Abstract Understanding the genetic basis of adaptation in natural populations to changing environmental conditions is challenging. The relatively simple genotype-to-phenotype relationship between opsin genes and visual pigments offers a particularly informative model to explore the molecular mechanisms underpinning adaptive phenotypic change in natural populations. Here we leveraged the natural experiment provided by the tectonic closure of the Central American seaway that created allopatric, sister taxa in multiple, independent lineages of marine organisms and exposed them to distinct underwater light environments: either the more turbid Tropical Eastern Pacific (TEP), or the spectrally broader Caribbean Sea. Using two species pairs of planktivorous teleosts, the Azurina multilineata / A. atrilobata damselfish and the Cephalopholis (Paranthias) furcifer / C. colonus groupers, we explore to what extent visual sensitivity converged to similar adaptations in response to similar foraging strategies and shared underwater light in each marine basin. We found that the compression of the underwater light field towards the central portion of the spectrum from Caribbean to TEP waters is reflected in similar shifts towards the centre of the light spectrum in overall single and double cone sensitivities in both families. Both TEP species have single (short-wavelength) cone sensitivities shifted to longer wavelengths and double (long-wavelength) cone sensitivities shifted to shorter wavelengths, compared to their Caribbean counterparts. These parallel shifts in visual sensitivities observed in response to shared underwater light environments are accomplished by different underlying opsin gene toolsets in the two lineages. Similarly, expression changes in pathways associated with the visual system revealed limited parallelism at the molecular level.

Over hundreds of years, breeders have selectively bred different strains of canaries for plumage and song characteristics. One strain, the Belgian Waterslager canary, has been bred for loud, low frequency song and coincidently has been found to have a high-frequency hearing loss due to damaged and missing hair cells in the basilar papilla. Here, we investigated the possible genetic basis for this hearing loss in the Belgian Waterslager canary by conducting whole-genome Illumina (San Diego, CA) sequencing in three canary strains. We identified a total of 16 Belgian Waterslager male-specific "high-impact" single nucleotide polymorphisms (SNP) variants with three mutations occurring within genes previously identified in mammalian hair cell abnormalities and hearing loss disorders: pericentriolar material 1 (PCM1), p21 (RAC1) activated kinase 3 (PAK3)-like, and protein tyrosine phosphatase receptor type K (PTPRK). Interestingly, we also identified three male-specific "high-impact" SNP variants in one of our control strains: the American Singer canary. One of these mutations occurs within genes previously associated with hearing loss in mammals. Since songbirds rely on hearing to develop a normal vocal repertoire, investigating the role of these genes in hearing loss at the molecular level may provide a valuable animal model for examining the relationship between hearing loss and vocal development in humans.

Sensory adaptation is widely hypothesized to drive ecological speciation, yet empirical evidence from natural populations undergoing early stage divergence remains limited. In Lake Masoko, a young crater lake in East Africa, the haplochromine cichlid Astatotilapia calliptera is undergoing early stage sympatric speciation into shallow-water littoral and deep-water benthic ecotypes that experience contrasting light environments. Here, we integrate retinal transcriptomics, phenotypic analyses, and visual modeling to uncover rapid sensory divergence associated with this ecological transition. We find striking shifts in cone opsin expression, with the benthic ecotype exhibiting a switch from short-wavelength sensitive SWS2B to SWS2A and an overall narrowing of cone sensitivity toward the center of the light spectrum, consistent with changes in deep-water light environment. In contrast, coding sequence variation in opsin genes was limited and no significant differences in allele frequencies were detected across nine polymorphic sites, pointing to expression regulation as the primary axis of early divergence in visual systems. In parallel, we observed divergence in male signaling traits, with benthic males displaying deeper red egg-spots, aligning with predictions from visual modeling of signal efficiency in different light environments. These results demonstrate rapid transcriptomic and phenotypic divergence in associated signaling traits—within ∼1,000 years—supporting a potential role for regulatory evolution in sensory adaptation during early ecological speciation.

