Extensive hybridization reveals multiple coloration genes underlying a complex plumage phenotype

Coloration is an important target of both natural and sexual selection. Discovering the genetic basis of colour differences can help us to understand how this visually striking phenotype evolves. Hybridizing taxa with both clear colour differences and shallow genomic divergences are unusually tractable for associating coloration phenotypes with their causal genotypes. Here, we leverage the extensive admixture between two common North American woodpeckers—yellow-shafted and red-shafted flickers—to identify the genomic bases of six distinct plumage patches involving both melanin and carotenoid pigments. Comparisons between flickers across approximately 7.25 million genome-wide SNPs show that these two forms differ at only a small proportion of the genome (mean F_ST = 0.008). Within the few highly differentiated genomic regions, we identify 368 SNPs significantly associated with four of the six plumage patches. These SNPs are linked to multiple genes known to be involved in melanin and carotenoid pigmentation. For example, a gene (CYP2J19) known to cause yellow to red colour transitions in other birds is strongly associated with the yellow versus red differences in the wing and tail feathers of these flickers. Additionally, our analyses suggest novel links between known melanin genes and carotenoid coloration. Our finding of patch-specific control of plumage coloration adds to the growing body of literature suggesting colour diversity in animals could be created through selection acting on novel combinations of coloration genes.     

The influence of carotenoid acquisition and utilization on the maintenance of species-typical plumage pigmentation in male American goldfinches (Carduelis tristis) and northern cardinals (Cardinalis cardinalis).

Birds display a tremendous variety of carotenoid-based colors in their plumage, but the mechanisms underlying interspecific variability in carotenoid pigmentation remain poorly understood. Because vertebrates cannot synthesize carotenoids de novo, access to pigments in the diet is one proximate factor that may shape species differences in carotenoid-based plumage coloration. However, some birds metabolize ingested carotenoids and deposit pigments that differ in color from their dietary precursors, indicating that metabolic capabilities may also contribute to the diversity of plumage colors we see in nature. In this study, we investigated how the acquisition and utilization of carotenoids influence the maintenance of species-typical plumage pigmentation in male American goldfinches (Carduelis tristis) and northern cardinals (Cardinalis cardinalis). We supplemented the diet of captive goldfinches with red carotenoids to determine whether males, which are typically yellow in color, were capable of growing red plumage. We also deprived cardinals of red dietary pigments to determine whether they could manufacture red carotenoids from yellow precursors to grow species-typical red plumage. We found that American goldfinches were able to deposit novel pigments in their plumage and develop a striking orange appearance. Thus, dietary access to pigments plays a role in determining the degree to which goldfinches express carotenoid-based plumage coloration. We also found that northern cardinals grew pale red feathers in the absence of red dietary pigments, indicating that their ability to metabolize yellow carotenoids in the diet contributes to the bright red plumage that they display.     

Dietary carotenoids predict plumage coloration in wild house finches

Carotenoid pigments are a widespread source of ornamental coloration in vertebrates and expression of carotenoid-based colour displays has been shown to serve as an important criterion in female mate choice in birds and fishes. Unlike other integumentary pigments, carotenoids cannot be synthesized; they must be ingested. Carotenoid-based coloration is condition-dependent and has been shown to be affected by both parasites and nutritional condition. A controversial hypothesis is that the expression of carotenoid-based coloration in wild vertebrates is also affected by the amount and types of carotenoid pigments that are ingested. We tested this carotenoid-limitation hypothesis by sampling the gut contents of moulting house finches and comparing the concentration of carotenoid pigments in their gut contents with the colour of growing feathers. We found a positive association: males that ingested food with a higher concentration of carotenoid pigments grew brighter ornamental plumage. We also compared the concentration of carotenoids in the gut contents of males from two subspecies of house finches with small and large patches of carotenoid-based coloration. Consistent with the hypothesis that carotenoid access drives the evolution of carotenoid-based colour displays, males from the population with limited ornamentation had much lower concentrations of carotenoids in their gut contents than males from the population with extensive ornamentation. These observations support the idea that carotenoid intake plays a part in determining the plumage brightness of male house finches.     

