Precise colocalization of interacting structural and pigmentary elements generates extensive color pattern variation in Phelsuma lizards

Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards

The joint expression of particular colors, morphologies, and behaviors is a common feature of adaptation, but the genetic basis for such "phenotypic syndromes" remains poorly understood. Here, we identified a complex genetic architecture associated with a sexually selected syndrome in common wall lizards, by capitalizing on the adaptive introgression of coloration and morphology into a distantly related lineage. Consistent with the hypothesis that the evolution of phenotypic syndromes in vertebrates is facilitated by developmental linkage through neural crest cells, most of the genes associated with the syndrome are involved in neural crest cell regulation. A major locus was a ~400-kb region, characterized by standing structural genetic variation and previously implied in the evolutionary innovation of coloration and beak size in birds. We conclude that features of the developmental and genetic architecture contribute to maintaining trait integration, facilitating the extensive and rapid introgressive spread of suites of sexually selected characters.

Multiple Routes to Color Convergence in a Radiation of Neotropical Poison Frogs

Convergent evolution is defined as the independent evolution of similar phenotypes in different lineages. Its existence underscores the importance of external selection pressures in evolutionary history, revealing how functionally similar adaptations can evolve in response to persistent ecological challenges through a diversity of evolutionary routes. However, many examples of convergence, particularly among closely related species, involve parallel changes in the same genes or developmental pathways, raising the possibility that homology at deeper mechanistic levels is an important facilitator of phenotypic convergence. Using the genus Ranitomeya, a young, color-diverse radiation of Neotropical poison frogs, we set out to 1) provide a phylogenetic framework for this group, 2) leverage this framework to determine if color phenotypes are convergent, and 3) to characterize the underlying coloration mechanisms to test whether color convergence occurred through the same or different physical mechanisms. We generated a phylogeny for Ranitomeya using ultraconserved elements and investigated the physical mechanisms underlying bright coloration, focusing on skin pigments. Using phylogenetic comparative methods, we identified several instances of color convergence, involving several gains and losses of carotenoid and pterin pigments. We also found a compelling example of nonparallel convergence, where, in one lineage, red coloration evolved through the red pterin pigment drosopterin, and in another lineage through red ketocarotenoids. Additionally, in another lineage, "reddish" coloration evolved predominantly through structural color mechanisms. Our study demonstrates that, even within a radiation of closely related species, convergent evolution can occur through both parallel and nonparallel mechanisms, challenging the assumption that similar phenotypes among close relatives evolve through the same mechanisms.

Analysis of the optical response of reptile tissues in the visible and UV applying the KKR method

Structural colors in nature are frequently produced by the ordered arrangement of nanoparticles. Interesting examples include reptiles and birds utilizing lattice-like formation of nanoparticles to produce a variety of colors. A famous example is the panther chameleon which is even able to change its color by actively varying the distance between guanine nanocrystals in its skin. Here, we demonstrate that the application of rigorous electromagnetic methods is important to determine the actual optical response of such biological systems. By applying the Korringa-Kohn-Rostoker (KKR) method we calculate the efficiencies of the reflected diffraction orders that can be viewed from directions other than the specular. Our results reveal that important characteristics of the reflectance spectra, especially within the ultraviolet (UV) and short visible wavelengths region, cannot be predicted by approximate models like the often-applied Maxwell-Garnett approach. Additionally, we show that the KKR method can be employed for the design of multi-layer structures with a desired optical response in the UV regime.

The Unreasonable Effectiveness of Reaction Diffusion in Vertebrate Skin Color Patterning

In 1952, Alan Turing published the reaction-diffusion (RD) mathematical framework, laying the foundations of morphogenesis as a self-organized process emerging from physicochemical first principles. Regrettably, this approach has been widely doubted in the field of developmental biology. First, we summarize Turing's line of thoughts to alleviate the misconception that RD is an artificial mathematical construct. Second, we discuss why phenomenological RD models are particularly effective for understanding skin color patterning at the meso/macroscopic scales, without the need to parameterize the profusion of variables at lower scales. More specifically, we discuss how RD models (a) recapitulate the diversity of actual skin patterns, (b) capture the underlying dynamics of cellular interactions, (c) interact with tissue size and shape, (d) can lead to ordered sequential patterning, (e) generate cellular automaton dynamics in lizards and snakes, (f) predict actual patterns beyond their statistical features, and (g) are robust to model variations. Third, we discuss the utility of linear stability analysis and perform numerical simulations to demonstrate how deterministic RD emerges from the underlying chaotic microscopic agents.

Genetics of yellow-orange color variation in a pair of sympatric sulphur butterflies

Continuous color polymorphisms can serve as a tractable model for the genetic and developmental architecture of traits. Here we investigated continuous color variation in Colias eurytheme and Colias philodice, two species of sulphur butterflies that hybridize in sympatry. Using quantitative trait locus (QTL) analysis and high-throughput color quantification, we found two interacting large-effect loci affecting orange-to-yellow chromaticity. Knockouts of red Malpighian tubules (red), likely involved in endosomal maturation, result in depigmented wing scales. Additionally, the transcription factor bric-a-brac can act as a modulator of orange pigmentation. We also describe the QTL architecture of other continuously varying traits, together supporting a large-X effect model where the genetic control of species-defining traits is enriched on sex chromosomes. This study sheds light on the range of possible genetic architectures that can underpin a continuously varying trait and illustrates the power of using automated measurement to score phenotypes that are not always conspicuous to the human eye.

