Revisiting old truths: The evolution of male coloration in guppies as a function of predation.

The Trinidadian guppy, Poecilia reticulata, is a long-studied model for the evolution of trade-offs in male nuptial coloration as a function of female mating preferences vs. predation risk. Previous work suggests that female mating preferences favour the evolution of increased conspicuous male coloration in low predation populations. In contrast, high predation risk shifts the balance towards reduced conspicuous coloration. In a From the Cover article in this issue of Molecular Ecology, Yong, Croft, Troscianko, Ramnarine, and Wilson (2021) use visual detection models to estimate the "conspicuousness" of male colour patterns as seen by guppies and their predators. The study fails to find robust patterns of increased conspicuousness in low predation populations. Only one of eight measures of conspicuousness showed parallel changes between high and low predation regimes, forcing us to reconsider the validity and repeatability of this classic example of parallel evolution.

Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers.

Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

Genomic Resources for Darters (Percidae: Etheostominae) Provide Insight into Postzygotic Barriers Implicated in Speciation.

Comparative genomic approaches are increasingly being used to study the evolution of reproductive barriers in nonmodel species. Although numerous studies have examined prezygotic isolation in darters (Percidae), investigations into postzygotic barriers have remained rare due to long generation times and a lack of genomic resources. Orangethroat and rainbow darters naturally hybridize and provide a remarkable example of male-driven speciation via character displacement. Backcross hybrids suffer from high mortality, which appears to promote behavioral isolation in sympatry. To investigate the genomic architecture of postzygotic isolation, we used Illumina and PacBio sequencing to generate a chromosome-level, annotated assembly of the orangethroat darter genome and high-density linkage maps for orangethroat and rainbow darters. We also analyzed genome-wide RADseq data from wild-caught adults of both species and laboratory-generated backcrosses to identify genomic regions associated with hybrid incompatibles. Several putative chromosomal translocations and inversions were observed between orangethroat and rainbow darters, suggesting structural rearrangements may underlie postzygotic isolation. We also found evidence of selection against recombinant haplotypes and transmission ratio distortion in backcross hybrid genomes, providing further insight into the genomic architecture of genetic incompatibilities. Notably, regions with high levels of genetic divergence between species were enriched for genes associated with developmental and meiotic processes, providing strong candidates for postzygotic isolating barriers. These findings mark significant contributions to our understanding of the genetic basis of reproductive isolation between species undergoing character displacement. Furthermore, the genomic resources presented here will be instrumental for studying speciation in darters, the most diverse vertebrate group in North America.

A potential role for overdominance in the maintenance of colour variation in the Neotropical tortoise beetle, Chelymorpha alternans.

The presence of persistent polymorphisms within natural populations elicits the question of how such polymorphisms are maintained. All else equal, genetic drift and natural selection should remove genetic variants from populations. Disassortative mating and overdominance are potential mechanisms for maintaining variation within populations. Here, we consider the potential role of these mechanisms in maintaining variation in colour pattern in the tortoise beetle, Chelymorpha alternans. Five colour morphs distinguished by elytral and pronotal coloration are largely determined by a single locus of large effect with four segregating alleles. As many as four morphs co-occur in natural populations. We first assessed whether disassortative mating might maintain this polymorphism. To test for assortative and disassortative mating, we paired females with two males, one with the same colour pattern as the female and one with a different colour pattern and examined the colour patterns of the offspring. We found strong evidence for random mating as a function of colour pattern. We next assessed whether differences in offspring survival among assortative and disassortative male-female pairs maintain colour variation. Crosses involving disassortative pairings had significantly higher offspring survival during development and resulted in more adult progeny. This result is consistent with the effects of overdominance, whereby outcrossed individuals have higher fitness than their homozygous counterparts. Overall, differences in offspring survival appear to play a greater role in maintaining polymorphisms than nonrandom mating in species.

Genomic landscape of reproductive isolation in Lucania killifish: The role of sex loci and salinity.