The mechanistic,genetic and evolutionary causes of bird eye colour variation

Birds display a rainbow of eye colours, but this trait has been little studied compared with plumage coloration. Avian eye colour variation occurs at all phylogenetic scales: it can be conserved throughout whole families or vary within one species, yet the evolutionary importance of this eye colour variation is under-studied. Here, we summarize knowledge of the causes of eye colour variation at three primary levels: mechanistic, genetic and evolutionary. Mechanistically, we show that avian iris pigments include melanin and carotenoids, which also play major roles in plumage colour, as well as purines and pteridines, which are often found as pigments in non-avian taxa. Genetically, we survey classical breeding studies and recent genomic work on domestic birds that have identified potential ‘eye colour genes’, including one associated with pteridine pigmentation in pigeons. Finally, from an evolutionary standpoint, we present and discuss several hypotheses explaining the adaptive significance of eye colour variation. Many of these hypotheses suggest that bird eye colour plays an important role in intraspecific signalling, particularly as an indicator of age or mate quality, although the importance of eye colour may differ between species and few evolutionary hypotheses have been directly tested. We suggest that future studies of avian eye colour should consider all three levels, including broad-scale iris pigment analyses across bird species, genome sequencing studies to identify loci associated with eye colour variation, and behavioural experiments and comparative phylogenetic analyses to test adaptive hypotheses. By examining these proximate and ultimate causes of eye colour variation in birds, we hope that our review will encourage future research to understand the ecological and evolutionary significance of this striking avian trait.     

Carotenoids in bird plumage: the complement of red pigments in the plumage of wild and captive bullfinch (Pyrrhula pyrrhula)

We have studied the carotenoid pigments in the red plumage of male bullfinch (Pyrrhula pyrrhula) immediately following capture and after the completion of the moult in captivity under dietary control. Astaxanthin, adonirubin, and alpha-doradexanthin, as well as papilioeritrinone and canthaxanthin (in lower amounts) are in every case the dominant carotenoids in the plumage pigment of wild individuals. alpha-Doradexanthin is responsible for the reddish-rose colour, which captive individuals adopt after a diet consisting mainly of lutein as disposable carotenoid. The red pigmentation biogenesis of captive bullfinch is compared with those of other red pigmented Carduelinae in which male individuals usually lose the red colour in captivity, namely Carpodacus roseus, Carpodacus rubricilloides, Uragus sibiricus, Carduelis cannabina, Carduelis flammea, Loxia curvirostra and Pinicola enucleator.     

Interspecific variation in the use of carotenoid-based coloration in birds: diet, life history and phylogeny

Birds show striking interspecific variation in their use of carotenoid-based coloration. Theory predicts that the use of carotenoids for coloration is closely associated with the availability of carotenoids in the diet but, although this prediction has been supported in single-species studies and those using small numbers of closely related species, there have been no broad-scale quantitative tests of the link between carotenoid coloration and diet. Here we test for such a link using modern comparative methods, a database on 140 families of birds and two alternative avian phylogenies. We show that carotenoid pigmentation is more common in the bare parts (legs, bill and skin) than in plumage, and that yellow coloration is more common than red. We also show that there is no simple, general association between the availability of carotenoids in the diet and the overall use of carotenoid-based coloration. However, when we look at plumage coloration separately from bare part coloration, we find there is a robust and significant association between diet and plumage coloration, but not between diet and bare part coloration. Similarly, when we look at yellow and red plumage colours separately, we find that the association between diet and coloration is typically stronger for red coloration than it is for yellow coloration. Finally, when we build multivariate models to explain variation in each type of carotenoid-based coloration we find that a variety of life history and ecological factors are associated with different aspects of coloration, with dietary carotenoids only being a consistent significant factor in the case of variation in plumage. All of these results remain qualitatively unchanged irrespective of the phylogeny used in the analyses, although in some cases the precise life history and ecological variables included in the multivariate models do vary. Taken together, these results indicate that the predicted link between carotenoid coloration and diet is idiosyncratic rather than general, being strongest with respect to plumage colours and weakest for bare part coloration. We therefore suggest that, although the carotenoid-based bird plumage may a good model for diet-mediated signalling, the use of carotenoids in bare part pigmentation may have a very different functional basis and may be more strongly influenced by genetic and physiological mechanisms, which currently remain relatively understudied.     

