Opsin gene duplication and diversification in the guppy, a model for sexual selection

The evolutionary history and spectral tuning of vertebrate visual opsins

Many animals depend on the sense of vision for survival. In eumetazoans, vision requires specialized, light-sensitive cells called photoreceptors. Light reaches the photoreceptors and triggers the excitation of light-detecting proteins called opsins. Here, we describe the story of visual opsin evolution from the ancestral bilaterian to the extant vertebrate lineages. We explain the mechanisms determining color vision of extant vertebrates, focusing on opsin gene losses, duplications, and the expression regulation of vertebrate opsins. We describe the sequence variation both within and between species that has tweaked the sensitivities of opsin proteins towards different wavelengths of light. We provide an extensive resource of wavelength sensitivities and mutations that have diverged light sensitivity in many vertebrate species and predict how these mutations were accumulated in each lineage based on parsimony. We suggest possible natural and sexual selection mechanisms underlying these spectral differences. Understanding how molecular changes allow for functional adaptation of animals to different environments is a major goal in the field, and therefore identifying mutations affecting vision and their relationship to photic selection pressures is imperative. The goal of this review is to provide a comprehensive overview of our current understanding of opsin evolution in vertebrates.

Light environment drives evolution of color vision genes in butterflies and moths

Opsins, combined with a chromophore, are the primary light-sensing molecules in animals and are crucial for color vision. Throughout animal evolution, duplications and losses of opsin proteins are common, but it is unclear what is driving these gains and losses. Light availability is implicated, and dim environments are often associated with low opsin diversity and loss. Correlations between high opsin diversity and bright environments, however, are tenuous. To test if increased light availability is associated with opsin diversification, we examined diel niche and identified opsins using transcriptomes and genomes of 175 butterflies and moths (Lepidoptera). We found 14 independent opsin duplications associated with bright environments. Estimating their rates of evolution revealed that opsins from diurnal taxa evolve faster-at least 13 amino acids were identified with higher dN/dS rates, with a subset close enough to the chromophore to tune the opsin. These results demonstrate that high light availability increases opsin diversity and evolution rate in Lepidoptera.

Vision adaptation in the laughing dove (Streptopelia senegalensis, Linnaeus, 1766) inferred from structural, ultrastructural, and genetic characterization

Neuroanatomy of the retina reflects adaptation and acclimation for dark and light conditions. Retinal cells and genes must be functionally adjusted to various environmental luminosities. Opsins are brilliant molecules to assess the adaptations at the genetic and phenotypic levels. Photic adaptations may reveal new mechanisms that enhance vision abilities. Through the investigation of histological, ultrastructural constituents of the whole retinal layers, and the sequencing of shortwave length sensitive opsin 1 (SWS1) of the laughing dove (Streptopelia senegalensis), the current study confirms the plasticity of the retina in response to the natural photic conditions. Retinal pigmented epithelium has plentiful melanosomes, signifying a highly adapted eye for maximum light perception and protection. Variously colored oil droplets signify high color vision ability. Stratified outer nuclear layer with many Müller cells suggests high sensitivity to dim conditions and high retinal regeneration. The penetration of outer limiting membrane by photoreceptor nuclei and Müller cell microvilli could minimize the light reflection. Oligodendrocytes establish thick myelination demanded for a keen visual acuity. A functional violet sensitive SWS1 with crucial Ser90 is presumed. Molecular phylogeny showed a secondary loss as color vision was shifted back from ultraviolet (UV) sensitivity to the ancestral avian violet sensitivity, thus improving visual resolution. However, SWS1 has some UV sensitive residues. These findings implicate not only spectral adaptations with high color vision ability and acuity but also photoinduced structural reorganizations. Further studies are needed to assess the secrets between photons and the structural genes.

Mechanistic insights into the evolution of the differential expression of tandemly arrayed cone opsin genes in zebrafish

The genome of many organisms contains several loci consisting of duplicated genes that are arrayed in tandem. The daughter genes produced by duplication typically exhibit differential expression patterns with each other or otherwise experience pseudogenization. Remarkably, opsin genes in fish are preserved after many duplications in different lineages. This fact indicates that fish opsin genes are characterized by a regulatory mechanism that could intrinsically facilitate the differentiation of the expression patterns. However, little is known about the mechanisms that underlie the differential expression patterns or how they were established during evolution. The loci of green (RH2)- and red (LWS)-sensitive cone opsin genes in zebrafish have been used as model systems to study the differential regulation of tandemly arrayed opsin genes. Over a decade of studies have uncovered several mechanistic features that might have assisted the differentiation and preservation of duplicated genes. Furthermore, recent progress in the understanding of the transcriptional process in general has added essential insights. In this article, the current understanding of the transcriptional regulation of differentially expressed tandemly arrayed cone opsin genes in zebrafish is summarized and a possible evolutionary scenario that could achieve this differentiation is discussed.

Coevolution of cognitive abilities and identity signals in individual recognition systems

Social interactions are mediated by recognition systems, meaning that the cognitive abilities or phenotypic diversity that facilitate recognition may be common targets of social selection. Recognition occurs when a receiver compares the phenotypes produced by a sender with a template. Coevolution between sender and receiver traits has been empirically reported in multiple species and sensory modalities, though the dynamics and relative exaggeration of traits from senders versus receivers have received little attention. Here, we present a coevolutionary dynamic model that examines the conditions under which senders and receivers should invest effort in facilitating individual recognition. The model predicts coevolution of sender and receiver traits, with the equilibrium investment dependent on the relative costs of signal production versus cognition. In order for recognition to evolve, initial sender and receiver trait values must be above a threshold, suggesting that recognition requires some degree of pre-existing diversity and cognitive abilities. The analysis of selection gradients demonstrates that the strength of selection on sender signals and receiver cognition is strongest when the trait values are furthest from the optima. The model provides new insights into the expected strength and dynamics of selection during the origin and elaboration of individual recognition, an important feature of social cognition in many taxa. This article is part of the theme issue 'Signal detection theory in recognition systems: from evolving models to experimental tests'.