Stripes and loss of color in ball pythons (Python regius) are associated with variants affecting endothelin signaling

Color patterns in nonavian reptiles are beautifully diverse, but little is known about the genetics and development of these patterns. Here, we investigated color patterning in pet ball pythons (Python regius), which have been bred to show color phenotypes that differ dramatically from the wildtype form. We report that several color phenotypes in pet animals are associated with putative loss-of-function variants in the gene encoding endothelin receptor EDNRB1: (1) frameshift variants in EDNRB1 are associated with conversion of the normal mottled color pattern to skin that is almost fully white, (2) missense variants affecting conserved sites of the EDNRB1 protein are associated with dorsal, longitudinal stripes, and (3) substitutions at EDNRB1 splice donors are associated with subtle changes in patterning compared to wildtype. We propose that these phenotypes are caused by loss of specialized color cells (chromatophores), with loss ranging from severe (fully white) to moderate (dorsal striping) to mild (subtle changes in patterning). Our study is the first to describe variants affecting endothelin signaling in a nonavian reptile and suggests that reductions in endothelin signaling in ball pythons can produce a variety of color phenotypes, depending on the degree of color cell loss.

Genetic mapping and molecular mechanism behind color variation in the Asian vine snake

BACKGROUND

Reptiles exhibit a wide variety of skin colors, which serve essential roles in survival and reproduction. However, the molecular basis of these conspicuous colors remains unresolved.

RESULTS

We investigate color morph-enriched Asian vine snakes (Ahaetulla prasina), to explore the mechanism underpinning color variations. Transmission electron microscopy imaging and metabolomics analysis indicates that chromatophore morphology (mainly iridophores) is the main basis for differences in skin color. Additionally, we assemble a 1.77-Gb high-quality chromosome-anchored genome of the snake. Genome-wide association study and RNA sequencing reveal a conservative amino acid substitution (p.P20S) in SMARCE1, which may be involved in the regulation of chromatophore development initiated from neural crest cells. SMARCE1 knockdown in zebrafish and immunofluorescence verify the interactions among SMARCE1, iridophores, and tfec, which may determine color variations in the Asian vine snake.

CONCLUSIONS

This study reveals the genetic associations of color variation in Asian vine snakes, providing insights and important resources for a deeper understanding of the molecular and genetic mechanisms related to reptilian coloration.

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

Color morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs-Albino, Lavender Albino, and Ultramel-show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.

The genomics of mimicry: Gene expression throughout development provides insights into convergent and divergent phenotypes in a Müllerian mimicry system

A common goal in evolutionary biology is to discern the mechanisms that produce the astounding diversity of morphologies seen across the tree of life. Aposematic species, those with a conspicuous phenotype coupled with some form of defence, are excellent models to understand the link between vivid colour pattern variations, the natural selection shaping it, and the underlying genetic mechanisms underpinning this variation. Mimicry systems in which multiple species share the same conspicuous phenotype can provide an even better model for understanding the mechanisms of colour production in aposematic species, especially if comimics have divergent evolutionary histories. Here we investigate the genetic mechanisms by which vivid colour and pattern are produced in a Müllerian mimicry complex of poison frogs. We did this by first assembling a high-quality de novo genome assembly for the mimic poison frog Ranitomeya imitator. This assembled genome is 6.8 Gbp in size, with a contig N50 of 300 Kbp R. imitator and two colour morphs from both Ranitomeya fantastica and R. variabilis which R. imitator mimics. We identified a large number of pigmentation and patterning genes that are differentially expressed throughout development, many of them related to melanocyte development, melanin synthesis, iridophore development and guanine synthesis. Polytypic differences within species may be the result of differences in expression and/or timing of expression, whereas convergence for colour pattern between species does not appear to be due to the same changes in gene expression. In addition, we identify the pteridine synthesis pathway (including genes such as qdpr and xdh) as a key driver of the variation in colour between morphs of these species. Finally, we hypothesize that genes in the keratin family are important for producing different structural colours within these frogs.

Pterin-based pigmentation in animals

Pterins are one of the major sources of bright coloration in animals. They are produced endogenously, participate in vital physiological processes and serve a variety of signalling functions. Despite their ubiquity in nature, pterin-based pigmentation has received little attention when compared to other major pigment classes. Here, we summarize major aspects relating to pterin pigmentation in animals, from its long history of research to recent genomic studies on the molecular mechanisms underlying its evolution. We argue that pterins have intermediate characteristics (endogenously produced, typically bright) between two well-studied pigment types, melanins (endogenously produced, typically cryptic) and carotenoids (dietary uptake, typically bright), providing unique opportunities to address general questions about the biology of coloration, from the mechanisms that determine how different types of pigmentation evolve to discussions on honest signalling hypotheses. Crucial gaps persist in our knowledge on the molecular basis underlying the production and deposition of pterins. We thus highlight the need for functional studies on systems amenable for laboratory manipulation, but also on systems that exhibit natural variation in pterin pigmentation. The wealth of potential model species, coupled with recent technological and analytical advances, make this a promising time to advance research on pterin-based pigmentation in animals.

Epistatic interactions between pterin and carotenoid genes modulate intra-morph color variation in a lizard

Color polymorphisms have become a major topic in evolutionary biology and substantial efforts have been devoted to the understanding of the mechanisms responsible for originating such colorful systems. Within-morph continuous variation, on the other hand, has been neglected in most of the studies. Here, we combine spectrophotometric/visual modeling and genetic data to study the mechanisms promoting continuous variation within categorical color morphs of Podarcis muralis. Our results suggest that intra-morph variability in the pterin-based orange morph is greater compared to white and yellow morphs. We also show that continuous variation within the orange morph is partially discriminable by conspecifics. Genotyping results indicate that allelic variants at the BCO2 locus (responsible for deposition of yellow carotenoids) contribute to generate continuous variation in orange individuals. However, other intrinsic and/or extrinsic mechanisms, such as body size, might be involved, opening a new avenue for future research on the drivers of continuous variation within-morphs.