Adaptation to different environments can directly and indirectly generate reproductive isolation between species. Bluefin killifish (Lucania goodei) and rainwater killifish (L. parva) are sister species that have diverged across a salinity gradient and are reproductively isolated by habitat, behavioural, extrinsic and intrinsic post-zygotic isolation. We asked if salinity adaptation contributes indirectly to other forms of reproductive isolation via linked selection and hypothesized that low recombination regions, such as sex chromosomes or chromosomal rearrangements, might facilitate this process. We conducted QTL mapping in backcrosses between L. parva and L. goodei to explore the genetic architecture of salinity tolerance, behavioural isolation and intrinsic isolation. We mapped traits relative to a chromosome that has undergone a centric fusion in L. parva (relative to L. goodei). We found that the sex locus appears to be male determining (XX-XY), was located on the fused chromosome and was implicated in intrinsic isolation. QTL associated with salinity tolerance were spread across the genome and did not overly co-localize with regions associated with behavioural or intrinsic isolation. This preliminary analysis of the genetic architecture of reproductive isolation between Lucania species does not support the hypothesis that divergent natural selection for salinity tolerance led to behavioural and intrinsic isolation as a by-product. Combined with previous studies in this system, our work suggests that adaptation as a function of salinity contributes to habitat isolation and that reinforcement may have contributed to the evolution of behavioural isolation instead, possibly facilitated by linkage between behavioural isolation and intrinsic isolation loci on the fused chromosome.

Sequence Analysis and Ontogenetic Expression Patterns of Cone Opsin Genes in the Bluefin Killifish (Lucania goodei).

Sensory systems allow for the transfer of environmental stimuli into internal cues that can alter physiology and behavior. Many studies of visual systems focus on opsins to compare spectral sensitivity among individuals, populations, and species living in different lighting environments. This requires an understanding of the cone opsins, which can be numerous. The bluefin killifish is a good model for studying the interaction between environments and visual systems as they are found in both clear springs and tannin-stained swamps. We conducted a genome-wide screening and demonstrated that the bluefin killifish has 9 cone opsins: 1 SWS1 (354 nm), 2 SWS2 (SWS2B: 359 nm, SWS2A: 448 nm), 2 RH2 (RH2-2: 476 nm, RH2-1: 537 nm), and 4 LWS (LWS-1: 569 nm, LWS-2: 524 nm, LWS-3: 569 nm, LWS-R: 560 or 569 nm). These 9 cone opsins were located on 4 scaffolds. One scaffold contained the 2 SWS2 and 3 of the 4 LWS opsins in the same syntenic order as found in other cyprinodontoid fishes. We also compared opsin expression in larval and adult killifish under clear water conditions, which mimic springs. Two of the newly discovered opsins (LWS-2 and LWS-3) were expressed at low levels (<0.2%). Whether these opsins make meaningful contributions to visual perception in other contexts (i.e., swamp conditions) is unclear. In contrast, there was an ontogenetic change from using LWS-R to LWS-1 opsin. Bluefin killifish adults may be slightly more sensitive to longer wavelengths, which might be related to sexual selection and/or foraging preferences.

Using Human Vision to Detect Variation in Avian Coloration: How Bad Is It?

Assessing variation in animal coloration is difficult, as animals differ in their visual system properties. This has led some to propose that human vision can never be used to evaluate coloration, yet many studies have a long history of relying on human vision. To reconcile these views, we compared the reflectance spectra of preserved avian plumage elements with two measures that are human biased: RGB values from digital photographs and the corresponding reflectance spectra from a field guide. We measured 73 plumage elements across 14 bird species. The field guide reflectance spectra were drastically different from that of the actual birds, particularly for blue elements. However, principal component analyses on all three data sets indicated remarkably similar data structure. We conclude that human vision can detect much of the variation in coloration in the visible range, providing fodder for subsequent studies in ecology, evolution, behavior, and visual ecology.

Agonistic character displacement of genetically based male colour patterns across darters.

Agonistic character displacement (ACD) occurs when selection to avoid maladaptive interspecific aggression leads to the evolution of agonistic signals and/or associated behavioural biases in sympatry. Here, we test for a pattern consistent with ACD in male colour pattern in darters (Percidae: Etheostoma). Male colour pattern has been shown to function in male-male competition rather than female mating preferences in several darter species. Additionally, males bias their aggression towards conspecific over heterospecific males in sympatry but not in allopatry, consistent with divergent ACD in male behavioural biases. We use a common garden approach to show that differences in male colour pattern among four closely related darter species are genetically based. Additionally, we demonstrate that some aspects of male colour pattern exhibit enhanced differences in sympatric compared to allopatric populations of two darter species, consistent with ACD. However, other male colour traits are more similar between species in sympatry compared with allopatry, indicating that not all signal components are under strong divergent selection in sympatry. This study provides evidence that interspecific male-male aggressive interactions alone can promote elaborate male signal evolution both between and within species. We discuss the implications this has for male-driven ACD and cascade ACD.

