The energetic cost of vision and the evolution of eyeless Mexican cavefish

Increased eye size is favoured in Trinidadian killifish experimentally transplanted into low light, high competition environments

Intraspecific variation in vertebrate eye size is well known. Ecological factors such as light availability are often correlated with shifts in relative eye size. However, experimental tests of selection on eye size are lacking. Trinidadian killifish (Anablepsoides hartii) are found in sites that differ in predation intensity. Sites that lack predators are characterized by lower light, high killifish densities, low resource availability, and intense competition for food. We previously found that killifish in sites that lack predators have evolved a larger "relative" eye size (eye size corrected for body size) than fish from sites with predators. Here, we used transplant experiments to test how selection operates on eye size when fish that are adapted to sites with predators are translocated into sites where predators are absent. We observed a significant "population × relative eye size" interaction; the relationship between relative eye size and a proxy for fitness (rates of individual growth) was positive in the transplanted fish. The trend was the opposite for resident fish. Such results provide experimental support that larger eyes enhance fitness and are favoured in environments characterized by low light and high competition.

Label-free multiphoton imaging reveals volumetric shifts across development in sensory-related brain regions of a miniature transparent vertebrate

Animals integrate information from different sensory modalities as they mature and perform increasingly complex behaviors. This may parallel differential investment in specific brain regions depending on the demands of changing sensory inputs. To investigate developmental changes in the volume of canonical sensory integration brain regions, we used third harmonic generation imaging for morphometric analysis of forebrain and midbrain regions from 5 to 90 days post fertilization (dpf) in Danionella dracula , a transparent, miniature teleost fish whose brain is optically accessible throughout its lifespan. Relative to whole brain volume, increased volume or investment in telencephalon, a higher order sensory integration center, and torus longitudinalis (TL), a midbrain visuomotor integration center, is relatively consistent from 5 to 30 dpf, until it increases at 60 dpf, followed by another increase at 90 dpf, as animals reach adulthood. In contrast, investment in midbrain optic tectum (TeO), a retinal-recipient target, progressively decreases from 30-90 dpf, whereas investment is relatively consistent across all stages for the midbrain torus semicircularis (TS), a secondary auditory and mechanosensory lateral line center, and the olfactory bulb (OB), a direct target of the olfactory epithelium. In sum, increased investment in higher order integration centers (telencephalon, TL) occurs as juveniles reach adulthood and exhibit more complex cognitive tasks, whereas investment in modality-dominant regions occurs in earlier stages (TeO) or is relatively consistent across development (TS, OB). Complete optical access throughout Danionella 's lifespan provides a unique opportunity to investigate how changing brain structure over development correlates with changes in connectivity, microcircuitry, or behavior.

Eye morphology contributes to the ecology and evolution of the aquatic avifauna

Aquatic birds are notable among the global avifauna for living in environments exposed to large amounts of light. Despite growing evidence that visual adaptations to light underly the ecology and evolution of the avian tree of life, no comprehensive comparative analysis of visual acuity as approximated by eyes size exists for the global aquatic avifauna. Here, I use Stanley Ritland's unpublished dataset of measurements for axial length collected from museum specimens to explore the ecology and evolution of eye size variation for half of the aquatic avifauna (N = 464 species). After correcting for body mass allometry and incorporating phylogenetic relationships, aquatic species had significantly smaller eyes compared to terrestrial species. Furthermore, species using hyperopic foraging manoeuvres, exhibiting carnivorous and insectivorous diets, and displaying nocturnal behaviour had larger eyes. Plunge-divers (e.g. boobies and tropic birds) and stalkers (e.g. herons) had the largest relative eye sizes, especially species identifying prey at higher altitudes or longer distances. Underwater pursuit-divers foraging at greater depths had larger eyes, likely due to the dramatic attenuation of light in the deep ocean. Overall, residual eye size was phylogenetically conserved (l = 0.94), with phylogeny alone explaining 62% of residual eye size variation. Collectively, these results suggest that the relatively bright environments found in aquatic ecosystems negate the adaptive benefits of costly metabolic investments associated with developing and maintaining larger eyes, while also reducing the potential occurrence of disability glare. Strong correlations between eye size and foraging ecology in different aquatic environments corroborate similar comparative studies of terrestrial birds and underscore the central role that vision has played in driving the ecology and evolution of the global avifauna.

Natural reversal of cavefish heart asymmetry is controlled by Sonic Hedgehog effects on the left-right organizer

The direction of left-right visceral asymmetry is conserved in vertebrates. Deviations of the standard asymmetric pattern are rare, and the underlying mechanisms are not understood. Here, we use the teleost Astyanax mexicanus, consisting of surface fish with normal left-oriented heart asymmetry and cavefish with high levels of reversed right-oriented heart asymmetry, to explore natural changes in asymmetry determination. We show that Sonic Hedgehog (Shh) signaling is increased at the posterior midline, Kupffer's vesicle (the teleost left-right organizer) is enlarged and contains longer cilia, and the number of dorsal forerunner cells is increased in cavefish. Furthermore, Shh increase in surface fish embryos induces asymmetric changes resembling the cavefish phenotype. Asymmetric expression of the Nodal antagonist Dand5 is equalized or reversed in cavefish, and Shh increase in surface fish mimics changes in cavefish dand5 asymmetry. Shh decrease reduces the level of right-oriented heart asymmetry in cavefish. Thus, naturally occurring modifications in cavefish heart asymmetry are controlled by the effects of Shh signaling on left-right organizer function.

Phylogenetic conservation of the interdependent homeostatic relationship of sleep regulation and redox metabolism

Sleep is an essential and evolutionarily conserved process that affects many biological functions that are also strongly regulated by cellular metabolism. The interdependence between sleep homeostasis and redox metabolism, in particular, is such that sleep deprivation causes redox metabolic imbalances in the form of over-production of ROS. Likewise (and vice versa), accumulation of ROS leads to greater sleep pressure. Thus, it is theorized that one of the functions of sleep is to act as the brain's "antioxidant" at night by clearing oxidation built up from daily stress of the active day phase. In this review, we will highlight evidence linking sleep homeostasis and regulation to redox metabolism by discussing (1) the bipartite role that sleep-wake neuropeptides and hormones have in redox metabolism through comparing cross-species cellular and molecular mechanisms, (2) the evolutionarily metabolic changes that accompanied the development of sleep loss in cavefish, and finally, (3) some of the challenges of uncovering the cellular mechanism underpinning how ROS accumulation builds sleep pressure and cellularly, how this pressure is cleared.

The prevalence of copy number increase at multiallelic copy number variants associated with cave colonization

Copy number variation is a common contributor to phenotypic diversity, yet its involvement in ecological adaptation is not easily discerned. Instances of parallelly evolving populations of the same species in a similar environment marked by strong selective pressures present opportunities to study the role of copy number variants (CNVs) in adaptation. By identifying CNVs that repeatedly occur in multiple populations of the derived ecotype and are not (or are rarely) present in the populations of the ancestral ecotype, the association of such CNVs with adaptation to the novel environment can be inferred. We used this paradigm to identify CNVs associated with recurrent adaptation of the Mexican tetra (Astyanax mexicanus) to cave environment. Using a read-depth approach, we detected CNVs from previously re-sequenced genomes of 44 individuals belonging to two ancestral surfaces and three derived cave populations. We identified 102 genes and 292 genomic regions that repeatedly diverge in copy number between the two ecotypes and occupy 0.8% of the reference genome. Functional analysis revealed their association with processes previously recognized to be relevant for adaptation, such as vision, immunity, oxygen consumption, metabolism, and neural function and we propose that these variants have been selected for in the cave or surface waters. The majority of the ecotype-divergent CNVs are multiallelic and display copy number increases in cavefish compared to surface fish. Our findings suggest that multiallelic CNVs - including gene duplications - and divergence in copy number provide a fast route to produce novel phenotypes associated with adaptation to subterranean life.