Brighter is darker: the Hamilton–Zuk hypothesis revisited in lizards

Several studies of lizards have made an erroneous interpretation of negative relationships between spectral brightness and parasite load, and thus provided misleading support for the Hamilton–Zuk hypothesis (HZH). The HZH predicts that infected hosts will produce poorer sexual ornamentation than uninfected individuals as a result of energetic trade-offs between immune and signalling functions. To test whether there is a negative relationship between spectral brightness and pigment content in the skin of lizards, we used spectrophotometry to quantify the changes in spectral brightness of colour patches of two species after chemically manipulating the contents of orange, yellow and black pigments in skin samples. Carotenoids were identified using high-performance liquid chromatography. In addition, we compared the spectral brightness in the colour patches of live individuals with differential expression of nuptial coloration. Overall, the analyses demonstrated that the more pigmented the colour patch, the darker the spectrum. We provide a comprehensive interpretation of how variation in pigment content affects the spectral brightness of the colour patches of lizards. Furthermore, we review 18 studies of lizards presenting 24 intraspecific tests of the HZH and show that 14 (58%) of the tests do not support the hypothesis.

Reaction-diffusion in a growing 3D domain of skin scales generates a discrete cellular automaton

We previously showed that the adult ocellated lizard skin colour pattern is effectively generated by a stochastic cellular automaton (CA) of skin scales. We additionally suggested that the canonical continuous 2D reaction-diffusion (RD) process of colour pattern development is transformed into this discrete CA by reduced diffusion coefficients at the borders of scales (justified by the corresponding thinning of the skin). Here, we use RD numerical simulations in 3D on realistic lizard skin geometries and demonstrate that skin thickness variation on its own is sufficient to cause scale-by-scale coloration and CA dynamics during RD patterning. In addition, we show that this phenomenon is robust to RD model variation. Finally, using dimensionality-reduction approaches on large networks of skin scales, we show that animal growth affects the scale-colour flipping dynamics by causing a substantial decrease of the relative length scale of the labyrinthine colour pattern of the lizard skin.

Comparative ultrastructural-functional characterizations of the skin in three reptile species; Chalcides ocellatus, Uromastyx aegyptia aegyptia, and Psammophis schokari aegyptia (FORSKAL, 1775): Adaptive strategies to their habitat

The current investigation was planned utilizing SEM, histological, and furthermore cytokeratin immunohistochemical to give a full depiction of skin of three reptiles species; Chalcides ocellatus (Scincidae), Uromastyx aegyptia aegyptia (Agamidae), and Psammophis schokari aegyptia (Colubridae) captured from Egypt with various ecological environment. Our SEM results showed different scales covered epidermis of three reptile's species with diverse surface microstructure. Overlapped rhomboid scales with numerous lenticular sense organs with numerous pores and oberhäutchen layer with microridges in C. ocellatus. In U. aegyptia, scales were overlapped elliptical-shaped possess lens-like sense structure with several scattered pits and oberhäutchen layer with polygonal outlined cells. While in P. schokari aegyptia, smooth scales flattened with two large dome-shaped scale receptors/sensilla and lens-like sense structure, moreover polygonal-shaped micro-ornamentation in scale hinge joints were observed. Histologically, skin of three species had outer epidermis with stratum germinativum, stratum corneum (α-keratin, β-keratin layer) capped by surface Oberhäutchen and inner dermis. Osteoderms were observed with dermis of C. ocellatus. There are marked variation within pigment cells types among examined species. Melanophores observed in dermal layer of C. ocellatus, while in U. aegyptia, three pigment cells in tegument dermis; melanophores, xanthophores, and iridophores whereas, P. schokari aegyptia had two forms of chromatophore cells (melanophores and iridophores) in dermis and few melanophores scattered between stratum germinativum cells. The highest cytokeratin immunostaining observed in epidermal cell layer of U. aegyptia aegyptia than two other species. Conclusion, dry scaly skin of reptiles reflects a great range of functional aspects and success to adapt with terrestrial life.

Untangling the structural and molecular mechanisms underlying colour and rapid colour change in a lizard, Agama atra

With functions as diverse as communication, protection and thermoregulation, coloration is one of the most important traits in lizards. The ability to change colour as a function of varying social and environmental conditions is thus an important innovation. While colour change is present in animals ranging from squids, to fish and reptiles, not much is known about the mechanisms behind it. Traditionally, colour change was attributed to migration of pigments, in particular melanin. More recent work has shown that the changes in nanostructural configuration inside iridophores are able to produce a wide palette of colours. However, the genetic mechanisms underlying colour, and colour change in particular, remain unstudied. Here we use a combination of transcriptomic and microscopic data to show that melanin, iridophores and pteridines are the main colour-producing mechanisms in Agama atra, and provide molecular and structural data suggesting that rapid colour change is achieved via melanin dispersal in combination with iridophore organization. This work demonstrates the power of combining genotypic (gene expression) and phenotypic (microscopy) information for addressing physiological questions, providing a basis for future studies of colour change.

Characterization of the Leucistic Texas Rat Snake Pantherophis obsoletus

Albinism and leucism are phenotypes resulting from impaired melanin pigmentation in the skin and skin appendages. However, melanin pigmentation of eyes remains unaffected in leucism. Here, using transmission electron microscopy, we show that the leucistic morph of the Texas rat snake (Pantherophis obsoletus lindheimeri) lacks both melanophores and xanthophores in its skin and exhibits a uniform ivory white color generated by iridophores and collagen fibers. In addition, we sequenced the full genome of a leucistic individual and obtained a highly-contiguous near-chromosome quality assembly of 1.69 Gb with an N50 of 14.5 Mb and an L50 of 29 sequences. Using a candidate-gene approach, we then identify in the leucistic genome a single-nucleotide deletion that generates a frameshift and a premature termination codon in the melanocyte inducing transcription factor (MITF) gene. This mutation shortens the translated protein from 574 to 286 amino acids, removing the helix-loop-helix DNA-binding domain that is highly conserved among vertebrates. Genotyping leucistic animals of independent lineages showed that not all leucistic individuals carry this single-nucleotide deletion. Subsequent gene expression analyses reveal that all leucistic individuals that we analyzed exhibit a significantly decreased expression of MITF. We thus suggest that mutations affecting the regulation and, in some cases, the coding sequence of MITF, the former probably predating the latter, could be associated with the leucistic phenotype in Texas rat snakes. MITF is involved in the development and survival of melanophores in vertebrates. In zebrafish, a classical model species for pigmentation that undergoes metamorphosis, larvae and adults of homozygous mitfa mutants lack melanophores, show an excess of iridophores and exhibit reduced yellow pigmentation. On the contrary, in the leucistic Texas rat snake, a non-metamorphic species, only iridophores persist. Our results suggest that fate determination of neural-crest derived melanophores and xanthophores, but not of iridophores, could require the expression of MITF during snake embryonic development.

