Chad M. Eliason

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.

Functionally Independent Components of Prey Capture Are Architecturally Constrained in Spider Orb Webs

Evolutionary conflict in trait performance under different ecological contexts is common, but may also arise from functional coupling between traits operating within the same context. Orb webs first intercept and then retain insects long enough to be attacked by spiders. Improving either function increases prey capture and they are largely determined by different aspects of web architecture. We manipulated the mesh width of orbs to investigate its effect, along with web size, on prey capture by spiders and found that they functioned independently. Probability of prey capture increased with web size but was not affected by mesh width. Conversely, spiders on narrow-meshed webs were almost three times more likely to capture energetically profitable large insects, which demand greater prey retention. Yet, the two functions are still constrained during web spinning because increasing mesh width maximizes web size and hence interception, while retention is improved by decreasing mesh width because more silk adheres to insects. The architectural coupling between prey interception and retention has probably played a key role in both the macroevolution of orb web shape and the expression of plasticity in the spinning behaviours of spiders.

How hollow melanosomes affect iridescent colour production in birds

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

A photonic heterostructure produces diverse iridescent colours in duck wing patches

The colours of birds are diverse but limited relative to the colours they can perceive. This mismatch may be partially caused by the properties of their colour-production mechanisms. Aside from pigments, several classes of highly ordered nanostructures (thin films, amorphous three-dimensional arrays) can produce a range of colours. However, the variability of any single nanostructural class has rarely been explored. Dabbling ducks are a speciose clade with substantial interspecific variation in the iridescent coloration of their wing patches (specula). Here, we use electron microscopy, spectrophotometry, polarization and refractive index-matching experiments, and optical modelling to examine these colours. We show that, in all species examined, speculum colour is produced by a photonic heterostructure consisting of both a single thin-film of keratin and a two-dimensional hexagonal lattice of melanosomes in feather barbules. Although the range of possible variations of this heterostructure is theoretically broad, only relatively close-packed, energetically stable variants producing more saturated colours were observed, suggesting that ducks are either physically constrained to these configurations or are under selection for the colours that they produce. These data thus reveal a previously undescribed biophotonic structure and suggest that both physical variability and constraints within single nanostructural classes may help explain the broader patterns of colour across Aves.

Decreased hydrophobicity of iridescent feathers: a potential cost of shiny plumage

SUMMARY Honest advertisement models posit that sexually selected traits are costly to produce, maintain or otherwise bear. Brightly coloured feathers are thought to be classic examples of these models, but evidence for a cost in feathers not coloured by carotenoid pigments is scarce. Unlike pigment-based colours, iridescent feather colours are produced by light scattering in modified feather barbules that are characteristically flattened and twisted towards the feather surface. These modifications increase light reflectance, but also expose more surface area for water adhesion, suggesting a potential trade-off between colour and hydrophobicity. Using light microscopy, spectrometry, contact angle goniometry and self-cleaning experiments, we show that iridescent feathers of mallards, Anas platyrhynchos, are less hydrophobic than adjacent non-iridescent feathers, and that this is primarily caused by differences in barbule microstructure. Furthermore, as a result of this decreased hydrophobicity, iridescent feathers are less efficient at self-cleaning than non-iridescent feathers. Together, these results suggest a previously unforeseen cost of iridescent plumage traits that may help to explain the evolution and distribution of iridescence in birds.

Rapid, reversible response of iridescent feather color to ambient humidity

Colorful traits can vary in response to neural control, hormone levels, reproductive state, or abiotic factors. In birds, colorful plumage traits are generally considered static ornaments that only vary irreversibly due to abrasion, bacterial degradation, or wear. However, in this work it is shown that iridescent feather color varies rapidly and reversibly in response to changes in ambient humidity. Based on optical models and sorption experiments, these changes appear to be caused by a swelling of the outer keratin cortex following water absorption. To our knowledge, this is the first study describing dynamic color changes in any keratinous biophotonic nanostructure.

