Stable correlation structure among multiple plumage colour traits: can they work as a single signal?

The presence of multiple distinct ornamental traits in the same species is frequently explained by context‐specificity and different information content. However, the expression of multiple ornaments is often correlated, and such traits may therefore function as a single, integrated signal. Delayed use of an integrated signal relative to production requires temporal stability in integration, which has seldom been examined. We used autumn and spring reflectance data from the breast, breast stripe, and crown of great tits (Parus major) to assess the stability and mating implications of colour signal integration, as well as the repeatability of any integrated colour trait and its correlation with condition during moult. We found high levels of stability between seasons, years, sexes, and ages in the correlation patterns of colour measures across the three plumage areas. The first principal component colour axis described joint variation of ultraviolet (UV) reflectance on the crown and the breast stripe, thereby representing an among‐trait UV chroma axis. However, only breast yellow chroma showed condition‐dependence, whereas temporally consistent and significant assortative mating was restricted to crown UV chroma. Our results therefore do not support the idea that the overall UV chroma of the breast stripe and the crown is special in condition‐dependence and repeatability, or that it plays a specific role in mutual sexual selection as an integrated signal. The results show that stable association between display traits is an existing phenomenon. They also indicate that, even in the presence of correlated traits, functional trait integration among these requires further scrutiny. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 114 , 92–108.     

Adaptation in temporally variable environments: stickleback armor in periodically breaching bar‐built estuaries

The evolutionary consequences of temporal variation in selection remain hotly debated. We explored these consequences by studying threespine stickleback in a set of bar‐built estuaries along the central California coast. In most years, heavy rains induce water flow strong enough to break through isolating sand bars, connecting streams to the ocean. New sand bars typically re‐form within a few weeks or months, thereby re‐isolating populations within the estuaries. These breaching events cause severe and often extremely rapid changes in abiotic and biotic conditions, including shifts in predator abundance. We investigated whether this strong temporal environmental variation can maintain within‐population variation while eroding adaptive divergence among populations that would be caused by spatial variation in selection. We used neutral genetic markers to explore population structure and then analysed how stickleback armor traits, the associated genes Eda and Pitx1 and elemental composition (%P) varies within and among populations. Despite strong gene flow, we detected evidence for divergence in stickleback defensive traits and Eda genotypes associated with predation regime. However, this among‐population variation was lower than that observed among other stickleback populations exposed to divergent predator regimes. In addition, within‐population variation was very high as compared to populations from environmentally stable locations. Elemental composition was strongly associated with armor traits, Eda genotype and the presence of predators, thus suggesting that spatiotemporal variation in armor traits generates corresponding variation in elemental phenotypes. We conclude that gene flow, and especially temporal environmental variation, can maintain high levels of within‐population variation while reducing, but not eliminating, among‐population variation driven by spatial environmental variation.     

Morphological and plumage colour variation in the Réunion grey white‐eye (Aves: Zosterops borbonicus): assessing the role of selection

The Réunion grey white‐eye (Zosterops borbonicus), a small passerine endemic to the island of Réunion (Mascarene archipelago), constitutes an extraordinary case of phenotypic variation within a bird species, with conspicuous plumage colour differentiation at a microgeographical scale. To understand whether natural selection could explain such variability, we compared patterns of variation in morphological and plumage colour traits within and among populations. To quantify morphological variation, we used measurements obtained by Frank Gill in the 1960s from 239 individuals collected in 60 localities distributed over the entire island of Réunion. To quantify colour variation, we measured the reflectance spectra of plumage patches of 50 males from a subset of Gill's specimens belonging to the five recognized plumage colour variants and used a visual model to project these colours in an avian‐appropriate, tetrachromatic, colour space. We found that variants occupy different regions of the avian colour space and that between‐variant differences for most plumage patches could be discriminated by the birds. Differences in morphology were also detected, but these were, in general, smaller than colour differences. Overall, we found that variation in both plumage colour and morphology among variants is greater than would be expected if genetic drift alone was responsible for phenotypic divergence. As the plumage colour variants correspond to four geographical forms, our results suggest that phenotypic evolution in the Réunion grey white‐eye is at least partly explained by divergent selection in different habitats or regions. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 459–473.     