Neon-green fluorescence in the desert gecko Pachydactylus rangei caused by iridophores

Biofluorescence is widespread in the natural world, but only recently discovered in terrestrial vertebrates. Here, we report on the discovery of iridophore-based, neon-green flourescence in the gecko Pachydactylus rangei, localised to the skin around the eyes and along the flanks. The maximum emission of the fluorescence is at a wavelength of 516 nm in the green spectrum (excitation maximum 465 nm, blue) with another, smaller peak at 430 nm. The fluorescent regions of the skin show large numbers of iridophores, which are lacking in the non-fluorescent parts. Two types of iridophores are recognized, fluorescent iridophores and basal, non-fluorescent iridophores, the latter of which might function as a mirror, amplifying the omnidirectional fluorescence. The strong intensity of the fluorescence (quantum yield of 12.5%) indicates this to be a highly effective mechanism, unique among tetrapods. Although the fluorescence is associated with iridophores, the spectra of emission and excitation as well as the small Stokes shifts argue against guanine crystals as its source, but rather a rigid pair of fluorophores. Further studies are necessary to identify their morphology and chemical structures. We hypothesise that this nocturnal gecko uses the neon-green fluorescence, excited by moonlight, for intraspecific signalling in its open desert habitat.

Genome mapping of a LYST mutation in corn snakes indicates that vertebrate chromatophore vesicles are lysosome-related organelles

Reptiles exhibit a spectacular diversity of skin colors and patterns brought about by the interactions among three chromatophore types: black melanophores with melanin-packed melanosomes, red and yellow xanthophores with pteridine- and/or carotenoid-containing vesicles, and iridophores filled with light-reflecting platelets generating structural colors. Whereas the melanosome, the only color-producing endosome in mammals and birds, has been documented as a lysosome-related organelle, the maturation paths of xanthosomes and iridosomes are unknown. Here, we first use 10x Genomics linked-reads and optical mapping to assemble and annotate a nearly chromosome-quality genome of the corn snake Pantherophis guttatus The assembly is 1.71 Gb long, with an N50 of 16.8 Mb and L50 of 24. Second, we perform mapping-by-sequencing analyses and identify a 3.9-Mb genomic interval where the lavender variant resides. The lavender color morph in corn snakes is characterized by gray, rather than red, blotches on a pink, instead of orange, background. Third, our sequencing analyses reveal a single nucleotide polymorphism introducing a premature stop codon in the lysosomal trafficking regulator gene (LYST) that shortens the corresponding protein by 603 amino acids and removes evolutionary-conserved domains. Fourth, we use light and transmission electron microscopy comparative analyses of wild type versus lavender corn snakes and show that the color-producing endosomes of all chromatophores are substantially affected in the LYST mutant. Our work provides evidence characterizing xanthosomes in xanthophores and iridosomes in iridophores as lysosome-related organelles.

Optical costs and benefits of disorder in biological photonic crystals

Photonic structures in ordered, quasi-ordered or disordered forms have evolved across many different animal and plant systems. They can produce complex and often functional optical responses through coherent and incoherent scattering processes, often too, in combination with broadband or narrowband absorbing pigmentation. Interestingly, these systems appear highly tolerant of faults in their photonic structures, with imperfections in their structural order appearing not to impact, discernibly, the systems' optical signatures. The extent to which any such biological system deviates from presenting perfect structural order can dictate the optical properties of that system and, thereby, the optical properties that system delivers. However, the nature and extent of the optical costs and benefits of imperfect order in biological systems demands further elucidation. Here, we identify the extent to which biological photonic systems are tolerant of defects and imperfections. Certainly, it is clear that often significant inherent variations in the photonic structures of these systems, for instance a relatively broad distribution of lattice constants, can consistently produce what appear to be effective visual appearances and optical performances. In this article, we review previously investigated biological photonic systems that present ordered, quasi-ordered or disordered structures. We discuss the form and nature of the optical behaviour of these structures, focusing particularly on the associated optical costs and benefits surrounding the extent to which their structures deviate from what might be considered ideal systems. Then, through detailed analyses of some well-known 1D and 2D structurally coloured systems, we analyse one of the common manifestations of imperfect order, namely, the extent and nature of positional disorder in the systems' spatial distribution of layers and scattering centres. We use these findings to inform optical modelling that presents a quantitative and qualitative description of the optical costs and benefits of such positional disorder among ordered and quasi-ordered 1D and 2D photonic systems. As deviation from perfectly ordered structures invariably limits the performance of technology-oriented synthetic photonic processes, we suggest that the use of bio-inspired fault tolerance principles would add value to applied photonic technologies.

