Molecular diversity, metabolic transformation, and evolution of carotenoid feather pigments in cotingas (Aves: Cotingidae)

Could alternative pathways for carotenoid transformation affect colour production efficiency? A correlative study in wild birds

In many vertebrates, dietary yellow carotenoids are enzymatically transformed into 4C-ketocarotenoid pigments, leading to conspicuous red colourations. These colourations may evolve as signals of individual quality under sexual selection. To evolve as signals, they must transmit reliable information benefiting both the receiver and the signaler. Some argue that the reliability of 4C-ketocarotenoid-based colourations is ensured by the tight link between individual quality and mitochondrial metabolism, which is supposedly involved in transforming yellow carotenoids. We studied how a range of carotenoids covary in the feathers and blood plasma of a large number (n > 140) of wild male common crossbills (Loxia curvirostra). Plumage redness was mainly due to 3-hydroxy-echinenone (3HOE). Two other, less abundant, red 4C-ketocarotenoids (astaxanthin and canthaxanthin) could have contributed to feather colour as they are redder pigments. This was demonstrated for astaxanthin but not canthaxanthin, whose feather levels were clearly uncorrelated to colouration. Moreover, moulting crossbills carried more 3HOE and astaxanthin in blood than non-moulting ones, whereas canthaxanthin did not differ. Canthaxanthin and 3HOE can be formed from echinenone, a probable product of dietary β-carotene ketolation. Echinenone could thus be ketolated or hydroxylated to produce canthaxanthin or 3HOE, respectively. In moulting birds, 3HOE blood levels positively correlated to astaxanthin, its product, but negatively to canthaxanthin levels. Redder crossbills also had lower plasma canthaxanthin values. A decrease in hydroxylation relative to ketolation could explain canthaxanthin production. We hypothesize that red colouration could indicate birds' ability to avoid inefficient deviations within the complex enzymatic pathways.

Transitions between colour mechanisms affect speciation dynamics and range distributions of birds

Several ecogeographical 'rules' have been proposed to explain colour variation at broad spatial and phylogenetic scales but these rarely consider whether colours are based on pigments or structural colours. However, mechanism can have profound effects on the function and evolution of colours. Here, we combine geographic information, climate data and colour mechanism at broad phylogenetic (9,409 species) and spatial scales (global) to determine how transitions between pigmentary and structural colours influence speciation dynamics and range distributions in birds. Among structurally coloured species, we find that rapid dispersal into tropical regions drove the accumulation of iridescent species, whereas the build-up of non-iridescent species in the tropics was driven by a combination of dispersal and faster in situ evolution in the tropics. These results could be explained by pleiotropic links between colouration and dispersal behaviour or ecological factors influencing colonization success. These data elucidate geographic patterns of colouration at a global scale and provide testable hypotheses for future work on birds and other animals with structural colours.

Feather carotenoids of the American Redstart (Setophaga ruticilla) across age and sex classes and the reliability of standard color metrics to capture pigment variation

Plumage ornaments act as important sexual signals, though the extent to which these ornaments act as honest signals-and the physiological mechanisms that maintain honesty-remain poorly understood. We studied the pigmentary basis of tail color in the American Redstart (Setophaga ruticilla), a species of songbird with sexual dichromatism and delayed plumage maturation; younger males resemble females, only replacing their yellow feathers for bright orange ones after the first breeding season. The yellow rectrices of females and young males and the orange feathers of older males largely contain the same pigments, but in vastly different proportions. Whereas the feathers of females and young males contain primarily lutein, 3'-dehydro-lutein and canary-xanthophylls, those of older males contain primarily 4-keto-carotenoids. The presence of lutein and the predominance of α-doradexanthin as 4-keto-carotenoid, a pigment with a shortened chain of conjugated double bonds compared to keto-carotenoids commonly found in red feathers, in the feathers of older males contribute to their uncommon orange hue. Since the orange coloration of the tail in the American redstart results from the combination of yellow, orange, and red pigments, this is a system where slight adjustments in the types of carotenoids deposited could significantly alter hue. Factors either work against achieving the most oxidized state in this species or the hue is maintained through stabilizing selection for a favored color. The color metrics of Carotenoid Chroma, Visible Hue, λR50 and tetrahedral θ best captured differences in pigment concentration and make-up, and are recommended in future spectrophotometric studies of carotenoid-based traits.