Cichlid fishes show remarkable variation in visual sensitivities through differential expression of seven cone opsin genes. Many species undergo spectral sensitivity shifts from shorter to longer wavelengths as they develop from larvae to adults. However, while some species retain larval-like short wavelength sensitivities, others show adult-like longer wavelength sensitivities throughout life. The riverine cichlid, Astatotilapia burtoni, shows a single cone progression from ultraviolet to violet to blue sensitivity, while their long wavelength double cones maintain green and red sensitivities throughout life. To identify mechanisms that regulate these sensitivities, we asked whether thyroid hormone (TH) or light environment can drive shifts. We find that developmental treatment with TH can speed shifts to longer wavelength sensitivity, but only in single cones. TH inhibition can short wavelength shift adult opsin expression. Exposure to light regimes containing UV wavelengths induce short wavelength shifts in single cones early in development. None of the treatments produces double cone shifts or significant expression of the shortest wavelength double cone opsin, rh2b, although we detect no cis-regulatory variation. This suggests that while single cones show both TH and light plasticity, A. burtoni double cones have lost this plasticity, perhaps through changes in trans-acting opsin regulation.

Coral reef fishes are diverse in ecology and behaviour and show remarkable colour variability. Investigating the visual pigment gene (opsin) expression in these fishes makes it possible to associate their visual genotype and phenotype (spectral sensitivities) to visual tasks, such as feeding strategy or conspecific detection. By studying all major damselfish clades (Pomacentridae) and representatives from five other coral reef fish families, we show that the long-wavelength-sensitive (lws) opsin is highly expressed in algivorous and less or not expressed in zooplanktivorous species. Lws is also upregulated in species with orange/red colours (reflectance >520 nm) and expression is highest in orange/red-coloured algivores. Visual models from the perspective of a typical damselfish indicate that sensitivity to longer wavelengths does enhance the ability to detect the red to far-red component of algae and orange/red-coloured conspecifics, possibly enabling social signalling. Character state reconstructions indicate that in the early evolutionary history of damselfishes, there was no lws expression and no orange/red coloration. Omnivory was most often the dominant state. Although herbivory was sometimes dominant, zooplanktivory was never dominant. Sensitivity to long wavelength (increased lws expression) only emerged in association with algivory but never with zooplanktivory. Higher lws expression is also exploited by social signalling in orange/red, which emerged after the transition to algivory. Although the relative timing of traits may deviate by different reconstructions and alternative explanations are possible, our results are consistent with sensory bias whereby social signals evolve as a correlated response to natural selection on sensory system properties in other contexts.

Organismal biology (OrgBio) comprises the diversity, structures, and functions of all organisms from bacteria to humans. Arguably, OrgBio is often the most poorly taught and least conceptually rigorous section of the introductory biology sequence offered at most U.S. institutions of higher education. This article reports on the successful implementation of conceptual and pedagogical reforms in an introductory OrgBio course offered at a large public university. Conceptual reforms were based on a theoretical framework consisting of universal physical and chemical laws, deep molecular homologies, and diverse structure–function relationships. Pedagogical reforms involved the development of group active engagements (GAEs) that were designed to encourage students to develop their abilities to engage in principles-based reasoning. A new model for characterizing different approaches toward principles-based reasoning in biology was developed to analyze these GAEs. Two surveys indicated that OrgBio students developed more favorable perceptions about the effectiveness of GAE-based course offerings, as compared to similar lecture-based versions.

Cichlid fish have undergone explosive radiation in a process aided by sexual selection. Thus, phenotypes that contribute to reproduction may partially explain the rate of radiation. One such phenotype is the presence of circular spots on the anal fin of the haplochromine cichlids. In 1963, Wickler postulated this phenotype acts as an egg mimic which enhances male fertilization success. However, it remained unclear whether cichlids can distinguish between eggs and egg spots in their natural environment. Further, studies have found differing effects of egg spot characteristics in female mate preference. In this study, we quantified the color of eggs, egg spots, and anal fins of two haplochromine species (Metriaclima benetos and Astatotilapia burtoni). Using a receptor noise limited (RNL) visual model, we found that these species are unable to distinguish the colors of eggs and egg spots in the lighting of their natural habitat. Further, only M. benetos could distinguish the color of egg spots from anal fins. This study supports Wickler’s egg spot mimicry hypothesis and potentially explains species differences in the roles of egg spots as sexually selected traits. It further points out the importance of avoiding human biases in quantifying what colors fish can and cannot distinguish.

