Colour patterns in Palaeozoic orthoceratoid cephalopods - diversification of striping

Problems Statement and Purpose. The colouration (when pigment is distributed more or less uniformly within skeletal substance) and colour patterns (when pigment is concentrated or arranged in bands, lines, spots, patches, etc.) of fossil brachiopod shells is poorly understood, since its preservation in the fossil record requires the coincidence of several, sometimes random, taphonomic factors. However, the study of the original colouration of fossil invertebrates is of great palaeoecological and taphonomic importance (e.g., to study of the evolution of vision, the development of predator-prey relationships). Records of Palaeozoic brachiopod shells with preserved colouration are quite rare and the shell colouration and colour patterns are currently known for only 15 genera. Data and Methods. Studied isolated valves of the lingulid brachiopods Lingularia mytiloides from the lower Moscovian Kamensk Formation of Luhansk Region (Ukraine) show a preserved colour pattern on the outer surface, represented mainly by light concentric bands. Studied remains are represented by small, 8–10 mm long and 6–7 mm wide, moderately convex ventral thin-shelled valves with elongate elliptical outlines, a rounded anterior margin, subparallel lateral margins and a small, pointed umbo. Valve surface is covered with thin concentric growth lines and weakly developed rugae. Results and Discussion. The studied specimens were divided into two groups based on shell colouration features, which may reflect some details of the colouration and colour patterns. However, these differences may be taphonomic artefacts. It is quite possible that the colour bands on the surface of the valves are evidence of sulphide oxidation, but even so, they likely still reflect the original colour patterns. Environmental conditions were important factors for the preservation of the colouration on the shells of the studied lingulid brachiopods. Among these conditions, the most important were slow sedimentation, absence of agents of mechanical and chemical destruction, such as high-energy water activity, encrustation by epibionts, etc., dysaerobic conditions, and rapid burial apparently accompanied by the activity of bacterial communities. The studied colour patterns on the shells of Lingularia mytiloides are similar to those on other fossil lingulids. The adaptive significance of this colouration for the studied lingulids, which lived infaunally, remains unclear and cannot be resolved with the available material.

Treating color patterns in a geometric morphometrics framework reveals rapid rates of color evolution that are explained by a combination of intrinsic organismal features (color variation among patches) and geography within a cosmopolitan radiation of birds.

Treating color patterns in a geometric morphometrics framework reveals rapid rates of color evolution that are explained by a combination of intrinsic organismal features (color variation among patches) and geography within a cosmopolitan radiation of birds.

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.

Colour variation in crocodilians is associated with size, environment and genetic structure, but little is known about colour variation in the genus Paleosuchus (Alligatoridae). Different genetic lineages of Paleosuchus palpebrosus (Dwarf caiman) occupy different environments throughout the species extensive distribution, and all are cryptically coloured. We captured 187 P. palpebrosus and recorded their head colour from four genetically distinct geographic clades between 2008 and 2019. Additionally, we determined the jaw and belly spot pattern of a subsample of 95 individuals (22–109 cm snout-vent length). PERMANCOVA was used to investigate the relationships between head colour and spot patterns, to the caiman size, sex, and geographic lineage, as well as ambient temperature. Variation in head colour, and jaw and belly spot patterns, were related to genetic lineage, snout-vent length and temperature, but the model explained only ∼45.4% of the variance in the data. Sex was not significantly related to the head colour, or jaw and belly spot patterns. Dwarf caimans inhabiting cooler climates tend to be darker than individuals from warmer areas, and individuals from the “Cerrado-Pantanal” and “Bolivia” lineages generally darker than the “Amazon” and “Madeira” lineages. However, individuals of a given size in different lineages overlap greatly in colour patterns and colour alone could not be used to distinguish lineages. The Natterer’s hypothesis of head-colour as diagnose from “Cerrado-Pantanal” lineage, cannot be completely accepted according our quantitative analysis, although there are a variation in the geographic distribution of these phenotypic traits, and the “Cerrado-Pantanal” lineage had been the most distinct among the lineages.

