Quantitative Colour Pattern Analysis (QCPA): A comprehensive framework for the analysis of colour patterns in nature

Automatic identification of bird females using egg phenotype

Individual identification is crucial for studying animal ecology and evolution. In birds this is often achieved by capturing and tagging. However, these methods are insufficient for identifying individuals/species that are secretive or difficult to catch. Here, we employ an automatic analytical approach to predict the identity of bird females based on the appearance of their eggs, using the common cuckoo (Cuculus canorus) as a model species. We analysed 192 cuckoo eggs using digital photography and spectrometry. Cuckoo females were identified from genetic sampling of nestlings, allowing us to determine the accuracy of automatic (unsupervised and supervised) and human assignment. Finally, we used a novel analytical approach to identify eggs that were not genetically analysed. Our results show that individual cuckoo females lay eggs with a relatively constant appearance and that eggs laid by more genetically distant females differ more in colour. Unsupervised clustering had similar cluster accuracy to experienced human observers, but supervised methods were able to outperform humans. Our novel method reliably assigned a relatively high number of eggs without genetic data to their mothers. Therefore, this is a cost-effective and minimally invasive method for increasing sample sizes, which may facilitate research on brood parasites and other avian species.

Motion: enhancing signals and concealing cues

Animal colour patterns remain a lively focus of evolutionary and behavioural ecology, despite the considerable conceptual and technical developments over the last four decades. Nevertheless, our current understanding of the function and efficacy of animal colour patterns remains largely shaped by a focus on stationary animals, typically in a static background. Yet, this rarely reflects the natural world: most animals are mobile in their search for food and mates, and their surrounding environment is usually dynamic. Thus, visual signalling involves not only animal colour patterns, but also the patterns of animal motion and behaviour, often in the context of a potentially dynamic background. While motion can reveal information about the signaller by attracting attention or revealing signaller attributes, motion can also be a means of concealing cues, by reducing the likelihood of detection (motion camouflage, motion masquerade and flicker-fusion effect) or the likelihood of capture following detection (motion dazzle and confusion effect). The interaction between the colour patterns of the animal and its local environment is further affected by the behaviour of the individual. Our review details how motion is intricately linked to signalling and suggests some avenues for future research.

This Review has an associated Future Leader to Watch interview with the first author.

Summary: While motion can reveal information about the signaller, motion can also be a means of concealing cues by reducing the likelihood of detection or the likelihood of capture following detection.

How visual system configuration can play a role in individual recognition: a visual modeling study

Many species rely on individual recognition (i.e., the use of individual signals to identify and remember a conspecific) to tune their social interactions. However, little is known about how the configuration of the sensory system may affect the perception of individual recognition signals over space. Utilizing a visual modeling approach, we quantified (1) the threshold distance between the receiver and the signaler at which individual recognition can no longer accurately occur, and (2) the regions of the head most likely to contain the individual recognition signals. We used chickens (Gallus gallus) as our study species, as they use visual individual recognition and additionally have a well-studied visual system. We took pictures of different individuals and followed a visual modeling approach considering color vision, visual acuity, and pattern processing of the receiver. We found that distance degrades the quality of information in potential individual recognition signals. We estimated that the neighbor distance at which a receiver may have difficulty recognizing a conspecific was between 0.25 and 0.30 m in chickens, which may be related to a decrease in available features of the potential signal. This signal perception threshold closely matches the recognition distance predicted by previous behavioral approaches. Additionally, we found that certain regions of the head (beak, cheek, comb, eye) may be good candidates for individual recognition signals. Overall, our findings support that recognition in chickens occurs at short distances due to constraints imposed by their visual system, which can affect the costs and benefits associated with social spacing in groups.

Generalist camouflage can be more successful than microhabitat specialisation in natural environments

BACKGROUND

Crypsis by background-matching is a critical form of anti-predator defence for animals exposed to visual predators, but achieving effective camouflage in patchy and variable natural environments is not straightforward. To cope with heterogeneous backgrounds, animals could either specialise on particular microhabitat patches, appearing cryptic in some areas but mismatching others, or adopt a compromise strategy, providing partial matching across different patch types. Existing studies have tested the effectiveness of compromise strategies in only a limited set of circumstances, primarily with small targets varying in pattern, and usually in screen-based tasks. Here, we measured the detection risk associated with different background-matching strategies for relatively large targets, with human observers searching for them in natural scenes, and focusing on colour. Model prey were designed to either 'specialise' on the colour of common microhabitat patches, or 'generalise' by matching the average colour of the whole visual scenes.

