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Animal colour patterns are a model system for understanding evolution because they are unusually accessible for study and experimental manipulation. This is possible because their functions are readily identifiable. In this final paper of the symposium we provide a diagram of the processes affecting colour patterns and use this to summarize their functions and put the other papers in a broad context. This allows us to identify significant ‘holes’ in the field that only become obvious when we see the processes affecting colour patterns, and their interactions, as a whole. We make suggestions about new directions of research that will enhance our understanding of both the evolution of colour patterns and visual signalling but also illuminate how the evolution of multiple interacting traits works. This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.

Color pattern plays a crucial role in various aspects of an organism’s biology, including camouflage, mating, and communication. Despite its significance, methods to quantify and study color pattern variation are often lacking, especially for complex patterns that defy simple categorization. In this study, we developed algorithms to capture and obtain data on 19 different pattern measurements from digital images of 55 individuals of the Eastern box turtle Terrapene carolina sampled in the field and in a museum. The Eastern box turtle is an ideal species to study variation of complex color patterns as this species is easily encountered in the field and in museum collections in Northeastern US, has a relatively easy to identify bright color pattern against a dark background, and has a rigid shell structure, which removes problems related to body distortion. The selected measurements capture the different aspects of the complexity of the color pattern, including the symmetry of the pattern on the turtles’ scutes, a critical component in developmental and evolutionary studies. We estimated the variation of each of these 19 measurements across our samples. We determined how much of this variation was influenced by the sensitivity of the pattern capture algorithm due to non-standardized elements of the image acquisition, lighting conditions, and animal shape on pattern variation. To our knowledge, this is the first study to use a comprehensive set of pattern measurements to capture variation in a complex color pattern while also assessing the susceptibility of each of these measurements to noise introduced during data collection. Additionally, we carried out a citizen science approach to characterize the complexity of the color pattern based on human perception and determine which of the 19 pattern measurements best describe this complexity. The most variable measurements across individuals were blue and yellow contrast between the pattern and non-pattern coloration and the average size of objects. From our estimates of the measurement noise due to image acquisition and analysis, we found that the contrast differences reflected true pattern variations between individual turtles, whereas differences in the average size of objects were influenced by both individual turtle variation and measurement inconsistencies. We found that due to the complexity of the patterns, measurements had lower variability if they did not depend on the algorithm defining a set of discrete objects. For example, total area had much less measurement variability than average object area. Our study provides a comprehensive workflow and tools to study variation in complex color patterns in organisms sampled under non-standardized conditions while also estimating the influence of noise due to biological and non-biological factors.

The diversity on coral reefs has long captivated observers. We examine the mechanisms of speciation, role of ecology in speciation, and patterns of species distribution in a typical reef-associated clade—the diverse and colorful Calcinus hermit crabs—to address the origin of tropical marine diversity. We sequenced COI, 16S, and H3 gene regions for ∼90% of 56 putative species, including nine undescribed, \"cryptic\" taxa, and mapped their distributions. Speciation in Calcinus is largely peripatric at remote locations. Allopatric species pairs are younger than sympatric ones, and molecular clock analyses suggest that >2 million years are needed for secondary sympatry. Substantial niche conservatism is evident within clades, as well as a few major ecological shifts between sister species. Color patterns follow species boundaries and evolve rapidly, suggesting a role in species recognition. Most species prefer and several are restricted to oceanic areas, suggesting great dispersal abilities and giving rise to an ocean-centric diversity pattern. Calcinus diversity patterns are atypical in that the diversity peaks in the west-central oceanic Pacific rather than in the Indo-Malayan \"diversity center.\" Calcinus speciation patterns do not match well-worn models put forth to explain the origin of Indo-West Pacific diversity, but underscore the complexity of marine diversification.

Diversification rates and evolutionary trajectories are known to be influenced by phenotypic traits and the geographic history of the landscapes that organisms inhabit. One of the most conspicuous traits in butterflies is their wing color pattern, which has been shown to be important in speciation. The evolution of many taxa in the Neotropics has also been influenced by major geological events. Using a dated, species‐level molecular phylogenetic hypothesis for Preponini, a colorful Neotropical butterfly tribe, we evaluated whether diversification rates were constant or varied through time, and how they were influenced by color pattern evolution and biogeographical events. We found that Preponini originated approximately 28 million years ago and that diversification has increased through time consistent with major periods of Andean uplift. Even though some clades show evolutionarily rapid transitions in coloration, contrary to our expectations, these shifts were not correlated with shifts in diversification. Involvement in mimicry with other butterfly groups might explain the rapid changes in dorsal color patterns in this tribe, but such changes have not increased species diversification in this group. However, we found evidence for an influence of major Miocene and Pliocene geological events on the tribe's evolution. Preponini apparently originated within South America, and range evolution has since been dynamic, congruent with Andean geologic activity, closure of the Panama Isthmus, and Miocene climate variability. We explore the potential role of phenotypic traits and major biogeographical events in explaining diversification dynamics and current distribution patterns of one of the most spectacularly colored butterfly groups in the Neotropics. We found that even though forewing color evolved fast in particular clades, these changes did not have a major influence on diversification dynamics. In contrast, we found that the Andean uplift was responsible for an increase in speciation rate and being responsible for current distribution patterns.

