Evidence for late Pleistocene origin of Astyanax mexicanus cavefish.

BACKGROUND: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. RESULTS: We reanalyzed the geographic distribution of mitochondrial and nuclear DNA polymorphisms and we found that these data do not support the existence of two cavefish lineages. Using IMa2, a program that allows dating population divergence in addition to demographic parameters, we found that microsatellite polymorphism strongly supports a very recent origin of cave populations (< 20,000 years). We identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of pools of embryos (Pool-seq) belonging to Pachón cave population and a surface population from Texas. Based on summary statistics that can be computed with this SNP data set together with simulations of evolution of SNP polymorphisms in two recently isolated populations, we looked for sets of demographic parameters that allow the computation of summary statistics with simulated populations that are similar to the ones with the sampled populations. In most simulations for which we could find a good fit between the summary statistics of observed and simulated data, the best fit occurred when the divergence between simulated populations was less than 30,000 years. CONCLUSIONS: Although it is often assumed that some cave populations have a very ancient origin, a recent origin of these populations is strongly supported by our analyses of independent sets of nuclear DNA polymorphism. Moreover, the observation of two divergent haplogroups of mitochondrial and nuclear genes with different geographic distributions support a recent admixture of two divergent surface populations, before the isolation of cave populations. If cave populations are indeed only several thousand years old, many phenotypic changes observed in cavefish would thus have mainly involved the fixation of genetic variants present in surface fish populations and within a very short period of time.

Revisiting the developmental and cellular role of the pigmentation gene yellow in Drosophila using a tagged allele.

Pigmentation is a diverse and ecologically relevant trait in insects. Pigment formation has been studied extensively at the genetic and biochemical levels. The temporality of pigment formation during animal development, however, is more elusive. Here, we examine this temporality, focusing on yellow, a gene involved in the formation of black melanin. We generated a protein-tagged yellow allele in the fruit fly Drosophila melanogaster, which allowed us to precisely describe Yellow expression pattern at the tissue and cellular levels throughout development. We found Yellow expressed in the pupal epidermis in patterns prefiguring black pigmentation. We also found Yellow expressed in a few central neurons from the second larval instar to adult stages, including a subset of neurons adjacent to the clock neurons marked by the gene Pdf. We then specifically examined the dynamics of Yellow expression domain and subcellular localization in relationship to pigment formation. In particular, we showed how a late step of re-internalization is regulated by the large low-density lipoprotein receptor-related protein Megalin. Finally we suggest a new function for Yellow in the establishment of sharp pigmentation pattern boundaries, whereby this protein may assume a structural role, anchoring pigment deposits or pigmentation enzymes in the cuticle.

Lens apoptosis in the Astyanax blind cavefish is not triggered by its small size or defects in morphogenesis.

Blindness is a convergent trait in many cave animals of various phyla. Astyanax mexicanus cavefish is one of the best studied cave animals; however the mechanisms underlying eye degeneration in this species are not yet completely understood. The lens seems to play a central role, but only relatively late differentiation defects have been implicated in the cavefish lens apoptosis phenotype so far. Here, we used genetic crosses between Astyanax cavefish and surface fish to confirm that during development, lens size is independent of retina size. We then investigated whether the small size of the cavefish lens could directly cause cell death. Laser ablation experiments of lens placode cells in surface fish embryos showed that a small lens size is not sufficient to trigger lens apoptosis. We further examined potential lens morphogenesis defects through classical histology and live-imaging microscopy. From lens placode to lens ball, we found that lens invagination and formation of the lens epithelium and fiber cells occur normally in cavefish. We conclude that the main and deleterious defect in the Astyanax cavefish lens must concern the molecular control of lens cell function.

Sensory evolution in blind cavefish is driven by early embryonic events during gastrulation and neurulation.

Natural variations in sensory systems constitute adaptive responses to the environment. Here, we compared sensory placode development in the blind cave-adapted morph and the eyed river-dwelling morph of Astyanax mexicanus Focusing on the lens and olfactory placodes, we found a trade-off between these two sensory components in the two morphs: from neural plate stage onwards, cavefish have larger olfactory placodes and smaller lens placodes. In a search for developmental mechanisms underlying cavefish sensory evolution, we analyzed the roles of Shh, Fgf8 and Bmp4 signaling, which are known to be fundamental in patterning the vertebrate head and are subtly modulated in space and time during cavefish embryogenesis. Modulating these signaling systems at the end of gastrulation shifted the balance toward a larger olfactory derivative. Olfactory tests to assess potential behavioral outcomes of such developmental evolution revealed that Astyanax cavefish are able to respond to a 105-fold lower concentration of amino acids than their surface-dwelling counterparts. We suggest that similar evolutionary developmental mechanisms may be used throughout vertebrates to drive adaptive sensory specializations according to lifestyle and habitat.

