Matthew D. Shawkey

pavo: an R package for the analysis, visualization and organization of spectral data

Summary Recent technical and methodological advances have led to a dramatic increase in the use of spectrometry to quantify reflectance properties of biological materials, as well as models to determine how these colours are perceived by animals, providing important insights into ecological and evolutionary aspects of animal visual communication. Despite this growing interest, a unified cross-platform framework for analysing and visualizing spectral data has not been available. We introduce pavo, an R package that facilitates the organization, visualization and analysis of spectral data in a cohesive framework. pavo is highly flexible, allowing users to (a) organize and manipulate data from a variety of sources, (b) visualize data using Rs state-of-the-art graphics capabilities and (c) analyse data using spectral curve shape properties and visual system modelling for a broad range of taxa. In this paper, we present a summary of the functions implemented in pavo and how they integrate in a workflow to explore and analyse spectral data. We also present an exact solution for the calculation of colour volume overlap in colourspace, thus expanding previously published methodologies. As an example of pavos capabilities, we compare the colour patterns of three African glossy starling species, two of which have diverged very recently. We demonstrate how both colour vision models and direct spectral measurement analysis can be used to describe colour attributes and differences between these species. Different approaches to visual models and several plotting capabilities exemplify the packages versatility and streamlined workflow. pavo provides a cohesive environment for handling spectral data and addressing complex sensory ecology questions, while integrating with Rs modular core for a broader and comprehensive analytical framework, automated management of spectral data and reproducible workflows for colour analysis.

Carotenoids need structural colours to shine.

The bright colours of feathers are among the most striking displays in nature and are frequently used as sexual signals. Feathers can be coloured by pigments or by ordered tissue, and these mechanisms have traditionally been treated as distinct modes of display. Here we show that some yellow plumage colour is created both by reflection of light from white structural tissue and absorption of light by carotenoids. Thus, structural components of feathers contribute substantially to yellow ‘carotenoid’ displays, but the effect of variation in structural components on variation in colour displays is, to our knowledge, unstudied. The presence of structural colour in some carotenoid-based colour displays will have to be considered in studies of colour signalling.

Nanostructure predicts intraspecific variation in ultraviolet-blue plumage colour †

Evidence suggests that structural plumage colour can be an honest signal of individual quality, but the mechanisms responsible for the variation in expression of structural coloration within a species have not been identified. We used full–spectrum spectrometry and transmission electron microscopy to investigate the effect of variation in the nanostructure of the spongy layer on expression of structural ultraviolet (UV)–blue coloration in eastern bluebird (Sialia sialis) feathers. Fourier analysis revealed that feather nanostructure was highly organized but did not accurately predict variation in hue. Within the spongy layer of feather barbs, the number of circular keratin rods significantly predicted UV–violet chroma, whereas the standard error of the diameter of these rods significantly predicted spectral saturation. These observations show that the precision of nanostructural arrangement determines some colour variation in feathers.

Plumage Color Patterns of an Extinct Dinosaur

Dinosaur Plumage Coloration and appearance provide important behavioral and evolutionary information in animals. However, for the most part, we do not know the coloration of fossil terrestrial animals. Li et al. (p. 1369, published online 4 February) have reconstructed the appearance of a theropod dinosaur by mapping features of its well-preserved feathers and comparing them with modern samples from birds. Feather color is partly determined by melanosome density and shape, and this information is preserved in a recently discovered fossil from China. The dinosaur was gray with white limbs and had a reddish crest and a speckled face. Comparison of melanosome shape and density between fossil feathers and modern ones reveals the appearance and color of a theropod. For as long as dinosaurs have been known to exist, there has been speculation about their appearance. Fossil feathers can preserve the morphology of color-imparting melanosomes, which allow color patterns in feathered dinosaurs to be reconstructed. Here, we have mapped feather color patterns in a Late Jurassic basal paravian theropod dinosaur. Quantitative comparisons with melanosome shape and density in extant feathers indicate that the body was gray and dark and the face had rufous speckles. The crown was rufous, and the long limb feathers were white with distal black spangles. The evolution of melanin-based within-feather pigmentation patterns may coincide with that of elongate pennaceous feathers in the common ancestor of Maniraptora, before active powered flight. Feathers may thus have played a role in sexual selection or other communication.

