absence of melanin pigmentation, is controlled by loss-of-function mutations in the oca2 gene. The mutation is accompanied by an increase in the melanin synthesis precursor l-tyrosine, which is also a precursor for catecholamine synthesis. In this study, we show a relationship between pigmentation loss, enhanced catecholamine synthesis and responsiveness to anaesthesia, determined as a proxy for catecholamine-related behaviours. We demonstrate that anaesthesia resistance (AR) is enhanced in multiple depigmented and albino cavefish (CF), inversely proportional to the degree of pigmentation loss, controlled by the oca2 gene, and can be modulated by experimental manipulations of l-tyrosine or the catecholamine norepinephrine (NE). Moreover, NE is increased in the brains of multiple albino and depigmented CF relative to surface fish. The results provide new insights into the evolution of pigment modification because NE controls a suite of adaptive behaviours similar to AR that may represent a target of natural selection. Thus, understanding the relationship between loss of pigmentation and AR may provide insight into the role of natural selection in the evolution of albinism via a melanin-catecholamine trade-off.

Neural Crest Transplantation Reveals Key Roles in the Evolution of Cavefish Development

Evolutionary changes in Astyanax mexicanus cavefish with respect to conspecific surface fish, including the regression of eyes, loss of pigmentation, and modification of the cranial skeleton, involve derivatives of the neural crest. However, the role of neural crest cells in cavefish evolution and development is poorly understood. One of the reasons is that experimental methods for neural crest analysis are not well developed in the Astyanax system. Here we describe neural crest transplantation between Astyanax surface fish and cavefish embryos. We found differences in the migration of cranial neural crest cells transplanted from the surface fish anterior hindbrain to the same region of surface fish or cavefish hosts. Cranial neural crest cells migrated extensively throughout the head, and to a lesser extent the trunk, in surface fish hosts but their migration was mostly restricted to the anterior and dorsal head regions in cavefish hosts. Cranial neural crest cells derived from the surface fish transplants invaded the degenerating eyes of cavefish hosts, resulting in increased eye size and suggesting that cavefish neural crest cells are defective in forming optic derivatives. We found that melanophores were formed in albino cavefish from grafts of surface fish trunk neural crest cells, showing that the cavefish tissue environment is conducive for pigment cell development, and implicating intrinsic changes in cavefish neural crest cells in loss of body pigmentation. It is concluded that changes in neural crest cells play key roles in the evolution of cavefish development.

Sweet fish: Fish models for the study of hyperglycemia and diabetes

Fish are good for your health in more ways than you may expect. For one, eating fish is a common dietary recommendation for a healthy diet. However, fish have much more to provide than omega-3 fatty acids to your circulatory system. Some fish species now serve as important and innovative model systems for diabetes research, providing novel and unique advantages compared with classical research models. Not surprisingly, the largest share of diabetes research in fish occurs in the laboratory workhorse among fish, the zebrafish (Danio rerio). Established as a genetic model system to study development, these small cyprinid fish have eventually conquered almost every scientific discipline and, over the past decade, have emerged as an important model system for metabolic diseases, including diabetes mellitus. In this review we highlight the practicability of using zebrafish to study diabetes and hyperglycemia, and summarize some of the recent research and breakthroughs made using this model. Equally exciting is the appearance of another emerging discipline, one that is taking advantage of evolution by studying cases of naturally occurring insulin resistance in fish species. We briefly discuss two such models in this review, namely the rainbow trout (Oncorhynchus mykiss) and the cavefish (Astyanax mexicanus).

Extreme Adaptation in Caves

Cave adaptation leads to unique anatomical specializations in many taxonomic groups. As the role of vision is reduced or disappears in a subterranean environment, other specializations arise to allow the organism to successfully detect and interact with their environment. A suite of unique, convergent phenotypes associated with subterranean adaptation has emerged (termed troglomorphy), with reduction or loss of pigmentation and eyes being the most conspicuous. Two vertebrate groups that have successfully colonized and adapted to subterranean environments are cavefishes and cave salamanders. There are many shared troglomorphic anatomical characters shared between these two groups, and we describe herein the morphological traits that are unique to fishes and salamanders that are adapted to caves and other subterranean habitats. Troglobionts, animals strictly bound and adapted to underground habitats, are outcomes of not just regressive evolution, but also constructive adaptation. There are skeletal changes, such as broadening and flattening of the head, as well as hypertrophy of non-visual modalities. Cavefishes and salamanders have lost eyes and pigmentation, but also enhanced mechanosenzation, chemosenzation and, in some cases, electroreception. Both cavefishes and cave salamanders have become important models in the study of the ecology, behavior, and evolution of subterranean colonization and adaptation. However, our knowledge is primarily limited to a few taxa and many questions remain to be studied. Anat Rec, 2018. © 2018 American Association for Anatomy.