Conserved visual sensitivities across divergent lizard lineages that differ in an ultraviolet sexual signal

The sensory drive hypothesis predicts the correlated evolution of signaling traits and sensory perception in differing environments. For visual signals, adaptive divergence in both color signals and visual sensitivities between populations may contribute to reproductive isolation and promote speciation, but this has rarely been tested or shown in terrestrial species. We tested whether opsin protein expression differs between divergent lineages of the tawny dragon (Ctenophorus decresii) that differ in the presence/absence of an ultraviolet sexual signal. We measured the expression of four retinal cone opsin genes (SWS1, SWS2, RH2, and LWS) using droplet digital PCR. We show that gene expression between lineages does not differ significantly, including the UV wavelength sensitive SWS1. We discuss these results in the context of mounting evidence that visual sensitivities are highly conserved in terrestrial systems. Multiple competing requirements may constrain divergence of visual sensitivities in response to sexual signals. Instead, signal contrast could be increased via alternative mechanisms, such as background selection. Our results contribute to a growing understanding of the roles of visual ecology, phylogeny, and behavior on visual system evolution in reptiles.

The Power of Fish Models to Elucidate Skin Cancer Pathogenesis and Impact the Discovery of New Therapeutic Opportunities

Animal models play important roles in investigating the pathobiology of cancer, identifying relevant pathways, and developing novel therapeutic tools. Despite rapid progress in the understanding of disease mechanisms and technological advancement in drug discovery, negative trial outcomes are the most frequent incidences during a Phase III trial. Skin cancer is a potential life-threatening disease in humans and might be medically futile when tumors metastasize. This explains the low success rate of melanoma therapy amongst other malignancies. In the past decades, a number of skin cancer models in fish that showed a parallel development to the disease in humans have provided important insights into the fundamental biology of skin cancer and future treatment methods. With the diversity and breadth of advanced molecular genetic tools available in fish biology, fish skin cancer models will continue to be refined and expanded to keep pace with the rapid development of skin cancer research. This review begins with a brief introduction of molecular characteristics of skin cancers, followed by an overview of teleost models that have been used in the last decades in melanoma research. Next, we will detail the importance of the zebrafish (Danio rerio) animal model and other emerging fish models including platyfish (Xiphophorus sp.), and medaka (Oryzias latipes) in future cutaneous malignancy studies. The last part of this review provides the recent development and genome editing applications of skin cancer models in zebrafish and the progress in small molecule screening.

Genomic Environment Impacts Color Vision Evolution in a Family with Visually Based Sexual Selection

Many models of evolution by sexual selection predict a coevolution of sensory systems and mate preferences, but the genomic architecture (number and arrangement of contributing loci) underlying these characters could constrain this coevolution. Here, we examine how the genomic organization and evolution of the opsin genes (responsible for tuning color vision) can influence the evolutionary trajectory of sexually selected traits across 15 species in the family Poeciliidae, which includes classic systems for studies of color-mediated sexual selection such as guppies, swordtails, and mollies. Although male coloration patterns and the importance of this coloration in female mate choice vary widely within and among genera, sequencing revealed low variability at amino acid sites that tune Long Wavelength-Sensitive (LWS) opsins in this speciose family. Although most opsin genes in these species appear to have evolved along traditional mutation-selection dynamics, we identified high rates of gene conversion between two of the LWS loci (LWS-1 and LWS-3), likely due to the inverted tandem repeat nature of these genes. Yet members of the subgenus Lebistes appear to resist LWS gene conversion. The LWS opsins are responsible for detecting and discriminating red and orange coloration-a key sexually selected trait in members of the subgenus Lebistes. Taken together these results suggest selection is acting against the homogenizing effects of gene conversion to maintain LWS-1/LWS-3 differences within this subgenus.

Genetic and plastic variation in opsin gene expression, light sensitivity, and female response to visual signals in the guppy

High diversity in sexual color signaling in animals has attracted considerable and sustained interest from evolution researchers. It has been suggested that variations in visual properties in guppies result in diverse female preference for sexual color signals, leading to genetic variation based on male body colors. Here, we report that opsin expression varies because of allelic differences as well as the different rearing light environments. The variation in opsin expression influences the diversity in visual light sensitivity. Moreover, the expression of multiple opsin genes influences female responsiveness to the luminous orange colors. Consequently, genetic and environmental variation in opsin gene expression could affect female responsiveness and preference for male sexual colors, facilitating male color polymorphisms.

According to the sensory drive model, variation in visual properties can lead to diverse female preferences, which in turn results in a range of male nuptial colors by way of sexual selection. However, the cause of variation in visual properties and the mechanism by which variation drives female response to visual signals remain unclear. Here, we demonstrate that both differences in the long-wavelength–sensitive 1 (LWS-1) opsin genotype and the light environment during rearing lead to variation in opsin gene expression. Opsin expression variation affects the visual sensitivity threshold to long wavelengths of light. Moreover, a behavioral assay using digitally modified video images showed that the expression of multiple opsin genes is positively correlated with the female responsiveness to images of males with luminous orange spots. The findings suggest that genetic polymorphisms and light environment in habitats induce variations in opsin gene expression levels. The variations may facilitate variations in visual sensitivity and female responsiveness to male body colors within and among populations.

Reviewing guppy color vision: integrating the molecular and physiological variation in visual tuning of a classic system for sensory drive

Sensory drive predicts coevolution of mate choice signals with the sensory systems detecting those signals. Guppies are a classic model for sensory drive as mate preferences based on coloration differ across individuals and populations. A large body of work has identified variation in color vision, yet we lack a direct tie between how such variation in color vision influences variation in color preference. Here we bring together studies that have investigated guppy vision over the past 40 years to: (1) highlight our current understanding of where variation occurs in the guppy color vision pathway and (2) suggest future avenues of research into sources of visual system variation that could influence guppy color preference. This will allow researchers to design careful studies that couple measures of color preference with measures of visual system variation from the same individual or population. Such studies will finally provide important answers as to what sets the direction and speed of mate preference evolution via sensory drive.

Photopigments and the dimensionality of animal color vision

Early color-matching studies established that normal human color vision is trichromatic. Subsequent research revealed a causal link between trichromacy and the presence in the retina of three classes of cone photopigments. Over the years, measurements of the photopigment complements of other species have expanded greatly and these are frequently used to predict the dimensionality of an animal's color vision. This review provides an account of how the linkage between the number of active photopigments and the dimensions of human color vision developed, summarizes the various mechanisms that can impact photopigment spectra and number, and provides an across-species survey to examine cases where the photopigment link to the dimensionality of color vision has been claimed. The literature reveals numerous instances where the human model fails to account for the ways in which the visual systems of other animals exploit information obtained from the presence of multiple photopigments in support of their behavior.