Fossil Evidence for Evolution of the Shape and Color of Penguin Feathers

Feather of the Penguin Penguins are highly adapted for their cold, aquatic environment. Changes in their wings and feathers have allowed rapid swimming and protection from the near-freezing water. Clarke et al. (p. 954, published online 30 September; see the cover) describe an early penguin, dating to about 35 million years ago, that includes well-preserved feathers. The melanosomes in the feathers, which influence their strength, as well as their color, are like those of many other aquatic birds and unlike those of present-day penguins, even though the morphology of the wings and feathers had already been modified. Thus, in penguins, the shape and form of the feather evolved before microstructural changes occurred. The melanosome arrangement also suggests that the penguin was mostly gray-brown. A fossil penguin shows that the wing and feather form evolved before distinctive microstructural changes in the feathers. Penguin feathers are highly modified in form and function, but there have been no fossils to inform their evolution. A giant penguin with feathers was recovered from the late Eocene (~36 million years ago) of Peru. The fossil reveals that key feathering features, including undifferentiated primary wing feathers and broad body contour feather shafts, evolved early in the penguin lineage. Analyses of fossilized color-imparting melanosomes reveal that their dimensions were similar to those of non-penguin avian taxa and that the feathering may have been predominantly gray and reddish-brown. In contrast, the dark black-brown color of extant penguin feathers is generated by large, ellipsoidal melanosomes previously unknown for birds. The nanostructure of penguin feathers was thus modified after earlier macrostructural modifications of feather shape linked to aquatic flight.

Reconstruction of Microraptor and the Evolution of Iridescent Plumage

Flashy Feathers Feather colors play key roles in the lives of birds, functioning in everything from camouflage, to thermoregulation, to sexual signaling. Much recent research has revealed that some dinosaurs also had feathers, and examination of feather components in fossil and preserved feathers has begun to reveal how feather color may have played a role in the lives of these dinosaurs. Li et al. (p. 1215) compared the characteristics of the melanosomes of the paravian dinosaur Microraptor to those found in extant birds, which suggest that its feathers were black and iridescent. The existence of this subtle color reflectance, together with morphological aspects of the feathered tail, suggests an important role for signaling in the early evolution of feathers. Iridescence in the feathers of a feathered dinosaur suggests an early role for feathers in ornamental display and signaling. Iridescent feather colors involved in displays of many extant birds are produced by nanoscale arrays of melanin-containing organelles (melanosomes). Data relevant to the evolution of these colors and the properties of melanosomes involved in their generation have been limited. A data set sampling variables of extant avian melanosomes reveals that those forming most iridescent arrays are distinctly narrow. Quantitative comparison of these data with melanosome imprints densely sampled from a previously unknown specimen of the Early Cretaceous feathered Microraptor predicts that its plumage was predominantly iridescent. The capacity for simple iridescent arrays is thus minimally inferred in paravian dinosaurs. This finding and estimation of Microraptor feathering consistent with an ornamental function for the tail suggest a centrality for signaling in early evolution of plumage and feather color.

Iridescent plumage in satin bowerbirds: structure, mechanisms and nanostructural predictors of individual variation in colour

SUMMARY Iridescence is produced by coherent scattering of light waves from alternating layers of materials of different refractive indices. In birds, iridescent colours are produced by feather barbules when light is scattered from alternating layers of keratin, melanin and air. The structure and organization of these layers, and hence the appearance of bird species with different types of plumage iridescence, varies extensively. One principal distinction between different types of iridescent colours is whether they are produced by a single pair of layers or by multiple pairs of layers. Multi-layer iridescence, such as that displayed by hummingbirds, has been relatively well characterized, but single-layer iridescence has only recently been modeled successfully. Here we use electron microscopy, spectrometry and thin-film optical modeling to investigate the glossy, ultraviolet-blue iridescent plumage colouration of adult male satin bowerbirds Ptilonorhynchus violaceus minor. The flattened barbules of adult males are composed of a superficial keratin layer overlying a melanin layer that is several granules thick. A thin-film model based on the thickness of the keratin layer and its two associated interfaces (air/keratin and keratin/melanin) generates predicted reflectance spectra that closely match measured spectra. In addition, hues predicted from this model are positively correlated with measured hues. As predicted from our thin-film model, measured hues shifted to shorter wavelengths at increasing angles of incidence and reflectance. Moreover, we found that individual variation in barbule nanostructure can predict measured variation in both hue and UV-chroma. Thus, we have characterized the microstructure of satin bowerbird barbules, uncovered the mechanisms responsible for producing ultraviolet iridescence in these barbules, and provided the first evidence of a nanostructural basis for individual variation in iridescent plumage colour.