Unraveling stress resilience: Insights from adaptations to extreme environments by Astyanax mexicanus cavefish

Extreme environmental conditions have profound impacts on shaping the evolutionary trajectory of organisms. Exposure to these conditions elicits stress responses, that can trigger phenotypic changes in novel directions. The Mexican Tetra, Astyanax mexicanus, is an excellent model for understanding evolutionary mechanisms in response to extreme or new environments. This fish species consists of two morphs; the classical surface-dwelling fish and the blind cave-dwellers that inhabit dark and biodiversity-reduced ecosystems. In this review, we explore the specific stressors present in cave environments and examine the diverse adaptive strategies employed by cave populations to not only survive but thrive as successful colonizers. By analyzing the evolutionary responses of A. mexicanus, we gain valuable insights into the genetic, physiological, and behavioral adaptations that enable organisms to flourish under challenging environmental conditions.

Evolution of neural circuitry and cognition

Neural circuits govern the interface between the external environment, internal cues and outwardly directed behaviours. To process multiple environmental stimuli and integrate these with internal state requires considerable neural computation. Expansion in neural network size, most readily represented by whole brain size, has historically been linked to behavioural complexity, or the predominance of cognitive behaviours. Yet, it is largely unclear which aspects of circuit variation impact variation in performance. A key question in the field of evolutionary neurobiology is therefore how neural circuits evolve to allow improved behavioural performance or innovation. We discuss this question by first exploring how volumetric changes in brain areas reflect actual neural circuit change. We explore three major axes of neural circuit evolution-replication, restructuring and reconditioning of cells and circuits-and discuss how these could relate to broader phenotypes and behavioural variation. This discussion touches on the relevant uses and limitations of volumetrics, while advocating a more circuit-based view of cognition. We then use this framework to showcase an example from the insect brain, the multi-sensory integration and internal processing that is shared between the mushroom bodies and central complex. We end by identifying future trends in this research area, which promise to advance the field of evolutionary neurobiology.

Daubenton's bats maintain stereotypical echolocation behaviour and a lombard response during target interception in light

Most bats hunt insects on the wing at night using echolocation as their primary sensory modality, but nevertheless maintain complex eye anatomy and functional vision. This raises the question of how and when insectivorous bats use vision during their largely nocturnal lifestyle. Here, we test the hypothesis that the small insectivorous bat, Myotis daubentonii, relies less on echolocation, or dispenses with it entirely, as visual cues become available during challenging acoustic noise conditions. We trained five wild-caught bats to land on a spherical target in both silence and when exposed to broad-band noise to decrease echo detectability, while light conditions were manipulated in both spectrum and intensity. We show that during noise exposure, the bats were almost three times more likely to use multiple attempts to solve the task compared to in silent controls. Furthermore, the bats exhibited a Lombard response of 0.18 dB/dBnoise and decreased call intervals earlier in their flight during masking noise exposures compared to in silent controls. Importantly, however, these adjustments in movement and echolocation behaviour did not differ between light and dark control treatments showing that small insectivorous bats maintain the same echolocation behaviour when provided with visual cues under challenging conditions for echolocation. We therefore conclude that bat echolocation is a hard-wired sensory system with stereotyped compensation strategies to both target range and masking noise (i.e. Lombard response) irrespective of light conditions. In contrast, the adjustments of call intervals and movement strategies during noise exposure varied substantially between individuals indicating a degree of flexibility that likely requires higher order processing and perhaps vocal learning.

Morphological disparity and structural performance of the dromaeosaurid skull informs ecology and evolutionary history

Non-avialan theropod dinosaurs had diverse ecologies and varied skull morphologies. Previous studies of theropod cranial morphology mostly focused on higher-level taxa or characteristics associated with herbivory. To better understand morphological disparity and function within carnivorous theropod families, here we focus on the Dromaeosauridae, 'raptors' traditionally seen as agile carnivorous hunters.We applied 2D geometric morphometrics to quantify skull shape, performed mechanical advantage analysis to assess the efficiency of bite force transfer, and performed finite element analysis to examine strain distribution in the skull during biting. We find that dromaeosaurid skull morphology was less disparate than most non-avialan theropod groups. Their skulls show a continuum of form between those that are tall and short and those that are flat and long. We hypothesise that this narrower morphological disparity indicates developmental constraint on skull shape, as observed in some mammalian families. Mechanical advantage indicates that Dromaeosaurus albertensis and Deinonychus antirrhopus were adapted for relatively high bite forces, while Halszkaraptor escuilliei was adapted for high bite speed, and other dromaeosaurids for intermediate bite forces and speeds. Finite element analysis indicates regions of high strain are consistent within dromaeosaurid families but differ between them. Average strain levels do not follow any phylogenetic pattern, possibly due to ecological convergence between distantly-related taxa.Combining our new morphofunctional data with a re-evaluation of previous evidence, we find piscivorous reconstructions of Halszkaraptor escuilliei to be unlikely, and instead suggest an invertivorous diet and possible adaptations for feeding in murky water or other low-visibility conditions. We support Deinonychus antirrhopus as being adapted for taking large vertebrate prey, but we find that its skull is relatively less resistant to bite forces than other dromaeosaurids. Given the recovery of high bite force resistance for Velociraptor mongoliensis, which is believed to have regularly engaged in scavenging behaviour, we suggest that higher bite force resistance in a dromaeosaurid taxon may reflect a greater reliance on scavenging rather than fresh kills.Comparisons to the troodontid Gobivenator mongoliensis suggest that a gracile rostrum like that of Velociraptor mongoliensis is ancestral to their closest common ancestor (Deinonychosauria) and the robust rostra of Dromaeosaurus albertensis and Deinonychus antirrhopus are a derived condition. Gobivenator mongoliensis also displays a higher jaw mechanical advantage and lower resistance to bite force than the examined dromaeosaurids, but given the hypothesised ecological divergence of troodontids from dromaeosaurids it is unclear which group, if either, represents the ancestral condition. Future work extending sampling to troodontids would therefore be invaluable and provide much needed context to the origin of skull form and function in early birds. This study illustrates how skull shape and functional metrics can discern non-avialan theropod ecology at lower taxonomic levels and identify variants of carnivorous feeding.

The Sensory Ecology of Speciation

In this work, we explore the potential influence of sensory ecology on speciation, including but not limited to the concept of sensory drive, which concerns the coevolution of signals and sensory systems with the local environment. The sensory environment can influence individual fitness in a variety of ways, thereby affecting the evolution of both pre- and postmating reproductive isolation. Previous work focused on sensory drive has undoubtedly advanced the field, but we argue that it may have also narrowed our understanding of the broader influence of the sensory ecology on speciation. Moreover, the clearest examples of sensory drive are largely limited to aquatic organisms, which may skew the influence of contributing factors. We review the evidence for sensory drive across environmental conditions, and in this context discuss the importance of more generalized effects of sensory ecology on adaptive behavioral divergence. Finally, we consider the potential of rapid environmental change to influence reproductive barriers related to sensory ecologies. Our synthesis shows the importance of sensory conditions for local adaptation and divergence in a range of behavioral contexts and extends our understanding of the interplay between sensory ecology and speciation.

Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies

The striking structural variation seen in arthropod visual systems can be explained by the overall quantity and spatio-temporal structure of light within habitats coupled with developmental and physiological constraints. However, little is currently known about how fine-scale variation in visual structures arises across shorter evolutionary and ecological scales. In this study, we characterise patterns of interspecific (between species), intraspecific (between sexes) and intraindividual (between eye regions) variation in the visual system of four ithomiine butterfly species. These species are part of a diverse 26-million-year-old Neotropical radiation where changes in mimetic colouration are associated with fine-scale shifts in ecology, such as microhabitat preference. Using a combination of selection analyses on visual opsin sequences, in vivo ophthalmoscopy, micro-computed tomography (micro-CT), immunohistochemistry, confocal microscopy and neural tracing, we quantify and describe physiological, anatomical and molecular traits involved in visual processing. Using these data, we provide evidence of substantial variation within the visual systems of Ithomiini, including: (i) relaxed selection on visual opsins, perhaps mediated by habitat preference, (ii) interspecific shifts in visual system physiology and anatomy, and (iii) extensive sexual dimorphism, including the complete absence of a butterfly-specific optic neuropil in the males of some species. We conclude that considerable visual system variation can exist within diverse insect radiations, hinting at the evolutionary lability of these systems to rapidly develop specialisations to distinct visual ecologies, with selection acting at the perceptual, processing and molecular level.

Convergent Anuran Middle Ear Loss Lacks a Universal, Adaptive Explanation

INTRODUCTION

Shared selection pressures often explain convergent trait loss, yet anurans (frogs and toads) have lost their middle ears at least 38 times with no obvious shared selection pressures unifying "earless" taxa. Anuran tympanic middle ear loss is especially perplexing because acoustic communication is dominant within Anura and tympanic middle ears enhance airborne hearing in most tetrapods.

METHODS

Here, we use phylogenetic comparative methods to examine whether particular geographic ranges, microhabitats, activity patterns, or aspects of acoustic communication are associated with anuran tympanic middle ear loss.

RESULTS

Although we find some differences between the geographic ranges of eared and earless species on average, there is plenty of overlap between the geographic distributions of eared and earless species. Additionally, we find a higher prevalence of diurnality in earless species, but not all earless species are diurnal. We find no universal adaptive explanation for the many instances of anuran tympanic middle ear loss.

CONCLUSION

The puzzling lack of universally shared selection pressures among earless species motivates discussion of alternative hypotheses, including genetic or developmental constraints, and the possibility that tympanic middle ear loss is maladaptive.

Metabolic shift toward ketosis in asocial cavefish increases social-like affinity

BACKGROUND

Social affinity and collective behavior are nearly ubiquitous in the animal kingdom, but many lineages feature evolutionarily asocial species. These solitary species may have evolved to conserve energy in food-sparse environments. However, the mechanism by which metabolic shifts regulate social affinity is not well investigated.

RESULTS

In this study, we used the Mexican tetra (Astyanax mexicanus), which features riverine sighted surface (surface fish) and cave-dwelling populations (cavefish), to address the impact of metabolic shifts on asociality and other cave-associated behaviors in cavefish, including repetitive turning, sleeplessness, swimming longer distances, and enhanced foraging behavior. After 1 month of ketosis-inducing ketogenic diet feeding, asocial cavefish exhibited significantly higher social affinity, whereas social affinity regressed in cavefish fed the standard diet. The ketogenic diet also reduced repetitive turning and swimming in cavefish. No major behavioral shifts were found regarding sleeplessness and foraging behavior, suggesting that other evolved behaviors are not largely regulated by ketosis. We further examined the effects of the ketogenic diet via supplementation with exogenous ketone bodies, revealing that ketone bodies are pivotal molecules positively associated with social affinity.

CONCLUSIONS

Our study indicated that fish that evolved to be asocial remain capable of exhibiting social affinity under ketosis, possibly linking the seasonal food availability and sociality.

The Mexican Tetra, Astyanax mexicanus, as a Model System in Cell and Developmental Biology

Our understanding of cell and developmental biology has been greatly aided by a focus on a small number of model organisms. However, we are now in an era where techniques to investigate gene function can be applied across phyla, allowing scientists to explore the diversity and flexibility of developmental mechanisms and gain a deeper understanding of life. Researchers comparing the eyeless cave-adapted Mexican tetra, Astyanax mexicanus, with its river-dwelling counterpart are revealing how the development of the eyes, pigment, brain, cranium, blood, and digestive system evolves as animals adapt to new environments. Breakthroughs in our understanding of the genetic and developmental basis of regressive and constructive trait evolution have come from A. mexicanus research. They include understanding the types of mutations that alter traits, which cellular and developmental processes they affect, and how they lead to pleiotropy. We review recent progress in the field and highlight areas for future investigations that include evolution of sex differentiation, neural crest development, and metabolic regulation of embryogenesis.

Origins and evolution of biological novelty

Understanding the origins and impacts of novel traits has been a perennial interest in many realms of ecology and evolutionary biology. Here, we build on previous evolutionary and philosophical treatments of this subject to encompass novelties across biological scales and eco-evolutionary perspectives. By defining novelties as new features at one biological scale that have emergent effects at other biological scales, we incorporate many forms of novelty that have previously been treated in isolation (such as novelty from genetic mutations, new developmental pathways, new morphological features, and new species). Our perspective is based on the fundamental idea that the emergence of a novelty, at any biological scale, depends on its environmental and genetic context. Through this lens, we outline a broad array of generative mechanisms underlying novelty and highlight how genomic tools are transforming our understanding of the origins of novelty. Lastly, we present several case studies to illustrate how novelties across biological scales and systems can be understood based on common mechanisms of change and their environmental and genetic contexts. Specifically, we highlight how gene duplication contributes to the evolution of new complex structures in visual systems; how genetic exchange in symbiosis alters functions of both host and symbiont, resulting in a novel organism; and how hybridisation between species can generate new species with new niches.

Trait Loss in Evolution: What Cavefish Have Taught Us about Mechanisms Underlying Eye Regression

Reduction or complete loss of traits is a common occurrence throughout evolutionary history. In spite of this, numerous questions remain about why and how trait loss has occurred. Cave animals are an excellent system in which these questions can be answered, as multiple traits, including eyes and pigmentation, have been repeatedly reduced or lost across populations of cave species. This review focuses on how the blind Mexican cavefish, Astyanax mexicanus, has been used as a model system for examining the developmental, genetic, and evolutionary mechanisms that underlie eye regression in cave animals. We focus on multiple aspects of how eye regression evolved in A. mexicanus, including the developmental and genetic pathways that contribute to eye regression, the effects of the evolution of eye regression on other traits that have also evolved in A. mexicanus, and the evolutionary forces contributing to eye regression. We also discuss what is known about the repeated evolution of eye regression, both across populations of A. mexicanus cavefish and across cave animals more generally. Finally, we offer perspectives on how cavefish can be used in the future to further elucidate mechanisms underlying trait loss using tools and resources that have recently become available.

Gadusol is a maternally provided sunscreen that protects fish embryos from DNA damage

Exposure to ultraviolet radiation (UVR) is harmful to living cells, leading organisms to evolve protective mechanisms against UVR-induced cellular damage and stress.1,2 UVR, particularly UVB (280-320 nm), can damage proteins and DNA, leading to errors during DNA repair and replication. Excessive UVR can induce cellular death. Aquatic organisms face risk of UV exposure as biologically harmful levels of UVB can penetrate >10 m in clear water.3 While melanin is the only known sunscreen in vertebrates, it often emerges late in embryonic development, rendering embryos of many species vulnerable during the earlier stages. Algae and microbes produce a class of sunscreening compounds known as mycosporine-like amino acids (MAAs).4 Fish eggs contain a similar compound called gadusol, whose role as a sunscreen has yet to be tested despite its discovery over 40 years ago.5 The recent finding that many vertebrate genomes contain a biosynthetic pathway for gadusol suggests that many fish may produce and use this molecule as a sunscreen.6 We generated a gadusol-deficient mutant zebrafish to investigate the role of gadusol in protecting fish embryos and larvae from UVR. Our results demonstrate that maternally provided gadusol is the primary sunscreen in embryonic and larval development, while melanin provides modest secondary protection. The gadusol biosynthetic pathway is retained in the vast majority of teleost genomes but is repeatedly lost in species whose young are no longer exposed to UVR. Our data demonstrate that gadusol is a maternally provided sunscreen that is critical for early-life survival in the most species-rich branch of the vertebrate phylogeny.