Differential sensitivity to estrogen-induced opsin expression in two poeciliid freshwater fish species

The sensory system shapes an individual's perception of the world, including social interactions with conspecifics, habitat selection, predator detection, and foraging behavior. Sensory signaling can be modulated by steroid hormones, making these processes particularly vulnerable to environmental perturbations. Here we examine the influence of exogenous estrogen manipulation on the visual physiology of female western mosquitofish (Gambusia affinis) and sailfin mollies (Poecilia latipinna), two poeciliid species that inhabit freshwater environments across the southern United States. We conducted two experiments to address this aim. First, we exposed females from both species to a one-week dose response experiment with three treatments of waterborne β-estradiol. Next, we conducted a one-week estrogen manipulation experiment with a waterborne estrogen (β-Estradiol), a selective estrogen receptor modulator (tamoxifen), or combination estrogen and tamoxifen treatment. We used quantitative PCR (qPCR) to examine the expression of cone opsins (SWS1, SWS2b, SWS2a, Rh2, LWS), rhodopsin (Rh1), and steroid receptor genes (ARα, ARβ, ERα, ERβ2, GPER) in the eyes of individual females from each species. Results from the dose response experiment revealed estradiol-sensitivity in opsin (SWS2a, Rh2, Rh1) and androgen receptor (ARα, ARβ) gene expression in mosquitofish females, but not sailfins. Meanwhile, our estrogen receptor modulation experiments revealed estrogen sensitivity in LWS opsin expression in both species, along with sensitivity in SWS1, SWS2b, and Rh2 opsins in mosquitofish. Comparisons of control females across experiments reveal species-level differences in opsin expression, with mosquitofish retinas dominated by short-wavelength sensitive opsins (SWS2b) and sailfins retinas dominated by medium- and long-wavelength sensitive opsins (Rh2 and LWS). Our research suggests that variation in exogenous levels of sex hormones within freshwater environments can modify the visual physiology of fishes in a species-specific manner.

Convergent evolution of SWS2 opsin facilitates adaptive radiation of threespine stickleback into different light environments

Repeated adaptation to a new environment often leads to convergent phenotypic changes whose underlying genetic mechanisms are rarely known. Here, we study adaptation of color vision in threespine stickleback during the repeated postglacial colonization of clearwater and blackwater lakes in the Haida Gwaii archipelago. We use whole genomes from 16 clearwater and 12 blackwater populations, and a selection experiment, in which stickleback were transplanted from a blackwater lake into an uninhabited clearwater pond and resampled after 19 y to test for selection on cone opsin genes. Patterns of haplotype homozygosity, genetic diversity, site frequency spectra, and allele-frequency change support a selective sweep centered on the adjacent blue- and red-light sensitive opsins SWS2 and LWS. The haplotype under selection carries seven amino acid changes in SWS2, including two changes known to cause a red-shift in light absorption, and is favored in blackwater lakes but disfavored in the clearwater habitat of the transplant population. Remarkably, the same red-shifting amino acid changes occurred after the duplication of SWS2 198 million years ago, in the ancestor of most spiny-rayed fish. Two distantly related fish species, bluefin killifish and black bream, express these old paralogs divergently in black- and clearwater habitats, while sticklebacks lost one paralog. Our study thus shows that convergent adaptation to the same environment can involve the same genetic changes on very different evolutionary time scales by reevolving lost mutations and reusing them repeatedly from standing genetic variation.

Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression

Background

Opsins are light sensitive receptors associated with visual processes. Insects typically possess opsins that are stimulated by ultraviolet, short and long wavelength (LW) radiation. Six putative LW-sensitive opsins predicted in the yellow fever mosquito, Aedes aegypti and malaria mosquito, Anopheles gambiae, and eight in the southern house mosquito, Culex quinquefasciatus, suggest gene expansion in the Family Culicidae (mosquitoes) relative to other insects. Here we report the first detailed molecular and evolutionary analyses of LW opsins in three mosquito vectors, with a goal to understanding the molecular basis of opsin-mediated visual processes that could be exploited for mosquito control.

Results

Time of divergence estimates suggest that the mosquito LW opsins originated from 18 or 19 duplication events between 166.9/197.5 to 1.07/0.94 million years ago (MY) and that these likely occurred following the predicted divergence of the lineages Anophelinae and Culicinae 145–226 MY. Fitmodel analyses identified nine amino acid residues in the LW opsins that may be under positive selection. Of these, eight amino acids occur in the N and C termini and are shared among all three species, and one residue in TMIII was unique to culicine species. Alignment of 5′ non-coding regions revealed potential Conserved Non-coding Sequences (CNS) and transcription factor binding sites (TFBS) in seven pairs of LW opsin paralogs.

Conclusions

Our analyses suggest opsin gene duplication and residues possibly associated with spectral tuning of LW-sensitive photoreceptors. We explore two mechanisms - positive selection and differential expression mediated by regulatory units in CNS – that may have contributed to the retention of LW opsin genes in Culicinae and Anophelinae. We discuss the evolution of mosquito LW opsins in the context of major Earth events and possible adaptation of mosquitoes to LW-dominated photo environments, and implications for mosquito control strategies based on disrupting vision-mediated behaviors.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0910-6) contains supplementary material, which is available to authorized users.

Intraspecific geographic variation in rod and cone visual pigment sensitivity of a parrot, Platycercus elegans

Variation in wavelength sensitivity among subspecies is unknown among vertebrates. The parrot Platycercus elegans has extreme plumage variation between subspecies ranging from pale yellow to crimson which, with differences in background colour and light environment between subspecies, makes it a good candidate for the evolution of within-species differences in vision. We report differences in visual pigments between populations of P. elegans from two subspecies, providing the first known support for population and subspecies variation in visual pigments within a vertebrate species; it is also the first instance of intraspecific variation in rod sensitivity within any vertebrate species. Differences in wavelength sensitivity of rods and cones corresponded to geographic differences in plumage colour. Between study populations, visual pigments varied but not oil droplets. Adaptive functions for the visual pigment differences are untested but they could cause divergence in behaviours associated with colour as well as in dim light, and provide insights into the role of senses in divergence and speciation.