African cichlids provide an ideal platform for studying genes responsible for mate choice and species divergence. These highly speciose fishes vary in expression of seven distinct cone opsin genes. Each species expresses a subset of these genes, leading to extensive diversity in visual sensitivities. In a genetic cross between two Lake Malawi cichlid species with varying opsin expression, we previously identified two quantitative trait loci responsible for differential expression of the short wavelength sensitive SWS2A opsin gene. We then identified the RX1 gene as contributing the largest effect. Here we aim to identify the second causative factor. We identify MITFA and BHE40 as candidate genes. Several lines of evidence suggest that an intronic insertion at the MITFA locus may be responsible for differential SWS2A expression. We tested the effect of MITFA on SWS2A expression using CRISPR/Cas9 coding sequence knockouts in Astatotilapia burtoni. Although the mutation altered SWS2A expression, its effect contradicted our expectations, with MITFA(d10/d10) mutants expressing more SWS2A opsin. This work provides some support for a role for MITFA, but additional work is needed to understand the mechanism by which MITFA acts, and to explore the potential role of other genes, including BHE40.

The Southern catfish ( Silurus meridionalis ) is a nocturnal and benthic freshwater fish endemic to the Yangtze River and its tributaries. In this study, we constructed a chromosome‐level draft genome of S . meridionalis using 69.7‐Gb Nanopore long reads and 49.5‐Gb Illumina short reads. The genome assembly was 741.2 Mb in size with a contig N50 of 13.19 Mb. An additional 116.4 Gb of Bionano and 77.4 Gb of Hi‐C data were applied to assemble contigs into scaffolds and further into 29 chromosomes, resulting in a 738.9‐Mb genome with a scaffold N50 of 28.04 Mb. A total of 22,965 protein‐coding genes were predicted from the genome with 22,519 (98.06%) genes functionally annotated. Comparative genomic and transcriptomic analyses revealed a rod‐dominated visual system which was responsible for scotopic vision. The absence of cone opsins SWS1 and SWS2 resulted in the lack of ultraviolet and blue violet sensitivity. Mutations at key amino acid sites of RH1.1, RH1.2 and RH2 resulted in spectral tuning good for dim light vision and narrow colour vision. A higher expression level of rod phototransduction genes than that of cone genes and higher rod‐to‐cone ratio led to higher optical sensitivity under dim light conditions. In addition, analysis of the genes involved in eye morphogenesis and development revealed the loss of some conserved noncoding elements, which might be associated with the small eyes in catfish. Together, our study provides important clues for the adaptation of the catfish visual system to the nocturnal and benthic lifestyles. The draft genome of S . meridionalis represents a valuable resource for studies of the molecular mechanisms of ecological adaptation.

The diversity of avian visual phenotypes provides a framework for studying mechanisms of trait diversification generally, and the evolution of vertebrate vision, specifically. Previous research has focused on opsins, but to fully understand visual adaptation, we must study the complete phototransduction cascade (PTC). Here, we developed a probe set that captures exonic regions of 46 genes representing the PTC and other light responses. For a subset of species, we directly compared gene capture between our probe set and low-coverage whole genome sequencing (WGS), and we discuss considerations for choosing between these methods. Finally, we developed a unique strategy to avoid chimeric assembly by using "decoy" reference sequences. We successfully captured an average of 64% of our targeted exome in 46 species across 14 orders using the probe set and had similar recovery using the WGS data. Compared to WGS or transcriptomes, our probe set: (1) reduces sequencing requirements by efficiently capturing vision genes, (2) employs a simpler bioinformatic pipeline by limiting required assembly and negating annotation, and (3) eliminates the need for fresh tissues, enabling researchers to leverage existing museum collections. We then utilized our vision exome data to identify positively selected genes in two evolutionary scenarios-evolution of night vision in nocturnal birds and evolution of high-speed vision specific to manakins (Pipridae). We found parallel positive selection of SLC24A1 in both scenarios, implicating the alteration of rod response kinetics, which could improve color discrimination in dim light conditions and/or facilitate higher temporal resolution.

Vision represents an excellent model for studying adaptation, given the genotype-to-phenotype map that has been characterized in a number of taxa. Fish possess a diverse range of visual sensitivities and adaptations to underwater light, making them an excellent group to study visual system evolution. In particular, some speciose but understudied lineages can provide a unique opportunity to better understand aspects of visual system evolution such as opsin gene duplication and neofunctionalization. In this study, we showcase the visual system evolution of neotropical Characiformes and the spectral tuning mechanisms they exhibit to modulate their visual sensitivities. Such mechanisms include gene duplications and losses, gene conversion, opsin amino acid sequence and expression variation, and A1 /A2 -chromophore shifts. The Characiforms we studied utilize three cone opsin classes (SWS2, RH2, LWS) and a rod opsin (RH1). However, the characiform's entire opsin gene repertoire is a product of dynamic evolution by opsin gene loss (SWS1, RH2) and duplication (LWS, RH1). The LWS- and RH1-duplicates originated from a teleost specific whole-genome duplication as well as characiform-specific duplication events. Both LWS-opsins exhibit gene conversion and, through substitutions in key tuning sites, one of the LWS-paralogues has acquired spectral sensitivity to green light. These sequence changes suggest reversion and parallel evolution of key tuning sites. Furthermore, characiforms' colour vision is based on the expression of both LWS-paralogues and SWS2. Finally, we found interspecific and intraspecific variation in A1 /A2 -chromophores proportions, correlating with the light environment. These multiple mechanisms may be a result of the diverse visual environments where Characiformes have evolved.