Teleasinae are commonly collected scelionids that are the only known egg parasitoids of carabid beetles and therefore play a crucial role in shaping carabid populations in natural and agricultural ecosystems. We review the available host information of Teleasinae, report a new host record, and revise Gryonoides Dodd, 1920, a morphologically distinct teleasine genus. We review the generic concept of Gryonoides and provide diagnoses and descriptions of thirteen Gryonoides species and two varieties: G. glabriceps Dodd, 1920, G. pulchellus Dodd, 1920 (= G. doddi Ogloblin, 1967, syn. nov. and G. pulchricornis Ogloblin, 1967, syn. nov. ), G. brasiliensis Masner & Mikó, sp. nov. , G. flaviclavus Masner & Mikó, sp. nov. , G. fuscoclavatus Masner & Mikó, sp. nov. , G. garciai Masner & Mikó, sp. nov. , G. mexicali Masner & Mikó, sp. nov. , G. mirabilicornis Masner & Mikó, sp. nov. , G. obtusus Masner & Mikó, sp. nov. , G. paraguayensis Masner & Mikó, sp. nov. , G. rugosus Masner & Mikó, sp. nov. , G. uruguayensis Masner & Mikó, sp. nov. We treat Gryonoides scutellaris Dodd, 1920, as status uncertain. Gryonoides mirabilicornis Masner & Mikó, sp. nov. is the only known teleasine with tyloids on two consecutive flagellomeres, a well-known trait of Sparasionidae. An illustrated identification key to species of Gryonoides , a queryable semantic representation of species descriptions using PhenoScript, and a simple approach for making Darwin Core Archive files in taxonomic revisions accessible are provided.

Background Body coloration is an ecologically important trait that is often involved in prey-predator interactions through mimicry and crypsis. Although this subject has attracted the interest of biologists and the general public, our scientific knowledge on the subject remains fragmentary. In the caterpillar of the swallowtail butterfly Papilio xuthus , spectacular changes in the color pattern are observed; the insect mimics bird droppings (mimetic pattern) as a young larva, and switches to a green camouflage coloration (cryptic pattern) in the final instar. Despite the wide variety and significance of larval color patterns, few studies have been conducted at a molecular level compared with the number of studies on adult butterfly wing patterns. Results To obtain a catalog of genes involved in larval mimetic and cryptic pattern formation, we constructed expressed sequence tag (EST) libraries of larval epidermis for P. xuthus , and P. polytes that contained 20,736 and 5,376 clones, respectively, representing one of the largest collections available in butterflies. A comparison with silkworm epidermal EST information revealed the high expression of putative blue and yellow pigment-binding proteins in Papilio species. We also designed a microarray from the EST dataset information, analyzed more than five stages each for six markings, and confirmed spatial expression patterns by whole-mount in situ hybridization. Hence, we succeeded in elucidating many novel marking-specific genes for mimetic and cryptic pattern formation, including pigment-binding protein genes, the melanin-associated gene yellow-h3 , the ecdysteroid synthesis enzyme gene 3-dehydroecdysone 3b-reductase , and Papilio -specific genes. We also found many cuticular protein genes with marking specificity that may be associated with the unique surface nanostructure of the markings. Furthermore, we identified two transcription factors, spalt and ecdysteroid signal-related E75 , as genes expressed in larval eyespot markings. This finding suggests that E75 is a strong candidate mediator of the hormone-dependent coordination of larval pattern formation. Conclusions This study is one of the most comprehensive molecular analyses of complicated morphological features, and it will serve as a new resource for studying insect mimetic and cryptic pattern formation in general. The wide variety of marking-associated genes (both regulatory and structural genes) identified by our screening indicates that a similar strategy will be effective for understanding other complex traits.