In this paper we propose a highly efficient novel algorithm named Automatic Feedback Error-Correcting Color-Weave Pattern Recognition algorithm (AFEC algorithm). This algorithm is capable of simultaneously recognizing the color and weave pattern of yarn dyed fabric. The AFEC algorithm consists of three main components: 1. Color pattern recognition, 2. Weave pattern recognition, and 3. Feedback error correction. The last two each include one additional sub-algorithm, namely, the Infill algorithm and the Rectification algorithm. The first component focuses mainly on using the simplest method to reduce the time demand of color pattern recognition. With this objective we have adopted an X-means clustering algorithm which has less time complexity than other common algorithms used in this field. Furthermore, since the detection of the yarn edge and color classification in this component are designed to be independent of one another, to save time they can be run in parallel. In the second component weave pattern is detected, based on the color pattern obtained in the first component. In the second component the Infill algorithm can identify the logic embedded in the incomplete weave pattern, and hence fill in the gaps to form a complete pattern. By contrasting the color and weave patterns of the fabric, the third and final component uses a Rectification algorithm to correct errors in the recognition of color and weave pattern that may have occurred in the earlier components. Theoretical analysis, and experiments conducted during the present study, indicate that without prior knowledge the AFEC algorithm can improve the accuracy and runtime required for recognizing the color and weave pattern of yarn-dyed fabrics.

Color variation is one of the most obvious examples of variation in nature, but biologically meaningful quantification and interpretation of variation in color and complex patterns are challenging. Many current methods for assessing variation in color patterns classify color patterns using categorical measures and provide aggregate measures that ignore spatial pattern, or both, losing potentially important aspects of color pattern.Here, we present Colormesh, a novel method for analyzing complex color patterns that offers unique capabilities. Our approach is based on unsupervised color quantification combined with geometric morphometrics to identify regions of putative spatial homology across samples, from histology sections to whole organisms. Colormesh quantifies color at individual sampling points across the whole sample.We demonstrate the utility of Colormesh using digital images of Trinidadian guppies (Poecilia reticulata), for which the evolution of color has been frequently studied. Guppies have repeatedly evolved in response to ecological differences between up‐ and downstream locations in Trinidadian rivers, resulting in extensive parallel evolution of many phenotypes. Previous studies have, for example, compared the area and quantity of discrete color (e.g., area of orange, number of black spots) between these up‐ and downstream locations neglecting spatial placement of these areas. Using the Colormesh pipeline, we show that patterns of whole‐animal color variation do not match expectations suggested by previous work.Colormesh can be deployed to address a much wider range of questions about color pattern variation than previous approaches. Colormesh is thus especially suited for analyses that seek to identify the biologically important aspects of color pattern when there are multiple competing hypotheses or even no a priori hypotheses at all.

BackgroundBody color and coloration patterns are important phenotypic traits to maintain survival and reproduction activities. The Oujiang color varieties of common carp (Cyprinus carpio var. color), with a narrow distribution in Zhejiang Province of China and a history of aquaculture for over 1,200 years, consistently exhibit a variety of body color patterns. The molecular mechanism underlying diverse color patterns in these variants is unknown. To the practical end, it is essential to develop molecular markers that can distinguish different phenotypes and assist selective breeding.Methodology/Principal FindingsIn this exploratory study, we conducted Roche 454 transcriptome sequencing of two pooled skin tissue samples of Oujiang common carp, which correspond to distinct color patterns, red with big black spots (RB) and whole white (WW), and a total of 737,525 sequence reads were generated. The reads obtained in this study were co-assembled jointly with common carp Roche 454 sequencing reads downloaded from NCBI SRA database, resulting in 43,923 isotigs and 546,676 singletons. Over 31 thousand (31,445; 71.6%) isotigs were found with significant BLAST matches (E<1e-10) to the nr protein database, which corresponds to 12,597 annotated zebrafish genes. A total of 70,947 isotigs and singletons (transcripts) were annotated with Gene Ontology, and 60,221 transcripts were found with corresponding EC numbers. Out of 145 zebrafish pigmentation genes, orthologs for 117 were recovered in Oujiang color carp transcriptome, including 18 found only among singletons. Our transcriptome analysis revealed over 52,902 SNPs in Oujiang common carp, and identified 63 SNP markers that are putatively unique either for RB or WW.ConclusionsThe transcriptome of Oujiang color varieties of common carp obtained through this study, along with the pigmentation genes recovered and the color pattern-specific molecular markers developed, will facilitate future research on the molecular mechanism of color patterns and promote aquaculture of Oujiang color varieties of common carp through molecular marker assisted-selective breeding.

