Evolutionary innovation and diversification of carotenoid‐based pigmentation in finches

The ornaments used by animals to mediate social interactions are diverse, and by reconstructing their evolutionary pathways we can gain new insights into the mechanisms underlying ornamental innovation and variability. Here, we examine variation in plumage carotenoids among the true finches (Aves: Fringillidae) using biochemical and comparative phylogenetic analyses to reconstruct the evolutionary history of carotenoid states and evaluate competing models of carotenoid evolution. Our comparative analyses reveal that the most likely ancestor of finches used dietary carotenoids as yellow plumage colorants, and that the ability to metabolically modify dietary carotenoids into more complex pigments arose secondarily once finches began to use modified carotenoids to create red plumage. Following the evolutionary “innovation” that enabled modified red carotenoid pigments to be deposited as plumage colorants, many finch species subsequently modified carotenoid biochemical pathways to create yellow plumage. However, no reversions to dietary carotenoids were observed. The finding that ornaments and their underlying mechanisms may be operating under different selection regimes—where ornamental trait colors undergo frequent reversions (e.g., between red and yellow plumage) while carotenoid metabolization mechanisms are more conserved—supports a growing empirical framework suggesting different evolutionary patterns for ornaments and the mechanistic innovations that facilitate their diversification.     

The color of greater flamingo feathers fades when no cosmetics are applied

Greater flamingos use cosmetic coloration by spreading uropygial secretions pigmented with carotenoids over their feathers, which makes the plumage redder. Because flamingos inhabit open environments that receive direct solar radiation during daytime, and carotenoids bleach when exposed to solar radiation, we expected that the plumage color would fade if there is no maintenance for cosmetic purposes. Here, we show that the concentrations of pigments inside feathers and on the surface of feathers were correlated, as well as that there was a correlation between the concentrations of pigments in the uropygial secretions and on the surface of feathers. There was fading in color (becoming less red) in feathers that received direct solar radiation when there was no plumage maintenance, but not so in others maintained in darkness. When we controlled for the initial color of feathers, the feathers of those individuals with higher concentration of pigments on the feather surfaces were those that lost less coloration after experimental exposure of feathers to sunny conditions. These results indicate that exposure to sunlight is correlated with the fading of feather color, which suggests that individuals need to regularly apply makeup to be more colorful. These results also reinforce the view that these birds use cosmetic coloration as a signal amplifier of plumage color. This may be important in species using highly variable habitats, such as wetlands, since the conditions experienced when molting may differ from those when the signal should be functional, usually months after molting.     

Coevolution of caudal skeleton and tail feathers in birds

Birds are capable of a wide range of aerial locomotor behaviors in part because of the derived structure and function of the avian tail. The tail apparatus consists of a several mobile (free) caudal vertebrae, a terminal skeletal element (the pygostyle), and an articulated fan of tail feathers that may be spread or folded, as well as muscular and fibroadipose structures that facilitate tail movements. Morphological variation in both the tail fan and the caudal skeleton that supports it are well documented. The structure of the tail feathers and the pygostyle each evolve in response to functional demands of differing locomotor behaviors. Here, I test whether the integument and skeleton coevolve in this important locomotor module. I quantified feather and skeletal morphology in a diverse sample of waterbirds and shorebirds using a combination of linear and geometric morphometrics. Covariation between tail fan shape and skeletal morphology was then tested using phylogenetic comparative methods. Pygostyle shape is found to be a good predictor of tail fan shape (e.g., forked, graduated), supporting the hypothesis that the tail fan and the tail skeleton have coevolved. This statistical relationship is used to reconstruct feather morphology in an exemplar fossil waterbird, Limnofregata azygosternon. Based on pygostyle morphology, this taxon is likely to have exhibited a forked tail fan similar to that of its extant sister clade Fregata, despite differing in inferred ecology and other aspects of skeletal anatomy. These methods may be useful in reconstructing rectricial morphology in other extinct birds and thus assist in characterizing the evolution of flight control surfaces in birds. J. Morphol. 275:1431–1440, 2014. © 2014 Wiley Periodicals, Inc.     