RESULTS

In both the field and an equivalent online computer-based search task, targets adopting the generalist strategy were more successful in evading detection than those matching microhabitat patches. This advantage occurred because, across all possible locations in these experiments, targets were typically viewed against a patchwork of different microhabitat areas; the putatively generalist targets were thus more similar on average to their various immediate surroundings than were the specialists.

CONCLUSIONS

Demonstrating close agreement between the results of field and online search experiments provides useful validation of online citizen science methods commonly used to test principles of camouflage, at least for human observers. In finding a survival benefit to matching the average colour of the visual scenes in our chosen environment, our results highlight the importance of relative scales in determining optimal camouflage strategies, and suggest how compromise coloration can succeed in nature.

Colour and motion affect a dune wasp's ability to detect its cryptic spider predators

Ambush predators depend on cryptic body colouration, stillness and a suitable hunting location to optimise the probability of prey capture. Detection of cryptic predators, such as crab spiders, by flower seeking wasps may also be hindered by wind induced movement of the flowers themselves. In a beach dune habitat, Microbembex nigrifrons wasps approaching flowerheads of the Palafoxia lindenii plant need to evaluate the flowers to avoid spider attack. Wasps may detect spiders through colour and movement cues. We tracked the flight trajectories of dune wasps as they approached occupied and unoccupied flowers under two movement conditions; when the flowers were still or moving. We simulated the appearance of the spider and the flower using psychophysical visual modelling techniques and related it to the decisions made by the wasp to land or avoid the flower. Wasps could discriminate spiders only at a very close range, and this was reflected in the shape of their trajectories. Wasps were more prone to making errors in threat assessment when the flowers are moving. Our results suggest that dune wasp predation risk is augmented by abiotic conditions such as wind and compromises their early detection capabilities.

Qualitative and quantitative methods show stability in patterns of Cepaea nemoralis shell polymorphism in the Pyrenees over five decades

Over the past century, the study of animal color has been critical in establishing some of the founding principles of biology, especially in genetics and evolution. In this regard, one of the emerging strengths of working with the land snail genus Cepaea is that historical collections can be compared against modern-day samples, for instance, to understand the impact of changing climate and habitat upon shell morph frequencies. However, one potential limitation is that prior studies scored shell ground color by eye into three discrete colours yellow, pink, or brown. This incurs both potential error and bias in comparative surveys. In this study, we therefore aimed to use a quantitative method to score shell color and evaluated it by comparing patterns of C. nemoralis shell color polymorphism in the Pyrenees, using both methods on present-day samples, and against historical data gathered in the 1960s using the traditional method. The main finding was that while quantitative measures of shell color reduced the possibility of error and standardized the procedure, the same altitudinal trends were recovered, irrespective of the method. The results also showed that there was a general stability in the local shell patterns over five decades, including altitudinal clines, with just some exceptions. Therefore, although subject to potential error human scoring of snail color data remains valuable, especially if persons have appropriate training. In comparison, while there are benefits in taking quantitative measures of color in the laboratory, there are also several practical disadvantages, mainly in terms of throughput and accessibility. In the future, we anticipate that genomic methods may be used to understand the potential role of selection in maintaining shell morph clines. In addition, photographs generated by citizen scientists conducting field surveys may be used with deep learning-based methods to survey color patterns.

Sexual selection on jumping spider color pattern: investigation with a new quantitative approach

How animals assess information encoded in individual color patches have been extensively studied, yet the role of both individual color patches and gross color pattern (i.e., the combination of color patches) remains understudied. We tested the functioning of both individual color patches and gross color pattern in sexual selection using the jumping spider Siler semiglaucus as a study system. We first quantified sexual dimorphism in S. semiglaucus in both individual patches and gross color pattern using the newly developed quantitative color pattern analysis (QCPA) framework. After detecting sexual differences in color coverage and pattern contrast, we manipulated the abdomen color pattern of males and had them engage in both female mate choice and male contest trials. Females spent more time watching males with lower pattern contrast and greater red coverage during mate assessment, suggesting that they evaluate information from both individual patches and gross color pattern of males. However, male color pattern had no significant effect on the outcomes of male contests. Thus, we suggest that the observed sexual color pattern dimorphism evolved primarily through female mate choice in S. semiglaucus. This is the first study to use QCPA framework to quantify sexual dimorphism in within-pattern conspicuousness from an intraspecific perspective in invertebrates. Our study also highlights the importance of both individual color patches and gross color pattern in sexual selection.