The Genome of the Trinidadian Guppy, Poecilia reticulata, and Variation in the Guanapo Population

For over a century, the live bearing guppy, Poecilia reticulata, has been used to study sexual selection as well as local adaptation. Natural guppy populations differ in many traits that are of intuitively adaptive significance such as ornamentation, age at maturity, brood size and body shape. Water depth, light supply, food resources and predation regime shape these traits, and barrier waterfalls often separate contrasting environments in the same river. We have assembled and annotated the genome of an inbred single female from a high-predation site in the Guanapo drainage. The final assembly comprises 731.6 Mb with a scaffold N50 of 5.3 MB. Scaffolds were mapped to linkage groups, placing 95% of the genome assembly on the 22 autosomes and the X-chromosome. To investigate genetic variation in the population used for the genome assembly, we sequenced 10 wild caught male individuals. The identified 5 million SNPs correspond to an average nucleotide diversity (π) of 0.0025. The genome assembly and SNP map provide a rich resource for investigating adaptation to different predation regimes. In addition, comparisons with the genomes of other Poeciliid species, which differ greatly in mechanisms of sex determination and maternal resource allocation, as well as comparisons to other teleost genera can begin to reveal how live bearing evolved in teleost fish.

The evolution of opsins and color vision: connecting genotype to a complex phenotype

Entender la base genética de los rasgos adaptativos es un paso crítico en el estudio de los procesos evolutivos. Para estudiar la conexión entre genotipo y fenotipo es importante definir el fenotipo a diferentes niveles: desde las proteínas que se construyen con base en un gen, hasta las características finales presentes en un organismo. Las opsinas y los fotopigmentos son elementos primordiales de la visión y entender cómo han evolucionado es fundamental en el estudio de la visión en los animales como un caracter derivado de selección natural o sexual. Este artículo se enfoca en este sistema, en el que se pueden conectar genotipo y fenotipo, como ejemplo de fenotipo complejo para ilustrar las dificultades de establecer una relación clara entre genotipo y fenotipo. Adicionalmente, este artículo tiene como objetivo discutir el funcionamiento del sistema de fotorrecepción, con énfasis particular en las aves, con el fin de enumerar varios factores que deben ser tenidos en cuenta para predecir cambios en la visión a partir del estudio de los fotopigmentos. Dado que los modelos basados en la visión de aves son cada vez más usados en diversas áreas de la biología evolutiva tales como: selección de pareja, depredación y camuflaje; se hace relevante entender los fundamentos y limitaciones de estos modelos. Por esta razón, en este artículo discuto los detalles y aspectos prácticos del uso de los modelos de visión existentes para aves, con el fin de facilitar su uso en futuras investigaciones en diversas áreas de evolución.

Effects of light environment during growth on the expression of cone opsin genes and behavioral spectral sensitivities in guppies (Poecilia reticulata)

BACKGROUND

The visual system is important for animals for mate choice, food acquisition, and predator avoidance. Animals possessing a visual system can sense particular wavelengths of light emanating from objects and their surroundings and perceive their environments by processing information contained in these visual perceptions of light. Visual perception in individuals varies with the absorption spectra of visual pigments and the expression levels of opsin genes, which may be altered according to the light environments. However, which light environments and the mechanism by which they change opsin expression profiles and whether these changes in opsin gene expression can affect light sensitivities are largely unknown. This study determined whether the light environment during growth induced plastic changes in opsin gene expression and behavioral sensitivity to particular wavelengths of light in guppies (Poecilia reticulata).

RESULTS

Individuals grown under orange light exhibited a higher expression of long wavelength-sensitive (LWS) opsin genes and a higher sensitivity to 600-nm light than those grown under green light. In addition, we confirmed that variations in the expression levels of LWS opsin genes were related to the behavioral sensitivities to long wavelengths of light.

CONCLUSIONS

The light environment during the growth stage alters the expression levels of LWS opsin genes and behavioral sensitivities to long wavelengths of light in guppies. The plastically enhanced sensitivity to background light due to changes in opsin gene expression can enhance the detection and visibility of predators and foods, thereby affecting survival. Moreover, changes in sensitivities to orange light may lead to changes in the discrimination of orange/red colors of male guppies and might alter female preferences for male color patterns.

Color vision varies more among populations than among species of live-bearing fish from South America

BACKGROUND

Sensory Bias models for the evolution of mate preference place a great emphasis on the role of sensory system variation in mate preferences. However, the extent to which sensory systems vary across- versus within-species remains largely unknown. Here we assessed whether color vision varies in natural locations where guppies (Poecilia reticulata) and their two closest relatives, Poecilia parae and Poecilia picta, occur in extreme sympatry and school together. All three species base mate preferences on male coloration but differ in the colors preferred.

RESULTS

Measuring opsin gene expression, we found that within sympatric locations these species have similar color vision and that color vision differed more across populations of conspecifics. In addition, all three species differ across populations in the frequency of the same opsin coding polymorphism that influences visual tuning.

CONCLUSIONS

Together, this shows sensory systems vary considerably across populations and supports the possibility that sensory system variation is involved in population divergence of mate preference.

Developmental plasticity in vision and behavior may help guppies overcome increased turbidity

Increasing turbidity in streams and rivers near human activity is cause for environmental concern, as the ability of aquatic organisms to use visual information declines. To investigate how some organisms might be able to developmentally compensate for increasing turbidity, we reared guppies (Poecilia reticulata) in either clear or turbid water. We assessed the effects of developmental treatments on adult behavior and aspects of the visual system by testing fish from both developmental treatments in turbid and clear water. We found a strong interactive effect of rearing and assay conditions: fish reared in clear water tended to decrease activity in turbid water, whereas fish reared in turbid water tended to increase activity in turbid water. Guppies from all treatments decreased activity when exposed to a predator. To measure plasticity in the visual system, we quantified treatment differences in opsin gene expression of individuals. We detected a shift from mid-wave-sensitive opsins to long wave-sensitive opsins for guppies reared in turbid water. Since long-wavelength sensitivity is important in motion detection, this shift likely allows guppies to salvage motion-detecting abilities when visual information is obscured in turbid water. Our results demonstrate the importance of developmental plasticity in responses of organisms to rapidly changing environments.

Human impact on fish sensory systems in the long term: an evolutionary perspective

Humans have severely impacted global ecosystems and this shows few signs of abating. Many aspects of an animal's biology, including its sensory systems, may be adversely influenced by pollutants and environmental noise. This review focuses on whether and/or how various environmental disturbances disrupt the sensory systems of fishes. As critical as it is to document and understand the current effects of the human footprint, it is also important to consider how organisms might adapt to these impacts over the long term. The present paper outlines the sources of genetic and genomic variation upon which natural selection can act and then reviews examples of known genetic contributions of variation in fish chemosensory, visual and acoustico-lateralis systems.

