CaveCrawler: An interactive analysis suite for cavefish bioinformatics

The growing use of genomics data in diverse animal models provides the basis for identifying genomic and transcriptional differences across species and contexts. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but are lacking for most emerging models of evolution. There is a rapidly expanding use of genomic, transcriptional, and functional genetic approaches to study diverse traits of the Mexican tetra, Astyanax mexicanus. This species exists as two morphs, eyed surface populations and at least 30 blind 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 can be processed with other analysis platforms including Gene Ontology (GO) to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built A. mexicanus can readily applied to other emerging model systems.

A Plethora of Senses

This chapter discusses the variety of animal senses, how they work, what they are used for, and why such a staggering array of senses exists in nature. The senses found across animal species, and even among individuals of the same species, vary according to many factors. Animal senses are carefully refined through evolution and development for the things that matter most to them. To accomplish the numerous tasks every individual must perform, the senses are tuned to work best in the habitats where the creature lives and to acquire the best available sources of information. Sometimes, one or more of the senses are exquisitely tuned to a few crucial tasks an animal must perform in order to survive and reproduce successfully. Investment in different senses can also be flexible depending on the conditions under which an animal grows up. Through adaptation over many generations, species like blind cave fish can decrease investment in one sense in favour of another, but individual animals can also do this during their lives.

The second known stygomorphic freshwater crab from China, Phasmon typhlops gen. nov. et sp. nov. (Crustacea, Decapoda, Potamidae), diverged at the beginning of the Late Miocene

A new genus and new species of blind freshwater cave crab are described from Chongzuo City, Guangxi Zhuang Autonomous Region, China based on morphology and mitochondrial 16S rDNA sequences. The new genus, Phasmongen. nov., is established for P. typhlopssp. nov., which is only the second blind cave crab known from China and East Asia. The combination of a very wide carapace, overall depigmentation, reduced orbits and vestigial unpigmented eyes of Phasmon immediately separates it from all known potamid genera. Molecular divergence estimates based on 16S rDNA suggest that the lineage to which the new genus belongs diverged from other potamids at the beginning of the Late Miocene (10.8 million years ago), much earlier than other Chinese cave crabs.

Social-like responses are inducible in the asocial and blind Mexican cavefish despite the continued exhibition of strong repetitive behavior

Collective behaviors, such as schooling of fishes and mass migrations of ungulates, are hallmark features of a wide variety of animal species. Such phenotypic characters can be lost, either through evolutionary process across generations or by certain environmental stressors within a generation. Such stressors simultaneously promote stereotypic repetitive behaviors in many mammals, such as those exhibited in certain ex-situ captive settings. However, in asocial species, it is unclear whether social ability is permanently lost or only suppressed. It is also unclear if this antagonistic regulation between repetitive and social behaviors is deeply conserved among vertebrates. An evolutionary model, the Mexican tetra, Astyanax mexicanus, has a blind cave-dwelling morph lacking collective behaviors but exhibiting repetitive circling. In contrast, the sighted surface riverine morph of A. mexicanus shows more normative behaviors. We here report that social-like interactions are recoverable in blind asocial cavefish under familiar environments but are suppressed under the stress-associated unfamiliar environments. In contrast, surface fish revealed robust social-like behaviors in the dark, regardless of familiarity to the environment. Treatment of a human antipsychotic drug also induced social-like interactions in cavefish even in unfamiliar environments. In addition, the level of repetitive behavior is positively correlated with that of asociality in cavefish, suggesting that the antagonistic regulation between repetitive and social-like behaviors is present in teleost fish. Asocial cavefish therefore, with a deeply conserved framework of behavioral regulation, are still capable of expressing social-like behavior following ca. 200,000 years of adaptation to caves.