Species identification using the characteristics of developmental stages is challenging. However, for insect taxonomy the coloration of larval stages can be an informative feature. The use of live specimens is recommended for this because the color fades in preserved specimens. In this study we examine the possibility of using variation in coloration and color pattern of larvae in order to distinguish between twoground beetlesspecies Epomis dejeani (Dejean, 1831) and Epomis circumscriptus (Duftschmid, 1812). We present an atlas and describe the coloration and body size of the three larval stages of the above species based on live specimens. An identification key is given for the three larval instars of the two Epomis species.The first instar larvae of the two Epomis species can be easily distinguished based on their color. From the second instar on, the variability in coloration and color patterns increases, creating an overlap in these attributes between larvae of the two species. Except for minor differences in color of the antennae and the base of the mandibles, larvae of the two species are indistinguishable at the second and third larval stages. To the best of our knowledge this is the first attempt to use variation in coloration and color pattern in live larvae in order to identify coleopterans. The color atlas of the larvae enables simple separation of the two Epomis species without requiring sophisticated magnifying devices, although it is less straightforward at the second and third larval stages.We found similar body lengths between the two species for all developmental stages, except for third instar larvae prior to pupation. In the two species the difference in larval body length before pupation positively correlated with that of the adult beetles. More than 70% of the adults’ length can be explained by the length of the late third-instar larva; i.e. the large larvae develop into large adults. The larger specimens are the females.

Evolution of aposematism and mimicry in butterflies: Causes, consequences and paradoxes

It has been observed that sympatric bumblebees species assemblages often exhibit similarities in their colour patterns (Plowright & Owen, 1980; Williams, 2007). An attractive suggestion is that this inter-specific similarity in coloration could result from learnt avoidance by avian predators: if a bird learns from adverse experience that a certain colour pattern is associated with a painful sting, it might subsequently generalize this experience to avoiding similar patterns displayed by other bee species, potentially leading aposematic insects to form local mimicry rings (Plowright & Owen, 1980; Williams, 2007). We recently tested this idea with reciprocal transplant experiments using bumblebees in which we compared the worker loss rates of foreign and local colour pattern variants. If local mimicry rings protect the local colour variant, we would expect foreign individuals, with unusual colour patterns, to be exposed to higher predation than local bee populations whose colour patterns should be familiar to local predators (Stelzer et al., 2010). The hypothesis that foragers that differ in coloration from the local native population would suffer higher predation risk was not upheld by our experiments. However, Owen (2014) now disputes the conclusions we draw from our empirical study. Having undertaken a re-analysis of our published data, he proposes a number of additional, alternative hypotheses, as yet unsupported by empirical evidence, to explain the perceived discrepancy between our data and the mimicry ring hypothesis. Owen suggests that if all the additional conditions he outlines apply, our data might be consistent with the mimicry ring hypothesis. Here, we carefully explore Owen’s hypotheses and provide evidence to reject them. Other explanations are therefore needed to explain the apparent convergence of bumblebee colour patterns in certain locations and its impact on predation rates. Insectivorous birds do not initially avoid aposematic insects but swiftly learn to associate visual patterns with aversive reinforcement (Mostler, 1935; Skelhorn & Rowe, 2006; Chittka & Osorio, 2007). Such learnt avoidance has been suggested to explain the observation that bumblebees from different species sometimes appear to display similar colour patterns, even though there is a remarkable diversity in coat colour both within and between bumblebee species (Williams, 2007). Support for this hypothesis requires more than just quantification of bumblebee colour patterns in various locations and an assessment of their apparent similarity from an avian predator’s perspective; it also requires an empirical demonstration that bumblebees with different colour patterns experience differential predation, depending on how similar their appearance is to the predominant local aposematic colour pattern(s). We explored whether diversity in bumblebee colour patterns, found in several locations in which different bee colorations naturally predominate, affects the loss rate of workers during foraging – some of which must be because of predation (Stelzer et al., 2010). However, although we found that there were pronounced differences in loss rates between bumblebees with different colour patterns in all locations tested, the native, local colour patterns did not provide consistently higher safety from being lost during foraging than non-native coloration (Stelzer et al., 2010). Owen (2014) observes that during summer (after fledging), the number of young, inexperienced birds can outnumber older, experienced individuals (King, Farner & Mewaldt, 1965). During this period, one might not expect local aposematic insects to be better protected because naive birds will initially sample all colour patterns equally. Our data allow us to test this hypothesis as two of the experiments were conducted during summer months (July and August in the UK and Germany) and compared loss rates of bees presenting native-like colour patterns with foreign ones (Stelzer et al., 2010). In the UK summer, the loss rate for the native-like colour pattern (Bombus terrestris dalmatinus) was consistently lower than for the non-native pattern (Bombus terrestris canariensis) in both years, though this difference was not statistically significant in our analysis (Stelzer et al., 2010). In Owen’s re-analysis of the same data using a different statistical test, he found a significant advantage for the native-like colour pattern (Owen, 2014) – refuting his own suggestion that there bs_bs_banner Journal of Zoology