Beauty in the eyes of the beholders: colour vision is tuned to mate preference in the Trinidadian guppy (Poecilia reticulata)

A broad range of animals use visual signals to assess potential mates, and the theory of sensory exploitation suggests variation in visual systems drives mate preference variation due to sensory bias. Trinidadian guppies (Poecilia reticulata), a classic system for studies of the evolution of female mate choice, provide a unique opportunity to test this theory by looking for covariation in visual tuning, light environment and mate preferences. Female preference co-evolves with male coloration, such that guppy females from 'low-predation' environments have stronger preferences for males with more orange/red coloration than do females from 'high-predation' environments. Here, we show that colour vision also varies across populations, with 'low'-predation guppies investing more of their colour vision to detect red/orange coloration. In independently colonized watersheds, guppies expressed higher levels of both LWS-1 and LWS-3 (the most abundant LWS opsins) in 'low-predation' populations than 'high-predation' populations at a time that corresponds to differences in cone cell abundance. We also observed that the frequency of a coding polymorphism differed between high- and low-predation populations. Together, this shows that the variation underlying preference could be explained by simple changes in expression and coding of opsins, providing important candidate genes to investigate the genetic basis of female preference variation in this model system.

Differentiation of visual spectra and nuptial colorations of two Paratanakia himantegus subspecies (Cyprinoidea: Acheilognathidae) in response to the distinct photic conditions of their habitats

BACKGROUND

Vision, an important sensory modality of many animals, exhibits plasticity in that it adapts to environmental conditions to maintain its sensory efficiency. Nuptial coloration is used to attract mates and hence should be tightly coupled to vision. In Taiwan, two closely related bitterlings (Paratanakia himantegus himantegus and Paratanakia himantegus chii) with different male nuptial colorations reside in different habitats. We compared the visual spectral sensitivities of these subspecies with the ambient light spectra of their habitats to determine whether their visual abilities correspond with photic parameters and correlate with nuptial colorations.

RESULTS

Theelectroretinogram (ERG) results revealed that the relative spectral sensitivity of P.h. himantegus was higher at 670 nm, but lower at 370 nm, than the sensitivity of P. h. chii. Both bitterlings could perceive and reflect UV light, but the UV reflection patterns differed between genders. Furthermore, the relative irradiance intensity of the light spectra in the habitat of P. h. himantegus was higher at long wavelengths (480-700 nm), but lower at short wavelengths (350-450 nm), than the light spectra in the habitats of P. h.chii.

CONCLUSIONS

Two phylogenetically closely related bitterlings, P. h. himantegus and P. h. chii, dwell in different waters and exhibit different nuptial colorations and spectral sensitivities, which may be the results of speciation by sensory drive. Sensory ability and signal diversity accommodating photic environment may promote diversity of bitterling fishes. UV light was demonstrated to be a possible component of bitterling visual communication. The UV cue may assist bitterlings in genderidentification.

Coexpression of three opsins in cone photoreceptors of the salamander Ambystoma tigrinum

Although more than one type of visual opsin is present in the retina of most vertebrates, it was thought that each type of photoreceptor expresses only one opsin. However, evidence has accumulated that some photoreceptors contain more than one opsin, in many cases as a result of a developmental transition from the expression of one opsin to another. The salamander UV-sensitive (UV) cone is particularly notable because it contains three opsins (Makino and Dodd [1996] J Gen Physiol 108:27-34). Two opsin types are expressed at levels more than 100 times lower than the level of the primary opsin. Here, immunohistochemical experiments identified the primary component as a UV cone opsin and the two minor components as the short wavelength-sensitive (S) and long wavelength-sensitive (L) cone opsins. Based on single-cell recordings of 156 photoreceptors, the presence of three components in UV cones of hatchlings and terrestrial adults ruled out a developmental transition. There was no evidence for multiple opsin types within rods or S cones, but immunohistochemistry and partial bleaching in conjunction with single-cell recording revealed that both single and double L cones contained low levels of short wavelength-sensitive pigments in addition to the main L visual pigment. These results raise the possibility that coexpression of multiple opsins in other vertebrates was overlooked because a minor component absorbing at short wavelengths was masked by the main visual pigment or because the expression level of a component absorbing at long wavelengths was exceedingly low.

Variation in the visual habitat may mediate the maintenance of color polymorphism in a poeciliid fish

The conspicuousness of animal signals is influenced by their contrast against the background. As such, signal conspicuousness will tend to vary in nature because habitats are composed of a mosaic of backgrounds. Variation in attractiveness could result in variation in conspecific mate choice and risk of predation, which, in turn, may create opportunities for balancing selection to maintain distinct polymorphisms. We quantified male coloration, the absorbance spectrum of visual pigments and the photic environment of Poecilia parae, a fish species with five distinct male color morphs: a drab (i.e., grey), a striped, and three colorful (i.e., blue, red and yellow) morphs. Then, using physiological models, we assessed how male color patterns can be perceived in their natural visual habitats by conspecific females and a common cichlid predator, Aequidens tetramerus. Our estimates of chromatic and luminance contrasts suggest that the three most colorful morphs were consistently the most conspicuous across all habitats. However, variation in the visual background resulted in variation in which morph was the most conspicuous to females at each locality. Likewise, the most colorful morphs were the most conspicuous morphs to cichlid predators. If females are able to discriminate between conspicuous prospective mates and those preferred males are also more vulnerable to predation, variable visual habitats could influence the direction and strength of natural and sexual selection, thereby allowing for the persistence of color polymorphisms in natural environments.

Divergent selection for opsin gene variation in guppy (Poecilia reticulata) populations of Trinidad and Tobago

The guppy is known to exhibit remarkable interindividual variations in spectral sensitivity of middle to long wavelength-sensitive (M/LWS) cone photoreceptor cells. The guppy has four M/LWS-type opsin genes (LWS-1, LWS-2, LWS-3 and LWS-4) that are considered to be responsible for this sensory variation. However, the allelic variation of the opsin genes, particularly in terms of their absorption spectrum, has not been explored in wild populations. Thus, we examined nucleotide variations in the four M/LWS opsin genes as well as blue-sensitive SWS2-B and ultraviolet-sensitive SWS1 opsin genes for comparison and seven non-opsin nuclear loci as reference genes in 10 guppy populations from various light environments in Trinidad and Tobago. For the first time, we discovered a potential spectral variation (180 Ser/Ala) in LWS-1 that differed at an amino acid site known to affect the absorption spectra of opsins. Based on a coalescent simulation of the nucleotide variation of the reference genes, we showed that the interpopulation genetic differentiation of two opsin genes was significantly larger than the neutral expectation. Furthermore, this genetic differentiation was significantly related to differences in dissolved oxygen (DO) level, and it was not explained by the spatial distance between populations. The DO levels are correlated with eutrophication that possibly affects the color of aquatic environments. These results suggest that the population diversity of opsin genes is significantly driven by natural selection and that the guppy could adapt to various light environments through color vision changes.