Phylogenetic biogeography and classification of the Drosophila montium species group (Diptera: Drosophilidae)

The Drosophila montium group is the largest clade of the subgenus Sophophora consisting of 94 palaeotropical species, whose phylogenetic relationships remain unclear. Here, I used a recent tree inferred from three nuclear genes and one mitochondrial gene for almost half of the species to reconstruct the historical biogeography of the group and propose a comprehensive classification for the totality of its species. The group originated in South-East Asia nearly 20 million years ago (mya), and dispersed to Africa in the Late Miocene. A second northward expansion into East Asia took place in the Pliocene. Based on morphological (male abdominal pigmentation and genitalia) and chorological traits congruent with the molecular tree, I divide the montium group into seven subgroups: parvula, montium, punjabiensis, serrata, kikkawai, seguyi and orosa. The polyphyletic status of some of the previously defined complexes (auraria, jambulina, serrata, kikkawai and nikananu) is also resolved.     

Astaxanthin is responsible for the pink plumage flush in Franklin's and Ring-billed gulls

ABSTRACT.   Carotenoid pigments produce the red, orange, and yellow plumage of many birds. Carotenoid-containing feathers are typically rich in color and displayed by all adult members of the species. In many gulls and terns, however, an unusual light pink coloring (or flush) to the normally white plumage can be found in highly variable proportions within and across populations. The carotenoid basis of plumage flush was determined in an Elegant Tern ( Sterna elegans ; Hudon and Brush 1990 ), but it is not clear if all larids use this same mechanism for pink plumage coloration. We examined the carotenoid content of pink feathers in Franklin's ( Larus pipixcan ) and Ring-billed ( Larus delawarensis ) gulls and found that a single carotenoid—astaxanthin—was present. Astaxanthin was primarily responsible for the flush in Elegant Terns as well, but was accompanied by other carotenoids (e.g., canthaxanthin and zeaxanthin), as is typical of most astaxanthin-containing bird feathers. In both gull and tern species, carotenoids were contained within feathers and did not occur on the plumage surface in preen oil, as some have previously speculated. We hypothesize that some gulls turn pink because they acquire unusually high amounts of astaxanthin in their diets at the time of feather growth. It is tempting to link the increase in sightings of pink Ring-billed Gulls since the late 1990s with the introduction of pure, synthetic astaxanthin to the diets of hatchery-raised salmon.     

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.     

Brain size and the expression of pheomelanin-based colour in birds

Eumelanin and pheomelanin are the most common vertebrate pigments. They generate different colours and are synthesized under different physiological conditions. While pheomelanogenesis requires high levels of a key intracellular antioxidant (glutathione, GSH), eumelanogenesis is inhibited by GSH. This implies that species that present the molecular basis to produce large amounts of pheomelanin might be more limited to perform other costly processes that generate oxidative stress than species that produce eumelanin. Brain development requires large amounts of energy and antioxidants during ontogeny, so that large-brained species may be constrained in their simultaneous synthesis of large amounts of pheomelanin, but not in their synthesis of eumelanin. Here, we tested this hypothesis in a large dataset of 323 bird species. After controlling for the effects of phylogeny, latitude and sexual dichromatism, the proportion of pheomelanic plumage colour was strongly negatively related to the relative brain mass of species, whereas no relationship was found for the proportion of eumelanic colour. This indicates that the production of pheomelanin is a costly process that cannot evolve together with complex neural structures and thus with large cognitive capacity. This is the first time that the expression of melanic traits is found to correlate with another phenotypic character across species.     

A continued role for signaling functions in the early evolution of feathers

Persons and Currie (2015) argued against either flight, thermoregulation, or signaling as a functional benefit driving the earliest evolution of feathers; rather, they favored simple feathers having an initial tactile sensory function, which changed to a thermoregulatory function as density increased. Here, we explore the relative merits of early simple feathers that may have originated as tactile sensors progressing instead toward a signaling, rather than (or in addition to) a thermoregulatory function. We suggest that signaling could act in concert with a sensory function more naturally than could thermoregulation. As such, the dismissal of a possible signaling function and the presumption that an initial sensory function led directly to a thermoregulatory function (implicit in the title “bristles before down”) are premature.     