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.

The cavefish genome reveals candidate genes for eye loss.

Natural populations subjected to strong environmental selection pressures offer a window into the genetic underpinnings of evolutionary change. Cavefish populations, Astyanax mexicanus (Teleostei: Characiphysi), exhibit repeated, independent evolution for a variety of traits including eye degeneration, pigment loss, increased size and number of taste buds and mechanosensory organs, and shifts in many behavioural traits. Surface and cave forms are interfertile making this system amenable to genetic interrogation; however, lack of a reference genome has hampered efforts to identify genes responsible for changes in cave forms of A. mexicanus. Here we present the first de novo genome assembly for Astyanax mexicanus cavefish, contrast repeat elements to other teleost genomes, identify candidate genes underlying quantitative trait loci (QTL), and assay these candidate genes for potential functional and expression differences. We expect the cavefish genome to advance understanding of the evolutionary process, as well as, analogous human disease including retinal dysfunction.

A mutation in the enzyme monoamine oxidase explains part of the Astyanax cavefish behavioural syndrome.

We use Astyanax mexicanus, a single species with surface-dwelling forms (SF) and blind de-pigmented cave forms (CF), to study mechanisms underlying the evolution of brain and behaviour. In CF, the origin of changes in complex motivated behaviours (social, feeding, sleeping, exploratory) is unknown. Here we find a hyper-aminergic phenotype in CF brains, including high levels and neurotransmission indexes for serotonin, dopamine and noradrenaline, and low monoamine oxidase (MAO) activity. Although MAO expression is unchanged in CF, a pro106leu mutation is identified in the MAO coding sequence. This mutation is responsible for low MAO activity and high serotonin neurotransmission index in CF brains. We find the same mutated allele in several natural CF populations, some being independently evolved. Such occurrence of the same allele in several caves may suggest that low MAO activity is advantageous for cave life. These results provide a genetic basis for several aspects of the cavefish 'behavioural syndrome'.

Differences in chemosensory response between eyed and eyeless Astyanax mexicanus of the Rio Subterráneo cave.

BACKGROUND: In blind cave-dwelling populations of Astyanax mexicanus, several morphological and behavioral shifts occurred during evolution in caves characterized by total and permanent darkness. Previous studies have shown that sensory systems such as the lateral line (mechanosensory) and taste buds (chemosensory) are modified in cavefish. It has long been hypothesized that another chemosensory modality, the olfactory system, might have evolved as well to provide an additional mechanism for food-searching in troglomorphic Astyanax populations. FINDINGS: During a March 2013 cave expedition to the Sierra de El Abra region of San Luís Potosi, Mexico, we tested chemosensory capabilities of the Astyanax mexicanus of the Rio Subterráneo cave. This cave hosts a hybrid population presenting a wide range of troglomorphic and epigean mixed phenotypes. During a behavioral test performed in situ in the cave, a striking correlation was observed between the absence of eyes and an increased attraction to food extract. In addition, eyeless troglomorphic fish possessed significantly larger naris size than their eyed, nontroglomorphic counterparts. CONCLUSIONS: Our findings suggest that chemosensory capabilities might have evolved in cave-dwelling Astyanax mexicanus and that modulation of naris size might at least partially underlie this likely adaptive change.

De novo sequencing of Astyanax mexicanus surface fish and Pachón cavefish transcriptomes reveals enrichment of mutations in cavefish putative eye genes.

Astyanax mexicanus, a teleost species with surface dwelling (surface fish) and cave adapted (cavefish) morphs, is an important model system in evolutionary developmental biology (evodevo). Astyanax cavefish differ from surface fish in numerous traits, including the enhancement of non-visual sensory systems, and the loss of eyes and pigmentation. The genetic bases for these differences are not fully understood as genomic and transcriptomic data are lacking. We here present de novo transcriptome sequencing of embryonic and larval stages of a surface fish population and a cavefish population originating from the Pachón cave using the Sanger method. This effort represents the first large scale sequence and clone resource for the Astyanax research community. The analysis of these sequences show low levels of polymorphism in cavefish compared to surface fish, confirming previous studies on a small number of genes. A high proportion of the genes mutated in cavefish are known to be expressed in the zebrafish visual system. Such a high number of mutations in cavefish putative eye genes may be explained by relaxed selection for vision during the evolution in the absence of light. Based on these sequence differences, we provide a list of 11 genes that are potential candidates for having a role in cavefish visual system degeneration.

Evolutionary shift from fighting to foraging in blind cavefish through changes in the serotonin network.