Ketocarotenoids adonirubin and adonixanthin: Properties, health benefits, current technologies, and emerging challenges

Given their multifaceted roles, carotenoids have garnered significant scientific interest, resulting in a comprehensive and intricate body of literature that occasionally presents conflicting findings concerning the proper characterization, quantification, and bioavailability of these compounds. Nevertheless, it is undeniable that the pursuit of novel carotenoids remains a crucial endeavor, as their diverse properties, functionalities and potential health benefits make them invaluable natural resources in agri-food and health promotion through the diet. In this framework, particular attention is given to ketocarotenoids, viz., astaxanthin (one of them) stands out for its possible multifunctional role as an antioxidant, anticancer, and antimicrobial agent. It has been widely explored in the market and utilized in different applications such as nutraceuticals, food additives, among others. Adonirubin and adonixanthin can be naturally found in plants and microorganisms. Due to the increasing significance of natural-based products and the remarkable opportunity to introduce these ketocarotenoids to the market, this review aims to provide an expert overview of the pros and cons associated with adonirubin and adonixanthin.

Carotenoid ornaments and the spandrels of physiology: a critique of theory to explain condition dependency

Even as numerous studies have documented that the red and yellow coloration resulting from the deposition of carotenoids serves as an honest signal of condition, the evolution of condition dependency is contentious. The resource trade-off hypothesis proposes that condition-dependent honest signalling relies on a trade-off of resources between ornamental display and body maintenance. By this model, condition dependency can evolve through selection for a re-allocation of resources to promote ornament expression. By contrast, the index hypothesis proposes that selection focuses mate choice on carotenoid coloration that is inherently condition dependent because production of such coloration is inexorably tied to vital cellular processes. These hypotheses for the origins of condition dependency make strongly contrasting and testable predictions about ornamental traits. To assess these two models, we review the mechanisms of production of carotenoids, patterns of condition dependency involving different classes of carotenoids, and patterns of behavioural responses to carotenoid coloration. We review evidence that traits can be condition dependent without the influence of sexual selection and that novel traits can show condition-dependent expression as soon as they appear in a population, without the possibility of sexual selection. We conclude by highlighting new opportunities for studying condition-dependent signalling made possible by genetic manipulation and expression of ornamental traits in synthetic biological systems.

The evolution of carotenoid-based plumage colours in passerine birds

Many birds use carotenoids to colour their plumage yellow to red. Because birds cannot synthesise carotenoids, they need to obtain these pigments from food, although some species metabolise dietary carotenoids (which are often yellow) into derived carotenoids (often red). Here, we study the occurrence of yellow and red carotenoid-based plumage colours in the passerines, the largest bird radiation and quantify the effects of potential ecological and life-history drivers on their evolution. We scored the presence/absence of yellow and red carotenoid-based plumage in nearly 6,000 species and use Bayesian phylogenetic mixed models to assess the effects of carotenoid-availability in diet, primary productivity, body size, habitat and sexual selection. We also test the widespread assumption that red carotenoid-based colours are more likely to be the result of metabolization. Finally, we analyse the pattern of evolutionary transitions between yellow and red carotenoid-based plumage colours to determine whether, as predicted, the evolution of yellow carotenoid-based colours precedes red. We show that, as expected, both colours are more likely to evolve in smaller species and in species with carotenoid-rich diets. Yellow carotenoid-based plumage colours, but not red, are more prevalent in species that inhabit environments with higher primary productivity and closed vegetation. In general, females were more likely to have yellow and males more likely to have red carotenoid-based plumage colours, closely matching the effects of sexual selection. Our analyses also confirm that red carotenoid-based colours are more likely to be metabolised than yellow carotenoid-based colours. Evolutionary gains and losses of yellow and red carotenoid-based plumage colours indicate that red colours evolved more readily in species that already deposited yellow carotenoids, while the reverse was rarely the case. Our study provides evidence for a general, directional evolutionary trend from yellow to red carotenoid-based colours, which are more likely to be the result of metabolization. This may render them potentially better indicators of quality, and thus favoured by sexual selection.