Real-time evolution of new genes by innovation, amplification, and divergence

Gene duplications allow evolution of genes with new functions. Here, we describe the innovation-amplification-divergence (IAD) model in which the new function appears before duplication and functionally distinct new genes evolve under continuous selection. One example fitting this model is a preexisting parental gene in Salmonella enterica that has low levels of two distinct activities. This gene is amplified to a high copy number, and the amplified gene copies accumulate mutations that provide enzymatic specialization of different copies and faster growth. Selection maintains the initial amplification and beneficial mutant alleles but is relaxed for other less improved gene copies, allowing their loss. This rapid process, completed in fewer than 3000 generations, shows the efficacy of the IAD model and allows the study of gene evolution in real time.

Hybridization leads to sensory repertoire expansion in a gynogenetic fish, the Amazon molly (poecilia formosa): a test of the hybrid-sensory expansion hypothesis

Expansions in sensory systems usually require processes such as gene duplication and divergence, and thus evolve slowly. We evaluate a novel mechanism leading to rapid sensory repertoire expansion: hybrid-sensory expansion (HSE). HSE occurs when two species with differently tuned sensory systems form a hybrid, bringing together alleles from each of the parental species. In one generation, a sensory repertoire is created that is the sum of the variance between parental species. The Amazon molly presents a unique opportunity to test the HSE hypothesis in a "frozen" hybrid. We compared opsin sequences of the Amazon molly, Poecilia formosa, to those of the parental species. Both parental species are homozygous at the RH2-1 locus and each of the four long wavelength sensitive loci, while P. formosa possess two different alleles at these loci; one matching each parental allele. Gene expression analysis showed P. formosa use the expanded opsin repertoire that was the result of HSE. Additionally, behavioral tests revealed P. formosa respond to colored stimuli in a manner similar or intermediate to the parental species P. mexicana and P. latipinna. Together these results strongly support the HSE hypothesis. Hybrid-sensory repertoire expansion is likely important in other hybrid species and in other sensory systems.

A new training procedure for studying discrimination learning in fish

The study of animal cognition and its neurobiological bases often requires the adoption of associative learning procedures. Though fish are increasingly being used as a model system in behavioral neuroscience, the availability of adequate learning protocols can be a limiting factor in this field of research. This study describes a novel training procedure to explore visual discrimination in fish. Subjects were singly housed in rectangular tanks. At intervals, two stimuli were introduced at opposite ends of the tank and food was delivered near the stimulus to be reinforced. Time spent near positive stimulus in probe trials was taken as a measure of discrimination performance. To validate the method, we replicated two published studies that used operant conditioning to investigate the mechanisms of numerical discrimination in mosquitofish. Our data indicate a complete overlap of the results obtained using the two different methods. The pros and cons of the new procedure are discussed in respect of traditional associative learning paradigms.

Opsin gene duplication and divergence in ray-finned fish

Opsin gene sequences were first reported in the 1980s. The goal of that research was to test the hypothesis that human opsins were members of a single gene family and that variation in human color vision was mediated by mutations in these genes. While the new data supported both hypotheses, the greatest contribution of this work was, arguably, that it provided the data necessary for PCR-based surveys in a diversity of other species. Such studies, and recent whole genome sequencing projects, have uncovered exceptionally large opsin gene repertoires in ray-finned fishes (taxon, Actinopterygii). Guppies and zebrafish, for example, have 10 visual opsin genes each. Here we review the duplication and divergence events that have generated these gene collections. Phylogenetic analyses revealed that large opsin gene repertories in fish have been generated by gene duplication and divergence events that span the age of the ray-finned fishes. Data from whole genome sequencing projects and from large-insert clones show that tandem duplication is the primary mode of opsin gene family expansion in fishes. In some instances gene conversion between tandem duplicates has obscured evolutionary relationships among genes and generated unique key-site haplotypes. We mapped amino acid substitutions at so-called key-sites onto phylogenies and this exposed many examples of convergence. We found that dN/dS values were higher on the branches of our trees that followed gene duplication than on branches that followed speciation events, suggesting that duplication relaxes constraints on opsin sequence evolution. Though the focus of the review is opsin sequence evolution, we also note that there are few clear connections between opsin gene repertoires and variation in spectral environment, morphological traits, or life history traits.

Patterns of positive selection and neutral evolution in the protein-coding genes of Tetraodon and Takifugu

Recent genome-wide analyses have revealed patterns of positive selection acting on protein-coding genes in humans and mammals. To assess whether the conclusions drawn from these analyses are valid for other vertebrates and to identify mammalian specificities, I have investigated the selective pressure acting on protein-coding genes of the puffer fishes Tetraodon and Takifugu. My results indicate that the strength of purifying selection in puffer fishes is similar to previous reports for murids but stronger in hominids, which have a smaller population size. Gene ontology analyses show that more than half of the biological processes targeted by positive selection in mammals are also targeted in puffer fishes, highlighting general patterns for vertebrates. Biological processes enriched with positively selected genes that are shared between mammals and fishes include immune and defense responses, signal transduction, regulation of transcription and several of their descendent terms. Mammalian-specific processes displaying an excess of positively selected genes are related to sensory perception and neurological processes. The comparative analyses also revealed that, for both mammals and fishes, genes encoding extracellular proteins are preferentially targeted by positive selection, indicating that adaptive evolution occurs more often in the extra-cellular environment rather than inside the cell. Moreover, I present here the first genome-wide characterization of neutrally-evolving regions of protein-coding genes. This analysis revealed an unexpectedly high proportion of genes containing both positively selected motifs and neutrally-evolving regions, uncovering a strong link between neutral evolution and positive selection. I speculate that neutrally-evolving regions are a major source of novelties screened by natural selection.