BACKGROUND: Within the species Astyanax mexicanus, there are several interfertile populations of river-dwelling sighted fish and cave-dwelling blind fish which have evolved morphological and behavioral adaptations, the origins of which are unknown. Here, we have investigated the neural, genetic, and developmental bases for the evolution of aggressive behavior in this teleost. RESULTS: We used an intruder-resident behavioral assay to compare aggressiveness quantitatively (attack counts) and qualitatively (pattern and nature of attacks) between the surface and cave populations of Astyanax. Using this paradigm, we characterize aggressive behavior in surface fish, bring support for the genetic component of this trait, and show that it is controlled by raphe serotonergic neurons and that it corresponds to the establishment of dominance between fish. Cavefish have completely lost such aggressive/dominance behavior. The few attacks performed by cavefish during the behavioral test instead correspond to food-seeking behavior, driven by the developmental evolution of their hypothalamic serotonergic paraventricular neurons, itself due to increased Sonic Hedgehog signaling during early forebrain embryogenesis. CONCLUSIONS: We propose that during evolution and adaptation to their cave habitat, cavefish have undergone a behavioral shift, due to modifications of their serotonergic neuronal network. They have lost the typical aggressive behavior of surface fish and evolved a food-seeking behavior that is probably more advantageous to surviving in the dark. We have therefore demonstrated a link between the development of a neuronal network and the likely adaptive behaviors it controls.

A developmental staging table for Astyanax mexicanus surface fish and Pachón cavefish.

Every model species requires its own developmental table. Astyanax mexicanus, a teleost fish comprising both sighted river and blind cave populations, is becoming more and more important in the field of developmental and evolutionary biology. As such, a developmental staging table is increasingly necessary, particularly since comparative analysis of early developmental events is widely employed by researchers. We collected freshly spawned embryos from surface fish and Pachón cavefish populations. Embryos were imaged every 10-12 min during the first day of development, and less frequently in the following days. The results provide an illustrated comparison of selected developmental stages from one cell to hatching of these two populations. The two morphs show an essentially synchronous development regarding major events such as epiboly, neurulation, somitogenesis, heart beating, or hatching. We also present data on particular morphological characters appearing during larval development, such as eye size, yolk regression, swim bladder, and fin development. Some details about the development of F1 Pachón cave×surface hybrids are also given. Comparisons are made with Danio rerio (zebrafish) development.

Restoring eye size in Astyanax mexicanus blind cavefish embryos through modulation of the Shh and Fgf8 forebrain organising centres.

The cavefish morph of the Mexican tetra (Astyanax mexicanus) is blind at adult stage, although an eye that includes a retina and a lens develops during embryogenesis. There are, however, two major defects in cavefish eye development. One is lens apoptosis, a phenomenon that is indirectly linked to the expansion of ventral midline sonic hedgehog (Shh) expression during gastrulation and that induces eye degeneration. The other is the lack of the ventral quadrant of the retina. Here, we show that such ventralisation is not extended to the entire forebrain because fibroblast growth factor 8 (Fgf8), which is expressed in the forebrain rostral signalling centre, is activated 2 hours earlier in cavefish embryos than in their surface fish counterparts, in response to stronger Shh signalling in cavefish. We also show that neural plate patterning and morphogenesis are modified in cavefish, as assessed by Lhx2 and Lhx9 expression. Inhibition of Fgf receptor signalling in cavefish with SU5402 during gastrulation/early neurulation mimics the typical surface fish phenotype for both Shh and Lhx2/9 gene expression. Fate-mapping experiments show that posterior medial cells of the anterior neural plate, which lack Lhx2 expression in cavefish, contribute to the ventral quadrant of the retina in surface fish, whereas they contribute to the hypothalamus in cavefish. Furthermore, when Lhx2 expression is rescued in cavefish after SU5402 treatment, the ventral quadrant of the retina is also rescued. We propose that increased Shh signalling in cavefish causes earlier Fgf8 expression, a crucial heterochrony that is responsible for Lhx2 expression and retina morphogenesis defect.

A subset of the histone H3 lysine 9 methyltransferases Suv39h1, G9a, GLP, and SETDB1 participate in a multimeric complex.

Lysine 9 of histone 3 (H3K9) can be mono-, di-, or trimethylated, inducing distinct effects on gene expression and chromatin compaction. H3K9 methylation can be mediated by several histone methyltransferases (HKMTs) that possess mono-, di-, or trimethylation activities. Here we provide evidence that a subset of each of the main H3K9 HKMTs, G9a/KMT1C, GLP/KMT1D, SETDB1/KMT1E, and Suv39h1/KMT1A, coexist in the same megacomplex. Moreover, in Suv39h or G9a null cells, the remaining HKMTs are destabilized at the protein level, indicating that the integrity of these HKMTs is interdependent. The four HKMTs are recruited to major satellite repeats, a known Suv39h1 genomic target, but also to multiple G9a target genes. Moreover, we report a functional cooperation between the four H3K9 HKMTs in the regulation of known G9a target genes. Altogether, our data identify a H3K9 methylation multimeric complex.