To colour a bird: The evolution of carotenoid-based colouration in passerines is shaped by sexual selection, ecology and life history

Research Highlight: Delhey, K., Valcu, M., Dale, J., & Kempenaers, B. (2022). The evolution of carotenoid-based plumage colours in passerine birds. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.13791. Carotenoids, a class of colour pigments, are responsible for red, yellow and orange hues in nature. They play an important role in visual animals, and specially birds, where dietary carotenoids can act as honest sexual signals. Long-standing interest in the function of carotenoid-based colours has led to different hypotheses for their evolutionary drivers. Yet, comparative studies testing the generality of these hypotheses have been previously limited in phylogenetic scope or resolution. In a recent study, Delhey et al. (2022) combined sexual dichromatism, life history and environmental data to investigate the evolution of carotenoid-based colouration in the largest avian radiation, the passerines (Order: Passeriformes). The authors show that the expression of carotenoid-based colours depends on environmental availability, dietary content and body size. They also show that red carotenoids are more often evolutionarily and metabolically derived, and suggest different colours are favoured by natural and sexual selection. These findings shine new light on commonly held hypotheses of carotenoid-colour evolution and contribute to our understanding of how phenotypic diversity evolves.

Lutein isolated from Scenedesmus obliquus microalga boosts immunity against cyclophosphamide-induced brain injury in rats

Lutein is a naturally potent antioxidant carotenoid synthesized in green microalgae with a potent ability to prevent different human chronic conditions. To date, there are no reports of the immune-stimulating effect of pure lutein isolated from Scenedesmus obliquus. Thus, we isolated the natural lutein from S. obliquus and evaluated its effectiveness as an immunostimulant against cyclophosphamide-induced brain injury. We purified all-E-(3R, 3'R, 6'R)-Lutein from S. obliquus using prep-HPLC and characterized it by ¹H- and ¹³C-NMR spectroscopy. We assigned rats randomly to four experimental groups: the Control group got a vehicle for lutein dimethyl sulfoxide for ten successive days. The Cyclophosphamide group received a single i.p injection of Cyclophosphamide (200 mg/kg). Lutein groups received 50 and 100 (mg/kg) of lutein one time per day for ten successive days after the cyclophosphamide dose. Lutein administration reduced brain contents of Macrophage inflammatory protein2 (MIP2), cytokine-induced- neutrophil chemoattractant (CINC), and Matrix metalloproteinase 1 (MMP1). Besides, it lowered the contents of interleukin 1 beta (IL-1β) and interleukin 18 (IL-18), associated with low content of NLR pyrin domain protein 3 (NLRP3) and consequently caspase-1 compared to the cyclophosphamide group. In the histomorphometric analysis, lutein groups (50 and 100 mg/Kg) showed mild histopathological alterations as they significantly reduced nuclear pyknosis numbers by 65% and 69% respectively, compared to the cyclophosphamide group. This is the first study that showed the immunomodulatory roles of lutein against cyclophosphamide-induced brain injury via decreasing neuroinflammation, chemokines recruitment, and neuron degeneration with the modulation of immune markers. Hence, lutein can be an effective immunomodulator against inflammation-related immune disorders.

A mechanism for red coloration in vertebrates

Red coloration is a salient feature of the natural world. Many vertebrates produce red color by converting dietary yellow carotenoids into red ketocarotenoids via an unknown mechanism. Here, we show that two enzymes, cytochrome P450 2J19 (CYP2J19) and 3-hydroxybutyrate dehydrogenase 1-like (BDH1L), are sufficient to catalyze this conversion. In birds, both enzymes are expressed at the sites of ketocarotenoid biosynthesis (feather follicles and red cone photoreceptors), and genetic evidence implicates these enzymes in yellow/red color variation in feathers. In fish, the homologs of CYP2J19 and BDH1L are required for ketocarotenoid production, and we show that these enzymes are sufficient to produce ketocarotenoids in cell culture and when ectopically expressed in fish skin. Finally, we demonstrate that the red-cone-enriched tetratricopeptide repeat protein 39B (TTC39B) enhances ketocarotenoid production when co-expressed with CYP2J19 and BDH1L. The discovery of this mechanism of ketocarotenoid biosynthesis has major implications for understanding the evolution of color diversity in vertebrates.