Mitochondrial phylogeography and molecular evolution of the rhodopsin visual pigment in troglobitic populations of Astyanax mexicanus (De Filippi, 1853)

Cave-adapted animals provide a unique opportunity to study the evolutionary mechanisms underlying phenotypic, metabolic, behavioral, and genetic evolution in response to cave environments. The Mexican tetra ( Astyanax mexicanus) is considered a unique model system as it shows both surface and cave-dwelling morphs. To date, at least 33 different cave populations have been identified, with phylogenetic studies suggesting an origin from at least two independent surface lineages, thereby providing a unique opportunity to study parallel evolution. In the present study, we carried out the most exhaustive phylogeographic study of A. mexicanus to date, including cave and surface localities, using two mitochondrial markers (cytochrome b (cyt b) and cytochrome c oxidase subunit I ( COI)) and nuclear rhodopsin visual pigment ( rho). Additionally, we inferred the molecular evolution of rho within the two contrasting environments (cave and surface) and across three geographic regions (Sierra de El Abra, Sierra de Guatemala, and Micos). In total, 267 individuals were sequenced for the two mitochondrial fragments and 268 individuals were sequenced for the rho visual pigment from 22 cave and 46 surface populations. Phylogeographic results based on the mitochondrial data supported the two-lineage hypothesis, except for the Pachón and Chica caves, whose introgression has been largely documented. The Sierra de El Abra region depicted the largest genetic diversity, followed by the Sierra de Guatemala region. Regarding the phylogeographic patterns of rho, we recovered exclusive haplogroups for the Sierra de El Abra (Haplogroup I) and Sierra de Guatemala regions (Haplogroup IV). Moreover, a 544 bp deletion in the rho gene was observed in the Escondido cave population from Sierra de Guatemala, reducing the protein from seven to three intramembrane domains. This change may produce a loss-of-function (LOF) but requires further investigation. Regarding nonsynonymous ( dN) and synonymous ( dS) substitution rates (omega values ω), our results revealed the prevailing influence of purifying selection upon the rho pigment for both cave and surface populations (ω<1), but relaxation at the El Abra region. Notably, in contrast to the other two regions, we observed an increase in the number of dN mutations for Sierra de El Abra. However, given that a LOF was exclusively identified in the Sierra de Guatemala region, we cannot dismiss the possibility of a pleiotropic effect on the Rho protein.

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.

Evolution of Avian Eye Size Is Associated with Habitat Openness, Food Type and Brain Size

The eye is the primary sensory organ that obtains information from the ecological environments and specifically bridges the brain with the extra environment. However, the coevolutionary relationships between eye size and ecological factors, behaviours and brain size in birds remain poorly understood. Here, we investigate whether eye size evolution is associated with ecological factors (e.g., habitat openness, food type and foraging habitat), behaviours (e.g., migration and activity pattern) and brain size among 1274 avian species using phylogenetically controlled comparative analyses. Our results indicate that avian eye size is significantly associated with habitat openness, food type and brain size. Species living in dense habitats and consuming animals exhibit larger eye sizes compared to species living in open habitats and consuming plants, respectively. Large-brained birds tend to possess larger eyes. However, migration, foraging habitat and activity pattern were not found to be significantly associated with eye size in birds, except for nocturnal birds having longer axial lengths than diurnal ones. Collectively, our results suggest that avian eye size is primarily influenced by light availability, food need and cognitive ability.

Selection-driven trait loss in independently evolved cavefish populations

Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found that phenotypic convergence is due to parallel genetic changes. This suggests a substantial role for constraint and determinism in evolution and indicates that certain mutations are more likely to contribute to phenotypic evolution. Here we use whole genome resequencing in the Mexican tetra, Astyanax mexicanus, to investigate how selection has shaped the repeated evolution of both trait loss and enhancement across independent cavefish lineages. We show that selection on standing genetic variation and de novo mutations both contribute substantially to repeated adaptation. Our findings provide empirical support for the hypothesis that genes with larger mutational targets are more likely to be the substrate of repeated evolution and indicate that features of the cave environment may impact the rate at which mutations occur.

Reduction of Paraoxonase Expression Followed by Inactivation across Independent Semiaquatic Mammals Suggests Stepwise Path to Pseudogenization

Convergent adaptation to the same environment by multiple lineages frequently involves rapid evolutionary change at the same genes, implicating these genes as important for environmental adaptation. Such adaptive molecular changes may yield either change or loss of protein function; loss of function can eliminate newly deleterious proteins or reduce energy necessary for protein production. We previously found a striking case of recurrent pseudogenization of the Paraoxonase 1 (Pon1) gene among aquatic mammal lineages-Pon1 became a pseudogene with genetic lesions, such as stop codons and frameshifts, at least four times independently in aquatic and semiaquatic mammals. Here, we assess the landscape and pace of pseudogenization by studying Pon1 sequences, expression levels, and enzymatic activity across four aquatic and semiaquatic mammal lineages: pinnipeds, cetaceans, otters, and beavers. We observe in beavers and pinnipeds an unexpected reduction in expression of Pon3, a paralog with similar expression patterns but different substrate preferences. Ultimately, in all lineages with aquatic/semiaquatic members, we find that preceding any coding-level pseudogenization events in Pon1, there is a drastic decrease in expression, followed by relaxed selection, thus allowing accumulation of disrupting mutations. The recurrent loss of Pon1 function in aquatic/semiaquatic lineages is consistent with a benefit to Pon1 functional loss in aquatic environments. Accordingly, we examine diving and dietary traits across pinniped species as potential driving forces of Pon1 functional loss. We find that loss is best associated with diving activity and likely results from changes in selective pressures associated with hypoxia and hypoxia-induced inflammation.

Increasing complexity of opsin expression across stomatopod development

Stomatopods are well studied for their unique visual systems, which can consist of up to 16 different photoreceptor types and 33 opsin proteins expressed in the adults of some species. The light-sensing abilities of larval stomatopods are comparatively less well understood with limited information about the opsin repertoire of these early-life stages. Early work has suggested that larval stomatopods may not possess the extensive light detection abilities found in their adult counterparts. However, recent studies have shown that these larvae may have more complex photosensory systems than previously thought. To examine this idea at the molecular level, we characterized the expression of putative light-absorbing opsins across developmental stages, from embryo to adult, in the stomatopod species Pullosquilla thomassini using transcriptomic methods with a special focus on ecological and physiological transition periods. Opsin expression during the transition from the larval to the adult stage was further characterized in the species Gonodactylaceus falcatus. Opsin transcripts from short, middle, and long wavelength-sensitive clades were found in both species, and analysis of spectral tuning sites suggested differences in absorbance within these clades. This is the first study to document the changes in opsin repertoire across development in stomatopods, providing novel evidence for light detection across the visual spectrum in larvae.