To gain a mechanistic understanding of color pattern formation, including molecular and genetic mechanisms, it is necessary to not only describe adult phenotypes, but also to understand color production and pattern formation during embryonic and postembryonic stages. Here, we review the pigment cell mechanisms underlying color production and pattern formation during embryonic development in lizards and snakes to provide a comprehensive pigment-cell–based understanding of color pattern formation. We first focus on different color production mechanisms in terms of epidermal and dermal pigment cell architectures and then discuss the genetic determinants of pattern formation considering both biologically relevant theoretical models and the processes of pigment cell specification, migration, and architecture differentiation. Clarifying the contributions of pigment cells and genetic factors improves our general understanding of reptilian color pattern evolution.

Research Highlight: van den Berg, C. P., Hassler, G., Blomberg, S., Wilson, N., Suchard, M., & Cheney, K. (2025). Diel activity correlates with colour pattern morphology of heterobranch sea slugs. Journal of Animal Ecology, https://doi.org/10.1111/1365-2656.70036. The ecological drivers of colour evolution in marine systems provide an important comparison to studies in terrestrial species that traditionally receive more research attention. However, many studies have historically been limited by lack of (1) standardised colour pattern data across well-resolved phylogenies and (2) methodological approaches that objectively assess colouration as a highly multidimensional trait. In a recent study, van den Berg etal. (2025) combined a novel phylogenetic tree with Quantitative Colour Pattern Analysis (QCPA) to test hypotheses about ecological correlates of colouration in highly charismatic Australian sea slugs. The authors found that diurnal activity was tightly correlated with bold patterning and high contrast of colour, luminance and overall pattern elements, and that a reliable set of 55 colour traits could accurately predict diel activity in nearly 90% of species. These results provide an exciting case study for future analyses of multidimensional colour patterns and advance our understanding of how ecological interactions can shape colour phenotypes that span highly variable signalling environments, especially in marine organisms so profoundly understudied relative to terrestrial taxa.

Alternative mating tactics in males of various taxa are associated with body color, body size, and social status. Chameleons are known for their ability to change body color following immediate environmental or social stimuli. In this study, we examined whether the differential appearance of male common chameleon during the breeding season is indeed an expression of alternative mating tactics. We documented body color of males and used computer vision techniques to classify images of individuals into discrete color patterns associated with seasons, individual characteristics, and social contexts. Our findings revealed no differences in body color and color patterns among males during the non-breeding season. However, during the breeding season males appeared in several color displays, which reflected body size, social status, and behavioral patterns. Furthermore, smaller and younger males resembled the appearance of small females. Consequently, we suggest that long-term color change in males during the breeding season reflects male alternative mating tactics. Upon encounter with a receptive female, males rapidly alter their appearance to that of a specific brief courtship display, which reflects their social status. The females, however, copulated indiscriminately in respect to male color patterns. Thus, we suggest that the differential color patterns displayed by males during the breeding season are largely aimed at inter-male signaling.

Coral reef fishes constitute one of the most diverse assemblages of vertebrates on the planet. Color patterns are known to serve a number of functions including intra- and inter-specific signaling, camouflage, mimicry, and defense. However, the relative importance of these and other factors in shaping color pattern evolution is poorly understood. Here we conduct a comparative phylogenetic analysis of color pattern evolution in the butterflyfishes (Chaetodontidae). Using recently developed tools for quantifying color pattern geometry as well as machine learning approaches, we investigate the tempo of evolution of color pattern elements and test whether ecological variables relating to defense, depth, and social behavior predict color pattern evolution. Butterflyfishes exhibit high diversity in measures of chromatic conspicuousness and the degrees of fine versus gross scale color patterning. Surprisingly, most diversity in color pattern was not predicted by any of the measures of ecology in our study, although we did find a significant but weak relationship between the level of fine scale patterning and some aspects of defensive morphology. We find that the tempo of color pattern diversification in butterflyfishes has increased toward the present and suggest that rapid evolution, presumably in response to evolutionary pressures surrounding speciation and lineage divergence, has effectively decoupled color pattern geometry from some aspects of ecology. Machine learning classification of color pattern appears to rely on a set of features that are weakly correlated with current color pattern geometry descriptors, but that may be better suited for the detection of discrete components of color pattern. A key challenge for future studies lies in determining whether rapid evolution has generally decoupled color patterns from ecology, or whether convergence in function produces convergence in color pattern at phylogenetic scales.