Ornamental evolution in Trinidadian guppies (Poecilia reticulata): insights from sensory processing‐based analyses of entire colour patterns

The evolution of exaggerated sexual ornamentation is classically thought to proceed as a compromise between opposing vectors of sexual and natural selection. In colour‐based ornamentation, as exhibited by guppies (Poecilia reticulata), heightened trait expression may be beneficial in promoting attractiveness, but costly in terms of predation. Opportunities to reconcile this compromise will exist if there are differences between conspecifics and predators in their sensory systems; in such situations guppies should evolve to exploit the ways in which their ornamentation would appear maximally conspicuous to conspecifics. In the present study, we addressed this hypothesis via a study of geographic variation employing the most sophisticated colour analysis yet attempted for Trinidadian guppies. We made two paired contrasts, one between two Aripo populations that vary in the presence of the potential predator Aequidens pulcher, and another between Quare and Marianne populations that vary in exposure to a predatory prawn, Macrobrachium crenulatum. We predicted that, if ornamentation is constrained by the presence of either predator, then guppy conspicuousness should change most markedly across each of the two paired populations as viewed by that predator. Although disparity analysis of entire colour patterns indicated significant differences in both contrasts, this prediction was most clearly supported for the Marianne/Quare contrast. Marianne fish, which co‐exist with prawns, exhibited larger black spots coupled with less extensive, less bright flank iridescence. The brightness reductions are notable because, as the only potential guppy predator with a dedicated ultraviolet (UV) photoreceptor, prawns may detect passing male guppies via their UV‐bright blues, violets and ‘UV/oranges’. We discuss our findings in light of the additional insights that might be obtained by combining spectral assessments and visual modeling with more traditional methods of colour pattern appraisal. © 2008 The Linnean Society of London, Biological Journal of the Linnean Society, 2008, 95 , 734–747.     

Female‐limited colour polymorphism in the crab spider Synema globosum (Araneae: Thomisidae)

Conspicuous colour variation, caused by the influence of the environment on phenotype or by genetic differences among individuals, is frequently observed in nature. If genetic in origin, colour variation can facilitate the study of mechanisms that contribute to the maintenance of true polymorphisms. Here we describe, for the first time, the female‐limited colour polymorphism in the crab spider, Synema globosum. We looked for associations between life‐history traits and female colour morph, and identified potential agents of selection that could influence the maintenance of the polymorphism. Our results showed that the polymorphism is discrete and heritable, and that differences in colour among morphs are likely to be detectable by honeybees, birds, and conspecifics. We found limited evidence of differences among morphs in morphology and ecology, and found no differences in components of reproduction. Based on the lines of evidence obtained in this study, we suggest that selection exerted by prey, predators, and/or mates is likely to influence the maintenance of the polymorphism observed in S. globosum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 368–383.     

Defining the colour pattern phenotype in bumble bees (Bombus): a new model for evo devo

Few insects exhibit the striking colour pattern radiation found in bumble bees (Bombus), which have diversified globally into a wide range of colours and patterns. Their potent sting is often advertised by conspicuous bands of contrasting colour commonly mimicked by scores of harmless (Batesian mimics) and noxious species (Müllerian co‐mimics). Despite extensive documentation of colour pattern diversification, next to nothing is known about the genetic regulation of pattern formation in bumble bees, hindering progress toward a more general model of the evolution of colour pattern mimicry. A critical first step in understanding the colour pattern genotype is an unambiguous understanding of the phenotype under selection, which has not been objectively defined in bumble bees. Here, we quantitatively define the principal colour pattern elements that comprise the phenotype array across all species. Matrix analysis of meticulously scored colour patterns of ～95% of described species indicates there are 12 discrete primary ‘ground plan’ elements in common among all species, many of which correspond to segmentation patterning. Additional secondary elements characterize individual species and geographical variants. The boundaries of these elements appear to correspond to expression patterns of Hox genes in Drosophila and Apis but also suggest novel post‐Hox specialization of abdominal patterning. Our findings provide the first foundation for exploring candidate genes regulating adaptive pattern variation in bumble bees and broaden the framework for understanding common genetic mechanisms of pattern evolution in insects. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 384–404.     