A synergistic combination of structural and pigmentary colour produces non-spectral colour in the purple-breasted cotinga, Cotinga cotinga (Passeriformes: Cotingidae)

Most studies of animal coloration focus on spectral colours, which are colours evoked by single peaks within the wavelengths of visible light. It is poorly understood how non-spectral colours (those produced by a combination of reflectance peaks) are produced, despite their potential significance to both animal communication and biomimicry. Moreover, although both pigmentary and structural colour production mechanisms have been well characterized in feathers independently, their interactions have received considerably less attention, despite their potential to broaden the available colour spectrum. Here, we investigate the colour production mechanisms of the purple feathers of the purple-breasted cotinga (Cotinga cotinga). The purple feather colour results from both the coherent scattering of light by a sphere-type nanomatrix of β-keratin and air (spongy layer) in the barbs, which produces a blue–green colour, and the selective absorption of light in the centre of the bird-visible spectrum by the methoxy-carotenoid, cotingin. This unusual combination of carotenoid and nanostructure with a central air vacuole, in the absence of melanin, is a blueprint of a synergistic way to produce a non-spectral colour that would be difficult to achieve with only a single colour production mechanism.

Carminic Acid Based Red Dye from Scale Insects Detected in Red Ruby-Crowned Kinglet Feathers by Surface-Enhanced Raman Scattering

In most birds, red feather color is linked to diet and attributed to carotenoids contained in plants and fruits. In the red crown feathers of the Ruby-crowned Kinglet (Regulus calendula), a new biopigment was identified based on carminic acid, the main coloring compound of cochineal (Dactylopius coccus) and other scale insects. This has revealed a potential new class of carminic acid-based biopigments, not previously identified in feathers. In this research, red crown feathers of a Ruby-crowned Kinglet were analyzed by surface-enhanced Raman scattering (SERS) employing synthesized silver star-shaped colloids as the nanoplasmonic platform. Results indicated peaks at 450, 670, 1290-1312, 1355, 1410, 1570, 1620 cm-1 in the feather SERS spectra characteristic of carminic acid. SERS has proven to be an extremely sensitive, non-destructive technique for the identification of different feather biopigments, even at trace quantities and in the presence of other predominant coloring substances.

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.

How do complex animal signals evolve?

Animal signals-involving combinations of acoustic, chemical, visual, and behavioral cues-are among the most diverse traits in nature. Testing hypotheses about signal evolution has been hampered by difficulties with comparing highly divergent signals among species. In this Primer, I describe recent advances in capturing signals and studying their evolution. I highlight new findings using an information theory-based approach to quantifying signal variation in the diverse birds-of-paradise. Growing access to signal databases in tandem with development of new analytical tools will open up new avenues for studying the proximate mechanisms and ultimate evolutionary causes of signal variation, both within and among species.

Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration

Background

As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst's pheasant (Chrysolophus amherstiae), exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds.

Results

We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons were conducted to investigate the complex features of plumage coloration. By identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant against different backgrounds, we found that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds showed some candidate genes related to carotenoid coloration in a broad range of birds. The transcriptome data further reveal important regulators of the two colorations, particularly one splicing transcript of the microphthalmia-associated transcription factor gene for pheomelanin synthesis.

Conclusions

Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage coloration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.