Bacteria as an agent for change in structural plumage color: correlational and experimental evidence.

Recent studies have documented that a diverse assemblage of bacteria is present on the feathers of wild birds and that uropygial oil affects these bacteria in diverse ways. These findings suggest that birds may regulate the microbial flora on their feathers. Birds may directly inhibit the growth of harmful microbes or promote the growth of other harmless microbes that competitively exclude them. If keratinolytic (i.e., feather‐degrading) bacteria degrade colored feathers, then plumage coloration could reveal the ability of individual birds to regulate microbial flora. We used field‐ and lab‐based methods to test whether male eastern bluebirds (Sialia sialis) with brighter blue structural plumage coloration were better able to regulate their microbial flora than duller males. When we sampled bluebirds in the field, individuals with brighter color had higher bacterial loads than duller individuals. In the lab, we tested whether bacteria could directly alter feather color. We found that keratinolytic bacteria increased the brightness and purity, decreased the ultraviolet chroma, and did not affect the hue of structural color. This change in spectral properties of feathers may occur through degradation of the cortex and spongy layer of structurally colored barbs. These data suggest that bacteria can alter structural plumage color through degradation.

A protean palette: colour materials and mixing in birds and butterflies

While typically classified as either ‘structural’ or ‘pigmentary’, bio-optical tissues of terrestrial animals are rarely homogeneous and typically contain both a structural material such as keratin or chitin and one or more pigments. These base materials interact physically and chemically to create colours. Combinations of structured base materials and embedded pigment molecules often interact optically to produce unique colours and optical properties. Therefore, to understand the mechanics and evolution of bio-optical tissues it is critical to understand their material properties, both in isolation and in combination. Here, we review the optics and evolution of coloured tissues with a focus on their base materials, using birds and butterflies as exemplar taxa owing to the strength of our current knowledge of colour production in these animals. We first review what is known of their base materials, and then discuss the consequences of these interactions from an optical perspective. Finally, we suggest directions for future research on colour optics and evolution that will be invaluable as we move towards a fuller understanding of colour in the natural world.

Concordant evolution of plumage colour, feather microstructure and a melanocortin receptor gene between mainland and island populations of a fairy–wren

Studies of the patterns of diversification of birds on islands have contributed a great deal to the development of evolutionary theory. In white–winged fairy–wrens, Malurus leucopterus, mainland males develop a striking blue nuptial plumage whereas those on nearby islands develop black nuptial plumage. We explore the proximate basis for this divergence by combining microstructural feather analysis with an investigation of genetic variation at the melanocortin–1 receptor locus (MC1R). Fourier analysis revealed that the medullary keratin matrix (spongy layer) of the feather barbs of blue males was ordered at the appropriate nanoscale to produce the observed blue colour by coherent light scattering. Surprisingly, the feather barbs of black males also contained a spongy layer that could produce a similar blue colour. However, black males had more melanin in their barbs than blue males, and this melanin may effectively mask any structural colour produced by the spongy layer. Moreover, the presence of this spongy layer suggests that black island males evolved from a blue–plumaged ancestor. We also document concordant patterns of variation at the MC1R locus, as five amino acid substitutions were perfectly associated with the divergent blue and black plumage phenotypes. Thus, with the possible involvement of a melanocortin receptor locus, increased melanin density may mask the blue–producing microstructure in black island males, resulting in the divergence of plumage coloration between mainland and island white–winged fairy–wrens. Such mechanisms may also be responsible for plumage colour diversity across broader geographical and evolutionary scales.