Eumelanin levels in rufous feathers explain plasma testosterone levels and survival in swallows

Pigment‐based plumage coloration and its physiological properties have attracted many researchers to explain the evolution of such ornamental traits. These studies, however, assume the functional importance of the predominant pigment while ignoring that of other minor pigments, and few studies have focused on the composition of these pigments. Using the pheomelanin‐based plumage in two swallow species, we studied the allocation of two pigments (the predominant pigment, pheomelanin, and the minor pigment, eumelanin) in relation to physiological properties and viability in populations under a natural and sexual selection. This is indispensable for studying the evolution of pheomelanin‐based plumage coloration. Pheomelanin and eumelanin share the same pathway only during their initial stages of development, which can be a key to unravel the functional importance of pigment allocation and thus of plumage coloration. Using the barn swallow, Hirundo rustica, a migratory species, we found that plasma testosterone levels increased with increasing the proportion of eumelanin pigments compared with pheomelanin pigments, but not with the amount of pheomelanin pigments, during the mating period. In the Pacific swallow Hirundo tahitica, a nonmigratory congener, we found that, during severe winter weathers, survivors had a proportionally smaller amount of eumelanin pigments compared with pheomelanin pigments than that in nonsurvivors, but no detectable difference was found in the pheomelanin pigmentation itself. These results indicated that a minor pigment, eumelanin, matters at least in some physiological measures and viability. Because the major pigment, pheomelanin, has its own physiological properties, a combination of major and minor pigments provides multiple information to the signal receivers, potentially enhancing the signaling function of pheomelanic coloration and its diversification across habitats.     

Not so colourful after all: eggshell pigments constrain avian eggshell colour space

Birds'' eggshells are renowned for their striking colours and varied patterns. Although often considered exceptionally diverse, we report that avian eggshell coloration, sampled here across the full phylogenetic diversity of birds, occupies only 0.08–0.10% of the avian perceivable colour space. The concentrations of the two known tetrapyrrole eggshell pigments (protoporphyrin and biliverdin) are generally poor predictors of colour, both intra- and interspecifically. Here, we show that the constrained diversity of eggshell coloration can be accurately predicted by colour mixing models based on the relative contribution of both pigments and we demonstrate that the models'' predictions can be improved by accounting for the reflectance of the eggshell''s calcium carbonate matrix. The establishment of these proximate links between pigmentation and colour will enable future tests of hypotheses on the functions of perceived avian eggshell colours that depend on eggshell chemistry. More generally, colour mixing models are not limited to avian eggshell colours but apply to any natural colour. Our approach illustrates how modelling can aid the understanding of constraints on phenotypic diversity.     

Changes in carotenoid‐based plumage colour in relation to age in European Serins Serinus serinus

Yearling birds generally display duller colours than adults. This may be due to selection favouring birds with more intensely coloured plumage or to an increase in colour after the first complete moult. Most research to date on the topic has been carried out on species with structural plumage coloration or with carotenoid‐based coloration that is produced by the unmodified deposition of pigments. However, no study has been carried out on species whose carotenoids are metabolically modified before deposition. In this study, we assess age‐related changes in the carotenoid‐based coloration of European Serins, a species that metabolically processes carotenoids before they can be deposited into feathers. Birds were captured over consecutive years and we carried out both cross‐sectional and longitudinal analysis. Adults had significantly greater values of lightness and chroma than yearling birds. However, there were no changes in plumage colour when analysing the same individuals captured in subsequent seasons. Plumage lightness and chroma of adult males after moult were related to body mass, suggesting a role of body condition on plumage coloration. Our results suggest that changes in plumage coloration with age in European Serins are due to a selection process that favours more intensely coloured individuals.     