Evolution of long-term coloration trends with biochemically unstable ingredients

The evolutionarily persistent and widespread use of carotenoid pigments in animal coloration contrasts with their biochemical instability. Consequently, evolution of carotenoid-based displays should include mechanisms to accommodate or limit pigment degradation. In birds, this could involve two strategies: (i) evolution of a moult immediately prior to the mating season, enabling the use of particularly fast-degrading carotenoids and (ii) evolution of the ability to stabilize dietary carotenoids through metabolic modification or association with feather keratins. Here, we examine evolutionary lability and transitions between the two strategies across 126 species of birds. We report that species that express mostly unmodified, fast-degrading, carotenoids have pre-breeding moults, and a particularly short time between carotenoid deposition and the subsequent breeding season. Species that expressed mostly slow-degrading carotenoids in their plumage accomplished this through increased metabolic modification of dietary carotenoids, and the selective expression of these slow-degrading compounds. In these species, the timing of moult was not associated with carotenoid composition of plumage displays. Using repeated samples from individuals of one species, we found that metabolic modification of dietary carotenoids significantly slowed their degradation between moult and breeding season. Thus, the most complex and colourful ornamentation is likely the most biochemically stable in birds, and depends less on ecological factors, such as moult timing and migration tendency. We suggest that coevolution of metabolic modification, selective expression and biochemical stability of plumage carotenoids enables the use of unstable pigments in long-term evolutionary trends in plumage coloration.

Structuring evolution: biochemical networks and metabolic diversification in birds

Background

Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a “global” carotenoid network – comprising of all known enzymatic reactions among naturally occurring carotenoids – with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds.

Results

We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network – compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution.

Conclusions

The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0731-z) contains supplementary material, which is available to authorized users.

Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird

The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue‐throated populations (Sierra Madre del Sur); two groups of amethyst‐throated populations (Trans‐Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue‐ and amethyst‐throated populations does not correspond to the 2‐MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest‐interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.

Tradeoff between robustness and elaboration in carotenoid networks produces cycles of avian color diversification

Background

Resolution of the link between micro- and macroevolution calls for comparing both processes on the same deterministic landscape, such as genomic, metabolic or fitness networks. We apply this perspective to the evolution of carotenoid pigmentation that produces spectacular diversity in avian colors and show that basic structural properties of the underlying carotenoid metabolic network are reflected in global patterns of elaboration and diversification in color displays. Birds color themselves by consuming and metabolizing several dietary carotenoids from the environment. Such fundamental dependency on the most upstream external compounds should intrinsically constrain sustained evolutionary elongation of multi-step metabolic pathways needed for color elaboration unless the metabolic network gains robustness – the ability to synthesize the same carotenoid from an additional dietary starting point.

Results

We found that gains and losses of metabolic robustness were associated with evolutionary cycles of elaboration and stasis in expressed carotenoids in birds. Lack of metabolic robustness constrained lineage’s metabolic explorations to the immediate biochemical vicinity of their ecologically distinct dietary carotenoids, whereas gains of robustness repeatedly resulted in sustained elongation of metabolic pathways on evolutionary time scales and corresponding color elaboration.

Conclusions

The structural link between length and robustness in metabolic pathways may explain periodic convergence of phylogenetically distant and ecologically distinct species in expressed carotenoid pigmentation; account for stasis in carotenoid colors in some ecological lineages; and show how the connectivity of the underlying metabolic network provides a mechanistic link between microevolutionary elaboration and macroevolutionary diversification.

Reviewers

This article was reviewed by Junhyong Kim, Eugene Koonin, and Fyodor Kondrashov. For complete reports, see the Reviewers’ reports section.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0073-6) contains supplementary material, which is available to authorized users.

Ancient origins and multiple appearances of carotenoid-pigmented feathers in birds

The broad palette of feather colours displayed by birds serves diverse biological functions, including communication and camouflage. Fossil feathers provide evidence that some avian colours, like black and brown melanins, have existed for at least 160 million years (Myr), but no traces of bright carotenoid pigments in ancient feathers have been reported. Insight into the evolutionary history of plumage carotenoids may instead be gained from living species. We visually surveyed modern birds for carotenoid-consistent plumage colours (present in 2956 of 9993 species). We then used high-performance liquid chromatography and Raman spectroscopy to chemically assess the family-level distribution of plumage carotenoids, confirming their presence in 95 of 236 extant bird families (only 36 family-level occurrences had been confirmed previously). Using our data for all modern birds, we modelled the evolutionary history of carotenoid-consistent plumage colours on recent supertrees. Results support multiple independent origins of carotenoid plumage pigmentation in 13 orders, including six orders without previous reports of plumage carotenoids. Based on time calibrations from the supertree, the number of avian families displaying plumage carotenoids increased throughout the Cenozoic, and most plumage carotenoid originations occurred after the Miocene Epoch (23 Myr). The earliest origination of plumage carotenoids was reconstructed within Passeriformes, during the Palaeocene Epoch (66-56 Myr), and not at the base of crown-lineage birds.