Rapid light-induced shifts in opsin expression: finding new opsins, discerning mechanisms of change, and implications for visual sensitivity

Light-induced shifts in cone frequency and opsin expression occur in many aquatic species. Yet little is known about how quickly animals can alter opsin expression and, thereby, track their visual environments. Similarly, little is known about whether adult animals can alter opsin expression or whether shifts in opsin expression are limited to critical developmental windows. We took adult wild-caught bluefin killifish (Lucania goodei) from three different lighting environments (spring, swamp and variable), placed them under two different lighting treatments (clear vs. tea-stained water) and monitored opsin expression over 4 weeks. We measured opsin expression for five previously described opsins (SWS1, SWS2B, SWS2A, RH2-1 and LWS) as well as RH2-2 which we discovered via 454 sequencing. We used two different metrics of opsin expression. We measured expression of each opsin relative to a housekeeping gene and the proportional expression of each opsin relative to the total pool of opsins. Population and lighting environment had large effects on opsin expression which were present at the earliest time points indicating rapid shifts in expression. The two measures of expression produced radically different patterns. Proportional measures indicated large effects of light on SWS1 expression, whereas relative measures indicated no such effect. Instead, light had large effects on the relative expression of SWS2B, RH2-2, RH2-1 and LWS. We suggest that proportional measures of opsin expression are best for making inferences about colour vision, but that measures relative to a housekeeping gene are better for making conclusions about which opsins are differentially regulated.

Sequencing and characterization of the guppy (Poecilia reticulata) transcriptome

Background

Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and we evaluate potential uses of this transcriptome, including detection of sex-specific transcripts and deployment as a reference for gene expression analysis in guppies and a related species. Guppies have been model organisms in ecology, evolutionary biology, and animal behaviour for over 100 years. An annotated transcriptome and other genomic tools will facilitate understanding the genetic and molecular bases of adaptation and variation in a vertebrate species with a uniquely well known natural history.

Results

We generated approximately 336 Mbp of mRNA sequence data from male brain, male body, female brain, and female body. The resulting 1,162,670 reads assembled into 54,921 contigs, creating a reference transcriptome for the guppy with an average read depth of 28×. We annotated nearly 40% of this reference transcriptome by searching protein and gene ontology databases. Using this annotated transcriptome database, we identified candidate genes of interest to the guppy research community, putative single nucleotide polymorphisms (SNPs), and male-specific expressed genes. We also showed that our reference transcriptome can be used for RNA-sequencing-based analysis of differential gene expression. We identified transcripts that, in juveniles, are regulated differently in the presence and absence of an important predator, Rivulus hartii, including two genes implicated in stress response. For each sample in the RNA-seq study, >50% of high-quality reads mapped to unique sequences in the reference database with high confidence. In addition, we evaluated the use of the guppy reference transcriptome for gene expression analyses in a congeneric species, the sailfin molly (Poecilia latipinna). Over 40% of reads from the sailfin molly sample aligned to the guppy transcriptome.

Conclusions

We show that next-generation sequencing provided a reliable and broad reference transcriptome. This resource allowed us to identify candidate gene variants, SNPs in coding regions, and sex-specific gene expression, and permitted quantitative analysis of differential gene expression.

RT-qPCR reveals opsin gene upregulation associated with age and sex in guppies (Poecilia reticulata) - a species with color-based sexual selection and 11 visual-opsin genes

Background

PCR-based surveys have shown that guppies (Poecilia reticulata) have an unusually large visual-opsin gene repertoire. This has led to speculation that opsin duplication and divergence has enhanced the evolution of elaborate male coloration because it improves spectral sensitivity and/or discrimination in females. However, this conjecture on evolutionary connections between opsin repertoire, vision, mate choice, and male coloration was generated with little data on gene expression. Here, we used RT-qPCR to survey visual-opsin gene expression in the eyes of males, females, and juveniles in order to further understand color-based sexual selection from the perspective of the visual system.

Results

Juvenile and adult (male and female) guppies express 10 visual opsins at varying levels in the eye. Two opsin genes in juveniles, SWS2B and RH2-2, accounted for >85% of all visual-opsin transcripts in the eye, excluding RH1. This relative abundance (RA) value dropped to about 65% in adults, as LWS-A180 expression increased from approximately 3% to 20% RA. The juvenile-to-female transition also showed LWS-S180 upregulation from about 1.5% to 7% RA. Finally, we found that expression in guppies' SWS2-LWS gene cluster is negatively correlated with distance from a candidate locus control region (LCR).

Conclusions

Selective pressures influencing visual-opsin gene expression appear to differ among age and sex. LWS upregulation in females is implicated in augmenting spectral discrimination of male coloration and courtship displays. In males, enhanced discrimination of carotenoid-rich food and possibly rival males are strong candidate selective pressures driving LWS upregulation. These developmental changes in expression suggest that adults possess better wavelength discrimination than juveniles. Opsin expression within the SWS2-LWS gene cluster appears to be regulated, in part, by a common LCR. Finally, by comparing our RT-qPCR data to MSP data, we were able to propose the first opsin-to-λ_max assignments for all photoreceptor types in the cone mosaic.

Gene duplication and divergence of long wavelength-sensitive opsin genes in the guppy, Poecilia reticulata

Female preference for male orange coloration in the genus Poecilia suggests a role for duplicated long wavelength-sensitive (LWS) opsin genes in facilitating behaviors related to mate choice in these species. Previous work has shown that LWS gene duplication in this genus has resulted in expansion of long wavelength visual capacity as determined by microspectrophotometry (MSP). However, the relationship between LWS genomic repertoires and expression of LWS retinal cone classes within a given species is unclear. Our previous study in the related species, Xiphophorus helleri, was the first characterization of the complete LWS opsin genomic repertoire in conjunction with MSP expression data in the family Poeciliidae, and revealed the presence of four LWS loci and two distinct LWS cone classes. In this study we characterized the genomic organization of LWS opsin genes by BAC clone sequencing, and described the full range of cone cell types in the retina of the colorful Cumaná guppy, Poecilia reticulata. In contrast to X. helleri, MSP data from the Cumaná guppy revealed three LWS cone classes. Comparisons of LWS genomic organization described here for Cumaná to that of X. helleri indicate that gene divergence and not duplication was responsible for the evolution of a novel LWS haplotype in the Cumaná guppy. This lineage-specific divergence is likely responsible for a third additional retinal cone class not present in X. helleri, and may have facilitated the strong sexual selection driven by female preference for orange color patterns associated with the genus Poecilia.