Increased juvenile predation is not associated with evolved differences in adult brain size in Trinidadian killifish (Rivulus hartii)

Vertebrates exhibit extensive variation in brain size. The long‐standing assumption is that this variation is driven by ecologically mediated selection. Recent work has shown that an increase in predator‐induced mortality is associated with evolved increases and decreases in brain size. Thus, the manner in which predators induce shifts in brain size remains unclear. Increased predation early in life is a key driver of many adult traits, including life‐history and behavioral traits. Such results foreshadow a connection between age‐specific mortality and selection on adult brain size. Trinidadian killifish, Rivulus hartii, are found in sites with and without guppies, Poecilia reticulata. The densities of Rivulus drop dramatically in sites with guppies because guppies prey upon juvenile Rivulus. Previous work has shown that guppy predation is associated with the evolution of adult life‐history traits in Rivulus. In this study, we compared second‐generation laboratory‐born Rivulus from sites with and without guppies for differences in brain size and associated trade‐offs between brain size and other components of fitness. Despite the large amount of existing research on the importance of early‐life events on the evolution of adult traits, and the role of predation on both behavior and brain size, we did not find an association between the presence of guppies and evolutionary shifts in Rivulus brain size. Such results argue that increased rates of juvenile mortality may not alter selection on adult brain size.     

Spatial processes and evolutionary models: a critical review

Evolution is a fundamentally population level process in which variation, drift and selection produce both temporal and spatial patterns of change. Statistical model fitting is now commonly used to estimate which kind of evolutionary process best explains patterns of change through time using models like Brownian motion, stabilizing selection (Ornstein–Uhlenbeck) and directional selection on traits measured from stratigraphic sequences or on phylogenetic trees. But these models assume that the traits possessed by a species are homogeneous. Spatial processes such as dispersal, gene flow and geographical range changes can produce patterns of trait evolution that do not fit the expectations of standard models, even when evolution at the local‐population level is governed by drift or a typical OU model of selection. The basic properties of population level processes (variation, drift, selection and population size) are reviewed and the relationship between their spatial and temporal dynamics is discussed. Typical evolutionary models used in palaeontology incorporate the temporal component of these dynamics, but not the spatial. Range expansions and contractions introduce rate variability into drift processes, range expansion under a drift model can drive directional change in trait evolution, and spatial selection gradients can create spatial variation in traits that can produce long‐term directional trends and punctuation events depending on the balance between selection strength, gene flow, extirpation probability and model of speciation. Using computational modelling that spatial processes can create evolutionary outcomes that depart from basic population‐level notions from these standard macroevolutionary models.     

Müllerian mimicry of a quantitative trait despite contrasting levels of genomic divergence and selection

Hybrid zones, where distinct populations meet and interbreed, give insight into how differences between populations are maintained despite gene flow. Studying clines in genetic loci and adaptive traits across hybrid zones is a powerful method for understanding how selection drives differentiation within a single species, but can also be used to compare parallel divergence in different species responding to a common selective pressure. Here, we study parallel divergence of wing colouration in the butterflies Heliconius erato and H. melpomene, which are distantly related Müllerian mimics which show parallel geographic variation in both discrete variation in pigmentation, and quantitative variation in structural colour. Using geographic cline analysis, we show that clines in these traits are positioned in roughly the same geographic region for both species, which is consistent with direct selection for mimicry. However, the width of the clines varies markedly between species. This difference is explained in part by variation in the strength of selection acting on colour traits within each species, but may also be influenced by differences in the dispersal rate and total strength of selection against hybrids between the species. Genotyping‐by‐sequencing also revealed weaker population structure in H. melpomene, suggesting the hybrid zones may have evolved differently in each species, which may also contribute to the patterns of phenotypic divergence in this system. Overall, we conclude that multiple factors are needed to explain patterns of clinal variation within and between these species, although mimicry has probably played a central role.     

Sexual selection as a promoter of population divergence in male phenotypic characters: a study on mainland and islet lizard populations

Sexual selection is often viewed as a promoter of population divergence, although some forms of sexual selection could rather hamper divergence. In the present study, we investigated whether sexual selection promotes divergence in sexually‐selected traits. We studied population variation in sexual selection in relation to colour morph and body size in islet and mainland populations of the Skyros wall lizard (Podarcis gaigeae). Females were most likely to mate with orange‐throated males with small body sizes, and male body size and coloration were therefore subject to correlational sexual selection. By contrast, male mating probabilities were not affected by any female phenotypic character. We also found variation in a female resistance trait (escape propensity), with females being more prone to escape when exposed to males from other habitats. Sexual selection could potentially affect the frequencies of throat colour morphs in this species by favouring orange‐throated males of small body size, although there was no evidence of sexual selection for local mates or rare phenotypes. The results obtained in the present study thus do not support a role for sexual selection as a promoter of population divergence in this species. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 374–389.     