Diversity, physiology, and evolution of avian plumage carotenoids and the role of carotenoid-protein interactions in plumage color appearance

The diversity of vibrant plumage colors in birds has evolved as a direct result of social and environmental pressures. To fully understand these underlying pressures it is necessary to elucidate the mechanisms for the creation of novel plumage colors which include the metabolic transformations of dietary carotenoids and spectral tuning of the molecules within the feather protein environment. Recent advances in this field have greatly expanded the number and breadth of avian species for which plumage pigmentation has been characterized, making it possible to reconstruct the phylogenetic history of carotenoid usage in plumage. Resonance Raman and classical Raman spectroscopic techniques have been employed with great effect in the study of carotenoids in situ. The application of these methods have two benefits: to identify carotenoids in feathers that are unavailable for destructive sampling; and to study the spectral tuning resulting from the interaction between the carotenoids and the proteins to which they are bound. This review presents a summary of recent advances in the understanding of the molecular factors controlling the coloration of avian carotenoid plumage obtained through the application of both bioanalytical and spectroscopic methodologies.

Plumage pigment differences underlying the yellow-red differentiation in the Northern Flicker (Colaptes auratus)

Elucidating the processes that create species differences is a central goal of evolutionary biology. The Northern Flicker (Colaptes auratus) exists as two well-differentiated subspecies groups in North America, the Yellow-shafted (auratus group) and Red-shafted Flickers (cafer group), which differ strikingly in the color of the underside and rachises of flight feathers, and of malar and nuchal patches. We investigated the physiological basis of these conspicuous phenotypic differences by identifying and quantifying the pigments involved. The yellow feathers of auratus contained carotenoids commonly found in nature (lutein, β-cryptoxanthin, zeaxanthin and β-carotene). The orange to red shafts/vanes of cafer and hybrids contained these carotenoids as well as mono- and diketo-carotenoids (notably adonirubin, α-doradexanthin, canthaxanthin, astaxanthin), representing oxygenated products at carbon C4(4') of the carotenoids present in auratus. Oxygenation of feather carotenoids at C4(4') correlated closely with shaft/vane redness. Carotenoid hydroxylation at C3(3') and the proportion of carotenoids with ε end-rings also varied with color and belie differences in the activity of several carotenoid-modifying enzymes between the two subspecies groups. Curiously, occasional yellow feathers in red-shafted individuals had the carotenoids of auratus, hence the differences are not constitutive in cafer, underscoring regulatory differences. The red malar stripe of cafer, the black malar stripe and red nuchal patch of auratus all contained similar types and amounts of carotenoids, mostly 3-hydroxy-4-keto-carotenoids. The biochemical differences between two strongly differentiated forms we uncovered shed light on how plumage coloration can change over evolutionary time and point to further avenues of research.

A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification

The Neotropical cotingas (Cotingidae: Aves) are a group of passerine birds that are characterized by extreme diversity in morphology, ecology, breeding system, and behavior. Here, we present a comprehensive phylogeny of the Neotropical cotingas based on six nuclear and mitochondrial loci (∼7500 bp) for a sample of 61 cotinga species in all 25 genera, and 22 species of suboscine outgroups. Our taxon sample more than doubles the number of cotinga species studied in previous analyses, and allows us to test the monophyly of the cotingas as well as their intrageneric relationships with high resolution. We analyze our genetic data using a Bayesian species tree method, and concatenated Bayesian and maximum likelihood methods, and present a highly supported phylogenetic hypothesis. We confirm the monophyly of the cotingas, and present the first phylogenetic evidence for the relationships of Phibalura flavirostris as the sister group to Ampelion and Doliornis, and the paraphyly of Lipaugus with respect to Tijuca. In addition, we resolve the diverse radiations within the Cotinga, Lipaugus, Pipreola, and Procnias genera. We find no support for Darwin's (1871) hypothesis that the increase in sexual selection associated with polygynous breeding systems drives the evolution of color dimorphism in the cotingas, at least when analyzed at a broad categorical scale. Finally, we present a new comprehensive phylogenetic classification of all cotinga species.