Male rock lizards may compensate reproductive costs of an immune challenge affecting sexual signals

Sexual signals can be evolutionarily stable if they are condition dependent or costly to the signaler. One of these costs may be the trade-off between maintaining the immune system and the elaboration of ornaments. Experimental immune challenges in captivity show a reduction in the expression of sexual signals, but it is not clear whether these detrimental effects are important in nature and, more importantly, whether they have reproductive consequences. We designed a field experiment to challenge the immune system of wild male Carpetan rock lizards, Iberolacerta cyreni, with a bacterial antigen (lipopolysaccharide). The immune challenge decreased relative reflectance of ultraviolet structural and melanin-dependent sexual coloration in the throat and the lateral ocelli, whereas the carotenoid-dependent dorsal green coloration was not affected. Immune activation also decreased proportions of ergosterol and cholesta-5,7-dien-3-ol in femoral secretions. These results support a trade-off between the immune system and both visual and chemical sexual ornaments. Moreover, the reproductive success of males, estimated with DNA microsatellites, depended on the expression of some color and chemical traits. However, the immune challenge did not cause overall differences in reproductive success, although it increased with body size/age in control but not in challenged males. This suggests the use of alternative reproductive strategies (e.g., forced matings) in challenged males, particularly in smaller ones. These males might consider that their survival probabilities are low and increase reproductive effort as a form of terminal investment in spite of their “low-quality” sexual signals and potential survival costs.

Lizard colour plasticity tracks background seasonal changes

Environmental heterogeneity on a spatial and temporal scale fosters an organism's capacity to plastically alter coloration. Predation risk might favour the evolution of phenotypic plasticity in colour patterns, as individuals who change colour throughout the year may be able to improve their fitness. Here we explored the change in dorsal pigmentation of the Italian wall lizard (Podarcis siculus campestris) at three time points (March, July, October) during a period of activity in a Mediterranean natural area in southern Italy. Following a preliminary investigation conducted in 2018, during 2019 we captured 135 lizards and took a picture of their ventral scales to check for possible recapture over the sessions. Lizard dorsal pictures were collected in the field with the support of a reference chart to quantitatively estimate chromatic variables (hue, saturation and value). At the same time, pictures of the environmental background were collected. Our findings suggest that lizards are capable of altering dorsal coloration during seasonal change. They vary from green at the onset of spring, to brownish in the middle of summer and to a greyish colour in October. This modification closely followed environmental background colour variation and enhanced lizard crypsis during each season.

Mechanisms for Color Convergence in a Mimetic Radiation of Poison Frogs

In animals, bright colors often evolve to mimic other species when a resemblance is selectively favored. Understanding the proximate mechanisms underlying such color mimicry can give insights into how mimicry evolves-for example, whether color convergence evolves from a shared set of mechanisms or through the evolution of novel color production mechanisms. We studied color production mechanisms in poison frogs (Dendrobatidae), focusing on the mimicry complex of Ranitomeya imitator. Using reflectance spectrometry, skin pigment analysis, electron microscopy, and color modeling, we found that the bright colors of these frogs, both within and outside the mimicry complex, are largely structural and produced by iridophores but that color production depends crucially on interactions with pigments. Color variation and mimicry are regulated predominantly by iridophore platelet thickness and, to a lesser extent, concentration of the red pteridine pigment drosopterin. Compared with each of the four morphs of model species that it resembles, R. imitator displays greater variation in both structural and pigmentary mechanisms, which may have facilitated phenotypic divergence in this species. Analyses of nonmimetic dendrobatids in other genera demonstrate that these mechanisms are widespread within the family and that poison frogs share a complex physiological "color palette" that can produce diverse and highly reflective colors.

Iridophoroma associated with the Lemon Frost colour morph of the leopard gecko (Eublepharis macularius)

The Lemon Frost is a new colour morph of the leopard gecko, which emerged in ca. 2015 as a result of selective breeding and spontaneous mutation. According to multiple breeders observation of Lemon Frost inbreeding with wild-type leopard geckos, Lemon Frost seems to be a codominant trait. Additionally breeders observed another, presumably associated trait - tumour-like skin lesions. Three private-owned Lemon Frost morph leopard geckos with tumour-like skin lesions were admitted to our clinic for examination, which included histopathology, X-ray and ultrasonography. The histopathological investigation of the biopsies indicated malignant iridophoroma; however, no changes were observed in diagnostic imaging. This research is the first report of clinical and histopathological findings of iridophoroma in leopard geckos.

Ecological, behavioral, and phylogenetic influences on the evolution of dorsal color pattern in geckos

The dorsal surfaces of many taxonomic groups often feature repetitive pattern elements consisting of stripes, spots, or bands. Here, we investigate how distinct categories of camouflage pattern work by relating them to ecological and behavioral traits in 439 species of gecko. We use phylogenetic comparative methods to test outstanding hypotheses based on camouflage theory and research in other taxa. We found that bands are associated with nocturnal activity, suggesting bands provide effective camouflage for motionless geckos resting in refugia during the day. A predicted association between stripes and diurnal activity was not supported, suggesting that stripes do not work via dazzle camouflage mechanisms in geckos. This, along with a lack of support for our prediction that plain patterning should be associated with open habitats, suggests that similar camouflage patterns do not work in consistent ways across taxa. We also found that plain and striped lineages frequently switched between using open or closed habitats, whereas spotted lineages rarely transitioned. This suggests that pattern categories differ in how specialized or generalized their camouflage is. This result has ramifications for theory on how camouflage compromises to background heterogeneity and how camouflage pattern might influence evolutionary trajectories.

Self-Organization in Pattern Formation

Self-organization is pervasive in development, from symmetry breaking in the early embryo to tissue patterning and morphogenesis. For a few model systems, the underlying molecular and cellular processes are now sufficiently characterized that mathematical models can be confronted with experiments, to explore the dynamics of pattern formation. Here, we review selected systems, ranging from cyanobacteria to mammals, where different forms of cell-cell communication, acting alone or together with positional cues, drive the patterning of cell fates, highlighting the insights that even very simple models can provide as well as the challenges on the path to a predictive understanding of development.