A mutation in monoamine oxidase (MAO) affects the evolution of stress behavior in the blind cavefish Astyanax mexicanus

ABSTRACTThe neurotransmitter serotonin controls a variety of physiological and behavioral processes. In humans, mutations affecting monoamine oxidase (MAO), the serotonin-degrading enzyme, are highly deleterious. Yet, blind cavefish of the species Astyanax mexicanus carry a partial loss-of-function mutation in MAO (P106L) and thrive in their subterranean environment. Here, we established four fish lines, corresponding to the blind cave-dwelling and the sighted river-dwelling morphs of this species, with or without the mutation, in order to decipher the exact contribution of mao P106L in the evolution of cavefish neurobehavioral traits. Unexpectedly, although mao P106L appeared to be an excellent candidate for the genetic determinism of the loss of aggressive and schooling behaviors in cavefish, we demonstrated that it was not the case. Similarly, the anatomical variations in monoaminergic systems observed between cavefish and surface fish brains were independent from mao P106L, and rather due to other, morph-dependent developmental processes. However, we found that mao P106L strongly affected anxiety-like behaviors. Cortisol measurements showed lower basal levels and an increased amplitude of stress response after a change of environment in fish carrying the mutation. Finally, we studied the distribution of the P106L mao allele in wild populations of cave and river A. mexicanus, and discovered that the mutant allele was present – and sometimes fixed – in all populations inhabiting caves of the Sierra de El Abra. The possibility that this partial loss-of-function mao allele evolves under a selective or a neutral regime in the particular cave environment is discussed.

A hypomorphic cystathionine ß-synthase gene contributes to cavefish eye loss by disrupting optic vasculature

Vestigial structures are key indicators of evolutionary descent, but the mechanisms underlying their development are poorly understood. This study examines vestigial eye formation in the teleost Astyanax mexicanus, which consists of a sighted surface-dwelling morph and multiple populations of blind cave morphs. Cavefish embryos initially develop eyes, but they subsequently degenerate and become vestigial structures embedded in the head. The mutated genes involved in cavefish vestigial eye formation have not been characterized. Here we identify cystathionine ß-synthase a (cbsa), which encodes the key enzyme of the transsulfuration pathway, as one of the mutated genes responsible for eye degeneration in multiple cavefish populations. The inactivation of cbsa affects eye development by increasing the transsulfuration intermediate homocysteine and inducing defects in optic vasculature, which result in aneurysms and eye hemorrhages. Our findings suggest that localized modifications in the circulatory system may have contributed to the evolution of vestigial eyes in cavefish.

A mutation in monoamine oxidase (MAO) affects the evolution of stress behavior in the blind cavefish Astyanax mexicanus

The neurotransmitter serotonin controls a great variety of physiological and behavioral processes. In humans, mutations affecting the monoamine oxidase or MAO, the serotonin-degrading enzyme, are highly deleterious. Yet, blind cavefish of the species A. mexicanus carry a partial loss-of-function mutation in MAO (P106L) and seem to thrive in their subterranean environment. Here, we established 4 fish lines, corresponding to the blind cave-dwelling and the sighted river-dwelling morphs of this species, with or without the mutation, in order to decipher the exact contribution of mao P106L in the evolution of cavefish neuro-behavioral traits. Unexpectedly, although mao P106L appeared as an excellent candidate for the genetic determinism of the loss of aggressive and schooling behaviors in cavefish, we demonstrated that it was not the case. Similarly, the anatomical variations in monoaminergic systems observed between cavefish and surface fish brains were independent from mao P106L, and rather due other, morph-dependent developmental processes. On the other hand, we found that mao P106L strongly affected anxiety-like behaviors. Cortisol measurements showed lower basal levels and an increased amplitude of stress response after a change of environment in fish carrying the mutation. Finally, we studied the distribution of the P106L mao allele in wild populations of cave and river A. mexicanus, and discovered that the mutant allele was present - and sometimes fixed - in all populations inhabiting caves of the Sierra de El Abra. The possibility that this partial loss-of-function mao allele evolves under a selective or a genetic drift regime in the particular cave environment is discussed.