Artificial selection for structural color on butterfly wings and comparison with natural evolution

Brilliant animal colors often are produced from light interacting with intricate nano-morphologies present in biological materials such as butterfly wing scales. Surveys across widely divergent butterfly species have identified multiple mechanisms of structural color production; however, little is known about how these colors evolved. Here, we examine how closely related species and populations of Bicyclus butterflies have evolved violet structural color from brown-pigmented ancestors with UV structural color. We used artificial selection on a laboratory model butterfly, B. anynana, to evolve violet scales from UV brown scales and compared the mechanism of violet color production with that of two other Bicyclus species, Bicyclus sambulos and Bicyclus medontias, which have evolved violet/blue scales independently via natural selection. The UV reflectance peak of B. anynana brown scales shifted to violet over six generations of artificial selection (i.e., in less than 1 y) as the result of an increase in the thickness of the lower lamina in ground scales. Similar scale structures and the same mechanism for producing violet/blue structural colors were found in the other Bicyclus species. This work shows that populations harbor large amounts of standing genetic variation that can lead to rapid evolution of scales' structural color via slight modifications to the scales' physical dimensions.

Mechanism of carotenoid coloration in the brightly colored plumages of broadbills (Eurylaimidae)

The plumage carotenoids of six species from five genera of broadbills (Eurylaimidae) have been examined. These plumages are crimson, violet, purple-maroon, or yellow. Two genera also have brilliant green plumages that are produced by a combination of structural coloration and unknown carotenoids. Six different carotenoids from nine different plumage patches were identified, including two previously unknown molecules, using high-performance liquid chromatography, mass spectrometry, and MS/MS fragment analysis. The yellow pigment in Eurylaimus javanicus and Eurylaimus ochromalus is identified as the novel carotenoid, 7,8-dihydro-3'-dehydro-lutein. The yellow and green plumages of Psarisomus dalhousiae contain the unmodified dietary carotenoids lutein and zeaxanthin. The brilliant green feathers of Calyptomena viridis contain a mixture of lutein and two other xanthophylls that have previously been found only in woodpeckers (Picinae). The crimson and violet colors of Cymbirhynchus, Sarcophanops, and Eurylaimus are produced by a novel pigment, which is identified as 2,3-didehydro-papilioerythrinone. The molecular structure of this carotenoid was confirmed using (1)H nuclear magnetic resonance, correlated two-dimensional spectroscopy, and two-dimensional nuclear Overhauser effect spectroscopy. Resonance Raman (rR) spectroscopy carried out at room and low temperatures was used to probe the configuration and conformation of 2,3-didehydro-papilioerythrinone in situ within crimson C. macrorhynchos and purple-red E. javanicus feathers. The rR spectra reveal that the pigment is in an all-trans configuration and appears to be relatively planar in the feathers. The likely metabolic pathways for the production of broadbill carotenoids from dietary precursors are discussed.

Vibrational and electronic spectroscopy of the retro-carotenoid rhodoxanthin in avian plumage, solid-state films, and solution

Rhodoxanthin is one of few retro-carotenoids in nature. These chromophores are defined by a pattern of single and double bond alternation that is reversed relative to most carotenoids. Rhodoxanthin is found in the plumage of several families of birds, including fruit doves (Ptilinopus, Columbidae) and the red cotingas (Phoenicircus, Cotingidae). The coloration associated with the rhodoxanthin-containing plumage of these fruit dove and cotinga species ranges from brilliant red to magenta or purple. In the present study, rhodoxanthin is characterized in situ by UV-Vis reflectance and resonance Raman spectroscopy to gain insights into the mechanisms of color-tuning. The spectra are compared with those of the isolated pigment in solution and in thin solid films. Key vibrational signatures are identified for three isomers of rhodoxanthin, primarily in the fingerprint region. Electronic structure (DFT) calculations are employed to describe the normal modes of vibration, and determine characteristic modes of retro-carotenoids. These results are discussed in the context of various mechanisms that change the electronic absorption, including structural distortion of the chromophore or enhanced delocalization of π-electrons in the ground-state. From the spectroscopic evidence, we suggest that the shift in absorption is likely a consequence of perturbations that primarily affect the excited state of the chromophore.