Metabolic constraints and individual variation shape the trade-off between physiological recovery and anti-predator responses in adult sockeye salmon

Metabolic scope represents the aerobic energy budget available to an organism to perform non-maintenance activities (e.g., escape a predator, recover from a fisheries interaction, compete for a mate). Conflicting energetic requirements can give rise to ecologically relevant metabolic trade-offs when energy budgeting is constrained. The objective of this study was to investigate how aerobic energy is utilized when individual sockeye salmon (Oncorhynchus nerka) are exposed to multiple acute stressors. To indirectly assess metabolic changes in free-swimming individuals, salmon were implanted with heart rate biologgers. The animals were then exercised to exhaustion or briefly handled as a control, and allowed to recover from this stressor for 48 h. During the first 2 h of the recovery period, individual salmon were exposed to 90 ml of conspecific alarm cues or water as a control. Heart rate was recorded throughout the recovery period. Recovery effort and time was higher in exercised fish, relative to control fish, whereas exposure to an alarm cue had no effect on either of these metrics. Individual routine heart rate was negatively correlated with recovery time and effort. Together, these findings suggest that metabolic energy allocation towards exercise recovery (i.e., an acute stressor; handling, chase, etc.) trumps anti-predator responses in salmon, although individual variation may mediate this effect at the population level.

Thalamic neurons drive distinct forms of motor asymmetry that are conserved in teleost and dependent on visual evolution

Brain laterality is a prominent feature in Bilateria, where neural functions are favored in a single brain hemisphere. These hemispheric specializations are thought to improve behavioral performance and are commonly observed as sensory or motor asymmetries, such as handedness in humans. Despite its prevalence, our understanding of the neural and molecular substrates instructing functional lateralization is limited. Moreover, how functional lateralization is selected for or modulated throughout evolution is poorly understood. While comparative approaches offer a powerful tool for addressing this question, a major obstacle has been the lack of a conserved asymmetric behavior in genetically tractable organisms. Previously, we described a robust motor asymmetry in larval zebrafish. Following the loss of illumination, individuals show a persistent turning bias that is associated with search pattern behavior with underlying functional lateralization in the thalamus. This behavior permits a simple yet robust assay that can be used to address fundamental principles underlying lateralization in the brain across taxa. Here, we take a comparative approach and show that motor asymmetry is conserved across diverse larval teleost species, which have diverged over the past 200 million years. Using a combination of transgenic tools, ablation, and enucleation, we show that teleosts exhibit two distinct forms of motor asymmetry, vision-dependent and - independent. These asymmetries are directionally uncorrelated, yet dependent on the same subset of thalamic neurons. Lastly, we leverage Astyanax sighted and blind morphs, which show that fish with evolutionarily derived blindness lack both retinal-dependent and -independent motor asymmetries, while their sighted surface conspecifics retained both forms. Our data implicate that overlapping sensory systems and neuronal substrates drive functional lateralization in a vertebrate brain that are likely targets for selective modulation during evolution.

Both Light Stimuli and Predation Risk Affect the Adult Behavior of a Stygobiont Crustacean

Stygobiont species show common, typical traits derived from their adaptation to subterranean life. Due to the general absence of light in cave environments, the majority of them are eyeless. Although the absence of eyes generally does not allow them to perceive luminous stimuli, some stygobionts still present phototaxis. Previous studies determined that different species of the eyeless amphipod crustaceans of the genus Niphargus are able to react to light; this has been interpreted as an adaptation to avoid dangerous surface habitats, even if recent studies suggest that this could also be an adaptation to exploit them when a situation is less dangerous (i.e., during the night). Niphargus thuringius is a stygobiont amphipod that can also be observed in spring environments despite possessing all the main morphological features of subterranean organisms, such as depigmentation and a lack of eyes. In the present study, we test how the species respond to light stimuli according to the light cycle and predation risk experienced during a conditioning period. We assessed the reactions to light stimuli of adult individuals of N. thuringius after 30 days of rearing in microcosms with different conditions of light occurrence (total darkness or a light/darkness daily cycle) and predation risk (without predators, with one predator, and with two predators). Both light stimuli during the test and rearing conditions affected the behavior of Niphargus thuringius. With light stimuli, individuals presented a strong photophobic response. Moreover, individuals reared in conditions of high predation risk preferred a more sheltered environment during behavioral tests than individuals reared in safe conditions. Our results add a new species to those of stygobiont amphipods known to display negative phototaxis, confirming that this pattern is widespread and conserved in the field. N. thuringius could be a good candidate model to perform further studies aiming to assess if differences occur between spring populations and populations present in deeper groundwater.

Gadusol is a maternally provided sunscreen that protects fish embryos from DNA damage

Ultraviolet radiation (UVR) and its deleterious effects on living cells selects for UVR-protective mechanisms. Organisms across the tree of life evolved a variety of natural sunscreens to prevent UVR-induced cellular damage and stress. However, in vertebrates, only melanin is known to act as a sunscreen. Here we demonstrate that gadusol, a transparent compound discovered over 40 years ago in fish eggs, is a maternally provided sunscreen required for survival of embryonic and larval zebrafish exposed to UVR. Mutating an enzyme involved in gadusol biosynthesis increases the formation of cyclobutane pyrimidine dimers, a hallmark of UVB-induced DNA damage. Compared to the contributions of melanin and the chorion, gadusol is the primary sunscreening mechanism in embryonic and larval fish. The gadusol biosynthetic pathway is retained in the vast majority of teleost genomes but is repeatedly lost in species whose young are no longer exposed to UVR. Our data demonstrate that gadusol is a maternally provided sunscreen that is critical for early-life survival in the most species-rich branch of the vertebrate phylogeny.

Natural selection versus neutral mutation in the evolution of subterranean life: A false dichotomy?

Throughout the evolutionary tree, there are gains and losses of morphological features, physiological processes, and behavioral patterns. Losses are perhaps nowhere so prominent as for subterranean organisms, which typically show reductions or losses of eyes and pigment. These losses seem easy to explain without recourse to natural selection. Its most modern form is the accumulation of selectively neutral, structurally reducing mutations. Selectionist explanations include direct selection, often involving metabolic efficiency in resource poor subterranean environments, and pleiotropy, where genes affecting eyes and pigment have other effects, such as increasing extra-optic sensory structures. This dichotomy echoes the debate in evolutionary biology in general about the sufficiency of natural selection as an explanation of evolution, e.g., Kimura’s neutral mutation theory. Tests of the two hypotheses have largely been one-sided, with data supporting that one or the other processes is occurring. While these tests have utilized a variety of subterranean organisms, the Mexican cavefish, Astyanax mexicanus, which has eyed extant ancestral-like surface fish conspecifics, is easily bred in the lab, and whose whole genome has been sequenced, is the favored experimental organism. However, with few exceptions, tests for selection versus neutral mutations contain limitations or flaws. Notably, these tests are often one sided, testing for the presence of one or the other process. In fact, it is most likely that both processes occur and make a significant contribution to the two most studied traits in cave evolution: eye and pigment reduction. Furthermore, narrow focus on neutral mutation hypothesis versus selection to explain cave-evolved traits often fails, at least in the simplest forms of these hypotheses, to account for aspects that are likely essential for understanding cave evolution: migration or epigenetic effects. Further, epigenetic effects and phenotypic plasticity have been demonstrated to play an important role in cave evolution in recent studies. Phenotypic plasticity does not by itself result in genetic change of course, but plasticity can reveal cryptic genetic variation which then selection can act on. These processes may result in a radical change in our thinking about evolution of subterranean life, especially the speed with which it may occur. Thus, perhaps it is better to ask what role the interaction of genes and environment plays, in addition to natural selection and neutral mutation.