DNA content and distribution in ancient feathers and potential to reconstruct the plumage of extinct avian taxa

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather ‘vane’ which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.     

Ecological, morphological and phylogenetic correlates of interspecific variation in plasma carotenoid concentration in birds

Carotenoids are important as pigments for bright coloration of animals, and as physiologically active compounds with a wide array of health-related benefits. However, the causes of variation in carotenoid acquisition and physiology among species are poorly known. We measured the concentration of carotenoids in the blood of 80 wild bird species differing in diet, body size and the extent of carotenoid-based traits. Preliminary analyses showed that diet significantly explains interspecific variability in plasma carotenoids. However, dietary influences were apparently overridden by phylogenetic relationships among species, which explained most (65%) of this variability. This phylogenetic effect could be due partly to its covariation with diet, but may also be caused by interspecific differences in carotenoid absorption from food to the blood stream, mediated, for example by endothelial carriers or gut parasites. Carotenoid concentrations also decreased with body size (which may be explained by the allometric relationship between ingestion rate and body mass), and correlated positively with the extent of carotenoid-dependent coloration of plumage and bare parts. Therefore, the acquisition of carotenoids from the diet and their use for both health and display functions seem to be constrained by ecological and physiological aspects linked to the phylogeny and size of the species.     

Asynchronous origins of ectomycorrhizal clades of Agaricales

The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.     

Plastid genomes reveal evolutionary shifts in elevational range and flowering time of Osmanthus (Oleaceae)

Species of Osmanthus are economically important ornamental trees, yet information regarding their plastid genomes (plastomes) have rarely been reported, thus hindering taxonomic and evolutionary studies of this small but enigmatic genus. Here, we performed comparative genomics and evolutionary analyses on plastomes of 16 of the 28 currently accepted species, with 11 plastomes newly sequenced. Phylogenetic studies identified four main lineages within the genus that are here designated the: “Caucasian Osmanthus” (corresponding to O. decorus), “Siphosmanthus” (corresponding to O. sect. Siphosmanthus), “O. serrulatus + O. yunnanensis,” and “Core Osmanthus: (corresponding to O. sect. Osmanthus + O. sect. Linocieroides). Molecular clock analysis suggested that Osmanthus split from its sister clade c. 15.83 Ma. The estimated crown ages of the lineages were the following: genus Osmanthus at 12.66 Ma; “Siphosmanthus” clade at 5.85 Ma; “O. serrulatus + O. yunnanensis” at 4.89 Ma; and “Core Osmanthus: clade at 6.2 Ma. Ancestral state reconstructions and trait mapping showed that ancestors of Osmanthus were spring flowering and originated at lower elevations. Phylogenetic principal component analysis clearly distinguished spring‐flowering species from autumn‐flowering species, suggesting that flowering time differentiation is related to the difference in ecological niches. Nucleotide substitution rates of 80 common genes showed slow evolutionary pace and low nucleotide variations, all genes being subjected to purifying selection.     

PLUMAGE EVOLUTION IN THE OROPENDOLAS AND CACIQUES: DIFFERENT DIVERGENCE RATES IN POLYGYNOUS AND MONOGAMOUS TAXA

Avian plumage colors are frequently used in studies of sexual selection, yet surprisingly little is known about how these traits evolve under different mating systems. We compared historical rates of divergence in male color patterns among the oropendolas and caciques (genera Cacicus , Gymnostinops, Ocyalus , and Psarocolius ), a group with both polygynous and monogamous representatives. Reconstructing the evolution of individual color patches on a molecular phylogeny showed that overall color patterns have changed much more rapidly in oropendolas, which comprise two groups that evolved polygyny independently, than in caciques, which are predominantly monogamous. None of these taxa are notably sexually dichromatic, however, suggesting that higher rates of plumage evolution occurred in both sexes rather than just males. Despite high rates of change, color patterns show few examples of convergence among taxa, similar to the lack of homoplasy in male song among oropendolas but in a stark contrast to the repeated convergence in both plumage and song patterns found in a closely related, monogamous clade, the New World orioles ( Icterus ). Our results support previous suggestions that display traits evolve more rapidly and with less homoplasy in polygynous mating systems, and we provide surprising evidence that these patterns may occur in both sexes.     