How hollow melanosomes affect iridescent colour production in birds

Developmental constraints and trade-offs can limit diversity, but organisms have repeatedly evolved morphological innovations that overcome these limits by expanding the range and functionality of traits. Iridescent colours in birds are commonly produced by melanin-containing organelles (melanosomes) organized into nanostructured arrays within feather barbules. Variation in array type (e.g. multilayers and photonic crystals, PCs) is known to have remarkable effects on plumage colour, but the optical consequences of variation in melanosome shape remain poorly understood. Here, we used a combination of spectrophotometric, experimental and theoretical methods to test how melanosome hollowness--a morphological innovation largely restricted to birds--affects feather colour. Optical analyses of hexagonal close-packed arrays of hollow melanosomes in two species, wild turkeys (Meleagris gallopavo) and violet-backed starlings (Cinnyricinclus leucogaster), indicated that they function as two-dimensional PCs. Incorporation of a larger dataset and optical modelling showed that, compared with solid melanosomes, hollow melanosomes allow birds to produce distinct colours with the same energetically favourable, close-packed configurations. These data suggest that a morphological novelty has, at least in part, allowed birds to achieve their vast morphological and colour diversity.

Key ornamental innovations facilitate diversification in an avian radiation

Patterns of biodiversity are often explained by ecological processes, where traits that promote novel ways of interacting with the environment (key innovations) play a fundamental role in promoting diversification. However, sexual selection and social competition can also promote diversification through rapid evolution of ornamental traits. Because selection can operate only on existing variation, the tendency of ornamental traits to constrain or enable the production of novel phenotypes is a crucial but often overlooked aspect of diversification. Starlings are a speciose group characterized by diverse iridescent colors produced by nanometer-scale arrays of melanin-containing organelles (melanosomes) that play a central role in sexual selection and social competition. We show that evolutionary lability of these colors is associated with both morphological and lineage diversification in African starlings. The solid rod-like melanosome morphology has evolved in a directional manner into three more optically complex forms that can produce a broader range of colors than the ancestral form, resulting in (i) faster color evolution, (ii) the occupation of novel, previously unreachable regions of colorspace, and ultimately (iii) accelerated lineage diversification. As in adaptive radiations, key innovations in ornament production can provide high phenotypic trait variability, leading to dramatic effects on the tempo and mode of diversification.

Genetics of colouration in birds

Establishing the links between phenotype and genotype is of great importance for resolving key questions about the evolution, maintenance and adaptive function of phenotypic variation. Bird colouration is one of the most studied systems to investigate the role of natural and sexual selection in the evolution of phenotypic diversity. Given the recent advances in molecular tools that allow discovering genetic polymorphisms and measuring gene and protein expression levels, it is timely to review the literature on the genetics of bird colouration. The present study shows that melanin-based colour phenotypes are often associated with mutations at melanogenic genes. Differences in melanin-based colouration are caused by switches of eumelanin to pheomelanin production or by changes in feather keratin structure, melanoblast migration and differentiation, as well as melanosome structure. Similar associations with other types of colourations are difficult to establish, because our knowledge about the molecular genetics of carotenoid-based and structural colouration is quasi inexistent. This discrepancy stems from the fact that only melanin-based colouration shows pronounced heritability estimates, i.e. the resemblance between related individuals is usually mainly explained by genetic factors. In contrast, the expression of carotenoid-based colouration is phenotypically plastic with a high sensitivity to variation in environmental conditions. It therefore appears that melanin-based colour traits are prime systems to understand the genetic basis of phenotypic variation. In this context, birds have a great potential to bring us to new frontiers where many exciting discoveries will be made on the genetics of phenotypic traits, such as colouration. In this context, a major goal of our review is to suggest a number of exciting future avenues.