Variation in individual temperature preferences, not behavioural fever, affects susceptibility to chytridiomycosis in amphibians.

The ability of wildlife populations to mount rapid responses to novel pathogens will be critical for mitigating the impacts of disease outbreaks in a changing climate. Field studies have documented that amphibians preferring warmer temperatures are less likely to be infected with the fungal pathogen Batrachochytrium dendrobatidis (Bd). However, it is unclear whether this phenomenon is driven by behavioural fever or natural variation in thermal preference. Here, we placed frogs in thermal gradients, tested for temperature preferences and measured Bd growth, prevalence, and the survival of infected animals. Although there was significant individual- and species-level variation in temperature preferences, we found no consistent evidence of behavioural fever across five frog species. Interestingly, for species that preferred warmer temperatures, the preferred temperatures of individuals were negatively correlated with Bd growth on hosts, while the opposite correlation was true for species preferring cooler temperatures. Our results suggest that variation in thermal preference, but not behavioural fever, might shape the outcomes of Bd infections for individuals and populations, potentially resulting in selection for individual hosts and host species whose temperature preferences minimize Bd growth and enhance host survival during epidemics.

The vertical distributions and spawning site choices of red and yellow bluefin killifish Lucania goodei colour morphs.

A genetic colour polymorphism is present in bluefin killifish Lucania goodei, where red and yellow anal-fin morphs coexist in clear springs, but the source of balancing selection is unknown. In a field study, vertical distributions did not differ between the morphs and there was little evidence that light environments differed qualitatively over the 200 cm at which fish were collected. A greenhouse study showed that both morphs preferred to spawn at shallow depths and hence vertical distribution and spawning site choice are unlikely to explain the maintenance of the colour polymorphism.

Exploring visual plasticity: dietary carotenoids can change color vision in guppies (Poecilia reticulata).

Differences in color vision can play a key role in an organism's ability to perceive and interact with the environment across a broad range of taxa. Recently, species have been shown to vary in color vision across populations as a result of differences in regulatory sequence and/or plasticity of opsin gene expression. For decades, biologists have been intrigued by among-population variation in color-based mate preferences of female Trinidadian guppies. We proposed that some of this variation results from variation in color vision caused by plasticity in opsin expression. Specifically, we asked about the role of dietary carotenoid availability, because carotenoids (1) are the precursors for vitamin A, which is essential for the creation of photopigments and (2) have been linked to variation in female mate choice. We raised guppies on different carotenoid-level diets and measured opsin expression. Guppies raised on high-carotenoid diets expressed higher levels of long wavelength sensitive opsin (LWS) opsins than those raised on lower levels of carotenoids. These results suggest that dietary effects on opsin expression represent a previously unaccounted for mechanism by which ecological differences across populations could lead to mate choice differences.

Behavioral Isolation due to Cascade Reinforcement in Lucania Killifish.

Reinforcement occurs when behavioral isolation is strengthened between species due to selection against hybridization in sympatry. Mate preferences and their target traits may change in sympatry as a consequence of reinforcement. This can potentially generate further behavioral isolation within species if sympatric populations evolve extreme preferences or traits that cause them to reject individuals from foreign populations as mates or be rejected as mates. This process is known as cascade reinforcement. We measured behavioral isolation between sympatric and allopatric populations of Lucania killifish to determine whether isolation evolves due to reinforcement between species and whether reinforcement affects preferences within species, consistent with the cascade reinforcement hypothesis. We measured mate preferences in both sexes between species (Lucania parva vs. Lucania goodei) and within species (among populations of L. parva). Between species, both male and female preferences for conspecifics were highest in sympatric populations. Within species, L. parva females from sympatric populations preferred their own native males over foreign males. Allopatric L. parva females and all L. parva males showed no preferences within species. Within species, behavioral isolation showed no association with ecological variables, such as salinity. Thus, reinforcement is a primary factor generating behavioral isolation in Lucania killifish, creating strong preferences in both sexes among species and leading to cascade reinforcement of female mate preference within species.