Fecundity selection does not vary along a large geographical cline of trait means in a passerine bird

Local environmental and ecological conditions are commonly expected to result in local adaptation, although there are few examples of variation in phenotypic selection across continent‐wide spatial scales. We collected standardized data on selection with respect to the highly variable plumage coloration of pied flycatcher (Ficedula hypoleuca Pall.) males from 17 populations across the species' breeding range. The observed selection on multiple male coloration traits via the annual number of fledged young was generally relatively weak. The main aim of the present study, however, was to examine whether the current directional selection estimates are associated with distance to the sympatric area with the collared flycatcher (Ficedula albicollis Temminck), a sister species with which the pied flycatcher is showing character displacement. This pattern was expected because plumage traits in male pied flycatchers are changing with the distance to these areas of sympatry. However, we did not find such a pattern in current selection on coloration. There were no associations between current directional selection on ornamentation and latitude or longitude either. Interestingly, current selection on coloration traits was not associated with the observed mean plumage traits of the populations. Thus, there do not appear to be geographical gradients in current directional fecundity selection on male plumage ornamentation. The results of the present study do not support the idea that constant patterns in directional fecundity selection would play a major role in the maintenance of coloration among populations in this species. By contrast, the tendency for relatively weak mosaic‐like variation in selection among populations could reflect just a snapshot of temporally variable, potentially environment‐dependent, selection, as suggested by other studies in this system. Such fine‐grained variable selection coupled with gene flow could maintain extensive phenotypic variation across populations. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 808–827.     

EVOLUTION OF VARIATION AND VARIABILITY UNDER FLUCTUATING,STABILIZING, AND DISRUPTIVE SELECTION

How variation and variability (the capacity to vary) may respond to selection remain open questions. Indeed, effects of different selection regimes on variational properties, such as canalization and developmental stability are under debate. We analyzed the patterns of among‐ and within‐individual variation in two wing‐shape characters in populations of Drosophila melanogaster maintained under fluctuating, disruptive, and stabilizing selection for more than 20 generations. Patterns of variation in wing size, which was not a direct target of selection, were also analyzed. Disruptive selection dramatically increased phenotypic variation in the two shape characters, but left phenotypic variation in wing size unaltered. Fluctuating and stabilizing selection consistently decreased phenotypic variation in all traits. In contrast, within‐individual variation, measured by the level of fluctuating asymmetry, increased for all traits under all selection regimes. These results suggest that canalization and developmental stability are evolvable and presumably controlled by different underlying genetic mechanisms, but the evolutionary responses are not consistent with an adaptive response to selection on variation. Selection also affected patterns of directional asymmetry, although inconsistently across traits and treatments.     

Plasticity and evolution in correlated suites of traits

When organisms are faced with new or changing environments, a central challenge is the coordination of adaptive shifts in many different phenotypic traits. Relationships among traits may facilitate or constrain evolutionary responses to selection, depending on whether the direction of selection is aligned or opposed to the pattern of trait correlations. Attempts to predict evolutionary potential in correlated traits generally assume that correlations are stable across time and space; however, increasing evidence suggests that this may not be the case, and flexibility in trait correlations could bias evolutionary trajectories. We examined genetic and environmental influences on variation and covariation in a suite of behavioural traits to understand if and how flexibility in trait correlations influences adaptation to novel environments. We tested the role of genetic and environmental influences on behavioural trait correlations by comparing Trinidadian guppies (Poecilia reticulata) historically adapted to high‐ and low‐predation environments that were reared under native and non‐native environmental conditions. Both high‐ and low‐predation fish exhibited increased behavioural variance when reared under non‐native vs. native environmental conditions, and rearing in the non‐native environment shifted the major axis of variation among behaviours. Our findings emphasize that trait correlations observed in one population or environment may not predict correlations in another and that environmentally induced plasticity in correlations may bias evolutionary divergence in novel environments.     

