Altered rest-activity patterns evolve via circadian independent mechanisms in cave adapted balitorid loaches

Divergent patterns of locomotor activity in cave isopods (Oniscidea: Styloniscidae) in Neotropics

In cave environments, stable conditions devoid of light-dark cycles and temperature fluctuations sustain circadian clock mechanisms across various species. However, species adapted to these conditions may exhibit disruption of circadian rhythm in locomotor activity. This study examines potential rhythm loss due to convergent evolution in five semi-aquatic troglobitic isopod species (Crustacea: Styloniscidae), focusing on its impact on locomotor activity. The hypothesis posits that these species display aperiodic locomotor activity patterns. Isopods were subjected to three treatments: constant red light (DD), constant light (LL), and light-dark cycles (LD 12:12), totaling 1656 h. Circadian rhythm analysis employed the Sokolove and Bushell periodogram chi-square test, Hurst coefficient calculation, intermediate stability (IS), and activity differences for each species. Predominantly, all species exhibited an infradian rhythm under DD and LL. There was synchronization of the locomotor rhythm in LD, likely as a result of masking. Three species displayed diurnal activity, while two exhibited nocturnal activity. The Hurst coefficient indicated rhythmic persistence, with LD showing higher variability. LD conditions demonstrated higher IS values, suggesting synchronized rhythms across species. Significant individual variations were observed within species across the three conditions. Contrary to the hypothesis, all species exhibited synchronization under light-dark conditions. Analyzing circadian activity provides insights into organism adaptation to non-cyclical environments, emphasizing the importance of exploring underlying mechanisms.

The interplay between sleep and ecophysiology, behaviour and responses to environmental change in fish

Evidence of behavioural sleep has been observed in every animal species studied to date, but current knowledge of the behaviour, neurophysiology and ecophysiology associated with sleep is concentrated on mammals and birds. Fish are a hugely diverse group that can offer novel insights into a variety of sleep-related behaviours across environments, but the ecophysiological relevance of sleep in fish has been largely overlooked. Here, we systematically reviewed the literature to assess the current breadth of knowledge on fish sleep, and surveyed the diverse physiological effects and behaviours associated with sleep. We also discuss possible ways in which unstudied external factors may alter sleep behaviours. For example, predation risk may alter sleep patterns, as has been shown in mammalian, avian and reptilian species. Other environmental factors - such as water temperature and oxygen availability - have the potential to alter sleep patterns in fish differently than for terrestrial endotherms. Understanding the ecological influences on sleep in fish is vital, as sleep deprivation has the potential to affect waking behaviour and fitness owing to cognitive and physiological impairments, possibly affecting ecological phenomena and sensitivity to environmental stressors in ways that have not been considered.

The ticking clock in the dark: Review of biological rhythms in cave invertebrates

Circadian clocks, internal mechanisms that generate 24-hour rhythms, play a crucial role in coordinating biological events with day-night cycles. In light-deprived environments such as caves, species, particularly isolated obligatory troglobites, may exhibit evolutionary adaptations in biological rhythms due to light exposure. To explore rhythm expression in these settings, we conducted a comprehensive literature review on invertebrate chronobiology in global subterranean ecosystems, analyzing 44 selected studies out of over 480 identified as of September 2023. These studies revealed significant taxonomic diversity, primarily among terrestrial species like Coleoptera, with research concentrated in the United States, Italy, France, Australia, and Brazil, and a notable gap in African records. Troglobite species displayed a higher incidence of aperiodic behavior, while troglophiles showed a robust association with rhythm expression. Locomotor activity was the most studied aspect (>60%). However, approximately 4% of studies lacked information on periodicity or rhythm asynchrony, and limited research under constant light conditions hindered definitive conclusions. This review underscores the need to expand chronobiological research globally, encompassing diverse geographical regions and taxa, to deepen our understanding of biological rhythms in subterranean species. Such insights are crucial for preserving the resilience of subsurface ecosystems facing threats like climate change and habitat loss.

Selection Maintains the Phenotypic Divergence of Cave and Surface Fish

AbstractGenetic divergence in the presence of gene flow has been well documented, but there is little information on the specific factors maintaining divergence. The present study investigates this in the Mexican tetra (Astyanax mexicanus), an excellent model for studying this question because surface and cave populations differ markedly in phenotype and genotype but are interfertile. Previous population studies documented significant gene flow among cave and surface populations, but they focused on analyses of neutral markers whose evolutionary dynamics likely differ from those of genes involved in cave adaptation. The present study advances our understanding of this question by focusing specifically on the genetics responsible for eye and pigmentation reduction, signature traits of cave populations. Direct observations of two cave populations over the course of 63 years verify that surface fish frequently move into the caves and even hybridize with the cave fish. Importantly, however, historical records show that surface alleles for pigmentation and eye size do not persist but are rapidly eliminated from the cave gene pool. It has been argued that regression of eyes and pigmentation was driven by drift, but the results of this study suggest that strong selection actively eliminates surface alleles from the cave populations.