ABSTRACT Knowledge of population dynamics is critical for species of conservation concern so wildlife researchers need to take advantage of biases in animals' behaviors that could help them monitor populations. This is particularly important for amphibians because many populations are declining and difficult to observe. Attraction of vertebrates to light is a well‐known navigational cue and some fisheries strategies utilize light sources to increase catch success. To optimize population monitoring of state‐endangered eastern tiger salamanders ( Ambystoma tigrinum ), we tested the utility of colored glow sticks (green, orange, pink, or yellow) as bait in traps in Maryland and Delaware, USA, during 2015–2016. We then measured intensities of the colored glow sticks and estimated photoreceptive quantum catches of each color according to the spectral sensitivities of eastern tiger salamanders. We found that eastern tiger salamanders' photoreceptors had greater quantum catches of photons from green and yellow glow sticks. However, traps baited with orange glow sticks were more than twice as likely to capture eastern tiger salamanders than were traps baited with green or yellow. There were no differences in the number of salamanders caught per successful trap among glow stick colors, perhaps due to attraction of salamanders to motion from previously captured salamanders. Our results indicate that biases other than perceived intensity of light sources may drive behavioral preferences. © 2020 The Wildlife Society.

Sensory systems are tuned by selection to maximize organismal fitness in particular environments. This tuning has implications for intraspecies communication, the maintenance of species boundaries, and speciation. Tuning of color vision largely depends on the sequence of the expressed opsin proteins. To improve tuning of visual sensitivities to shifts in habitat or foraging ecology over the course of development, many organisms change which opsins are expressed. Changes in this developmental sequence (heterochronic shifts) can create differences in visual sensitivity among closely related species. The genetic mechanisms by which these developmental shifts occur are poorly understood. Here, we use quantitative trait locus analyses, genome sequencing, and gene expression studies in African cichlid fishes to identify a role for the transcription factor Tbx2a in driving a switch between long wavelength sensitive (LWS) and Rhodopsin-like (RH2) opsin expression. We identify binding sites for Tbx2a in the LWS promoter and the highly conserved locus control region of RH2 which concurrently promote LWS expression while repressing RH2 expression. We also present evidence that a single change in Tbx2a regulatory sequence has led to a species difference in visual tuning, providing the first mechanistic model for the evolution of rapid switches in sensory tuning. This difference in visual tuning likely has important roles in evolution as it corresponds to differences in diet, microhabitat choice, and male nuptial coloration.

Canaries have been selectively bred for specific song characteristics (song canaries) or for morphology or plumage (type canaries) for centuries. Type canaries (e.g., Border and Gloster strains) retain song characteristics that are quite similar to those of wild canaries. By contrast, song canaries (e.g., Belgian Waterslager and Roller strains) have been selected for song types pleasing to the human ear, resulting in songs that, in most cases, are less complex, lower-pitched, and narrower in a frequency range than songs from wild canaries. We now suspect that song selection in the Belgian Waterslager song canary has either directly or indirectly resulted in high-frequency hearing loss associated with hair cell abnormalities. Here, we compare hearing in the Belgian Waterslager and several other type and song canaries including the American Singer Canary. Though bred only since the 1930s, American Singer canaries may also have a high-frequency hearing loss that looks very similar to that of the Belgian Waterslager and may involve similar pathologies. Illumina whole-genome sequencing has preliminarily identified a number of high-impact SnpEff variants in Belgian Waterslager and American Singer Canaries, some of which are related to deafness genes in mammals.