Evaluation of the effectiveness of cryptic coloration of the Carolina anole’s skin

Cryptic coloration of animals’ integument is one of the effective adaptations that allow them to lead an active lifestyle while being protected from natural enemies due to visual disguise. This is achieved by the similarity of body color of a particular individual to the background of various substrates in its environment. The morphological and functional basis of cryptic coloration in vertebrates, including reptiles, is ensured by the skin pigmentation. Using bioinformatic methods, we calculated the skin camouflage index of the Carolina anole (Anolis carolinensis Voigt, 1832) in various conditions of its habitat. The skin camouflage index (Ic) is the ratio of the sum of the average values of rgb coordinates of the skin color to the sum of the average values of rgb coordinates of the color of the external substrate. Ic satisfies the effective level of adaptation to habitat conditions if it falls within the range of 0.80–1.20. It has been shown that rgb-values of the dominant color of the dorsal skin of green anoles slightly differ from the similar parameters characteristic of the deciduous habitat, which is reflected by Ic of its skin (0.94). In the brown anoles on a background of woody substrate, the Ic value of its skin (0.88) is also optimal, since it exceeds the lower limit (0.80), which indicates close values of the sums of the rgb coordinates of the skin color and the color of the external background. In the mixed green-brown anoles, the deciduous habitat is preferable to the woody one. In the first case, Ic (1.11) is in the optimum zone, and in the second case, Ic (0.70) goes beyond the lower limit of the optimum, which indicates a greater vulnerability of the animal to external threats. We have confirmed the relativity of visual hiding of the skin that is effective only in the habitat conditions in which the camouflage abilities of the skin manifest as fully as possible.

Body coloration and mechanisms of colour production in Archelosauria: the case of deirocheline turtles

Animal body coloration is a complex trait resulting from the interplay of multiple mechanisms. While many studies address the functions of animal coloration, the mechanisms of colour production still remain unknown in most taxa. Here we compare reflectance spectra, cellular, ultra- and nano-structure of colour-producing elements, and pigment types in two freshwater turtles with contrasting courtship behaviour, Trachemys scripta and Pseudemys concinna. The two species differ in the distribution of pigment cell-types and in pigment diversity. We found xanthophores, melanocytes, abundant iridophores and dermal collagen fibres in stripes of both species. The yellow chin and forelimb stripes of both P. concinna and T. scripta contain xanthophores and iridophores, but the post-orbital regions of the two species differ in cell-type distribution. The yellow post-orbital region of P. concinna contains both xanthophores and iridophores, while T. scripta has only xanthophores in the yellow-red postorbital/zygomatic regions. Moreover, in both species, the xanthophores colouring the yellow-red skin contain carotenoids, pterins and riboflavin, but T. scripta has a higher diversity of pigments than P. concinna. Trachemys s. elegans is sexually dichromatic. Differences in the distribution of pigment cell types across body regions in the two species may be related to visual signalling but do not match predictions based on courtship position. Our results demonstrate that archelosaurs share some colour production mechanisms with amphibians and lepidosaurs (i.e. vertical layering/stacking of different pigment cell types and interplay of carotenoids and pterins), but also employ novel mechanisms (i.e. nano-organization of dermal collagen) shared with mammals.

Tissue Transparency In Vivo

In vivo tissue transparency in the visible light spectrum is beneficial for many research applications that use optical methods, whether it involves in vivo optical imaging of cells or their activity, or optical intervention to affect cells or their activity deep inside tissues, such as brain tissue. The classical view is that a tissue is transparent if it neither absorbs nor scatters light, and thus absorption and scattering are the key elements to be controlled to reach the necessary transparency. This review focuses on the latest genetic and chemical approaches for the decoloration of tissue pigments to reduce visible light absorption and the methods to reduce scattering in live tissues. We also discuss the possible molecules involved in transparency.

Variation in pigmentation gene expression is associated with distinct aposematic color morphs in the poison frog Dendrobates auratus

Background

Color and pattern phenotypes have clear implications for survival and reproduction in many species. However, the mechanisms that produce this coloration are still poorly characterized, especially at the genomic level. Here we have taken a transcriptomics-based approach to elucidate the underlying genetic mechanisms affecting color and pattern in a highly polytypic poison frog. We sequenced RNA from the skin from four different color morphs during the final stage of metamorphosis and assembled a de novo transcriptome. We then investigated differential gene expression, with an emphasis on examining candidate color genes from other taxa.

Results

Overall, we found differential expression of a suite of genes that control melanogenesis, melanocyte differentiation, and melanocyte proliferation (e.g., tyrp1, lef1, leo1, and mitf) as well as several differentially expressed genes involved in purine synthesis and iridophore development (e.g., arfgap1, arfgap2, airc, and gart).

Conclusions

Our results provide evidence that several gene networks known to affect color and pattern in vertebrates play a role in color and pattern variation in this species of poison frog.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1410-7) contains supplementary material, which is available to authorized users.

Dynamic pigmentary and structural coloration within cephalopod chromatophore organs

Chromatophore organs in cephalopod skin are known to produce ultra-fast changes in appearance for camouflage and communication. Light-scattering pigment granules within chromatocytes have been presumed to be the sole source of coloration in these complex organs. We report the discovery of structural coloration emanating in precise register with expanded pigmented chromatocytes. Concurrently, using an annotated squid chromatophore proteome together with microscopy, we identify a likely biochemical component of this reflective coloration as reflectin proteins distributed in sheath cells that envelop each chromatocyte. Additionally, within the chromatocytes, where the pigment resides in nanostructured granules, we find the lens protein Ω- crystallin interfacing tightly with pigment molecules. These findings offer fresh perspectives on the intricate biophotonic interplay between pigmentary and structural coloration elements tightly co-located within the same dynamic flexible organ - a feature that may help inspire the development of new classes of engineered materials that change color and pattern.