Evidence of ancestral nocturnality, locomotor clock regression, and cave zone-adjusted sleep duration modes in a cave beetle

The small carrion beetle Ptomaphagus hirtus is an abundant inhabitant of the exceptionally biodiverse Mammoth Cave system. Previous studies revealed negative phototaxis and the expression of biological clock genes in this microphthalmic cave beetle. Here we present results from probing P. hirtus for the entrainment of locomotor rhythms using the TriKinetics activity monitor setup. Although curtailed by low adjustment frequency of animals to the test environment, the data obtained from successfully monitoring two animals in constant darkness (DD) and six animals exposed to 12 hour light-dark cycles (LD) revealed a strong effect of light on locomotor activity in P. hirtus. In LD, activity was prevalent during the artificial night phases while close to absent during the presumptive day phases, suggesting conserved nocturnality. Upon transitioning LD animals to constant darkness, none displayed detectable evidence of free-running activity rhythms, suggesting complete regression of the central circadian clock. Equally notable, overall locomotor activity of the two DD-monitored animals was about three-fold lower compared to LD animals due to longer rest durations in the former. We, therefore, propose the existence of cave zone-specific energy expenditure modes that are mediated through light schedule responsive modification of sleep duration in P. hirtus.

Cavefishes in Chronobiological Research: A Narrative Review

Cavefish are vertebrates living in extreme subterranean environments with no light, temperature changes, and limited food. Circadian rhythms in these fish are suppressed in natural habitats. However, they can be found in artificial light-dark cycles and other zeitgebers. The molecular circadian clock has its peculiarities in cavefish. In Astyanax mexicanus, the core clock mechanism is tonically repressed in the caves due to the overactivation of the light input pathway. A lack of functional light input pathway but rather the entrainment of circadian genes' expression by scheduled feeding were revealed in more ancient Phreatichthys andruzzii. Different evolutionarily determined irregularities in the functioning of molecular circadian oscillators can be expected in other cavefish. The unique property of some species is the existence of surface and cave forms. Along with the ease of maintenance and breeding, it made cavefish a promising model for chronobiological studies. At the same time, a divergence of the circadian system between cavefish populations requires the strain of origin to be indicated in further research.

Telling the Seasons Underground: The Circadian Clock and Ambient Temperature Shape Light Exposure and Photoperiodism in a Subterranean Rodent

Living organisms anticipate the seasons by tracking the proportion of light and darkness hours within a day—photoperiod. The limits of photoperiod measurement can be investigated in the subterranean rodents tuco-tucos (Ctenomys aff. knighti), which inhabit dark underground tunnels. Their exposure to light is sporadic and, remarkably, results from their own behavior of surface emergence. Thus, we investigated the endogenous and exogenous regulation of this behavior and its consequences to photoperiod measurement. In the field, animals carrying biologgers displayed seasonal patterns of daily surface emergence, exogenously modulated by temperature. In the laboratory, experiments with constant lighting conditions revealed the endogenous regulation of seasonal activity by the circadian clock, which has a multi-oscillatory structure. Finally, mathematical modeling corroborated that tuco-tuco’s light exposure across the seasons is sufficient for photoperiod encoding. Together, our results elucidate the interrelationship between the circadian clock and temperature in shaping seasonal light exposure patterns that convey photoperiod information in an extreme photic environment.

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.

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.

Convergence on reduced stress behavior in the Mexican blind cavefish

Responding appropriately to stress is essential for survival, yet in pathological states, these responses can develop into debilitating conditions such as post-traumatic stress disorder and generalized anxiety. While genetic models have provided insight into the neurochemical and neuroanatomical pathways that underlie stress, little is known about how evolutionary processes and naturally occurring variation contribute to the diverse responses to stressful stimuli observed in the animal kingdom. The Mexican cavefish is a powerful system to address how altered genetic and neuronal systems can give rise to altered behaviors. When introduced into a novel tank, surface fish and cavefish display a stereotypic stress response, characterized by reduced exploratory behavior and increased immobility, akin to "freezing". The stress response in cave and surface forms is reduced by pharmacological treatment with the anxiolytic drug, buspirone, fortifying the notion that behavior in the assay represents a conserved stress state. We find that cave populations display reduced behavioral measures of stress compared to surface conspecifics, including increased time in the top half of the tank and fewer periods of immobility. Further, reduced stress responses are observed in multiple independently derived cavefish populations, suggesting convergence on loss of behavioral stress responses in the novel tank assay. These findings provide evidence of a naturally occurring species with two drastically different forms in which a shift in predator-rich ecology to one with few predators corresponds to a reduction in stress behavior.

