scholarly journals Quantitative Colour Pattern Analysis (QCPA): A Comprehensive Framework for the Analysis of Colour Patterns in Nature

2019 ◽  
Author(s):  
Cedric P. van den Berg ◽  
Jolyon Troscianko ◽  
John A. Endler ◽  
N. Justin Marshall ◽  
Karen L. Cheney
Keyword(s):  
Pattern Analysis ◽  
Digital Photography ◽  
Colour Pattern ◽  
Strength Analysis ◽  
List Type ◽  
Spatial Acuity ◽  
Visual Contrast ◽  
Colour Patterns ◽  
User Friendly ◽  
Receptor Noise

AbstractTo understand the function of colour signals in nature, we require robust quantitative analytical frameworks to enable us to estimate how animal and plant colour patterns appear against their natural background as viewed by ecologically relevant species. Due to the quantitative limitations of existing methods, colour and pattern are rarely analysed in conjunction with one another, despite a large body of literature and decades of research on the importance of spatiochromatic colour pattern analyses. Furthermore, key physiological limitations of animal visual systems such as spatial acuity, spectral sensitivities, photoreceptor abundances and receptor noise levels are rarely considered together in colour pattern analyses.Here, we present a novel analytical framework, called the ‘Quantitative Colour Pattern Analysis’ (QCPA). We have overcome many quantitative and qualitative limitations of existing colour pattern analyses by combining calibrated digital photography and visual modelling. We have integrated and updated existing spatiochromatic colour pattern analyses, including adjacency, visual contrast and boundary strength analysis, to be implemented using calibrated digital photography through the ‘Multispectral Image Analysis and Calibration’ (MICA) Toolbox.This combination of calibrated photography and spatiochromatic colour pattern analyses is enabled by the inclusion of psychophysical colour and luminance discrimination thresholds for image segmentation, which we call ‘Receptor Noise Limited Clustering’, used here for the first time. Furthermore, QCPA provides a novel psycho-physiological approach to the modelling of spatial acuity using convolution in the spatial or frequency domains, followed by ‘Receptor Noise Limited Ranked Filtering’ to eliminate intermediate edge artefacts and recover sharp boundaries following smoothing. We also present a new type of colour pattern analysis, the ‘Local Edge Intensity Analysis’ (LEIA) as well as a range of novel psycho-physiological approaches to the visualisation of spatiochromatic data.QCPA combines novel and existing pattern analysis frameworks into what we hope is a unified, user-friendly, free and open source toolbox and introduce a range of novel analytical and data-visualisation approaches. These analyses and tools have been seamlessly integrated into the MICA toolbox providing a dynamic and user-friendly workflow.QCPA is a framework for the empirical investigation of key theories underlying the design, function and evolution of colour patterns in nature. We believe that it is compatible with, but more thorough than, other existing colour pattern analyses.

scholarly journals Boundary Strength Analysis: Combining colour pattern geometry and coloured patch visual properties for use in predicting behaviour and fitness

2018 ◽  
Author(s):  
John A. Endler ◽  
Gemma L. Cole ◽  
Alexandrea Kranz
Keyword(s):  
Poecilia Reticulata ◽  
Colour Pattern ◽  
Strength Analysis ◽  
Noise Estimate ◽  
Darwinian Fitness ◽  
The Mean ◽  
Colour Patterns ◽  
Visual Properties ◽  
Colour Patch ◽  
Boundary Strength

AbstractColour patterns are used by many species to make decisions that ultimately affect their Darwinian fitness. Colour patterns consist of a mosaic of patches that differ in geometry and visual properties. Although traditionally pattern geometry and colour patch visual properties are analysed separately, these components are likely to work together as a functional unit. Despite this, the combined effect of patch visual properties, patch geometry, and the effects of the patch boundaries on animal visual systems, behaviour and fitness are relatively unexplored. Here we describe Boundary Strength Analysis (BSA), a novel way to combine the geometry of the edges (boundaries among the patch classes) with the receptor noise estimate (ΔS) of the intensity of the edges. The method is based upon known properties of vertebrate and invertebrate retinas. The mean and SD of ΔS (mΔS, sΔS) of a colour pattern can be obtained by weighting each edge class ΔS by its length, separately for chromatic and achromatic ΔS. This assumes those colour patterns, or parts of the patterns used in signalling, with larger mΔS and sΔS are more stimulating and hence more salient to the viewers. BSA can be used to examine both colour patterns and visual backgrounds. BSA was successful in assessing the estimated conspicuousness of colour pattern variants in two species, guppies (Poecilia reticulata) and Gouldian finches (Erythrura gouldiae), both polymorphic for patch colour, luminance and geometry. The pattern difference between chromatic and achromatic edges in both species reveals the possibility that chromatic and achromatic edges could function differently. BSA can be applied to any colour pattern used in intraspecific and interspecific behaviour. Seven predictions and four questions about colour patterns are presented.