Ecological genomics in full colour

Colour patterns in animals have long offered an opportunity to observe adaptive traits in natural populations. Colour plays myriad roles in interactions within and among species, from reproductive signalling to predator avoidance, leading to multiple targets of natural and sexual selection and opportunities for diversification. Understanding the genetic and developmental underpinnings of variation in colour promises a fuller understanding of these evolutionary processes, but the path to unravelling these connections can be arduous. The advent of genomic techniques suitable for nonmodel organisms is now beginning to light the way. Two new studies in this issue of Molecular Ecology use genomic sequencing of laboratory crosses to map colour traits in cichlid fishes, a remarkably diverse group in which coloration has played a major role in diversification. They illustrate how genomic approaches, specifically RAD sequencing, can rapidly identify both simple and more complex genetic variation underlying ecologically important traits. In the first, Henning et al. ( 2014 ) detect a single locus that appears to control in a Mendelian fashion the presence of horizontal stripes, a trait that has evolved in numerous cichlid lineages. In the second, Albertson et al. ( 2014 ) identify several genes and epistatic interactions affecting multiple colour traits, as well as a novel metric describing integration across colour traits. Albertson et al. ( 2014 ) go further, by quantifying differential expression of parental alleles at a candidate locus and by relating differentiation among natural populations at mapped loci to trait divergence. Herein lies the promise of ecological genomics – efficiently integrating genetic mapping of phenotypes with population genomic data to both identify functional genes and unravel their evolutionary history. These studies offer guidance on how genomic techniques can be tailored to a research question or study system, and they also add to the growing body of empirical examples addressing basic questions about how ecologically important traits evolve in natural populations.     

The static allometry of sexual and nonsexual traits in vervet monkeys

Sexual traits vary tremendously in static allometry. This variation may be explained in part by body size‐related differences in the strength of selection. We tested this hypothesis in two populations of vervet monkeys, using estimates of the level of condition dependence for different morphological traits as a proxy for body size‐related variation in the strength of selection. In support of the hypothesis, we found that the steepness of allometric slopes increased with the level of condition dependence. One trait of particular interest, the penis, had shallow allometric slopes and low levels of condition dependence, in agreement with one of the most consistent patterns yet detected in the study of allometry, namely that of genitalia exhibiting shallow allometries. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 527–537.     

Effect of migration and environmental heterogeneity on the maintenance of quantitative genetic variation: a simulation study

The paradox of high genetic variation observed in traits under stabilizing selection is a long‐standing problem in evolutionary theory, as mutation rates appear too low to explain observed levels of standing genetic variation under classic models of mutation–selection balance. Spatially or temporally heterogeneous environments can maintain more standing genetic variation within populations than homogeneous environments, but it is unclear whether such conditions can resolve the above discrepancy between theory and observation. Here, we use individual‐based simulations to explore the effect of various types of environmental heterogeneity on the maintenance of genetic variation (V_A) for a quantitative trait under stabilizing selection. We find that V_A is maximized at intermediate migration rates in spatially heterogeneous environments and that the observed patterns are robust to changes in population size. Spatial environmental heterogeneity increased variation by as much as 10‐fold over mutation–selection balance alone, whereas pure temporal environmental heterogeneity increased variance by only 45% at max. Our results show that some combinations of spatial heterogeneity and migration can maintain considerably more variation than mutation–selection balance, potentially reconciling the discrepancy between theoretical predictions and empirical observations. However, given the narrow regions of parameter space required for this effect, this is unlikely to provide a general explanation for the maintenance of variation. Nonetheless, our results suggest that habitat fragmentation may affect the maintenance of V_A and thereby reduce the adaptive capacity of populations.     

Parallel phenotypic evolution in a wolf spider radiation on Galápagos

Within island archipelagos, repeated ecological settings may lead to radiations wherein similar niches are recurrently occupied. Although it has been shown that species with common habitat requirements share particular traits, it remains relatively unexplored to what extent this may lead to the repeated evolution of almost identical phenotypes (phenocopies) and how this correlates with traits subjected to sexual selection. Exploring divergence patterns of ecological and sexual relevant traits within spiders seem promising to enhance our understanding of the relative role of natural and sexual selection. Here, we conduct a detailed morphological analysis on a large set of genital and non‐genital traits (morphometrics, colour pattern) within a radiation of the wolf spider genus Hogna Simon, 1885 on Galápagos and interpret these data, taking into account their known phylogenetic relationship. Our results show that recurrent environmental gradients have led to the parallel evolution of almost identical phenotypes, which not only proves that natural selection has driven morphological divergence, but also suggests that a similar genetic or developmental basis most likely underlies this divergence. Among‐species variation in genital traits in contrast rather reflects the phylogenetic relationships on Santa Cruz and San Cristóbal. The combination of these data indicate that speciation in this system is driven by the combined effect of ecological mechanisms and allopatric divergence in sexual traits. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 123–136.     

