Evolutionary Genetics of the Cavefish Astyanax mexicanus

Lung adenocarcinomas without driver genes converge to common adaptive strategies through diverse genetic, epigenetic, and niche construction evolutionary pathways

Somatic evolution selects cancer cell phenotypes that maximize survival and proliferation in dynamic environments. Although cancer cells are molecularly heterogeneous, we hypothesized convergent adaptive strategies to common host selection forces can be inferred from patterns of epigenetic and genetic evolutionary selection in similar tumors. We systematically investigated gene mutations and expression changes in lung adenocarcinomas with no common driver genes (n = 313). Although 13,461 genes were mutated in at least one sample, only 376 non-synonymous mutations evidenced positive evolutionary selection with conservation of 224 genes, while 1736 and 2430 genes exhibited ≥ two-fold increased and ≥ 50% decreased expression, respectively. Mutations under positive selection are more frequent in genes with significantly altered expression suggesting they often "hardwire" pre-existing epigenetically driven adaptations. Conserved genes averaged 16-fold higher expression in normal lung tissue compared to those with selected mutations demonstrating pathways necessary for both normal cell function and optimal cancer cell fitness. The convergent LUAD phenotype exhibits loss of differentiated functions and cell-cell interactions governing tissue organization. Conservation with increased expression is found in genes associated with cell cycle, DNA repair, p53 pathway, epigenetic modifiers, and glucose metabolism. No canonical driver gene pathways exhibit strong positive selection, but extensive down-regulation of membrane ion channels suggests decreased transmembrane potential may generate persistent proliferative signals. NCD LUADs perform niche construction generating a stiff, immunosuppressive microenvironment through selection of specific collagens and proteases. NCD LUADs evolve to a convergent phenotype through a network of interconnected genetic, epigenetic, and ecological pathways.

The nature and distribution of putative non-functional alleles suggest only two independent events at the origins of Astyanax mexicanus cavefish populations

BACKGROUND

Several studies suggested that cavefish populations of Astyanax mexicanus settled during the Late Pleistocene. This implies that the cavefish's most conspicuous phenotypic changes, blindness and depigmentation, and more cryptic characters important for cave life, evolved rapidly.

RESULTS

Using the published genomes of 47 Astyanax cavefish from la Cueva de El Pachón, El Sótano de la Tinaja, La Cueva Chica and El Sótano de Molino, we searched for putative loss-of-function mutations in previously defined sets of genes, i.e., vision, circadian clock and pigmentation genes. Putative non-functional alleles for four vision genes were identified. Then, we searched genome-wide for putative non-functional alleles in these four cave populations. Among 512 genes with segregating putative non-functional alleles in cavefish that are absent in surface fish, we found an enrichment in visual perception genes. Among cavefish populations, different levels of shared putative non-functional alleles were found. Using a subset of 12 genes for which putative loss-of-function mutations were found, we extend the analysis of shared pseudogenes to 11 cave populations. Using a subset of six genes for which putative loss-of-function mutations were found in the El Sótano del Toro population, where extensive hybridization with surface fish occurs, we found a correlation between the level of eye regression and the amount of putative non-functional alleles.

CONCLUSIONS

We confirm that very few putative non-functional alleles are present in a large set of vision genes, in accordance with the recent origin of Astyanax mexicanus cavefish. Furthermore, the genome-wide analysis indicates an enrichment of putative loss-of-function alleles in genes with vision-related GO-terms, suggesting that visual perception may be the function chiefly impacted by gene losses related to the shift from a surface to a cave environment. The geographic distribution of putative loss-of-function alleles newly suggests that cave populations from Sierra de Guatemala and Sierra de El Abra share a common origin, albeit followed by independent evolution for a long period. It also supports that populations from the Micos area have an independent origin. In El Sótano del Toro, the troglomorphic phenotype is maintained despite massive introgression of the surface genome.