Diversity of color vision: not all Australian marsupials are trichromatic

Color vision in marsupials has recently emerged as a particularly interesting case among mammals. It appears that there are both dichromats and trichromats among closely related species. In contrast to primates, marsupials seem to have evolved a different type of trichromacy that is not linked to the X-chromosome. Based on microspectrophotometry and retinal whole-mount immunohistochemistry, four trichromatic marsupial species have been described: quokka, quenda, honey possum, and fat-tailed dunnart. It has, however, been impossible to identify the photopigment of the third cone type, and genetically, all evidence so far suggests that all marsupials are dichromatic. The tammar wallaby is the only Australian marsupial to date for which there is no evidence of a third cone type. To clarify whether the wallaby is indeed a dichromat or trichromatic like other Australian marsupials, we analyzed the number of cone types in the “dichromatic” wallaby and the “trichromatic” dunnart. Employing identical immunohistochemical protocols, we confirmed that the wallaby has only two cone types, whereas 20–25% of cones remained unlabeled by S- and LM-opsin antibodies in the dunnart retina. In addition, we found no evidence to support the hypothesis that the rod photopigment (rod opsin) is expressed in cones which would have explained the absence of a third cone opsin gene. Our study is the first comprehensive and quantitative account of color vision in Australian marsupials where we now know that an unexpected diversity of different color vision systems appears to have evolved.

Teasing apart the many effects of lighting environment on opsin expression and foraging preference in bluefin killifish

Coloration and color vision covary with lighting in many taxa. Determining the mechanisms underlying these patterns is difficult because lighting environments can have multiple effects on signaling that occur at multiple timescales. Lighting environments can (1) immediately affect signal propagation and transmission, which determine the radiance spectrum reaching the receiver; (2) induce variation in visual systems via developmental plasticity; and (3) lead to genetic differences in visual systems due to a history of selection in different habitats. We tease apart these effects on pecking preference and examine the relationship between pecking preference and opsin expression. Using killifish from two visually distinct populations (clear vs. tea-stained water), we performed crosses (genetics), raised animals under different lighting conditions (developmental plasticity), and assayed the preference to peck at different-colored dots under different lighting conditions (immediate effects). Pecks are interpreted as foraging preference. Developmental plasticity affected both pecking preference and opsin expression. Lighting environments also had immediate effects on pecking preference, but these depended on the lighting conditions animals experienced during development. Genetic effects were detected in opsin expression, but there were no corresponding effects on pecking preference. Overall, only 3.36% of the variation in pecking preference was accounted for by opsin expression.

Determination of onset of sexual maturation and mating behavior by melanocortin receptor 4 polymorphisms

Polymorphisms in reproductive strategies are among the most extreme and complex in nature. A prominent example is male body size and the correlated reproductive strategies in some species of platyfish and swordtails of the genus Xiphophorus. This polymorphism is controlled by a single Mendelian locus (P) that determines the onset of sexual maturity of males. Because males cease growth after reaching puberty, this results in a marked size polymorphism. The different male size classes show pronounced behavioral differences (e.g., courtship versus sneak mating), and females prefer large over small males. We show that sequence polymorphisms of the melanocortin receptor 4 gene (mc4r) comprise both functional and non-signal-transducing versions and that variation in copy number of mc4r genes on the Y chromosome underlies the P locus polymorphism. Nonfunctional Y-linked mc4r copies in larger males act as dominant-negative mutations and delay the onset of puberty. Copy number variation, as a regulating mechanism, endows this system with extreme genetic flexibility that generates extreme variation in phenotype. Because Mc4r is critically involved in regulation of body weight and appetite, a novel link between the physiological system controlling energy balance and the regulation of reproduction becomes apparent.

Effects of polyandry on male phenotypic diversity

Polyandry has the potential to affect the distribution of phenotypes and to shape the direction of sexual selection. Here, we explore this potential using Trinidadian guppies as a model system and ask whether polyandry leads to directional and/or diversifying selection of male phenotypic traits. In this study, we compare the phenotypic diversity of offspring from multiply and singly sired broods. To quantify phenotypic diversity, we first combine phenotypic traits using multivariate methods, and then take the dispersion of individuals in multivariate space as our measure of diversity. We show that, when each trait is examined separately, polyandry generates offspring with a higher proportion of bright coloration, indicating directional selection. However, our multivariate approach reveals that this directionality is accompanied by an increase in phenotypic diversity. These results suggest that polyandry (i) selects for the production of sons with the preferred brighter colour phenotypes whereas (ii) enhancing the diversity of male sexual traits. Promoting phenotypic diversity may be advantageous in coping with environmental and reproductive variability by increasing long-term fitness.

Genomic organization of duplicated short wave-sensitive and long wave-sensitive opsin genes in the green swordtail, Xiphophorus helleri

Background

Long wave-sensitive (LWS) opsin genes have undergone multiple lineage-specific duplication events throughout the evolution of teleost fishes. LWS repertoire expansions in live-bearing fishes (family Poeciliidae) have equipped multiple species in this family with up to four LWS genes. Given that color vision, especially attraction to orange male coloration, is important to mate choice within poeciliids, LWS opsins have been proposed as candidate genes driving sexual selection in this family. To date the genomic organization of these genes has not been described in the family Poeciliidae, and little is known about the mechanisms regulating the expression of LWS opsins in any teleost.

Results

Two BAC clones containing the complete genomic repertoire of LWS opsin genes in the green swordtail fish, Xiphophorus helleri, were identified and sequenced. Three of the four LWS loci identified here were linked in a tandem array downstream of two tightly linked short wave-sensitive 2 (SWS2) opsin genes. The fourth LWS opsin gene, containing only a single intron, was not linked to the other three and is the product of a retrotransposition event. Genomic and phylogenetic results demonstrate that the LWS genes described here share a common evolutionary origin with those previously characterized in other poeciliids. Using qualitative RT-PCR and MSP we showed that each of the LWS and SWS2 opsins, as well as three other cone opsin genes and a single rod opsin gene, were expressed in the eyes of adult female and male X. helleri, contributing to six separate classes of adult retinal cone and rod cells with average λ_max values of 365 nm, 405 nm, 459 nm, 499 nm, 534 nm and 568 nm. Comparative genomic analysis identified two candidate teleost opsin regulatory regions containing putative CRX binding sites and hormone response elements in upstream sequences of LWS gene regions of seven teleost species, including X. helleri.

Conclusions

We report the first complete genomic description of LWS and SWS2 genes in poeciliids. These data will serve as a reference for future work seeking to understand the relationship between LWS opsin genomic organization, gene expression, gene family evolution, sexual selection and speciation in this fish family.