Assessment of tissue-specific multifactor effects in environmental -omics studies of heterogeneous biological samples: Combining hyperspectral image information and chemometrics

The use of hyperspectral imaging techniques in biological studies has increased in the recent years. Hyperspectral images (HSI) provide chemical information and preserve the morphology and original structure of heterogeneous biological samples, which can be potentially useful in environmental -omics studies when effects due to several factors, e.g., contaminant exposure, phenotype,…, at a specific tissue level need to be investigated. Yet, no available strategies exist to exploit adequately this kind of information. This work offers a novel chemometric strategy to pass from the raw image information to useful knowledge in terms of statistical assessment of the multifactor effects of interest in -omic studies. To do so, unmixing of the hyperspectral image measurement is carried out to provide tissue-specific information. Afterwards, several specific ANOVA-Simultaneous Component Analysis (ASCA) models are generated to properly assess and interpret the diverse effect of the factors of interest on the spectral fingerprints of the different tissues characterized. The unmixing step is performed by Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS) on multisets of biological images related to each studied condition and provides reliable HSI spectral signatures and related image maps for each specific tissue in the regions imaged. The variability associated with these signatures within a population is obtained through an MCR-based resampling step on representative pixel subsets of the images analyzed. All spectral fingerprints obtained for a particular tissue in the different conditions studied are used to obtain the related ASCA model that will help to assess the significance of the factors studied on the tissue and, if relevant, to describe the associated fingerprint modifications. The potential of the approach is assessed in a real case of study linked to the investigation of the effect of exposure time to chlorpyrifos-oxon (CPO) on ocular tissues of different phenotypes of zebrafish larvae from Raman HSI of eye cryosections. The study allowed the characterization of melanin, crystalline and internal eye tissue and the phenotype, exposure time and the interaction of the two factors were found to be significant in the changes found in all kind of tissues. Factor-related changes in the spectral fingerprint were described and interpreted per each kind of tissue characterized.

Ontogenetic and phylogenetic simplification during white stripe evolution in clownfishes

Background

Biologists have long been fascinated by the striking diversity of complex color patterns in tropical reef fishes. However, the origins and evolution of this diversity are still poorly understood. Disentangling the evolution of simple color patterns offers the opportunity to dissect both ultimate and proximate causes underlying color diversity.

Results

Here, we study clownfishes, a tribe of 30 species within the Pomacentridae that displays a relatively simple color pattern made of zero to three vertical white stripes on a dark body background. Mapping the number of white stripes on the evolutionary tree of clownfishes reveals that their color pattern diversification results from successive caudal to rostral losses of stripes. Moreover, we demonstrate that stripes always appear with a rostral to caudal stereotyped sequence during larval to juvenile transition. Drug treatments (TAE 684) during this period leads to a dose-dependent loss of stripes, demonstrating that white stripes are made of iridophores and that these cells initiate the stripe formation. Surprisingly, juveniles of several species (e.g., Amphiprion frenatus) have supplementary stripes when compared to their respective adults. These stripes disappear caudo-rostrally during the juvenile phase leading to the definitive color pattern. Remarkably, the reduction of stripe number over ontogeny matches the sequences of stripe losses during evolution, showing that color pattern diversification among clownfish lineages results from changes in developmental processes. Finally, we reveal that the diversity of striped patterns plays a key role for species recognition.

Conclusions

Overall, our findings illustrate how developmental, ecological, and social processes have shaped the diversification of color patterns during the radiation of an emblematic coral reef fish lineage.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0559-7) contains supplementary material, which is available to authorized users.

The chemical fingerprint of hair melanosomes by infrared nano-spectroscopy

In situ characterization of the chemical and structural properties of black and white sheep hair was performed with a spatial resolution of 25 nm using infrared nano-spectroscopy. Comparing data sets from two types of hair allowed us to isolate the keratin FTIR fingerprint and so mark off chemical properties of the hair's melanosomes. From a polarization sensitive analysis of the nano-FTIR spectra, we showed that keratin intermediate filaments (IFs) present anisotropic molecular ordering. In stark contrast with white hair which does not contain melanosomes, in black hair, we spatially resolved single melanosomes and achieved unprecedented assignment of the vibrational modes of pheomelanin and eumelanin. The in situ experiment presented here avoids harsh chemical extractive methods used in previous studies. Our findings offer a basis for a better understanding of the keratin chemical and structural packing in different hair phenotypes as well as the involvement of melanosomes in hair color and biological functionality.

Interactions between colour-producing mechanisms and their effects on the integumentary colour palette

Animal integumentary coloration plays a crucial role in visual communication and camouflage, and varies extensively among and within species and populations. To understand the pressures underlying such diversity, it is essential to elucidate the mechanisms by which animals have created novel integumentary coloration. Colours can be produced by selective absorption of light by skin pigments, through light scattering by structured or unstructured tissues, or by a combination of pigments and nanostructures. In this review, we highlight our current understanding of the interactions between pigments and structural integumentary tissues and molecules. We analyse the available evidence suggesting that these combined mechanisms are capable of creating colours and optical properties unachievable by either mechanism alone, thereby effectively expanding the animal colour palette. Moreover, structural and pigmentary colour mechanisms frequently interact in unexpected and overlooked ways, suggesting that classification of colours as being of any particular type may be difficult. Finally, we discuss how these mixtures are useful for investigating the largely unknown genetic, developmental and physical processes generating phenotypic diversity.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

Genomics of coloration in natural animal populations

Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

Combining hyperspectral imaging and chemometrics to assess and interpret the effects of environmental stressors on zebrafish eye images at tissue level

Changes on an organism by the exposure to environmental stressors may be characterized by hyperspectral images (HSI), which preserve the morphology of biological samples, and suitable chemometric tools. The approach proposed allows assessing and interpreting the effect of contaminant exposure on heterogeneous biological samples monitored by HSI at specific tissue levels. In this work, the model example used consists of the study of the effect of the exposure of chlorpyrifos-oxon on zebrafish tissues. To assess this effect, unmixing of the biological sample images followed by tissue-specific classification models based on the unmixed spectral signatures is proposed. Unmixing and classification are performed by multivariate curve resolution-alternating least squares (MCR-ALS) and partial least squares-discriminant analysis (PLS-DA), respectively. Crucial aspects of the approach are: (1) the simultaneous MCR-ALS analysis of all images from 1 population to take into account biological variability and provide reliable tissue spectral signatures, and (2) the use of resolved spectral signatures from control and exposed populations obtained from resampling of pixel subsets analyzed by MCR-ALS multiset analysis as information for the tissue-specific PLS-DA classification models. Classification results diagnose the presence of a significant effect and identify the spectral regions at a tissue level responsible for the biological change.