Multiple transitions between realms shape relict lineages of Proteus cave salamanders

In comparison to biodiversity on Earth's surface, subterranean biodiversity has largely remained concealed. The olm (Proteus anguinus) is one of the most enigmatic extant cave inhabitants, and until now little was known regarding its genetic structure and evolutionary history. Olms inhabit subterranean waters throughout the Dinaric Karst of the western Balkans, with a seemingly uniform phenotypic appearance of cave-specialized traits: an elongate body, snout and limbs, degenerated eyes and loss of pigmentation ("white olm"). Only a single small region in southeastern Slovenia harbours olms with a phenotype typical of surface animals: pigmented skin, eyes, a blunt snout and short limbs ("black olm"). We used a combination of mitochondrial DNA and genome-wide single nucleotide polymorphism data to investigate the molecular diversity, evolutionary history and biogeography of olms along the Dinaric Karst. We found nine deeply divergent species-level lineages that separated between 17 and 4 million years ago, while molecular diversity within lineages was low. We detected no signal of recent admixture between lineages and only limited historical gene flow. Biogeographically, the contemporaneous distribution of lineages mostly mirrors hydrologically separated subterranean environments, while the historical separation of olm lineages follows microtectonic and climatic changes in the area. The reconstructed phylogeny suggests at least four independent transitions to the cave phenotype. Two of the species-level lineages have miniscule ranges and may represent Europe's rarest amphibians. Their rarity and the decline in other lineages call for protection of their subterranean habitats.

Full-length transcriptome reveals the circularly polarized light response-related molecular genetic characteristics of Oratosquilla oratoria

The mantis shrimp is the only animal that can recognize circularly polarized light (CPL), but its molecular genetic characteristics are unclear. Multi-tissue level full-length (FL) transcriptome sequencing of Oratosquilla oratoria, a representative widely distributed mantis shrimp, was performed in the present study. We used comparative transcriptomics to explore the critical genes of O. oratoria selected by CPL and the GNβ gene associated with CPL signal transduction was hypothesized to be positively selected. Furthermore, the FL transcriptomes of O. oratoria compound eyes under five light conditions were sequenced and used to detect alternative splicing (AS). The ASs associated with CPL recognition mainly occurred in the LWS, ARR and TRPC regions. The number of FL transcripts with AS events and annotation information also provided evidence that O. oratoria could recognize LCPL. Additionally, 51 sequences belonging to the LWS, UV and Peropsin gene families were identified based on conserved 7tm domains. The LWS, UV and Peropsin opsins have similar 3D structures with seven domains across the cell membrane and conserved KSLRTPSN, DRY, and QAKK motifs. In conclusion, these results are undoubtedly valuable for perfecting the vision theory of O. oratoria and other mantis shrimp.

From darkness to discovery: evolutionary, adaptive, and translational genetic insights from cavefish

How genotype determines phenotype is a well-explored question, but genotype-environment interactions and their heritable impact on phenotype over the course of evolution are not as thoroughly investigated. The fish Astyanax mexicanus, consisting of surface and cave ecotypes, is an ideal emerging model to study the genetic basis of adaptation to new environments. This model has permitted quantitative trait locus mapping and whole-genome comparisons to identify the genetic bases of traits such as albinism and insulin resistance and has helped to better understand fundamental evolutionary mechanisms. In this review, we summarize recent advances in A. mexicanus genetics and discuss their broader impact on the fields of adaptation and evolutionary genetics.

CaveCrawler: an interactive analysis suite for cavefish bioinformatics

The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.

From Cave Dragons to Genomics: Advancements in the Study of Subterranean Tetrapods

Throughout most of the kingdom Animalia, evolutionary transitions from surface life to a life permanently bound to caves and other subterranean habitats have occurred innumerous times. Not so in tetrapods, where a mere 14 cave-obligate species-all plethodontid and proteid salamanders-are known. We discuss why cave tetrapods are so exceptional and why only salamanders have made the transition. Their evolution follows predictable and convergent, albeit independent pathways. Among the many known changes associated with transitions to subterranean life, eye degeneration, starvation resistance, and longevity are especially relevant to human biomedical research. Recently, sequences of salamander genomes have become available opening up genomic research for cave tetrapods. We discuss new genomic methods that can spur our understanding of the evolutionary mechanisms behind convergent phenotypic change, the relative roles of selective and neutral evolution, cryptic species diversity, and data relevant for conservation such as effective population size and demography.