Disentangling the effects of intraspecies variability,phylogeny, space,and climate on the evolution of shell morphology in endemic Greek land snails of the genus Codringtonia

Extensive variation in land snail shell morphology has been widely documented, although few studies have attempted to investigate the ecological and evolutionary drivers of this variation. Within a comparative phylogenetic framework, we investigated the temporal and spatial evolution of the shell morphology of the Greek endemic land snail genus Codringtonia. The contribution of both inter‐ and intraspecies shell differentiation in the overall shell variability is assessed. The effect of climate, space, and evolutionary history on the shell variability was inferred using a variance partitioning framework. For Codringtonia species, intraspecies divergence of shell traits contributes substantially to the overall shell variability. By decomposing this variability, it was shown that the overall shell size of Codringtonia clades is phylogenetically constrained, related to early speciation events, and strongly affected by large‐scale spatial variability (latitudinal gradient). The effect of climate on shell size cannot be disentangled from phylogeny and space. Shell and, to a larger extent, aperture shape are not phylogenetically constrained, and appear to be mostly related to conspecific populations divergence events. Shell shape is substantially explained by both climate and space that greatly overlap. Aperture shape is mainly interpreted by medium to small‐scale spatial variables. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 796–813.     

Clinal colour variation within a panmictic population of tree squirrels,Tamiasciurus douglasii (Rodentia: Sciuridae), across an ecological gradient

Local adaptation occurs when a population in a heterogeneous environment experiences divergent ecological selection but only if selection is stronger than the homogenizing effects of gene flow. The forest environments of Oregon vary along a physical and biotic gradient from a wet, closed‐canopy forest near the coast to a drier open‐canopy forest eastward across the Cascade Mountains. The present study explores patterns of local adaptation in Douglas squirrels (Tamiasciurus douglasii) in relation to these transitions in forest structure and ecology. We test for the presence of morphological clines in relation to gene flow and, more specifically, whether any such character clines correspond with environmental clines. We sampled animals at six locations (10 specimens each) and evaluated environmental parameters across a 240‐km west‐to‐east transect. Population structure analysis of 18 microsatellite loci indicates a single, panmictic squirrel population across the entire transect. Coalescent‐based estimates show bidirectional gene flow at similar west–east intensities between squirrels in coastal and interior forests. Of the four skull traits examined, none shows a significant clinal transition. By contrast, ventral fur colour shows a strong clinal transition, from deep‐orange in coastal forest to whitish–yellow in the interior forest. This pattern of phenotypic divergence coincides with the gradient in tree‐canopy cover. Ventral fur colour of T. douglasii exemplifies a gradation of continuous phenotypic variation maintained despite ongoing gene flow in a panmictic population. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 113 , 536–546.     

Age,sex and beauty: methodological dependence of age‐ and sex‐dichromatism in the great tit Parus major

Carotenoid‐based colour expression is frequently involved in sexual dichromatism, particularly in bird plumage, suggesting a role in sexual selection. Despite much work on expression of the carotenoid‐based ventral plumage coloration of the great tit (Parus major), which represents a popular model in evolution and ecology, a consensus on even the most basic demographic patterns of variation (e.g. age and sex differences) is lacking. This may reflect the use of variable methods for analysing colour variation, although what is not clear, either in this case or in general, is the extent to which these alternative methods are equally effective at describing age‐ and sex‐related dichromatism. Using data obtained over 4 years from a large sample of free‐ranging great tits, we examined how colour‐scoring methodology influences estimates of age‐ and sex‐related dichromatism. We compare: (1) principal components analysis‐derived scores; (2) tristimulus colour variables; (3) a visual model‐independent, carotenoid‐focussed colour score; and (4) two colour scoring methods based on avian visual models, examining how they assess colour variation with respect to age and sex to determine how methodology may influence results. We demonstrate clear age‐ and sex‐dependent expression of this colour trait, both in our own data and in meta‐analyses of results from great tit populations across Europe, and discuss the merits of the various colour scores, which yield very different estimates of the extent of age‐ and sex‐dependent dichromatism. We show variation is likely to be visible to conspecifics and propose a novel, visual model‐derived scoring system for describing variation in carotenoid‐based colour patches, where the perceived signal is divided into independent chromatic and achromatic components, in line with current understanding of visual perception. The present study highlights the impact of colour‐scoring methodology and shows that, as novel measures continue to be developed, researchers should consider carefully how they quantify colour expression. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 101 , 777–796.