Physiological or genetic assays and computational modeling are valuable tools for understanding animals’ visual discrimination capabilities. Yet sometimes, the results generated by these methods appear not to jive with other aspects of an animal’s appearance or natural history, and behavioral confirmatory tests are warranted. Here we examine the peculiar case of a male jumping spider that displays red, black, white, and UV color patches during courtship despite the fact that, according to microspectrophotometry and color vision modeling, they are unlikely able to discriminate red from black. To test whether some optical or neurological component could have been missed using these methods, we conduct mate choice experiments. Some females are presented with a choice between males with their red leg coloration painted over with either red or black paint, while other females are presented with a choice between males with the same coloration painted over by either red or white paint. This latter pairing of red and white males should have been easily distinguishable to the spiders and served as a control to ensure our experimental setup was conducive to natural mating behavior. Red males were more likely to mate than white males ( P = 0.035), whereas red and black males had identical mating success ( P = 1.0). This suggests that previous physiological and computational work on these spiders was correct in concluding that they are unable to discriminate between red and black. Any functional significance of displaying both colors, rather than only black, remains unresolved.

Animal coloration patterns, from zebra stripes to bird egg speckles, are remarkably varied. With research on the perception, function, and evolution of animal patterns growing rapidly, we require a convenient framework for quantifying their diversity, particularly in the contexts of camouflage, mimicry, mate choice, and individual recognition. Ideally, patterns should be defined by their locations in a low-dimensional pattern space that represents their appearance to their natural receivers, much as color is represented by color spaces. This synthesis explores the extent to which animal patterns, like colors, can be described by a few perceptual dimensions in a pattern space. We begin by reviewing biological spatial vision, focusing on early stages during which neurons act as spatial filters or detect simple features such as edges. We show how two methods from computational vision—spatial filtering and feature detection—offer qualitatively distinct measures of animal coloration patterns. Spatial filters provide a measure of the image statistics, captured by the spatial frequency power spectrum. Image statistics give a robust but incomplete representation of the appearance of patterns, whereas feature detectors are essential for sensing and recognizing physical objects, such as distinctive markings and animal bodies. Finally, we discuss how pattern space analyses can lead to new insights into signal design and macroevolution of animal phenotypes. Overall, pattern spaces open up new possibilities for exploring how receiver vision may shape the evolution of animal pattern signals.

Advances in digital imaging and software tools have provided increasingly accessible datasets and methods for analysing colour evolution. Despite the variety of computational packages available, most rely on colour classification before running analyses. Previous methods to characterize colour limit the ability to analyse large‐scale image databases and are not always representative of biologically relevant colour classes, which decrease the accuracy of downstream analyses. Here, we present charisma, an R package designed to characterize the distribution of distinct colour classes in images suitable for large‐scale studies of biological organisms. We demonstrate the utility of our package through an analysis of colour evolution in a sample of diverse and charismatic birds, tanagers, in the subfamily Thraupinae. We show that charisma can quickly and accurately classify every pixel in an image and validate these results using pre‐identified, canonical colour swatches. We find that charisma colour classifications are consistent with those made by colour pattern experts in the field. Applying charisma to tanager colour evolution, we find that charisma outputs seamlessly integrate with downstream evolutionary analyses. Our results demonstrate that using charisma to manually curate and characterize colours in images provides a standardized, reliable and reproducible framework for high‐throughput colour classification.

Background Biologists have long been fascinated by the striking diversity of complex color patterns in tropical reef fishes. However, the origins and evolution of this diversity are still poorly understood. Disentangling the evolution of simple color patterns offers the opportunity to dissect both ultimate and proximate causes underlying color diversity. Results Here, we study clownfishes, a tribe of 30 species within the Pomacentridae that displays a relatively simple color pattern made of zero to three vertical white stripes on a dark body background. Mapping the number of white stripes on the evolutionary tree of clownfishes reveals that their color pattern diversification results from successive caudal to rostral losses of stripes. Moreover, we demonstrate that stripes always appear with a rostral to caudal stereotyped sequence during larval to juvenile transition. Drug treatments (TAE 684) during this period leads to a dose-dependent loss of stripes, demonstrating that white stripes are made of iridophores and that these cells initiate the stripe formation. Surprisingly, juveniles of several species (e.g., Amphiprion frenatus ) have supplementary stripes when compared to their respective adults. These stripes disappear caudo-rostrally during the juvenile phase leading to the definitive color pattern. Remarkably, the reduction of stripe number over ontogeny matches the sequences of stripe losses during evolution, showing that color pattern diversification among clownfish lineages results from changes in developmental processes. Finally, we reveal that the diversity of striped patterns plays a key role for species recognition. Conclusions Overall, our findings illustrate how developmental, ecological, and social processes have shaped the diversification of color patterns during the radiation of an emblematic coral reef fish lineage.