Diurnal lighting patterns and habitat alter opsin expression and colour preferences in a killifish.

Spatial variation in lighting environments frequently leads to population variation in colour patterns, colour preferences and visual systems. Yet lighting conditions also vary diurnally, and many aspects of visual systems and behaviour vary over this time scale. Here, we use the bluefin killifish (Lucania goodei) to compare how diurnal variation and habitat variation (clear versus tannin-stained water) affect opsin expression and the preference to peck at different-coloured objects. Opsin expression was generally lowest at midnight and dawn, and highest at midday and dusk, and this diurnal variation was many times greater than variation between habitats. Pecking preference was affected by both diurnal and habitat variation but did not correlate with opsin expression. Rather, pecking preference matched lighting conditions, with higher preferences for blue at noon and for red at dawn/dusk, when these wavelengths are comparatively scarce. Similarly, blue pecking preference was higher in tannin-stained water where blue wavelengths are reduced. In conclusion, L. goodei exhibits strong diurnal cycles of opsin expression, but these are not tightly correlated with light intensity or colour. Temporally variable pecking preferences probably result from lighting environment rather than from opsin production. These results may have implications for the colour pattern diversity observed in these fish.

Differences in offspring size predict the direction of isolation asymmetry between populations of a placental fish.

Crosses between populations or species often display an asymmetry in the fitness of reciprocal F1 hybrids. This pattern, referred to as isolation asymmetry or Darwin's Corollary to Haldane's Rule, has been observed in taxa from plants to vertebrates, yet we still know little about which factors determine its magnitude and direction. Here, we show that differences in offspring size predict the direction of isolation asymmetry observed in crosses between populations of a placental fish, Heterandria formosa. In crosses between populations with differences in offspring size, high rates of hybrid inviability occur only when the mother is from a population characterized by small offspring. Crosses between populations that display similarly sized offspring, whether large or small, do not result in high levels of hybrid inviability in either direction. We suggest this asymmetric pattern of reproductive isolation is due to a disruption of parent-offspring coadaptation that emerges from selection for differently sized offspring in different populations.

Polyphenisms and polymorphisms: Genetic variation in plasticity and color variation within and among bluefin killifish populations.

The presence of stable color polymorphisms within populations begs the question of how genetic variation is maintained. Consistent variation among populations in coloration, especially when correlated with environmental variation, raises questions about whether environmental conditions affect either the fulcrum of those balanced polymorphisms, the plastic expression of coloration, or both. Color patterns in male bluefin killifish provoke both types of questions. Red and yellow morphs are common in all populations. Blue males are more common in tannin-stained swamps relative to clear springs. Here, we combined crosses with a manipulation of light to explore how genetic variation and phenotypic plasticity shape these patterns. We found that the variation in coloration is attributable mainly to two axes of variation: (1) a red-yellow axis with yellow being dominant to red, and (2) a blue axis that can override red-yellow and is controlled by genetics, phenotypic plasticity, and genetic variation for phenotypic plasticity. The variation among populations in plasticity suggests it is adaptive in some populations but not others. The variation among sires in plasticity within the swamp population suggests balancing selection may be acting not only on the red-yellow polymorphism but also on plasticity for blue coloration.

Visual Background Choice and Light Environment Affect Male Guppy Visual Contrast.

Male guppies (Poecilia reticulata) have multiple colored spots and perform courtship displays near the edges of streams in Trinidad in shallow water flowing through rainforest. Depending upon the orientation of the pair, the female sees the male displays against gravel or other stream bed substrates or against the spacelight-the roughly uniform light coming from the water column away from the bank. We observed courting pairs in two adjacent natural streams and noted the directions of each male display. We found that the female sees the male more often against spacelight than against gravel when females either faced the spacelight from the opposite bank or from downstream, or both. Visual modelling using natural substrate reflectances and field light measurements showed higher chromatic contrast of males against spacelight than against substrates independent of the two ambient light environments used during displays, but achromatic contrast depended upon the ambient light habitat. This suggests that courtship involves both chromatic and achromatic contrast. We conclude that the orientation of courting pairs and the ambient light spectrum should be accounted for in studies of mate choice, because the visual background and light affect visibility, and these differ with orientation.