Antimicrobial properties of a nanostructured eggshell from a compost-nesting bird

Infection is an important source of mortality for avian embryos but parental behaviors and eggs themselves can provide a network of antimicrobial defenses. Mound builders (Aves: Megapodiidae) are unique among birds in that they produce heat for developing embryos not by sitting on eggs but by burying them in carefully tended mounds of soil and microbially decomposing vegetation. The low infection rate of eggs of one species in particular, the Australian brush-turkey (Alectura lathami), suggests that they possess strong defensive mechanisms. To identify some of these mechanisms, we first quantified antimicrobial albumen proteins and characterized eggshell structure, finding that albumen was not unusually antimicrobial, but that eggshell cuticle was composed of nanometer-sized calcite spheres. Experimental tests revealed that these modified eggshells were significantly more hydrophobic and better at preventing bacterial attachment and penetration into the egg contents than chicken eggs. Our results suggest that these mechanisms may contribute to the antimicrobial defense system of these eggs, and may provide inspiration for new biomimetic anti-fouling surfaces.

Structural color change following hydration and dehydration of iridescent mourning dove (Zenaida macroura) feathers

Dynamic changes in integumentary color occur in cases as diverse as the neurologically controlled iridiphores of cephalopod skin and the humidity-responsive cuticles of longhorn beetles. By contrast, feather colors are generally assumed to be relatively static, changing by small amounts only over periods of months. However, this assumption has rarely been tested even though structural colors of feathers are produced by ordered nanostructures that are analogous to those in the aforementioned dynamic systems. Feathers are neither innervated nor vascularized and therefore any color change must be caused by external stimuli. Thus, we here explore how feathers of iridescent mourning doves Zenaida macroura respond to a simple stimulus: addition and evaporation of water. After three rounds of experimental wetting and subsequent evaporation, iridescent feather color changed hue, became more chromatic and increased in overall reflectance by almost 50%. To understand the mechanistic basis of this change, we used electron microscopy to examine macro- and nanostructures before and after treatment. Transmission electron microscopy and transfer matrix thin-film models revealed that color is produced by thin-film interference from a single (∼ 35 nm layer of keratin around the edge of feather barbules, beneath which lies a layer of air and melanosomes. After treatment, the most striking morphological difference was a twisting of colored barbules that exposed more of their surface area for reflection, explaining the observed increase in brightness. These results suggest that some plumage colors may be more malleable than previously thought, leading to new avenues for research on dynamic plumage color.

Coos, booms, and hoots: The evolution of closed‐mouth vocal behavior in birds

Most birds vocalize with an open beak, but vocalization with a closed beak into an inflating cavity occurs in territorial or courtship displays in disparate species throughout birds. Closed‐mouth vocalizations generate resonance conditions that favor low‐frequency sounds. By contrast, open‐mouth vocalizations cover a wider frequency range. Here we describe closed‐mouth vocalizations of birds from functional and morphological perspectives and assess the distribution of closed‐mouth vocalizations in birds and related outgroups. Ancestral‐state optimizations of body size and vocal behavior indicate that closed‐mouth vocalizations are unlikely to be ancestral in birds and have evolved independently at least 16 times within Aves, predominantly in large‐bodied lineages. Closed‐mouth vocalizations are rare in the small‐bodied passerines. In light of these results and body size trends in nonavian dinosaurs, we suggest that the capacity for closed‐mouth vocalization was present in at least some extinct nonavian dinosaurs. As in birds, this behavior may have been limited to sexually selected vocal displays, and hence would have co‐occurred with open‐mouthed vocalizations.

Evolutionary shifts in the melanin-based color system of birds

Melanin pigments contained in organelles (melanosomes) impart earthy colors to feathers. Such melanin‐based colors are distributed across birds and thought to be the ancestral color‐producing mechanism in birds. However, we have had limited data on melanin‐based color and melanosome diversity in Palaeognathae, which includes the flighted tinamous and large‐bodied, flightless ratites and is the sister taxon to all other extant birds. Here, we use scanning electron microscopy and spectrophotometry to assess melanosome morphology and quantify reflected color for 19 species within this clade. We find that brown colors in ratites are uniquely associated with elongated melanosomes nearly identical in shape to those associated with black colors. Melanosome and color diversity in large‐bodied ratites is limited relative to other birds (including flightless penguins) and smaller bodied basal maniraptoran dinosaur outgroups of Aves, whereas tinamous show a wider range of melanosome forms similar to neognaths. The repeated occurrence of novel melanosome forms in the nonmonophyletic ratites suggests that melanin‐based color tracks changes in body size, physiology, or other life history traits associated with flight loss, but not feather morphology. We further anticipate these findings will be useful for future color reconstructions in extinct species, as variation in melanosome shape may potentially be linked to a more nuanced palette of melanin‐based colors.