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

2019 ◽  
Vol 11 (2) ◽  
pp. 316-332 ◽  
Author(s):  
Cedric P. van den Berg ◽  
Jolyon Troscianko ◽  
John A. Endler ◽  
N. Justin Marshall ◽  
Karen L. Cheney
Keyword(s):  
Pattern Analysis ◽  
Colour Pattern ◽  
Colour Patterns ◽  
Comprehensive Framework

scholarly journals Dog colour patterns explained by modular promoters of ancient canid origin

2021 ◽  
Author(s):  
Danika L. Bannasch ◽  
Christopher B. Kaelin ◽  
Anna Letko ◽  
Robert Loechel ◽  
Petra Hug ◽  
...  
Keyword(s):  
Colour Pattern ◽  
Hair Cycle ◽  
Temporal And Spatial Distribution ◽  
Multiple Alleles ◽  
Haplotype Combination ◽  
Regulatory Modules ◽  
Regulatory Module ◽  
Temporal And Spatial ◽  
Selection For ◽  
Colour Patterns

AbstractDistinctive colour patterns in dogs are an integral component of canine diversity. Colour pattern differences are thought to have arisen from mutation and artificial selection during and after domestication from wolves but important gaps remain in understanding how these patterns evolved and are genetically controlled. In other mammals, variation at the ASIP gene controls both the temporal and spatial distribution of yellow and black pigments. Here, we identify independent regulatory modules for ventral and hair cycle ASIP expression, and we characterize their action and evolutionary origin. Structural variants define multiple alleles for each regulatory module and are combined in different ways to explain five distinctive dog colour patterns. Phylogenetic analysis reveals that the haplotype combination for one of these patterns is shared with Arctic white wolves and that its hair cycle-specific module probably originated from an extinct canid that diverged from grey wolves more than 2 million years ago. Natural selection for a lighter coat during the Pleistocene provided the genetic framework for widespread colour variation in dogs and wolves.

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

2020 ◽  
Author(s):  
Adélaïde Sibeaux ◽  
Thomas Camduras ◽  
John A Endler
Keyword(s):  
Mate Choice ◽  
Coefficient Of Variation ◽  
Color Pattern ◽  
Strength Analysis ◽  
Visual Contrast ◽  
Female Preferences ◽  
Signal Amplifier ◽  
Polymorphic Species ◽  
Adjacent Patch

Abstract 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.

scholarly journals Stabilizing selection on individual pattern elements of aposematic signals

2017 ◽  
Vol 284 (1861) ◽  
pp. 20170926 ◽  
Author(s):  
Anne E. Winters ◽  
Naomi F. Green ◽  
Nerida G. Wilson ◽  
Martin J. How ◽  
Mary J. Garson ◽  
...  
Keyword(s):  
Pattern Analysis ◽  
Marine Organism ◽  
Warning Signal ◽  
Colour Pattern ◽  
Stabilizing Selection ◽  
Warning Signals ◽  
Fish Predator ◽  
Selection For ◽  
Aposematic Signals ◽  
Behavioural Experiments

Warning signal variation is ubiquitous but paradoxical: low variability should aid recognition and learning by predators. However, spatial variability in the direction and strength of selection for individual elements of the warning signal may allow phenotypic variation for some components, but not others. Variation in selection may occur if predators only learn particular colour pattern components rather than the entire signal. Here, we used a nudibranch mollusc, Goniobranchus splendidus , which exhibits a conspicuous red spot/white body/yellow rim colour pattern, to test this hypothesis. We first demonstrated that secondary metabolites stored within the nudibranch were unpalatable to a marine organism. Using pattern analysis, we demonstrated that the yellow rim remained invariable within and between populations; however, red spots varied significantly in both colour and pattern. In behavioural experiments, a potential fish predator, Rhinecanthus aculeatus , used the presence of the yellow rims to recognize and avoid warning signals. Yellow rims remained stable in the presence of high genetic divergence among populations. We therefore suggest that how predators learn warning signals may cause stabilizing selection on individual colour pattern elements, and will thus have important implications on the evolution of warning signals.