Novel genome sequence of Chinese cavefish (Triplophysa rosa) reveals pervasive relaxation of natural selection in cavefish genomes

All cavefishes, living exclusively in caves across the globe, exhibit similar phenotypic traits, including the characteristic loss of eyes. To understand whether such phenotypic convergence shares similar genomic bases, here we investigated genome-wide evolutionary signatures of cavefish phenotypes by comparing whole-genome sequences of three pairs of cavefishes and their surface fish relatives. Notably, we newly sequenced and generated a whole-genome assembly of the Chinese cavefish Triplophysa rosa. Our comparative analyses revealed several shared features of cavefish genome evolution. Cavefishes had lower mutation rates than their surface fish relatives. In contrast, the ratio of nonsynonymous to synonymous substitutions (ω) was significantly elevated in cavefishes compared to in surface fishes, consistent with the relaxation of purifying selection. In addition, cavefish genomes had an increased mutational load, including mutations that alter protein hydrophobicity profiles, which were considered harmful. Interestingly, however, we found no overlap in positively selected genes among different cavefish lineages, indicating that the phenotypic convergence in cavefishes was not caused by positive selection of the same sets of genes. Analyses of previously identified candidate genes associated with cave phenotypes supported this conclusion. Genes belonging to the lipid metabolism functional ontology were under relaxed purifying selection in all cavefish genomes, which may be associated with the nutrient-poor habitat of cavefishes. Our work reveals previously uncharacterized patterns of cavefish genome evolution and provides comparative insights into the evolution of cave-associated phenotypic traits.

Modulating antioxidant systems as a therapeutic approach to retinal degeneration

The human retina is facing a big challenge of reactive oxygen species (ROS) from endogenous and exogenous sources. Excessive ROS can cause damage to DNA, lipids, and proteins, triggering abnormal redox signaling, and ultimately lead to cell death. Thus, oxidative stress has been observed in inherited retinal diseases as a common hallmark. To counteract the detrimental effect of ROS, cells are equipped with various antioxidant defenses. In this review, we will focus on the antioxidant systems in the retina and how they can protect retina from oxidative stress. Both small antioxidants and antioxidant enzymes play a role in ROS removal. Particularly, the thioredoxin and glutaredoxin systems, as the major antioxidant systems in mammalian cells, exert functions in redox signaling regulation via modifying cysteines in proteins. In addition, the thioredoxin-like rod-derived cone viability factor (RdCVFL) and thioredoxin interacting protein (TXNIP) can modulate metabolism in photoreceptors and promote their survival. In conclusion, elevating the antioxidant capacity in retina is a promising therapy to curb the progress of inherited retinal degeneration.

Biogeography and eye size evolution of the ogre-faced spiders

Net-casting spiders (Deinopidae) comprise a charismatic family with an enigmatic evolutionary history. There are 67 described species of deinopids, placed among three genera, Deinopis, Menneus, and Asianopis, that are distributed globally throughout the tropics and subtropics. Deinopis and Asianopis, the ogre-faced spiders, are best known for their giant light-capturing posterior median eyes (PME), whereas Menneus does not have enlarged PMEs. Molecular phylogenetic studies have revealed discordance between morphology and molecular data. We employed a character-rich ultra-conserved element (UCE) dataset and a taxon-rich cytochrome-oxidase I (COI) dataset to reconstruct a genus-level phylogeny of Deinopidae, aiming to investigate the group's historical biogeography, and examine PME size evolution. Although the phylogenetic results support the monophyly of Menneus and the single reduction of PME size in deinopids, these data also show that Deinopis is not monophyletic. Consequently, we formally transfer 24 Deinopis species to Asianopis; the transfers comprise all of the African, Australian, South Pacific, and a subset of Central American and Mexican species. Following the divergence of Eastern and Western deinopids in the Cretaceous, Deinopis/Asianopis dispersed from Africa, through Asia and into Australia with its biogeographic history reflecting separation of Western Gondwana as well as long-distance dispersal events.

Functional and ecomorphological evolution of orbit shape in mesozoic archosaurs is driven by body size and diet

The orbit is one of several skull openings in the archosauromorph skull. Intuitively, it could be assumed that orbit shape would closely approximate the shape and size of the eyeball resulting in a predominantly circular morphology. However, a quantification of orbit shape across Archosauromorpha using a geometric morphometric approach demonstrates a large morphological diversity despite the fact that the majority of species retained a circular orbit. This morphological diversity is nearly exclusively driven by large (skull length > 1000 mm) and carnivorous species in all studied archosauromorph groups, but particularly prominently in theropod dinosaurs. While circular orbit shapes are retained in most herbivores and smaller species, as well as in juveniles and early ontogenetic stages, large carnivores adopted elliptical and keyhole-shaped orbits. Biomechanical modelling using finite element analysis reveals that these morphologies are beneficial in mitigating and dissipating feeding-induced stresses without additional reinforcement of the bony structure of the skull.

Out of water in the dark: Plasticity in visual structures and function in an amphibious fish

Many fishes encounter periods of prolonged darkness within their lifetime, yet the consequences for the visual system are poorly understood. We used an amphibious fish (Kryptolebias marmoratus) that occupies dark terrestrial environments during seasonal droughts to test whether exposure to prolonged darkness diminishes visual performance owing to reduced optic tectum (OT) size and/or neurogenesis. We performed a 3-week acclimation with a 2  ×$\times $  2 factorial design, in which fish were either acclimated to a 12 h:12 h or 0 h:24 h light:dark photoperiod in water or in air. We found that water-exposed fish had poorer visual acuity when acclimated to the dark, while air-acclimated fish had poorer visual acuity regardless of photoperiod. The ability of K. marmoratus to capture aerial prey from water followed a similar trend, suggesting that good vision is important for hunting effectively. Changes in visual acuity did not result from changes in OT size, but air-acclimated fish had 37% fewer proliferating cells in the OT than water-acclimated fish. As K. marmoratus are unable to eat on land, reducing cell proliferation in the OT may serve as a mechanism to reduce maintenance costs associated with the visual system. Overall, we suggest that prolonged darkness and air exposure can impair vision in K. marmoratus, and that changes in visual performance may be mediated, in part, by OT neurogenesis. More broadly, we show that plastic changes to the visual system of fishes can have potential consequences for organismal performance and fitness.

Comparative Effects of Embryonic Metformin Exposure on Wild and Laboratory-Spawned Fathead Minnow (Pimephales promelas) Populations

Metformin is routinely detected in aquatic ecosystems because of its widespread use as a treatment for Type 2 diabetes. Laboratory studies have shown that exposure to environmentally relevant concentrations of metformin can alter metabolic pathways and impact the growth of early life stage (ELS) fish; however, it is unknown whether these effects occur in wild populations. Herein, we evaluate whether findings from laboratory studies are representative and describe the relative sensitivities of both populations. Duplicate exposures (0, 5, or 50 μg/L metformin) were conducted using wild- and lab-spawned fathead minnow (Pimephales promelas) embryos. Apart from the water source, exposure conditions remained constant. Wild embryos were exposed to previously dosed lake water to account for changes in bioavailability, while reconstituted freshwater was used for the laboratory study. Developmental metformin exposure differentially impacted the growth and morphology of both cohorts, with energy dyshomeostasis and visual effects indicated. The fitness of wild-spawned larvae was impacted to a greater extent relative to lab-spawned fish. Moreover, baseline data reveal important morphological differences between wild- and lab-spawned ELS fatheads that may diminish representativeness of lab studies. Findings also confirm the bioavailability of metformin in naturally occurring systems and suggest current exposure scenarios may be sufficient to negatively impact developing fish.