African cichlid fishes are a prime model for studying the mechanisms of speciation. Despite the development of extensive genomic resources, it has been difficult to determine which sources of genetic variation are responsible for variation in cichlid phenotypes. Cichlids have some of the largest known shifts in vertebrate visual sensitivity. These shifts arise mainly from the differential expression of seven cone opsin genes. By mapping expression quantitative trait loci (eQTL) in intergeneric crosses of Lake Malawi (LM) cichlids, we have thus far identified four causative genetic variants that correspond to indels in the promoters of either key transcription factors or of the opsin gene itself. Here we show that these indels are caused by the movement of transposable elements (TEs). These precise indels are not found outside of LM, suggesting that these TEs are recently active and are segregating within the Malawi cichlid lineage. A similar indel has arisen independently outside of LM at one locus, suggesting that some locations are primed for TE insertion and the resulting indels. Increased TE mobility may be associated with interspecific hybridization, which disrupt mechanisms of TE suppression. Overall, our study suggests that TEs may contribute to key regulatory changes, and may facilitate rapid phenotypic change and possibly speciation in African cichlids.

AbstractSensory systems are tuned by selection to maximize organismal fitness in particular environments. This tuning has implications for intraspecies communication, the maintenance of species boundaries, and speciation. Tuning of color vision largely depends on the sequence of the expressed opsin proteins. To improve tuning of visual sensitivities to shifts in habitat or foraging ecology over the course of development, many organisms change which opsins are expressed. Changes in this developmental sequence (heterochronic shifts) can create differences in visual sensitivity among closely related species. The genetic mechanisms by which these developmental shifts occur are poorly understood. Here, we use quantitative trait locus analyses, genome sequencing, and gene expression studies in African cichlid fishes to identify a role for the transcription factor Tbx2a in driving a switch between long wavelength sensitive (LWS) and Rhodopsin-like (RH2) opsin expression. We identify binding sites for Tbx2a in the LWS promoter and the highly conserved locus control region of RH2 which concurrently promote LWS expression while repressing RH2 expression. We also present evidence that a single change in Tbx2a regulatory sequence has led to a species difference in visual tuning, providing the first mechanistic model for the evolution of rapid switches in sensory tuning. This difference in visual tuning likely has important roles in evolution as it corresponds to differences in diet, microhabitat choice, and male nuptial coloration.

The family Cichlidae contains approximately 2000 species that live in diverse freshwater habitats including murky lakes, turbid rivers, and clear lakes from both the Old and New Worlds. Their visual systems are similarly diverse and have evolved specific sensitivities that differ along several axes of variation. Variation in cornea and lens transmission affect which wavelengths reach the retina. Variation in photoreceptor number and distribution affect brightness sensitivity, spectral sensitivity and resolution. Probably their most dynamic characteristic is the variation in visual pigment peak sensitivities. Visual pigments can be altered through changes in chromophore, opsin sequence and opsin expression. Opsin expression varies by altering which of the seven available cone opsins in their genomes are turned on. These opsins can even be coexpressed to produce seemingly infinitely tunable cone sensitivities. Both chromophore and opsin expression can vary on either rapid (hours or days), slower (seasonal or ontogenetic) or evolutionary timescales. Such visual system shifts have enabled cichlids to adapt to different habitats and foraging styles. Through both short term plasticity and longer evolutionary adaptations, cichlids have proven to be ecologically successful and an excellent model for studying organismal adaptation.

Among vertebrates, teleost eye diversity exceeds that found in all other groups. Their spectral sensitivities range from ultraviolet to red, and the number of visual pigments varies from 1 to over 40. This variation is correlated with the different ecologies and life histories of fish species, including their variable aquatic habitats: murky lakes, clear oceans, deep seas and turbulent rivers. These ecotopes often change with the season, but fish may also migrate between ecotopes diurnally, seasonally or ontogenetically. To survive in these variable light habitats, fish visual systems have evolved a suite of mechanisms that modulate spectral sensitivities on a range of timescales. These mechanisms include: (1) optical media that filter light, (2) variations in photoreceptor type and size to vary absorbance and sensitivity, and (3) changes in photoreceptor visual pigments to optimize peak sensitivity. The visual pigment changes can result from changes in chromophore or changes to the opsin. Opsin variation results from changes in opsin sequence, opsin expression or co-expression, and opsin gene duplications and losses. Here, we review visual diversity in a number of teleost groups where the structural and molecular mechanisms underlying their spectral sensitivities have been relatively well determined. Although we document considerable variability, this alone does not imply functional difference per se. We therefore highlight the need for more studies that examine species with known sensitivity differences, emphasizing behavioral experiments to test whether such differences actually matter in the execution of visual tasks that are relevant to the fish.