Differential accumulation and pigmenting ability of dietary carotenoids in colorful finches

Many animals develop bright red, orange, or yellow carotenoid pigmentation that they use to attract mates. Colorful carotenoid pigments are acquired from the diet and are either directly incorporated as integumentary colorants or metabolized into other forms before deposition. Because animals often obtain several different carotenoids from plant and animal food sources, it is possible that these pigments are accumulated at different levels in the body and may play unique roles in shaping the ultimate color expression of individuals. We studied patterns of carotenoid accumulation and integumentary pigmentation in two colorful finch species--the American goldfinch (Carduelis tristis) and the zebra finch (Taeniopygia guttata). Both species acquire two main hydroxycarotenoids, lutein and zeaxanthin, from their seed diet but transform these into a series of metabolites that are used as colorful pigments in the plumage (goldfinches only) and beak (both species). We conducted a series of carotenoid-supplementation experiments to investigate the relative extent to which lutein and zeaxanthin are accumulated in blood and increase carotenoid coloration in feathers and bare parts. First, we supplemented the diets of both species with either lutein or zeaxanthin and measured plasma pigment status, feather carotenoid concentration (goldfinches only), and integumentary color. Zeaxanthin-supplemented males grew more colorful feathers and beaks than lutein-supplemented males, and in goldfinches incorporated a different ratio of carotenoids in feathers (favoring the accumulation of canary xanthophyll B). We also fed goldfinches different concentrations of a standard lutein-zeaxanthin mix and found that at physiologically normal and high concentrations, birds circulated proportionally more zeaxanthin over lutein than occurred in the diet. Collectively, these results demonstrate that zeaxanthin is preferentially accumulated in the body and serves as a more potent substrate for pigmentation than lutein in these finches.     

Blue‐green eggshell coloration reflects yolk antioxidant content in spotless starlings Sturnus unicolor

The hypothesis that eggshell colouration is a sexually selected trait of female birds is based on the fact that biliverdin, the pigment responsible for blue‐green colours of the eggshell, is a potent antioxidant and that only females with high antioxidant capacity can deposit higher concentrations of biliverdin as eggshell pigment. Antioxidants (e.g. carotenoids, vitamins) are also abundant in the egg yolk, which serve as nutrient reserves for the developing embryo, and eggshell colour intensity may reflect maternal investment in yolk antioxidants. Here, we test the relationship between blue‐green eggshell colour intensity and concentration and amount of carotenoids, vitamin A, and vitamin E in the egg yolk of spotless starling Sturnus unicolor, a species for which we have previously shown good evidence of sexual selection driving egg coloration. As could be extrapolated from the hypothesis of sexual selection driving the evolution of blue‐green eggshells, we found that eggshell colour intensity was positively related to the concentration and amount of carotenoids and vitamin E in the yolk. Thus, mothers may use egg colour intensity to signal to fathers the antioxidant status of their offspring. Moreover, we provide evidence suggesting that maternal yolk investment in more coloured eggs can also explain the detected association between feeding decisions of males and egg colour intensity that we have found previously in this species.     

Season-, sex-, and age-specific accumulation of plasma carotenoid pigments in free-ranging white-winged crossbills Loxia leucoptera

Many birds acquire carotenoid pigments from foods and deposit these pigments into feathers and bare‐parts to become sexually attractive, but little work has been done on the interindividual and temporal variability in the types and amounts of carotenoids that free‐ranging individuals have available for use in coloration or other functions (e.g., in immunomodulation). To address this issue, we studied intra‐annual variation in plasma carotenoid profiles of juvenile and adult white‐winged crossbills Loxia leucoptera of both sexes. Adult male crossbills exhibit bright red carotenoid‐based plumage pigmentation, whereas females uniformly display drab yellow feather coloration and juvenile males only occasionally display some orange or pink color. Yellow xanthophylls (e.g., lutein, zeaxanthin) were predominant in plasma of birds from both sexes and age classes throughout the year. Plasma xanthophylls levels tended to be highest in the summer, when crossbills increase seed consumption for breeding as well as supplement their diet with insects. Blood accumulation of three other, less common plasma carotenoids‐β‐cryptoxanthin, rubixanthin, and gazaniaxanthin‐varied in a highly season‐, sex‐, and age‐dependent fashion. These carotenoids were virtually absent in juvenile or adult female plasma at all times of year and were only present in male plasma, at higher concentrations in adults than juveniles, during the period of feather growth (Sept.–Nov.). These pigments have been reported as valuable precursors of the metabolically derived red pigments (e.g., 3‐hydroxy‐echinenone, 4‐oxo‐rubixanthin, and 4‐oxo‐gazaniaxanthin, respectively) that appear in the plumage of male crossbills. These findings suggest that male crossbills either adopt a season‐specific foraging strategy to acquire foods rich in these pigments at the time they are needed to develop red coloration, or have a unique physiological ability to metabolically produce these pigments or absorb them from food during molt, in order to maximize color production.     