Behavioural thresholds of blue tit colour vision and the effect of background chromatic complexity

Vision is a vital attribute to foraging, navigation, mate selection and social signalling in animals, which often have a very different colour perception in comparison to humans. For understanding how animal colour perception works, vision models provide the smallest colour difference that animals of a given species are assumed to detect. To determine the just-noticeable-difference, or JND, vision models use Weber fractions that set discrimination thresholds of a stimulus compared to its background. However, although vision models are widely used, they rely on assumptions of Weber fractions since the exact fractions are unknown for most species. Here, we test; i) which Weber fractions in long-, middle- and shortwave (i.e. L, M, S) colour channels best describe the blue tit (Cyanistes caeruleus) colour discrimination, ii) how changes in hue of saturated colours and iii) chromatic background noise impair search behaviour in blue tits. We show that the behaviourally verified Weber fractions on achromatic backgrounds were L: 0.05, M: 0.03 and S: 0.03, indicating a high colour sensitivity. In contrast, on saturated chromatic backgrounds, the correct Weber fractions were considerably higher for L: 0.20, M: 0.17 and S: 0.15, indicating a less detailed colour perception. Chromatic complexity of backgrounds affected the longwave channel, while middle- and shortwave channels were mostly unaffected. We caution that using a vision model whereby colour discrimination is determined in achromatic viewing conditions, as they often are, can lead to misleading interpretations of biological interactions in natural - colourful - environments.

Decontextualized learning for interpretable hierarchical representations of visual patterns

Apart from discriminative modeling, the application of deep convolutional neural networks to basic research utilizing natural imaging data faces unique hurdles. Here, we present decontextualized hierarchical representation learning (DHRL), designed specifically to overcome these limitations. DHRL enables the broader use of small datasets, which are typical in most studies. It also captures spatial relationships between features, provides novel tools for investigating latent variables, and achieves state-of-the-art disentanglement scores on small datasets. DHRL is enabled by a novel preprocessing technique inspired by generative model chaining and an improved ladder network architecture and regularization scheme. More than an analytical tool, DHRL enables novel capabilities for virtual experiments performed directly on a latent representation, which may transform the way we perform investigations of natural image features, directly integrating analytical, empirical, and theoretical approaches.

The role of boundary length and adjacent patch contrast in guppy mate choice

The presence of various combinations of adjacent colors within polymorphic species’ color pattern could have a major impact on mate choice. We studied the role of pattern geometry in predicting mate choice in guppies using boundary strength analysis (BSA). BSA estimates the visual contrast intensity between two adjacent color patches (ΔS) weighted by the lengths of the boundaries between these adjacent color patches. We measured both the chromatic (hue and saturation) and achromatic (luminance) ΔS for each pair of adjacent patches. For each male’s color pattern, we measured BSA as both mean (mΔS) and coefficient of variation (cvΔS) of all ΔS weighted by their corresponding boundary lengths. We also determined if specific color patch boundaries had an impact on female preferences and whether these predicted overall male contrast (mΔS). We found that males with a higher mΔS were more attractive to females and that six boundaries containing either fuzzy black or black as one of the pair colors significantly affected female preferences, indicating that 1) females favored highly conspicuous males and 2) melanin-based patches could be used as a signal amplifier, not only for orange but for other colors.

The Paradox of Iridescent Signals

Signals reliably convey information to a receiver. To be reliable, differences between individuals in signal properties must be consistent and easily perceived and evaluated by receivers. Iridescent objects are often striking and vivid, but their appearance can change dramatically with viewing geometry and illumination. The changeable nature of iridescent surfaces creates a paradox: how can they be reliable signals? We contend that iridescent color patches can be reliable signals only if accompanied by specific adaptations to enhance reliability, such as structures and behaviors that limit perceived hue shift or enhance and control directionality. We highlight the challenges of studying iridescence and key considerations for the evaluation of its adaptive significance.