Studying the Evolution of the Vertebrate Circadian Clock: The Power of Fish as Comparative Models

The utility of any model species cannot be judged solely in terms of the tools and approaches it provides for genetic analysis. A fundamental consideration is also how its biology has been shaped by the environment and the ecological niche which it occupies. By comparing different species occupying very different habitats we can learn how molecular and cellular mechanisms change during evolution in order to optimally adapt to their environment. Such knowledge is as important as understanding how these mechanisms work. This is illustrated by the use of fish models for studying the function and evolution of the circadian clock. In this review we outline our current understanding of how fish clocks sense and respond to light and explain how this differs fundamentally from the situation with mammalian clocks. In addition, we present results from comparative studies involving two species of blind cavefish, Astyanax mexicanus and Phreatichthys andruzzii. This work reveals the consequences of evolution in perpetual darkness for the circadian clock and its regulation by light as well as for other mechanisms such as DNA repair, sleep, and metabolism which directly or indirectly are affected by regular exposure to sunlight. Major differences in the cave habitats inhabited by these two cavefish species have a clear impact on shaping the molecular and cellular adaptations to life in complete darkness.

Evolutionary Genetics of the Cavefish Astyanax mexicanus

Blind and depigmented fish belonging to the species Astyanax mexicanus are outstanding models for evolutionary genetics. During their evolution in the darkness of caves, they have undergone a number of changes at the morphological, physiological, and behavioral levels, but they can still breed with their river-dwelling conspecifics. The fertile hybrids between these two morphotypes allow forward genetic approaches, from the search of quantitative trait loci to the identification of the mutations underlying the evolution of troglomorphism. We review here the past 30years of evolutionary genetics on Astyanax: from the first crosses and the discovery of convergent evolution of different Astyanax cavefish populations to the most recent evolutionary transcriptomics and genomics studies that have provided researchers with potential candidate genes to be tested using functional genetic approaches. Although significant progress has been made and some genes have been identified, cavefish have not yet fully revealed the secret of their adaptation to the absence of light. In particular, the genetic determinism of their loss of eyes seems complex and still puzzles researchers. We also discuss future research directions, including searches for the origin of cave alleles and searches for selection genome-wide, as well as the necessary but missing information on the timing of cave colonization by surface fish.

Life in a dark biosphere: a review of circadian physiology in "arrhythmic" environments

Most of the life with which humans interact is exposed to highly rhythmic and extremely predictable changes in illumination that occur with the daily events of sunrise and sunset. However, while the influence of the sun feels omnipotent to surface dwellers such as ourselves, life on earth is dominated, in terms of biomass, by organisms isolated from the direct effects of the sun. A limited understanding of what life is like away from the sun can be inferred from our knowledge of physiology and ecology in the light biosphere, but a full understanding can only be gained by studying animals from the dark biosphere, both in the laboratory and in their natural habitats. One of the least understood aspects of life in the dark biosphere is the rhythmicity of physiology and what it means to live in an environment of low or no rhythmicity. Here we describe methods that may be used to understand rhythmic physiology in the dark and summarise some of the studies of rhythmic physiology in "arrhythmic" environments, such as the poles, deep sea and caves. We review what can be understood about the adaptive value of rhythmic physiology on the Earth's surface from studies of animals from arrhythmic environments and what role a circadian clock may play in the dark.

Genomic consequences of ecological speciation in astyanax cavefish

The cave environment is consistently radically different than the surface environment because it lacks light, and animals adapting to cave life are subject to strong selective forces much different than those experienced by their ancestors who evolved in the presence of light. As such, their divergence from surface ancestors and eventual speciation is likely to be driven by the shift in ecology. We report here that hybrids between cave and surface Astyanax mexicanus fishes produce offspring with allelic frequencies that differ significantly from Mendelian expectations both for transmission ratios and for independent assortment of unlinked markers. Comparison of allelic content of DNA from fin clips and sperm pools show that the transmission ratio distortion likely occurs during spermatogenesis. Departures from expectations of independent assortment are essentially epistatic phenomena generating linkage disequilibrium. A novel analysis of the epistatic interactions reveals an apparent network of interactions among genes known or suspected to be involved in cave adaptation, implying that the epistasis arose as a "by product" of the divergence due to cave adaptation.

Effects of fasting and feeding on the brain mRNA expressions of orexin, tyrosine hydroxylase (TH), PYY and CCK in the Mexican blind cavefish (Astyanax fasciatus mexicanus)

The effects of fasting and feeding on the brain expression of orexin (OX), tyrosine hydroxylase (TH), peptide Y (PY) and cholecystokinin (CCK) were examined in the blind cavefish Astyanax fasciatus mexicanus. A 10-days fasting period induced increases in both OX and TH brain mRNA expression but had no effect on PYY and CCK expression. Periprandial changes in expression were seen for OX, TH and PYY but not for CCK. OX brain expression peaked 1h prior to a scheduled meal and decreased 1h post feeding in fed fish. A peak in TH expression was seen 1h post feeding in unfed fish whereas a peak in PYY expression was seen 1h post feeding in fed fish. Our result indicates that brain OX, TH and PYY might be involved in the central regulation of feeding of blind cavefish.