Melanin coloration in New World orioles I: carotenoid masking and pigment dichromatism in the orchard oriole complex

Carotenoids produce the brilliant red, orange, and yellow colors of many animals. However, melanin pigments can also confer some of these same hues. Because carotenoid and melanin colors are produced in different ways and may serve different signaling functions, either within or between species, it is important to establish whether one or both types of pigment are responsible for coloration. We have discovered what appears to be an evolutionary switch from carotenoid- to melanin-based color in two sexually dichromatic New World orioles. Using a combination of reflectance spectrometry and chromatographic analyses of plumage pigments, we found that the chestnut plumage of adult male orchard orioles Icterus spurius is produced predominantly by phaeomelanins. Orchard oriole feathers also contain carotenoids, which appear to be masked by the high concentration of phaeomelanins. In contrast, both carotenoids and phaeomelanins appear to contribute to color in adult male Fuertes's orioles I. fuertesi . Moreover, yellow yearling male and female plumage in both species is produced by carotenoids alone. The masking of carotenoids with phaeomelanins in orchard orioles is interesting in light of the signaling roles that carotenoids are thought to play. In addition, these plumage differences produce a unique case of age and sexual pigment dimorphism in orchard and Fuertes's orioles.     

Seasonal changes in carotenoid- and melanin-based plumage coloration in the Great Tit Parus major

Plumage coloration plays an important role as a signal of individual quality. We studied plumage coloration in two Great Tit Parus major populations to test the hypothesis that coloration changes during the year without moult. As expected, the coloration of 'yellow' and 'dark green' areas in the breast and back changed with time but not the colour characteristics of the 'black' crown. This suggests that colours based on carotenoids could be more exposed to abrasion or fading than melanin-derived colours, although other factors could affect the patterns of change found. Our results show that effects of colour alteration could be important to the understanding of the potential for reliable signalling of different colours. Seasonal changes in plumage colour should be considered in future analysis of intraspecific variation in coloration.     

Eggshell biliverdin concentration does not sufficiently predict eggshell coloration

Avian eggshell coloration may have arisen due to selection on the biological, chemical, or physical properties of the pigments embedded within the eggshell, or due to selection on the coloration that emerges due to pigment deposition. Within both hypothetical frameworks, pigment‐based eggshell coloration would be related to metrics of egg quality; however, no one has evaluated the relative strength of coloration and pigment concentration in predicting egg quality. Here, we examined 66 European starling Sturnus vulgaris eggs and quantified eggshell biliverdin concentration (an antioxidant that produces the eggshell's blue coloration) and used 28 different coloration metrics derived from both photographic and spectrophotometric data. We also measured egg size, eggshell thickness, concentration of carotenoids in the yolk, and concentration of lysozyme in the albumen to capture variation in egg quality. We found that throughout the laying sequence, biliverdin concentration increased while eggshell thickness, yolk carotenoid concentration, and lysozyme concentration in the albumen all decreased, but this variation was not captured by any eggshell coloration metric. Both eggshell coloration and biliverdin concentration were negatively associated with yolk carotenoid concentration, but only eggshell biliverdin concentration was negatively associated with yolk mass. Lastly, biliverdin concentration explained, at most, only 46% of the variation for all eggshell coloration metrics. Our results suggest biliverdin concentration is a better predictor of egg quality than egg coloration in European starlings, supporting the hypothesis that eggshell pigment concentration per se may be the target of selection.     