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.     

Visual modelling suggests a weak relationship between the evolution of ultraviolet vision and plumage coloration in birds

Birds have sophisticated colour vision mediated by four cone types that cover a wide visual spectrum including ultraviolet (UV) wavelengths. Many birds have modest UV sensitivity provided by violet‐sensitive (VS) cones with sensitivity maxima between 400 and 425 nm. However, some birds have evolved higher UV sensitivity and a larger visual spectrum given by UV‐sensitive (UVS) cones maximally sensitive at 360–370 nm. The reasons for VS–UVS transitions and their relationship to visual ecology remain unclear. It has been hypothesized that the evolution of UVS‐cone vision is linked to plumage colours so that visual sensitivity and feather coloration are ‘matched’. This leads to the specific prediction that UVS‐cone vision enhances the discrimination of plumage colours of UVS birds while such an advantage is absent or less pronounced for VS‐bird coloration. We test this hypothesis using knowledge of the complex distribution of UVS cones among birds combined with mathematical modelling of colour discrimination during different viewing conditions. We find no support for the hypothesis, which, combined with previous studies, suggests only a weak relationship between UVS‐cone vision and plumage colour evolution. Instead, we suggest that UVS‐cone vision generally favours colour discrimination, which creates a nonspecific selection pressure for the evolution of UVS cones.     

Sexual, seasonal, and environmental variation in plasma carotenoids in great tits, Parus major

In many birds, carotenoids have dual functions as irreversible plumage pigments and as physiologically essential vitamins and antioxidants. They must be obtained through the diet and may therefore be a limiting resource, a constraint that is likely to vary with factors such as sex, habitat, and time of year. In the present study, we investigated signs of carotenoid limitation in great tits, Parus major , in relation to sex, season, year, and within an urban versus a rural habitat. The two main carotenoids, lutein and zeaxanthin, were analysed by high-performance liquid chromatography in the plasma and in the yellow carotenoid-based breast feathers. We found that plasma carotenoid concentrations were significantly influenced by sex, season, and year, but not by urban versus rural habitat. At moult, plasma concentration was positively correlated with feather pigmentation, independent of body condition and sex. During the breeding season, however, circulating carotenoid concentrations were negatively related to the feather pigmentation (i.e. from previous autumn moult). We suggest that great tits are carotenoid deprived before leaf emergence, and that carotenoid utilization and limitations are sex-specific, but that there are neither any obvious honesty-maintaining costs of pigmentation, nor any fitness consequences of the colour variation.  © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 92 , 521–527.     

Size scaling and stiffness of avian primary feathers: implications for the flight of Mesozoic birds

The primary feathers of birds are subject to cyclical forces in flight causing their shafts (rachises) to bend. The amount the feathers deflect during flight is dependent upon the flexural stiffness of the rachises. By quantifying scaling relationships between body mass and feather linear dimensions in a large data set of living birds, we show that both feather length and feather diameter scale much closer to predictions for geometric similarity than they do to elastic similarity. Scaling allometry also indicates that the primary feathers of larger birds are relatively shorter and their rachises relatively narrower, compared to those of smaller birds. Two-point bending tests indicated that larger birds have more flexible feathers than smaller species. Discriminant functional analyses (DFA) showed that body mass, primary feather length and rachis diameter can be used to differentiate between different magnitudes of feather bending stiffness, with primary feather length explaining 63% of variance in rachis stiffness. Adding fossil measurement data to our DFA showed that Archaeopteryx and Confuciusornis do not overlap with extant birds. This strongly suggests that the bending stiffness of their primary feathers was different to extant birds and provides further evidence for distinctive flight styles and likely limited flight ability in Archaeopteryx and Confuciusornis.