More than noise: context-dependent luminance contrast discrimination in a coral reef fish (Rhinecanthus aculeatus)

Achromatic (luminance) vision is used by animals to perceive motion, pattern, space and texture. Luminance contrast sensitivity thresholds are often poorly characterised for individual species and are applied across a diverse range of perceptual contexts using over-simplified assumptions of an animal's visual system. Such thresholds are often estimated using the receptor noise limited model (RNL). However, the suitability of the RNL model to describe luminance contrast perception remains poorly tested. Here, we investigated context-dependent luminance discrimination using triggerfish (Rhinecanthus aculeatus) presented with large achromatic stimuli (spots) against uniform achromatic backgrounds of varying absolute and relative contrasts. 'Dark' and 'bright' spots were presented against relatively dark and bright backgrounds. We found significant differences in luminance discrimination thresholds across treatments. When measured using Michelson contrast, thresholds for bright spots on a bright background were significantly higher than for other scenarios, and the lowest threshold was found when dark spots were presented on dark backgrounds. Thresholds expressed in Weber contrast revealed lower thresholds for spots darker than their backgrounds, which is consistent with the literature. The RNL model was unable to estimate threshold scaling across scenarios as predicted by the Weber-Fechner law, highlighting limitations in the current use of the RNL model to quantify luminance contrast perception. Our study confirms that luminance contrast discrimination thresholds are context dependent and should therefore be interpreted with caution.

Molecular Plasticity in Animal Pigmentation: Emerging Processes Underlying Color Changes

Animal coloration has been rigorously studied and has provided morphological implications for fitness with influences over social behavior, predator–prey interactions, and sexual selection. In vertebrates, its study has developed our understanding across diverse fields ranging from behavior to molecular biology. In the search for underlying molecular mechanisms, many have taken advantage of pedigree-based and genome-wide association screens to reveal the genetic architecture responsible for pattern variation that occurs in early development. However, genetic differences do not provide a full picture of the dynamic changes in coloration that are most prevalent across vertebrates at the molecular level. Changes in coloration that occur in adulthood via phenotypic plasticity rely on various social, visual, and dietary cues independent of genetic variation. Here, I will review the contributions of pigment cell biology to animal color changes and recent studies describing their molecular underpinnings and function. In this regard, conserved epigenetic processes such as DNA methylation play a role in lending plasticity to gene regulation as it relates to chromatophore function. Lastly, I will present African cichlids as emerging models for the study of pigmentation and molecular plasticity for animal color changes. I posit that these processes, in a dialog with environmental stimuli, are important regulators of variation and the selective advantages that accompany a change in coloration for vertebrate animals.

Visual acuity and egg spatial chromatic contrast predict egg rejection behavior of American robins

Color and spatial vision is critical for recognition and discrimination tasks affecting fitness, including finding food and mates, and recognizing offspring. For example, as a counter defense to avoid the cost of raising the unrelated offspring of obligate interspecific avian brood parasites, many host species routinely view, recognize and remove the foreign egg(s) from their nests. Recent research has shown that host species visually attend to both chromatic and spatial pattern features of eggs; yet how hosts simultaneously integrate these features together when recognizing eggs remains an open question. Here, we tested egg rejection responses of American robins (Turdus migratorius) using a range of 3D-printed model eggs covered with blue and yellow checkered patterns differing in relative square sizes. We predicted that robins would reject a model egg if they could visually resolve the blue and yellow squares as separate features, or accept it if the squares blended together and appeared similar in color to the natural blue-green color of robin eggs as perceived by the avian visual system. As predicted, the probability of robins rejecting a model egg increased with greater sizes of its blue and yellow squares. Our results suggest that chromatic visual acuity and viewing distance have the potential to limit the ability of a bird to recognize a foreign egg in its nest, thus providing a limitation to host egg recognition that obligate interspecific avian brood parasites may exploit.

Flies improve the salience of iridescent sexual signals by orienting toward the sun

Sunlight is the ultimate source of most visual signals. Theory predicts strong selection for its effective use during communication, with functional links between signal designs and display behaviors a likely result. This is particularly true for iridescent structural colors, whose moment-to-moment appearance bears a heightened sensitivity to the position of signalers, receivers, and the sun. Here, we experimentally tested this prediction using Lispe cana, a muscid fly in which males present their structurally colored faces and wings to females during ground-based sexual displays. In field-based assays, we found that males actively bias the orientation of their displays toward the solar azimuth under conditions of full sunlight and do so across the entire day. This bias breaks down, however, when the sun is naturally concealed by heavy cloud or experimentally obscured. Our modeling of the appearance of male signals revealed clear benefits for the salience of male ornaments, with a roughly 4-fold increase in subjective luminance achievable through accurate display orientation. These findings offer fine-scale, causal evidence for the active control of sexual displays to enhance the appearance of iridescent signals. More broadly, they speak to predicted coevolution between dynamic signal designs and presentation behaviors, and support arguments for a richer appreciation of the fluidity of visual communication.