Parallel decay of vision genes in subterranean water beetles

In the framework of neutral theory of molecular evolution, genes specific to the development and function of eyes in subterranean animals living in permanent darkness are expected to evolve by relaxed selection, ultimately becoming pseudogenes. However, definitive empirical evidence for the role of neutral processes in the loss of vision over evolutionary time remains controversial. In previous studies, we characterized an assemblage of independently-evolved water beetle (Dytiscidae) species from a subterranean archipelago in Western Australia, where parallel vision and eye loss have occurred. Using a combination of transcriptomics and exon capture, we present evidence of parallel coding sequence decay, resulting from the accumulation of frameshift mutations and premature stop codons, in eight phototransduction genes (arrestins, opsins, ninaC and transient receptor potential channel genes) in 32 subterranean species in contrast to surface species, where these genes have open reading frames. Our results provide strong evidence to support neutral evolutionary processes as a major contributing factor to the loss of phototransduction genes in subterranean animals, with the ultimate fate being the irreversible loss of a light detection system.

Alterations to cavefish red blood cells provide evidence of adaptation to reduced subterranean oxygen

Animals inhabiting extreme environments allow the powerful opportunity to examine adaptive evolution in response to diverse pressures. One such pressure is reduced oxygen, commonly present at high-altitude and subterranean environments. Cave-dwelling animals must also deal with darkness and starvation, both of which have been rigorously studied as key forces driving the evolution of cave-associated traits. Interestingly, hypoxia as an environmental pressure has received less attention. Here we examined putatively adaptive phenotypes evolving in a freshwater teleost fish, Astyanax mexicanus, which includes both surface- and cave-dwelling forms. This model system also provides the opportunity to identify convergent responses to hypoxia, owing to the presence of numerous natural and independently-colonised cave populations, alongside closely-related surface conspecifics. The focus of this study is hemoglobin, an essential molecule for oxygen transport and delivery. We found that multiple cave populations harbor a higher concentration of hemoglobin in their blood, which is coincident with an increase in cave morph erythrocyte size compared to surface fish. Interestingly, both cave and surface morphs have comparable numbers of erythrocytes per unit of blood, suggesting elevated hemoglobin is not due to overproduction of red blood cells. Alternatively, owing to an increased cell area of erythrocytes in cavefish, we reason that they contain more hemoglobin per erythrocyte. These findings support the notion that cavefish have adapted to hypoxia in caves through modulation of both hemoglobin production and erythrocyte size. This work reveals an additional adaptive feature of Astyanax cavefish, and demonstrates that coordinated changes between cellular architecture and molecular changes are necessary for organisms evolving under intense environmental pressure.

A natural history of vertebrate vision loss: Insight from mammalian vision for human visual function

Research on the origin of vision and vision loss in naturally "blind" animal species can reveal the tasks that vision fulfills and the brain's role in visual experience. Models that incorporate evolutionary history, natural variation in visual ability, and experimental manipulations can help disentangle visual ability at a superficial level from behaviors linked to vision but not solely reliant upon it, and could assist the translation of ophthalmological research in animal models to human treatments. To unravel the similarities between blind individuals and blind species, we review concepts of 'blindness' and its behavioral correlates across a range of species. We explore the ancestral emergence of vision in vertebrates, and the loss of vision in blind species with reference to an evolution-based classification scheme. We applied phylogenetic comparative methods to a mammalian tree to explore the evolution of visual acuity using ancestral state estimations. Future research into the natural history of vision loss could help elucidate the function of vision and inspire innovations in how to address vision loss in humans.

Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia-inducible genes

Dark caves lacking primary productivity can expose subterranean animals to hypoxia. We used the surface-dwelling (surface fish) and cave-dwelling (cavefish) morphs of Astyanax mexicanus as a model for understanding the mechanisms of hypoxia tolerance in the cave environment. Primitive hematopoiesis, which is restricted to the posterior lateral mesoderm in other teleosts, also occurs in the anterior lateral mesoderm in Astyanax, potentially pre-adapting surface fish for hypoxic cave colonization. Cavefish have enlarged both hematopoietic domains and develop more erythrocytes than surface fish, which are required for normal development in both morphs. Laboratory-induced hypoxia suppresses growth in surface fish but not in cavefish. Both morphs respond to hypoxia by overexpressing hypoxia-inducible factor 1 (hif1) pathway genes, and some hif1 genes are constitutively upregulated in normoxic cavefish to similar levels as in hypoxic surface fish. We conclude that cavefish cope with hypoxia by increasing erythrocyte development and constitutive hif1 gene overexpression.

Evolution of orbit size in toothed whales (Artiodactyla: Odontoceti)

For many marine tetrapods, vision is important for finding food and navigating underwater, and eye size has increased to improve the capture of light in dim ocean depths. Odontocete whales, in contrast, rely instead on echolocation for navigation and prey capture. We tested whether the evolution of echolocation has influenced the orbit size, a proxy for eye size, and examined how orbit size evolved over time. We also assessed variation in orbit size amongst whales and tested how body size, diving ability, sound production, foraging habitat, and prey capture strategy influenced the orbit size using phylogenetic independent contrasts and phylogenetic ANOVAs. Using measurements of orbit length and bizygomatic width, we calculated proportional orbit size for 70 extant and 29 extinct whale taxa, with an emphasis on Odontoceti. We then performed ancestral character state reconstruction on a time-calibrated composite phylogeny. Our analysis revealed that there was no shift in proportional orbit size from archaeocetes through stem odontocetes, indicating that the evolution of echolocation did not influence the orbit size. Proportional orbit size increased in Ziphiidae, Phocoenidae, and Cephalorhynchus. Proportional orbit size decreased in Balaenidae, Physeteridae, Platanistidae, and Lipotidae. Body size, diving ability, foraging environment, and prey capture strategy had a significant influence on orbit size, but only without phylogenetic correction. An increase in orbit size is associated with deep diving behavior in beaked whales, while progenesis and retention of juvenile features into adulthood explain the pattern observed in Phocoenidae and Cephalorhynchus. Decrease in proportional orbit size is associated with adaptation toward murky freshwater environments in odontocetes and skim feeding in balaenids. Our study reveals that the evolution of echolocation had little effect on orbit size, which is variable in whales, and that adaptation for different feeding modes and habitat explains some of this variance.

Experience-expectant brain plasticity corresponds to caste-specific abiotic challenges in dampwood termites (Zootermopsis angusticollis and Z. nevadensis)

Hypotheses for adaptive brain investment predict associations between the relative sizes of functionally distinct brain regions and the sensory/cognitive demands animals confront. We measured developmental differences in the relative sizes of visual processing brain regions (optic lobes) among dampwood termite castes to test whether optic lobe investment matches caste differences in exposure to visually complex environments. The winged primary reproductives (Kings/Queens) on mating flights are the only caste to leave the dark nest cavities and as predicted, Kings/Queens showed greater relative investment in optic lobe tissue than nestbound (neotenic) reproductives and soldiers in two dampwood termite species (Zootermopsis angusticollis and Z. nevadensis). Relative optic lobe size spanned more than an order of magnitude among the castes we studied, suggesting the growth of the optic lobes incurs substantial tissue costs. Optic lobe growth was experience-expectant: the optic lobes of Z. angusticollis brachypterous nymphs, which typically develop into Kings/Queens, were relatively larger than the optic lobes of apterous nymphs, which precede neotenics and soldiers, and relative optic lobe size of nestbound brachypterous nymphs was statistically similar to that of Kings/Queens. Experience-expectant brain tissue growth is rarely documented in insects, likely because it entails high potential costs of tissue production and maintenance and relatively low immediate sensory/cognitive benefits. We develop hypotheses for the conditions under which experience-expectant growth in brain regions could be favored by natural selection.

Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes

Epigenetic variation modulates gene expression and can be heritable. However, knowledge of the contribution of epigenetic divergence to adaptive diversification in nature remains limited. The massive evolutionary radiation of Lake Malawi cichlid fishes displaying extensive phenotypic diversity despite extremely low sequence divergence is an excellent system to study the epigenomic contribution to adaptation. Here, we present a comparative genome-wide methylome and transcriptome study, focussing on liver and muscle tissues in phenotypically divergent cichlid species. In both tissues we find substantial methylome divergence among species. Differentially methylated regions (DMR), enriched in evolutionary young transposons, are associated with transcription changes of ecologically-relevant genes related to energy expenditure and lipid metabolism, pointing to a link between dietary ecology and methylome divergence. Unexpectedly, half of all species-specific DMRs are shared across tissues and are enriched in developmental genes, likely reflecting distinct epigenetic developmental programmes. Our study reveals substantial methylome divergence in closely-related cichlid fishes and represents a resource to study the role of epigenetics in species diversification.

No Evidence for Effects of Ecological and Behavioral Factors on Eye Size Evolution in Anurans

Eye size varies markedly among taxonomic levels, and this variation is often related to the patterns shaped by phylogeny and ecological and behavioral factors. The selective pressures underlying eye size evolution are especially studied in fishes, anurans, birds, and mammals. However, selective pressures underlying the eye size evolution in anurans have inconsistent scaling rules. Here, we investigated the links between eye size and both ecological (e.g., light availability and habitat type) and behavioral factors (e.g., activity time, foraging mobility, defensive strategy, and mating system) among 252 species of anurans by using phylogenetically controlled generalized least-squared (PGLS) regression. Results show that anuran eye size scales hypo-allometrically with body size. However, eye size was not significantly influenced by ecological and behavioral factors, including habitat type, activity time, light availability, foraging mobility, defensive strategy, and mating system. Therefore, neither ecology nor behavior plays a key role in promoting eye size evolution in frogs.

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

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

Domestication-induced reduction in eye size revealed in multiple common garden experiments: The case of Atlantic salmon (Salmo salar L.)

Domestication leads to changes in traits that are under directional selection in breeding programmes, though unintentional changes in nonproduction traits can also arise. In offspring of escaping fish and any hybrid progeny, such unintentionally altered traits may reduce fitness in the wild. Atlantic salmon breeding programmes were established in the early 1970s, resulting in genetic changes in multiple traits. However, the impact of domestication on eye size has not been studied. We measured body size corrected eye size in 4000 salmon from six common garden experiments conducted under artificial and natural conditions, in freshwater and saltwater environments, in two countries. Within these common gardens, offspring of domesticated and wild parents were crossed to produce 11 strains, with varying genetic backgrounds (wild, domesticated, F1 hybrids, F2 hybrids and backcrosses). Size-adjusted eye size was influenced by both genetic and environmental factors. Domesticated fish reared under artificial conditions had smaller adjusted eye size when compared to wild fish reared under identical conditions, in both the freshwater and marine environments, and in both Irish and Norwegian experiments. However, in parr that had been introduced into a river environment shortly after hatching and sampled at the end of their first summer, differences in adjusted eye size observed among genetic groups were of a reduced magnitude and were nonsignificant in 2-year-old sea migrating smolts sampled in the river immediately prior to sea entry. Collectively, our findings could suggest that where natural selection is present, individuals with reduced eye size are maladapted and consequently have reduced fitness, building on our understanding of the mechanisms that underlie a well-documented reduction in the fitness of the progeny of domesticated salmon, including hybrid progeny, in the wild.

Contrasting physiological responses between invasive sea lamprey and non-target bluegill in response to acute lampricide exposure

Control of invasive sea lamprey (Petromyzon marinus) in the Laurentian Great Lakes of North America uses lampricides, which consist of 3-trifluoromethyl-4-nitrophenol (TFM) and niclosamide. Lampricides are thought to inhibit aerobic energy synthesis, with TFM having a relatively greater selective action against lampreys. While the toxicity and physiological effects of TFM are known, the impacts associated with exposure to niclosamide and TFM:niclosamide mixtures are poorly characterized in fishes. Therefore, focusing on energy metabolism, we quantified the physiological responses of larval sea lamprey and bluegill (Lepomis macrochirus), a non-target, native species. Exposures consisted of each lampricide alone (TFM at the species-specific 24 h LC₁₀; niclosamide at 1.5% of the mixture's TFM concentration) or a mixture of the two (larval sea lamprey at TFM 24 h LC₁₀ + 1.5% niclosamide; bluegill at sea lamprey's TFM 24 h LC_99.9 + 1.5% niclosamide) for 24 h. Tissues (brain, skeletal muscle, and liver) were sampled at 6, 12, and 24 h of exposure and assayed for concentrations of ATP, phosphocreatine, glycogen, lactate, and glucose and tissue lampricide levels. In larval sea lamprey, TFM had little effect on brain and skeletal muscle, but niclosamide resulted in a depletion of high energy substrates in both tissues. Mixture-exposed lamprey showed depletion of high energy substrates, accumulation of lactate, and high mortality rates. Bluegill were largely unaffected by toxicant exposures. However, bluegill liver showed lower glycogen and lactate under all three toxicant exposures suggesting increased metabolic turnover. Bluegill also had lower concentrations of TFM and niclosamide in their tissues when compared to lamprey. Our results indicate that lampricide toxicity in sea lamprey larvae is mediated through a depletion of high energy substrates because of impaired aerobic ATP synthesis. We also confirmed that non-target bluegill showed high tolerance to lampricide exposure, an effect potentially mediated through a high detoxification capacity relative to lampreys.

Insights into the vision of the hadal snailfish Pseudoliparis swirei through proteomic analysis of the eye

No sunlight can reach the hadal trench, but some fishes dwelling there still have apparent eye morphology. However, whether they are capable of sensing light remains unknown. In this study, the eyes of the dominant hadal endemic snailfish Pseudoliparis swirei from the Mariana Trench were analyzed using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). A total of 2088 proteins were identified in the eye proteome, most of which had at least one hit against public databases and could be mapped to 316 metabolic pathways. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways directly contributing to visual phototransduction were significantly enriched from the top 10% dominant proteins, implying abundant metabolic activities in the eye and it is still a functional visual organ. One rhodopsin was identified in the eye proteome, sequence analysis indicated that it might have an absorption maximum at ∼480 nm and be sensitive to dim blue light. In addition, proteins that might contribute to extreme environment adaptation, such as heat shock proteins and chaperonin-containing T-complex protein 1, were also highly expressed in the eye. Overall, these results provide insights into the molecular mechanism underlying the vision of hadal snailfish and provide a useful database for further research.

Have the eyes of bioluminescent scale worms adapted to see their own light? A comparative study of eyes and vision in Harmothoe imbricata and Lepidonotus squamatus

Annelids constitute a diverse phylum with more than 19,000 species, which exhibit greatly varying morphologies and lifestyles ranging from sessile detritivores to fast swimming active predators. The lifestyle of an animal is closely linked to its sensory systems, not least the visual equipment. Interestingly, many errantian annelid species from different families, such as the scale worms (Polynoidae), have two pairs of eyes on their prostomium. These eyes are typically 100-200 µm in diameter and structurally similar judged from their gross morphology. The polynoids Harmothoe imbricata and Lepidonotus squamatus from the North Atlantic are both benthic predators preying on small invertebrates but only H. imbricata can produce bioluminescence in its scales. Here, we examined the eye morphology, photoreceptor physiology and light-guided behaviour in these two scale worms to assess their visual capacity and visual ecology. The structure and physiology of the two pairs of eyes are remarkably similar within each species, with the only difference being the gaze direction. The photoreceptor physiology, however, differs between species. Both species express a single opsin in their eyes, but in H. imbricata the peak sensitivity is green shifted and the temporal resolution is lower, suggesting that the eyes of H. imbricata are adapted to detect their own bioluminescence. The behavioural experiments showed that both species are strictly night active but yielded no support for the hypothesis that H. imbricata is repelled by its own bioluminescence.