Energetic constraints on expression of carotenoid-based plumage coloration

Carotenoid pigments are used by many bird species as feather colorants, creating brilliant yellow, orange, and red plumage displays. Such carotenoid-based plumage coloration has been shown to function as an honest signal that is used in female mate choice. Despite recent interest in carotenoid-based ornamental traits, the basis for individual variation in expression of carotenoid-based plumage coloration remains incompletely understood. I tested the hypothesis that, independent of carotenoid access, food stress during molt would cause reduced expression of carotenoid pigmentation. I fed molting male House Finches Carpodacus mexicanus seed diets supplemented with either the red carotenoid pigment canthaxanthin or the yellow/orange carotenoid pigment β-cryptoxanthin (in the form of tangerine juice). Within each diet treatment, one group of males was given restricted food access and the other group was given unrestricted food access. Carotenoid supplements were placed in water so carotenoid access was controlled independent of food access. The results indicated a strong effect of both carotenoid access and food access on color display. Some males in the β-cryptoxanthin-supplemented group grew red plumage, suggesting that they can metabolically modify yellow pigments into red pigments, but no bird supplemented with β-cryptoxanthin grew plumage as red as birds supplemented with canthaxanthin. Males in the unrestricted food groups grew redder and more intensely pigmented plumage than males in the restricted food groups. These observations provide the best evidence to date of an energetic cost of carotenoid utilization in the generation of colorful plumage.     

Eggshell coloration is an indicator of dietary calcium in Common Pheasants (Phasianus colchicus)

According to the structural-function hypothesis, the eggshell pigment protoporphyrin, deposited at weak spots, can strengthen the shell structure when calcium is lacking in avian species. However, this hypothesis has not been tested in species that produce pigmented eggs of uniform ground colour without spotting patterns. We tested the structural-function hypothesis using 435 eggs produced on seven calcium diets (0.2–4.5%) given to Common Pheasants Phasianus colchicus, a species that produces a large number of eggs on a low-calcium diet with unspotted eggshells composed of a uniform ground colour of mainly protoporphyrin. We found that pheasants on the lowest calcium diet (0.2%), which had thinner eggshells, produced eggs containing more protoporphyrin-based coloration than four of six other diets, suggesting this species employs pigmentation as ground colour to strengthen eggshells when available calcium is low. Our results provide the first, at least partial support for a structural function for eggshell pigments producing ground colour without spotting in a species that is often calcium-limited. This pattern may be more widespread in other ground-nesting taxa that also produce large numbers of eggs with protoporphyrin-based ground colour and are potentially limited by calcium during breeding.     

Melanin-based plumage coloration in the house finch is unaffected by coccidial infection

For most species of birds, ornamental plumage coloration may result from two types of pigments: carotenoids and melanins. Despite the fact that melanin pigments can be synthesized by birds from basic, amino acid precursors, while carotenoids cannot be synthesized by birds and must be ingested, melanin-based plumage coloration and carotenoid-based plumage coloration have often been treated as a single trait in investigations of the function and evolution of plumage coloration. Expression of carotenoid-based coloration is known to be dependent on condition, while the effects of individual condition have not been well-tested for expression of melanin-based coloration. In this study, we experimentally tested the effect of coccidial infection of the intestinal tract of male house finches during moult on expression of melanin-based plumage coloration. Coccidial infection had a significant negative effect on carotenoid-based coloration, but it had no significant effect on melanin-based feather coloration. Unlike carotenoid-based coloration, melanin-based coloration may be cheap to produce, and honesty of melanin-based coloration my require social mediation.     

EVOLUTION OF CAROTENOID PIGMENTATION IN CACIQUES AND MEADOWLARKS (ICTERIDAE): REPEATED GAINS OF RED PLUMAGE COLORATION BY CAROTENOID C4‐OXYGENATION

Many animals use carotenoid pigments to produce yellow, orange, and red coloration. In birds, at least 10 carotenoid compounds have been documented in red feathers; most of these are produced through metabolic modification of dietary precursor compounds. However, it is poorly understood how lineages have evolved the biochemical mechanisms for producing red coloration. We used high‐performance liquid chromatography to identify the carotenoid compounds present in feathers from 15 species across two clades of blackbirds (the meadowlarks and allies, and the caciques and oropendolas; Icteridae), and mapped their presence or absence on a phylogeny. We found that the red plumage found in meadowlarks includes different carotenoid compounds than the red plumage found in caciques, indicating that these gains of red color are convergent. In contrast, we found that red coloration in two closely related lineages of caciques evolved twice by what appear to be similar biochemical mechanisms. The C4‐oxygenation of dietary carotenoids was responsible for each observed transition from yellow to red plumage coloration, and has been commonly reported by other researchers. This suggests that the C4‐oxygenation pathway may be a readily evolvable means to gain red coloration using carotenoids.