Evolutionary innovation and diversification of carotenoid‐based pigmentation in finches

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 carotenoid redshift: Physical basis and implications for visual signaling

Carotenoid pigments are the basis for much red, orange, and yellow coloration in nature and central to visual signaling. However, as pigment concentration increases, carotenoid signals not only darken and become more saturated but they also redshift; for example, orange pigments can look red at higher concentration. This occurs because light experiences exponential attenuation, and carotenoid-based signals have spectrally asymmetric reflectance in the visible range. Adding pigment disproportionately affects the high-absorbance regions of the reflectance spectra, which redshifts the perceived hue. This carotenoid redshift is substantial and perceivable by animal observers. In addition, beyond pigment concentration, anything that increases the path length of light through pigment causes this redshift (including optical nano- and microstructures). For example, male Ramphocelus tanagers appear redder than females, despite the same population and concentration of carotenoids, due to microstructures that enhance light-pigment interaction. This mechanism of carotenoid redshift has sensory and evolutionary consequences for honest signaling in that structures that redshift carotenoid ornaments may decrease signal honesty. More generally, nearly all colorful signals vary in hue, saturation, and brightness as light-pigment interactions change, due to spectrally asymmetrical reflectance within the visible range of the relevant species. Therefore, the three attributes of color need to be considered together in studies of honest visual signaling.

Feather function and the evolution of birds

The ability of feathers to perform many functions either simultaneously or at different times throughout the year or life of a bird is integral to the evolutionary history of birds. Many studies focus on single functions of feathers, but any given feather performs many functions over its lifetime. These functions necessarily interact with each other throughout the evolution and development of birds, so our knowledge of avian evolution is incomplete without understanding the multifunctionality of feathers, and how different functions may act synergistically or antagonistically during natural selection. Here, we review how feather functions interact with avian evolution, with a focus on recent technological and discovery-based advances. By synthesising research into feather functions over hierarchical scales (pattern, arrangement, macrostructure, microstructure, nanostructure, molecules), we aim to provide a broad context for how the adaptability and multifunctionality of feathers have allowed birds to diversify into an astounding array of environments and life-history strategies. We suggest that future research into avian evolution involving feather function should consider multiple aspects of a feather, including multiple functions, seasonal wear and renewal, and ecological or mechanical interactions. With this more holistic view, processes such as the evolution of avian coloration and flight can be understood in a broader and more nuanced context.

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.

Evolution: The biochemistry of honest sexual signaling

The discovery of a new enzyme required for production of red carotenoid pigments in vertebrates provides insights for how shared biochemical pathways may be the key to understanding honest signaling via plumage coloration.

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.

Avian Coloration Genetics: Recent Advances and Emerging Questions

The colorful phenotypes of birds have long provided rich source material for evolutionary biologists. Avian plumage, beaks, skin, and eggs-which exhibit a stunning range of cryptic and conspicuous forms-inspired early work on adaptive coloration. More recently, avian color has fueled discoveries on the physiological, developmental, and-increasingly-genetic mechanisms responsible for phenotypic variation. The relative ease with which avian color traits can be quantified has made birds an attractive system for uncovering links between phenotype and genotype. Accordingly, the field of avian coloration genetics is burgeoning. In this review, we highlight recent advances and emerging questions associated with the genetic underpinnings of bird color. We start by describing breakthroughs related to 2 pigment classes: carotenoids that produce red, yellow, and orange in most birds and psittacofulvins that produce similar colors in parrots. We then discuss structural colors, which are produced by the interaction of light with nanoscale materials and greatly extend the plumage palette. Structural color genetics remain understudied-but this paradigm is changing. We next explore how colors that arise from interactions among pigmentary and structural mechanisms may be controlled by genes that are co-expressed or co-regulated. We also identify opportunities to investigate genes mediating within-feather micropatterning and the coloration of bare parts and eggs. We conclude by spotlighting 2 research areas-mechanistic links between color vision and color production, and speciation-that have been invigorated by genetic insights, a trend likely to continue as new genomic approaches are applied to non-model species.