Evolution in Sinocyclocheilus cavefish is marked by rate shifts, reversals, and origin of novel traits

Background

Natural model systems are indispensable for exploring adaptations in response to environmental pressures. Sinocyclocheilus of China, the most diverse cavefish clade in the world (75 species), provide unique opportunities to understand recurrent evolution of stereotypic traits (such as eye loss and sensory expansion) in the context of a deep and diverse phylogenetic group. However, they remain poorly understood in terms of their morphological evolution. Therefore, we explore key patterns of morphological evolution, habitat utilization and geographic distribution in these fishes.

Results

We constructed phylogenies and categorized 49 species based on eye-related condition (Blind, Micro-eyed, and Normal-eyed), habitat types (Troglobitic—cave-restricted; Troglophilic—cave-associated; Surface—outside caves) and existence of horns. Geometric-morphometric analyses show Normal-eyed morphs with fusiform shapes segregating from Blind/Micro-eyed deeper bodied morphs along the first principal-component axis; second axis accounts for shape complexity related to horns. The body shapes showed a significant association with eye-related condition and horn, but not habitat types. Ancestral reconstructions suggest at least three independent origins of Blind morphs, each with different levels of modification in relation to their ancestral Normal-eyed morphs; Sinocyclocheilus are also pre-adapted for cave dwelling. Our geophylogeny shows an east-to-west diversification spanning Pliocene and Pleistocene, with early-diversifying Troglobitic species dominating subterranean habitats of karstic plains whereas predominantly Surface forms inhabit hills to the west. Evolutionary rates analyses suggest that lineages leading to Blind morphs were characterized by significant rate shifts, such as a slowdown in body size evolution and a 5–20 fold increase in rate of eye regression, possibly explained by limited resource availability. Body size and eye size have undergone reversals, but not horns, a trait entailing considerable time to form.

Conclusions

Sinocyclocheilus occupied cave habitats in response to drying associated with aridification of China during late Miocene and the Pliocene. The prominent cave-adaptations (eye-regression, horn-evolution) occur in clades associated with the extensive subterranean cave system in Guangxi and Guizhou provinces. Integration of morphology, phylogeny, rate analyses, molecular-dating and distribution show not only several remarkable patterns of evolution, but also interesting exceptions to these patterns signifying the diversification of Sinocyclocheilus as an invaluable model system to explore evolutionary novelty.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12862-021-01776-y.

A chromosome-level genome of Astyanax mexicanus surface fish for comparing population-specific genetic differences contributing to trait evolution

Identifying the genetic factors that underlie complex traits is central to understanding the mechanistic underpinnings of evolution. Cave-dwelling Astyanax mexicanus populations are well adapted to subterranean life and many populations appear to have evolved troglomorphic traits independently, while the surface-dwelling populations can be used as a proxy for the ancestral form. Here we present a high-resolution, chromosome-level surface fish genome, enabling the first genome-wide comparison between surface fish and cavefish populations. Using this resource, we performed quantitative trait locus (QTL) mapping analyses and found new candidate genes for eye loss such as dusp26. We used CRISPR gene editing in A. mexicanus to confirm the essential role of a gene within an eye size QTL, rx3, in eye formation. We also generated the first genome-wide evaluation of deletion variability across cavefish populations to gain insight into this potential source of cave adaptation. The surface fish genome reference now provides a more complete resource for comparative, functional and genetic studies of drastic trait differences within a species.