A Matador-like Predator Diversion Strategy Driven by Conspicuous Coloration in Guppies

Understanding the adaptive function of conspicuous coloration has been a major focus of evolutionary biology for much of the last century. Although considerable progress has been made in explaining how conspicuous coloration can be used in functions as diverse as sexual and social signaling, startling predators, and advertising toxicity [1], there remain a multitude of species that display conspicuous coloration that cannot be explained by existing theory. Here we detail a new "matador-like" divertive antipredator strategy based on conspicuous coloration in Trinidadian guppies (Poecilia reticulata). Guppies encountering predatory fish rapidly enhance the conspicuousness of their eyes by blackening their irises. By pitting biomimetic robotic guppies against real predatory fish, we show this conspicuous eye coloration diverts attacks away from the guppies' center of mass to their head. To determine the function of this seemingly counterintuitive behavior, we developed a method for simulating escape probabilities when live prey interact with ballistic attacking predators, and find this diversion effect significantly benefits black-eyed guppies because they evade capture by rapidly pivoting away from the predator once it has committed to its attack. Remarkably, this antipredator strategy reverses the commonly observed negative scaling relationship between prey size and evasive ability, with larger fish benefiting most from diverting predators. Taken together, our results introduce a new antipredator divertive strategy that may be widely used by conspicuously colored prey that rely on agility to escape their predators.

Does reproductive mode affect sexually-selected coloration? Evaluating UV-blue spots in parthenogenetic and bisexual lizards of the genus Darevskia

Sexual selection often leads to evolution of conspicuous signals, raising the chances of attracting not only potential mates, but also predators. In lacertid lizards, ultraviolet (UV)–blue spots on flanks and shoulders represent such a trait. Some level of correlation between male and female ornamentation is also known to exist. Therefore, the phenotype of females may change in the absence of sexual selection. We tested this hypothesis on a complex of parthenogenetic and bisexual lizards of the genus Darevskia. We evaluated area, counts, and chromatic properties (UV opponency, saturation) of UV–blue spots and compared the values between the clones and their bisexual progenitor species. We found a fair heterogeneity between the parthenogenetic species, but no general tendency toward higher crypsis or conspicuousness. Values of the parthenogens were not significantly different from the values of sexual females. A possible explanation is that the changes in selective forces associated with parthenogenetic reproduction are too small to affect the resulting pattern of selective pressures on the studied traits, or that the phenotypes of the parthenogens result from the unique combination of parental genomes and are conserved by clonal reproduction.

Climate Predicts UV Floral Pattern Size, Anthocyanin Concentration, and Pollen Performance in Clarkia unguiculata

Given that flower size and pigmentation can mediate plant-pollinator interactions, many studies have focused on pollinator-driven selection on these floral traits. However, abiotic factors such as precipitation, temperature, and solar radiation also contribute to geographic variation in floral color, pattern, and size within multiple species. Several studies have described an ecogeographic pattern within species in which high temperature, high ultraviolet (UV) radiation, low precipitation and/or low latitudes are associated with increased floral anthocyanin production, smaller flowers, and/or larger UV-absorbing floral patterns (nectar guides or bullseyes). However, latitude or elevation is often used as a proxy variable to study variation in floral traits associated with a wide range of climatic variables, making the proximate abiotic drivers of variation difficult to identify. In this study, we tested and corroborated several predictions for how the abiotic environment may directly or indirectly shape geographic patterns of floral color, pattern, and size in Clarkia unguiculata (Onagraceae). This study provides the first report of geographic variation in multispectral floral color and pattern in C. unguiculata, while also providing an experimental test of the putative protective role of UV absorption for pollen performance. We quantified geographic variation among greenhouse-raised populations in UV floral pattern size, mean UV petal reflectance, anthocyanin concentration, and petal area in C. unguiculata across its natural range in California and, using 30 year climate normals for each population, we identified climatic and topographic attributes that are correlated with our focal floral traits. In addition, we examined pollen performance under high and low UV light conditions to detect the protective function (if any) of UV floral patterns in this species. Contrary to our expectations, the nectar guide and the proportion of the petal occupied by the UV nectar guide were largest in low solar UV populations. Estimated floral anthocyanin concentration was highest in populations with high solar UV, which does support our predictions. The size of the UV nectar guide did not affect pollen performance in either of the light treatments used in this study. We conclude that, under the conditions examined here, UV-absorbing floral patterns do not serve a direct "pollen protection" function in C. unguiculata. Our results only partially align with expected ecogeographic patterns in these floral traits, highlighting the need for research in a wider range of taxa in order to detect and interpret broad scale patterns of floral color variation.