Genomic investigation of colour polymorphism and phylogeographic variation among populations of black-headed bulbul (Brachypodius atriceps) in insular southeast Asia

Intraspecific polymorphism in birds, especially plumage colour polymorphism, and the mechanisms that control it are an area of active research in evolutionary biology. The black-headed bulbul (Brachypodius atriceps) is a polymorphic species with two distinct morphs, yellow and grey. This species inhabits the mainland and virtually all continental islands of Southeast Asia where yellow morphs predominate, but on two islands in the Sunda region, Bawean and Maratua, grey morphs are common or exclusive. Here, we generated a high-quality reference genome of a yellow individual and resequenced genomes of multiple individuals of both yellow and grey morphs to study the genetic basis of coloration and population history of the species. Using PCA and STRUCTURE analysis, we found the Maratua Island population (which is exclusively grey) to be distinct from all other B. atriceps populations, having been isolated c. 1.9 million years ago (Ma). In contrast, Bawean grey individuals (a subset of yellow and grey individuals on that island) are embedded within an almost panmictic Sundaic clade of yellow birds. Using F_ST and d_xy to compare variable genomic segments between Maratua and yellow individuals, we located peaks of divergence and identified candidate loci involved in the colour polymorphism. Tests of selection among coding-proteins in high F_ST regions, however, did not indicate selection on the candidate genes. Overall, we report on some loci that are potentially responsible for the grey/yellow polymorphism in a species that otherwise shows little genetic diversification across most of its range.

Avian color expression and perception: is there a carotenoid link?

Carotenoids color many of the red, orange and yellow ornaments of birds and also shape avian vision. The carotenoid-pigmented oil droplets in cone photoreceptors filter incoming light and are predicted to aid in color discrimination. Carotenoid use in both avian coloration and color vision raises an intriguing question: is the evolution of visual signals and signal perception linked through these pigments? Here, we explore the genetic, physiological and functional connections between these traits. Carotenoid color and droplet pigmentation share common mechanisms of metabolic conversion and are both affected by diet and immune system challenges. Yet, the time scale and magnitude of these effects differ greatly between plumage and the visual system. Recent observations suggest a link between retinal carotenoid levels and color discrimination performance, but the mechanisms underlying these associations remain unclear. Therefore, we performed a modeling exercise to ask whether and how changes in droplet carotenoid content could alter the perception of carotenoid-based plumage. This exercise revealed that changing oil droplet carotenoid concentration does not substantially affect the discrimination of carotenoid-based colors, but might change how reliably a receiver can predict the carotenoid content of an ornament. These findings suggest that, if present, a carotenoid link between signal and perception is subtle. Deconstructing this relationship will require a deeper understanding of avian visual perception and the mechanisms of color production. We highlight several areas where we see opportunities to gain new insights, including comparative genomic studies of shared mechanisms of carotenoid processing and alternative approaches to investigating color vision.

Microstructures amplify carotenoid plumage signals in tanagers

Brilliantly-colored birds are a model system for research into evolution and sexual selection. Red, orange, and yellow carotenoid-colored plumages have been considered honest signals of condition; however, sex differences in feather pigments and microstructures are not well understood. Here, we show that microstructures, rather than carotenoid pigments, seem to be a major driver of male-female color differences in the social, sexually-dimorphic tanager genus Ramphocelus. We comprehensively quantified feather (i) color (using spectrophotometry), (ii) pigments (using liquid chromatography-mass spectrometry (LC-MS)), and (iii) microstructures (using scanning electron microscopy (SEM) and finite-difference time-domain (FDTD) optical modeling). Males have significantly more saturated color patches than females. However, our exploratory analysis of pigments suggested that males and females have concordant carotenoid pigment profiles across all species (MCMCglmm model, female:male ratio = 0.95). Male, but not female, feathers have elaborate microstructures which amplify color appearance. Oblong, expanded feather barbs in males enhance color saturation (for the same amount of pigment) by increasing the transmission of optical power through the feather. Dihedral barbules (vertically-angled, strap-shaped barbules) in males reduce total reflectance to generate "super black" and "velvet red" plumage. Melanin in females explains some, but not all, of the male-female plumage differences. Our results suggest that a widely cited index of honesty, carotenoid pigments, cannot fully explain male appearance. We propose that males are selected to evolve amplifiers-in this case, microstructures that enhance appearance-that are not necessarily themselves linked to quality.

Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

Identifying the genetic bases for colour patterns has provided important insights into the control and expression of pigmentation and how these characteristics influence fitness. However, much more is known about the genetic bases for traits based on melanin pigments than for traits based on another major class of pigments, carotenoids. Here, we use natural admixture in a hybrid zone between Audubon's and myrtle warblers (Setophaga coronata auduboni/S. c. coronata) to identify genomic regions associated with both types of pigmentation. Warblers are known for rapid speciation and dramatic differences in plumage. For each of five plumage coloration traits, we found highly significant associations with multiple single-nucleotide polymorphisms (SNPs) across the genome and these were clustered in discrete regions. Regions near significantly associated SNPs were enriched for genes associated with keratin filaments, fibrils that make up feathers. A carotenoid-based trait that differs between the taxa-throat colour-had more than a dozen genomic regions of association. One cluster of SNPs for this trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene. Other scavenger receptors are presumed to be expressed at target tissues and involved in the selective movement of carotenoids into the target cells, making SCARF2 a plausible new candidate for carotenoid processing. In addition, two melanin-based plumage traits-colours of the eye line and eye spot-show very strong associations with a single genomic region mapping to chromosome 20 in the zebra finch. These findings indicate that only a subset of the genomic regions differentiated between these two warblers are associated with the plumage differences between them and demonstrate the utility of reduced-representation genomic scans in hybrid zones.

Synergistic selection regimens drive the evolution of display complexity in birds of paradise

Integrated visual displays that combine gesture with colour are nearly ubiquitous in the animal world, where they are shaped by sexual selection for their role in courtship and competition. However, few studies assess how multiple selection regimens operate on different components of these complex phenotypes on a macroevolutionary scale. Here, we study this issue by assessing how both sexual and ecological selection work together to influence visual display complexity in the birds of paradise. We first find that sexual dichromatism is highest in lekking species, which undergo more intense sexual selection by female choice, than non-lekking species. At the same time, species in which males directly compete with one another at communal display courts have more carotenoid-based ornaments and fewer melanin ornaments. Meanwhile, display habitat influences gestural complexity. Species that dance in the cluttered understorey have more complex dances than canopy-displaying species. Taken together, our results illustrate how distinct selection regimens each operate on individual elements comprising a complex display. This supports a modular model of display evolution, wherein the ultimate integrated display is the product of synergy between multiple factors that select for different types of phenotypic complexity.

Expression of a carotenoid-modifying gene and evolution of red coloration in weaverbirds (Ploceidae)

Red carotenoid colours in birds are widely assumed to be sexually selected quality indicators, but this rests on a very incomplete understanding of genetic mechanisms and honesty-mediating costs. Recent progress was made by the implication of the gene CYP2J19 as an avian carotenoid ketolase, catalysing the synthesis of red C4-ketocarotenoids from yellow dietary precursors, and potentially a major mechanism behind red coloration in birds. Here, we investigate the role of CYP2J19 in the spectacular colour diversification of African weaverbirds (Ploceidae), represented by five genera and 16 species: eight red, seven yellow and one without carotenoid coloration. All species had a single copy of CYP2J19, unlike the duplication found in the zebra finch, with high expression in the retina, confirming its function in colouring red oil droplets. Expression was weak or undetected in skin and follicles of pigment-depositing feather buds, as well as in beaks and tarsi, including those of the red-billed quelea. In contrast, the hepatic (liver) expression of CYP2J19 was consistently higher (>14-fold) in seven species with C4-ketocarotenoid coloration than in species without (including one red species), an association strongly supported by a phylogenetic comparative analysis. The results suggest a critical role of the candidate ketolase, CYP2J19, in the evolution of red C4-ketocarotenoid colour variation in ploceids. As ancestral state reconstruction suggests that ketocarotenoid coloration has evolved twice in this group (once in Euplectes and once in the Quelea/Foudia clade), we argue that while CYP2J19 has retained its ancestral role in the retina, it has likely been co-opted for red coloration independently in the two lineages, via increased hepatic expression.