An Alternative Molecular View of Evolution: How DNA was Altered over Geological Time

Four natural phenomena are cited for their defiance of conventional neo-Darwinian analysis: human intelligence; cat domesticity; the Cambrian explosion; and convergent evolution. 1. Humans are now far more intelligent than needed in their hunting-gathering days >10,000 years ago. 2. Domestic cats evolved from wildcats via major genetic and physical changes, all occurring in less than 12,000 years. 3. The Cambrian explosion refers to the remarkable expansion of species that mystifies evolutionists, as there is a total lack of fossil evidence for precursors of this abundant new life. 4. Convergent evolution often involves formation of complex, multigene traits in two or more species that have no common ancestor. These four evolutionary riddles are discussed in terms of a proposed "preassembly" mechanism in which genes and gene precursors are collected silently and randomly over extensive time periods within huge non-coding sections of DNA. This is followed by epigenetic release of the genes, when the environment so allows, and by natural selection. In neo-Darwinism, macroevolution of complex traits involves multiple mutation/selections, with each of the resulting intermediates being more favorable to the species than the previous one. Preassembly, in contrast, invokes natural selection only after a partially or fully formed trait is already in place. Preassembly does not supplant neo-Darwinism but, instead, supplements neo-Darwinism in those important instances where the classical theory is wanting.

Diversity of Olfactory Responses and Skills in Astyanax Mexicanus Cavefish Populations Inhabiting different Caves

Animals in many phyla are adapted to and thrive in the constant darkness of subterranean environments. To do so, cave animals have presumably evolved mechano- and chemosensory compensations to the loss of vision, as is the case for the blind characiform cavefish, Astyanax mexicanus. Here, we systematically assessed the olfactory capacities of cavefish and surface fish of this species in the lab as well as in the wild, in five different caves in northeastern Mexico, using an olfactory setup specially developed to test and record olfactory responses during fieldwork. Overall cavefish showed lower (i.e., better) olfactory detection thresholds than surface fish. However, wild adult cavefish from the Pachón, Sabinos, Tinaja, Chica and Subterráneo caves showed highly variable responses to the three different odorant molecules they were exposed to. Pachón and Subterráneo cavefish showed the highest olfactory capacities, and Chica cavefish showed no response to the odors presented. We discuss these data with regard to the environmental conditions in which these different cavefish populations live. Our experiments in natural settings document the diversity of cave environments inhabited by a single species of cavefish, A. mexicanus, and highlight the complexity of the plastic and genetic mechanisms that underlie cave adaptation.

Astyanax surface and cave fish morphs

The small teleost fish Astyanax mexicanus has emerged as an outstanding model for studying many biological topics in the context of evolution. A major attribute is conspecific surface dwelling (surface fish) and blind cave dwelling (cavefish) morphs that can be raised in the laboratory and spawn large numbers of transparent and synchronously developing embryos. More than 30 cavefish populations have been discovered, mostly in northeastern Mexico, and some are thought to have evolved independently from surface fish ancestors, providing excellent models of parallel and convergent evolution. Cavefish have evolved eye and pigmentation regression, as well as modifications in brain morphology, behaviors, heart regenerative capacity, metabolic processes, and craniofacial organization. Thus, the Astyanax model provides researchers with natural "mutants" to study life in the challenging cave environment. The application of powerful genetic approaches based on hybridization between the two morphs and between the different cavefish populations are key advantages for deciphering the developmental and genetic mechanisms regulating trait evolution. QTL analysis has revealed the genetic architectures of gained and lost traits. In addition, some cavefish traits resemble human diseases, offering novel models for biomedical research. Astyanax research is supported by genome assemblies, transcriptomes, tissue and organ transplantation, gene manipulation and editing, and stable transgenesis, and benefits from a welcoming and interactive research community that conducts integrated community projects and sponsors the International Astyanax Meeting (AIM).

Comparative Transcriptome Profiling of the Loaches Triplophysa bleekeri and Triplophysa rosa Reveals Potential Mechanisms of Eye Degeneration