Developmental mechanisms of longitudinal stripes in the Japanese four-lined snake

The developmental mechanisms of color patterns formation and its evolution remain unclear in reptilian sauropsids. We, therefore, studied the pigment cell mechanisms of stripe pattern formation during embryonic development of the snake Elaphe quadrivirgata. We identified 10 post-ovipositional embryonic developmental stages based on external morphological characteristics. Examination for the temporal changes in differentiation, distribution, and density of pigment cells during embryonic development revealed that melanophores first appeared in myotome and body cavity but not in skin surface at Stage 5. Epidermal melanophores were first recognized at Stage 7, and dermal melanophores and iridophores appeared in Stage 9. Stripe pattern first appeared to establish at Stage 8 as a spatial density gradient of epidermal melanophores between the regions of future dark brown longitudinal stripes and light colored background. Our study, thus, provides a comprehensive pigment-cell-based understanding of stripe pattern formation during embryonic development. We briefly discuss the importance of the gene expression studies by considering the biologically relevant theoretical models with standard developmental staging for understanding reptilian color pattern evolution.

Stress-induced changes in color expression mediated by iridophores in a polymorphic lizard

Stress is an important potential factor mediating a broad range of cellular pathways, including those involved in condition‐dependent (i.e., honest) color signal expression. However, the cellular mechanisms underlying the relationship between stress and color expression are largely unknown. We artificially elevated circulating corticosterone levels in male tawny dragon lizards, Ctenophorus decresii, to assess the effect of stress on the throat color signal. Corticosterone treatment increased luminance (paler throat coloration) and decreased the proportion of gray, thereby influencing the gray reticulations that produce unique patterning. The magnitude of change in luminance for corticosterone‐treated individuals in our study was around 6 “just noticeable differences” to the tawny dragon visual system, suggesting that lizards are likely to be able to perceive the measured variation. Transmission electron microscopy (TEM) of iridophore cells indicated that luminance increased with increasing density of iridophore cells and increased spacing (and/or reduced size) of crystalline guanine platelets within them. Crystal spacing within iridophores also differed between skin colors, being greater in cream than either gray or yellow skin and greater in orange than yellow skin. Our results demonstrate that stress detectably impacts signal expression (luminance and patterning), which may provide information on individual condition. This effect is likely to be mediated, at least in part, by structural coloration produced by iridophore cells.

Eumelanin and pheomelanin are predominant pigments in bumblebee (Apidae: Bombus) pubescence

BACKGROUND

Bumblebees (Hymenoptera: Apidae: Bombus) are well known for their important inter- and intra-specific variation in hair (or pubescence) color patterns, but the chemical nature of the pigments associated with these patterns is not fully understood. For example, though melanization is believed to provide darker colors, it still unknown which types of melanin are responsible for each color, and no conclusive data are available for the lighter colors, including white.

METHODS

By using dispersive Raman spectroscopy analysis on 12 species/subspecies of bumblebees from seven subgenera, we tested the hypothesis that eumelanin and pheomelanin, the two main melanin types occurring in animals, are largely responsible for bumblebee pubescence coloration.

RESULTS

Eumelanin and pheomelanin occur in bumblebee pubescence. Black pigmentation is due to prevalent eumelanin, with visible signals of additional pheomelanin, while the yellow, orange, red and brown hairs clearly include pheomelanin. On the other hand, white hairs reward very weak Raman signals, suggesting that they are depigmented. Additional non-melanic pigments in yellow hair cannot be excluded but need other techniques to be detected. Raman spectra were more similar across similarly colored hairs, with no apparent effect of phylogeny and both melanin types appeared to be already used at the beginning of bumblebee radiation.

DISCUSSION

We suggest that the two main melanin forms, at variable amounts and/or vibrational states, are sufficient in giving almost the whole color range of bumblebee pubescence, allowing these insects to use a single precursor instead of synthesizing a variety of chemically different pigments. This would agree with commonly seen color interchanges between body segments across Bombus species.

Manipulation of parasite load induces significant changes in the structural-based throat color of male iberian green lizards

The honesty of structural-based ornaments is controversial. Sexual selection theory predicts that the honesty of a sexual signal relies on its cost of production or maintenance. Therefore, environmental factors with negative impact on individuals could generate high costs and affect the expression of these sexual signals. In this sense, parasites are a main cost for their hosts. To probe the effect of parasites on the structural-based coloration of a lacertid species Lacerta schreiberi, we have experimentally removed ticks from a group of male Iberian green lizards using an acaricide treatment (i.e., the broad-use insecticide fipronil). All individuals were radio-tracked and recaptured after 15 days to study changes in coloration in both the ultraviolet (UV)-blue (structural-based) and UV-yellow (structural and pigment-based) ornamentations after manipulation, as well as changes in endo- and ectoparasitic load and body condition. Additionally, after the experiment, we measured the skin inflammatory response to a mitogen. The fipronil treatment was effective in reducing ticks and it was associated with a significant reduction of hemoparasite load. Throughout the season, individuals treated with fipronil tended to maintain the brightness of the UV-blue throat coloration while control lizards tended to increase it. However, individuals treated with fipronil that were not infected with hemoparasites significantly reduced the brightness of the UV-blue throat coloration. Individuals with a higher initial tick load exhibited a lower UV saturation increment (UV-blue) and a higher brightness increment (UV-yellow) during the experiment. Overall these results experimentally support the idea that parasites adversely influence the expression of the structural-based coloration of male Iberian green lizards. This adds evidence to the hypothesis that sexual ornaments in lizards function as honest signals.