Craniofacial skeleton of MEXICAN tetra (Astyanax mexicanus): As a bone disease model

A small fresh water fish, the Mexican tetra (Astyanax mexicanus) is a novel animal model in evolutionary developmental biology. The existence of morphologically distinct surface and cave morphs of this species allows simultaneous comparative analysis of phenotypic changes at different life stages. The cavefish harbors many favorable constructive traits (i.e., large jaws with an increased number of teeth, neuromast cells, enlarged olfactory pits and excess storage of adipose tissues) and regressive traits (i.e., reduced eye structures and pigmentation) which are essential for cave adaptation. A wide spectrum of natural craniofacial morphologies can be observed among the different cave populations. Recently, the Mexican tetra has been identified as a human disease model. The fully sequenced genome along with modern genome editing tools has allowed researchers to generate transgenic and targeted gene knockouts with phenotypes that resemble human pathological conditions. This review will discuss the anatomy of the craniofacial skeleton of A. mexicanus with a focus on morphologically variable facial bones, jaws that house continuously replacing teeth and pharyngeal skeleton. Furthermore, the possible applications of this model animal in identifying human congenital and metabolic skeletal disorders is addressed. Developmental Dynamics 248:153-161, 2019. © 2018 Wiley Periodicals, Inc.

Genetic analysis reveals candidate genes for activity QTL in the blind Mexican tetra, Astyanax mexicanus

Animal models provide useful tools for exploring the genetic basis of morphological, physiological and behavioral phenotypes. Cave-adapted species are particularly powerful models for a broad array of phenotypic changes with evolutionary, developmental and clinical relevance. Here, we explored the genetic underpinnings of previously characterized differences in locomotor activity patterns between the surface-dwelling and Pachón cave-dwelling populations of Astyanax mexicanus. We identified multiple novel QTL underlying patterns in overall levels of activity (velocity), as well as spatial tank use (time spent near the top or bottom of the tank). Further, we demonstrated that different regions of the genome mediate distinct patterns in velocity and tank usage. We interrogated eight genomic intervals underlying these activity QTL distributed across six linkage groups. In addition, we employed transcriptomic data and draft genomic resources to generate and evaluate a list of 36 potential candidate genes. Interestingly, our data support the candidacy of a number of genes, but do not suggest that differences in the patterns of behavior observed here are the result of alterations to certain candidate genes described in other species (e.g., teleost multiple tissue opsins, melanopsins or members of the core circadian clockwork). This study expands our knowledge of the genetic architecture underlying activity differences in surface and cavefish. Future studies will help define the role of specific genes in shaping complex behavioral phenotypes in Astyanax and other vertebrate taxa.

Characterization and comparison of activity profiles exhibited by the cave and surface morphotypes of the blind Mexican tetra, Astyanax mexicanus

Departure from normal circadian rhythmicity and exposure to atypical lighting cues has been shown to adversely affect human health and wellness in a variety of ways. In contrast, adaptation to extreme environments has led many species to alter or even entirely abandon their reliance upon cyclic environmental inputs, principally daily cycles of light and darkness. The extreme darkness, stability and isolation of cave ecosystems has made cave-adapted species particularly attractive systems in which to study the consequences of life without light and the strategies that allow species to survive and even thrive in such environments. In order to further explore these questions, we have assessed the rhythmicity of locomotion in the blind Mexican tetra, Astyanax mexicanus, under controlled laboratory conditions. Using high-resolution video tracking assays, we characterized patterns in locomotor activity and spatial tank usage for members of the surface and Pachón cave populations. Here we demonstrate that cavefish have a higher overall level of activity and use the space within the trial tank differently than surface fish. Further, Pachón cavefish show circadian rhythmicity in both activity and spatial tank usage under a 12:12 light/dark cycle. We provide further evidence that these cavefish retain a weakly light-entrainable, endogenous circadian oscillator with limited capability to sustain rhythms in activity, but not spatial tank usage, in the absence of photic cues. Finally, we demonstrate a putative behavioral "masking effect" contributing to behavioral rhythms and provide evidence that exposure to constant darkness during development may alter behavioral patterns later in life.

An epigenetic mechanism for cavefish eye degeneration

Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss-of-eyes phenotype in the Pachón blind cave morph of the Mexican tetra Astyanax mexicanus, no inactivating mutations have been found in any of these genes. Here, we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave A. mexicanus. By performing parallel analyses in A. mexicanus cave and surface morphs, and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and downregulated genes in the cave morph are also linked to human eye disorders, suggesting that the function of these genes is conserved across vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.

Investigating gene flow between the blind cavefish Garra barreimiae and its conspecific surface populations

Cave-dwelling taxa often share the same phenotypic modifications like absence of eyes and pigmentation. These “troglomorphic characters” are expressed in the populations of Garra barreimiae from the Al Hoota Cave and nearby Hoti Pit in Northern Oman. Surface morphotypes of this cyprinid species are common throughout the distribution area. Very rarely individuals with intermediate phenotypes can be found. In the present study, potential gene flow between cave and surface populations was tested and population structure within five sampling sites was assessed. Overall, 213 individuals were genotyped at 18 microsatellite loci. We found that the cave populations have lower genetic diversity and are clearly isolated from the surface populations, which seem to be sporadically in contact with each other. The results indicate a recent genetic bottleneck in the cave populations. Thus, it can be assumed that during climatic changes the connection between cave and surface water bodies was disjoined, leaving a subpopulation trapped inside. Nevertheless, occasional gene flow between the morphotypes is detectable, but hybridisation seems only possible in cave habitat with permanent connection to surface water. Individuals from surface sites bearing intermediate phenotypes but cave genotypes imply that phenotypic plasticity might play a role in the development of the phenotype.