Eye degeneration is one of the most obvious characteristics of organisms restricted to subterranean habitats. In cavefish, eye degeneration has evolved independently numerous times and each process is associated with different genetic mechanisms. To gain a better understanding of these mechanisms, we compared the eyes of adult individuals of the cave loach Triplophysa rosa and surface loach Triplophysa bleekeri. Compared with the normal eyes of the surface loach, those of the cave loach were found to possess a small abnormal lens and a defective retina containing photoreceptor cells that lack outer segments. Sequencing of the transcriptomes of both species to identify differentially expressed genes (DEGs) and genes under positive selection revealed 4,802 DEGs and 50 genes under positive selection (dN/dS > 1, FDR < 0.1). For cave loaches, we identified one Gene Ontology category related to vision that was significantly enriched in downregulated genes. Specifically, we found that many of the downregulated genes, including pitx3, lim2, crx, gnat2, rx1, rho, prph2, and β|γ-crystallin are associated with lens/retinal development and maintenance. However, compared with those in the surface loach, the lower dS rates but higher dN rates of the protein-coding sequences in T. rosa indicate that changes in amino acid sequences might be involved in the adaptation and visual degeneration of cave loaches. We also found that genes associated with light perception and light-stimulated vision have evolved at higher rates (some genes dN/dS > 1 but FDR > 0.1). Collectively, the findings of this study indicate that the degradation of cavefish vision is probably associated with both gene expression and amino acid changes and provide new insights into the mechanisms underlying the degeneration of cavefish eyes.

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.

Maternally regulated gastrulation as a source of variation contributing to cavefish forebrain evolution

Sequential developmental events, starting from the moment of fertilization, are crucial for the acquisition of animal body plan. Subtle modifications in such early events are likely to have major impacts in later morphogenesis, bringing along morphological diversification. Here, comparing the blind cave and the surface morphotypes of Astyanax mexicanus fish, we found heterochronies during gastrulation that produce organizer and axial mesoderm tissues with different properties (including differences in the expression of dkk1b) that may have contributed to cavefish brain evolution. These variations observed during gastrulation depend fully on maternal factors. The developmental evolution of retinal morphogenesis and hypothalamic patterning are among those traits that retained significant maternal influence at larval stages. Transcriptomic analysis of fertilized eggs from both morphotypes and reciprocal F₁ hybrids showed a strong and specific maternal signature. Our work strongly suggests that maternal effect genes and developmental heterochronies that occur during gastrulation have impacted morphological brain change during cavefish evolution.

Towards an integrated approach to understand Mexican cavefish evolution

The Mexican tetra, Astyanax mexicanus, comes in two forms: a classical river-dwelling fish and a blind and depigmented cave-dwelling fish. The two morphotypes are used as models for evolutionary biology, to decipher mechanisms of morphological and behavioural evolution in response to environmental change. Over the past 40 years, insights have been obtained from genetics, developmental biology, physiology and metabolism, neuroscience, genomics, population biology and ecology. Here, we promote the idea that A. mexicanus, as a model, has reached a stage where an integrated approach or a multi-disciplinary method of analysis, whereby a phenomenon is examined from several angles, is a powerful tool that can be applied to understand general evolutionary processes. Mexican cavefish have undergone considerable selective pressure and extreme morphological evolution, an obvious advantage to contribute to our understanding of evolution through comparative analyses and to pinpoint the specific traits that may have helped their ancestors to colonize caves.

Microbial eukaryotes in the suboxic chemosynthetic ecosystem of Movile Cave, Romania

Movile Cave is a small system of partially inundated galleries in limestone settings close to the Black Sea in Southeast Romania. Isolated from the surface for 6 million years, its sulfidic, methane and ammonia-rich waters harbour unique chemosynthetic prokaryotic communities that include sulphur and ammonium-metabolizing chemolithotrophs, methanogens, methanotrophs and methylotrophs. The cave also harbours cave-dwelling invertebrates and fungi, but the diversity of other microbial eukaryotes remained completely unknown. Here, we apply an 18S rRNA gene-based metabarcoding approach to study the composition of protist communities in floating microbial mats and plankton from a well-preserved oxygen-depleted cave chamber. Our results reveal a wide protist diversity with, as dominant groups, ciliates (Alveolata), Stramenopiles, especially bicosoecids, and jakobids (Excavata). Ciliate sequences dominated both, microbial mats and plankton, followed by either Stramenopiles or excavates. Stramenopiles were more prominent in microbial mats, whereas jakobids dominated the plankton fraction of the oxygen-depleted water column. Mats cultured in the laboratory were enriched in Cercozoa. Consistent with local low oxygen levels, Movile Cave protists are most likely anaerobic or microaerophilic. Several newly detected OTU clades were very divergent from cultured species or environmental sequences in databases and represent phylogenetic novelty, notably within jakobids. Movile Cave protists likely cover a variety of ecological roles in this ecosystem including predation, parasitism, saprotrophy and possibly diverse prokaryote-protist syntrophies.

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.

Neuroendocrinology of reproduction: Is gonadotropin-releasing hormone (GnRH) dispensable?

Gonadotropin releasing hormone (GnRH) is a highly conserved neuroendocrine decapeptide that is essential for the onset of puberty and the maintenance of the reproductive state. First identified in mammals, the GnRH signaling pathway is found in all classes of vertebrates; homologues of GnRH have also been identified in invertebrates. In addition to its role as a hypothalamic releasing hormone, GnRH has multiple functions including modulating neural activity within specific regions of the brain. These various functions are mediated by multiple isoforms, which are expressed at diverse locations within the central nervous system. Here we discuss the GnRH signaling pathways in light of new reports that reveal that some vertebrate genomes lack GnRH1. Not only do other isoforms of GnRH not compensate for this gene loss, but elements upstream of GnRH1, including kisspeptins, appear to also be dispensable. We discuss routes that may compensate for the loss of the GnRH1 pathway.

Breeding behavior in the blind Mexican cavefish and its river-dwelling conspecific

Fish reproductive patterns are very diverse in terms of breeding frequency, mating system, sexual dimorphisms and selection, mate choice, spawning site choice, courtship patterns, spawning behaviors and parental care. Here we have compared the breeding behavior of the surface-dwelling and cave-dwelling morphs of the characiform A. mexicanus, with the goals of documenting the spawning behavior in this emerging model organism, its possible evolution after cave colonization, and the sensory modalities involved. Using infrared video recordings, we showed that cave and surface Astyanax spawning behavior is identical, occurs in the dark, and can be divided into 5 rapid phases repeated many times, about once per minute, during spawning sessions which last about one hour and involve one female and several males. Such features may constitute "pre-adaptive traits" which have facilitated fish survival after cave colonization, and may also explain how the two morphs can hybridize in the wild and in the laboratory. Accordingly, cross-breeding experiments involving females of one morphotype and males of the other morphotype showed the same behavior including the same five phases. However, breeding between cavefish females and surface fish males was more frequent than the reverse. Finally, cavefish female pheromonal solution was able to trigger strong behavioral responses in cavefish males-but not on surface fish males. Lastly, egg production seemed higher in surface fish females than in cavefish females. These results are discussed with regards to the sensory modalities involved in triggering reproductive behavior in the two morphs, as well as its possible ongoing evolution.

The origins and evolution of sleep

Sleep is nearly ubiquitous throughout the animal kingdom, yet little is known about how ecological factors or perturbations to the environment shape the duration and timing of sleep. In diverse animal taxa, poor sleep negatively impacts development, cognitive abilities and longevity. In addition to mammals, sleep has been characterized in genetic model organisms, ranging from the nematode worm to zebrafish, and, more recently, in emergent models with simplified nervous systems such as Aplysia and jellyfish. In addition, evolutionary models ranging from fruit flies to cavefish have leveraged natural genetic variation to investigate the relationship between ecology and sleep. Here, we describe the contributions of classical and emergent genetic model systems to investigate mechanisms underlying sleep regulation. These studies highlight fundamental interactions between sleep and sensory processing, as well as a remarkable plasticity of sleep in response to environmental changes. Understanding how sleep varies throughout the animal kingdom will provide critical insight into fundamental functions and conserved genetic mechanisms underlying sleep regulation. Furthermore, identification of naturally occurring genetic variation regulating sleep may provide novel drug targets and approaches to treat sleep-related diseases.

Morphogenesis and motility of the Astyanax mexicanus gastrointestinal tract

Through the course of evolution, the gastrointestinal (GI) tract has been modified to maximize nutrient absorption, forming specialized segments that are morphologically and functionally distinct. Here we show that the GI tract of the Mexican tetra, Astyanax mexicanus, has distinct regions, exhibiting differences in morphology, motility, and absorption. We found that A. mexicanus populations adapted for life in subterranean caves exhibit differences in the GI segments compared to those adapted to surface rivers. Cave-adapted fish exhibit bi-directional churning motility in the stomach region that is largely absent in river-adapted fish. We investigated how this motility pattern influences intestinal transit of powdered food and live prey. We found that powdered food is more readily emptied from the cavefish GI tract. In contrast, the transit of live rotifers from the stomach region to the midgut occurs more slowly in cavefish compared to surface fish, consistent with the presence of churning motility. Differences in intestinal motility and transit likely reflect adaptation to unique food sources available to post-larval A. mexicanus in the cave and river environments. We found that cavefish grow more quickly than surface fish when fed ad libitum, suggesting that altered GI function may aid in nutrient consumption or absorption. We did not observe differences in enteric neuron density or smooth muscle organization between cavefish and surface fish. Altered intestinal motility in cavefish could instead be due to changes in the activity or patterning of the enteric nervous system. Exploring this avenue will lead to a better understanding of how the GI tract evolves to maximize energy assimilation from novel food sources.

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.

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.

Pigmentation pattern and developmental constraints: flight muscle attachment sites delimit the thoracic trident of Drosophila melanogaster

In their seminal paper published in 1979, Gould and Lewontin argued that some traits arise as by-products of the development of other structures and not for direct utility in themselves. We show here that this applies to the trident, a pigmentation pattern observed on the thorax of Drosophila melanogaster. Using reporter constructs, we show that the expression domain of several genes encoding pigmentation enzymes follows the trident shape. This domain is complementary to the expression pattern of stripe (sr), which encodes an essential transcription factor specifying flight muscle attachment sites. We demonstrate that sr limits the expression of these pigmentation enzyme genes to the trident by repressing them in its own expression domain, i.e. at the flight muscle attachment sites. We give evidence that repression of not only yellow but also other pigmentation genes, notably tan, is involved in the trident shape. The flight muscle attachment sites and sr expression patterns are remarkably conserved in dipterans reflecting the essential role of sr. Our data suggest that the trident is a by-product of flight muscle attachment site patterning that arose when sr was co-opted for the regulation of pigmentation enzyme coding genes.

Comparing growth in surface and cave morphs of the species Astyanax mexicanus: insights from scales

Background

Life in the darkness of caves is accompanied, throughout phyla, by striking phenotypic changes including the loss or severe reduction in eyes and pigmentation. On the other hand, cave animals have undergone constructive changes, thought to be adaptive, to survive in this extreme environment. The present study addresses the question of the evolution of growth in caves, taking advantage of the comparison between the river-dwelling and the cave-dwelling morphs of the Mexican tetra, Astyanax mexicanus.

Results

A sclerochronology approach was undertaken to document the growth of the species in these two very distinct habitats. Scales from 158 wild Astyanax mexicanus specimens were analyzed from three caves (Pachón, Tinaja and Subterráneo) and two rivers (Rio Gallinas and Arroyo Lagarto) in San Luis Potosi and Tamaulipas, Mexico. A 10–13% reduction in scales size was observed in the cave morphs compared to the surface morphs. Age could be reliably inferred from annual growth increments on the scales from the two morphs of the species. Further comparisons with growth curves in laboratory conditions, obtained using the von Bertalanffy growth model, were also performed. In the wild and in the laboratory, cavefish originating from the Pachón cave reached smaller sizes than surface fish from three different locations: Rio Gallinas and Arroyo Lagarto (wild sampling) and Texas (laboratory population), respectively. Wild Pachón cavefish also seemed to grow to smaller sizes than the two other wild cavefish populations studied, Tinaja and Subterráneo. Finally, growth in the laboratory was faster than in the wild, particularly in the two first years of life.

Conclusions

These data suggest that cavefish originating from the Pachón cave are subjected to an intrinsic limitation of their final size, which is at least in part independent from energy/food availability. This growth limitation may be an advantageous way of limiting energy expenditure and food needs in the cave environment. Moreover, growth regulation evolved differently in independently evolved cave populations. These results are discussed with regard to the sources of energy or general ecological conditions present in caves, and to the differences in behavior or feeding skills known in cavefish.

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.