Molecular phylogeny of Clibanarius Dana, 1852 from the Indo-West Pacific: evolution of pereopod colour pattern and habitat adaptation

Crustaceana ◽  
2019 ◽  
Vol 92 (7) ◽  
pp. 799-839 ◽  
Author(s):  
Akihiro Yoshikawa ◽  
Kazuho Ikeo ◽  
Junichi Imoto ◽  
Wachirah Jaingam ◽  
Lily Surayya Eka Putri ◽  
...  
Keyword(s):  
Histone H3 ◽  
Hermit Crabs ◽  
Colour Pattern ◽  
12S Rrna ◽  
Habitat Adaptation ◽  
Soft Sediments ◽  
Mitochondrial 12S Rrna ◽  
Nuclear Histone ◽  
Colour Patterns ◽  
Hard Substrates

Abstract Species of hermit crabs in the genus Clibanarius Dana, 1852 have adapted to various environments in the intertidal areas, including hard substrates and soft sediments. These species often bear a close morphological resemblance to each other, therefore, the colouration on the pereopods can be one of the reliable characteristics to distinguish the species. However, the evolutionary relationships among species with different colour patterns and relationships between colour patterns and habitat adaptation have not previously been investigated. Therefore, we reconstructed the phylogenetic relationships among 19 species of Clibanarius based on mitochondrial [12S rRNA, 16S rRNA and cytochrome oxidase I] and nuclear [histone H3] DNA markers. The results suggest that the striped and solid colour elements have evolved multiple times independently, with the ancestral colour pattern potentially being scattered, bright colour spots with a bright colour band. Our findings also suggest that evolutionary adaptation from hard substrates to mudflats and soft sediments may have occurred at least twice.

scholarly journals Sexually dimorphic dorsal coloration in a jumping spider: testing a potential case of sex-specific mimicry

2021 ◽  
Vol 8 (6) ◽  
pp. 210308
Author(s):  
Collette Cook ◽  
Erin C. Powell ◽  
Kevin J. McGraw ◽  
Lisa A. Taylor
Keyword(s):  
Colour Pattern ◽  
Sexually Dimorphic ◽  
Sham Control ◽  
Jumping Spider ◽  
Negative Results ◽  
Potential Case ◽  
Opposite Sex ◽  
Colour Patterns ◽  
Hymenopteran Insects ◽  
Predation Rates

To avoid predation, many animals mimic behaviours and/or coloration of dangerous prey. Here we examine potential sex-specific mimicry in the jumping spider Habronattus pyrrithrix . Previous work proposed that males' conspicuous dorsal coloration paired with characteristic leg-waving (i.e. false antennation) imperfectly mimics hymenopteran insects (e.g. wasps and bees), affording protection to males during mate-searching and courtship. By contrast, less active females are cryptic and display less leg-waving. Here we test the hypothesis that sexually dimorphic dorsal colour patterns in H. pyrrithrix are most effective when paired with sex-specific behaviours. We manipulated spider dorsal coloration with makeup to model the opposite sex and exposed them to a larger salticid predator ( Phidippus californicus ). We predicted that males painted like females should suffer higher predation rates than sham-control males. Likewise, females painted like males should suffer higher predation rates than sham-control females. Contrary to expectations, spiders with male-like coloration were attacked more than those with female-like coloration, regardless of their actual sex. Moreover, males were more likely to be captured, and were captured sooner, than females (regardless of colour pattern). With these unexpected negative results, we discuss alternative functional hypotheses for H. pyrrithrix colours, as well as the evolution of defensive coloration generally.

scholarly journals FIREcaller: Detecting Frequently Interacting Regions from Hi-C Data

2019 ◽  
Author(s):  
Cheynna Crowley ◽  
Yuchen Yang ◽  
Yunjiang Qiu ◽  
Benxia Hu ◽  
Armen Abnousi ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Spatial Organization ◽  
R Package ◽  
Specific Gene ◽  
List Type ◽  
Cell Type ◽  
R Software ◽  
Computational Tools ◽  
Cell Type Specific ◽  
User Friendly

AbstractHi-C experiments have been widely adopted to study chromatin spatial organization, which plays an essential role in genome function. We have recently identified frequently interacting regions (FIREs) and found that they are closely associated with cell-type-specific gene regulation. However, computational tools for detecting FIREs from Hi-C data are still lacking. In this work, we present FIREcaller, a stand-alone, user-friendly R package for detecting FIREs from Hi-C data. FIREcaller takes raw Hi-C contact matrices as input, performs within-sample and cross-sample normalization, and outputs continuous FIRE scores, dichotomous FIREs, and super-FIREs. Applying FIREcaller to Hi-C data from various human tissues, we demonstrate that FIREs and super-FIREs identified, in a tissue-specific manner, are closely related to gene regulation, are enriched for enhancer-promoter (E-P) interactions, tend to overlap with regions exhibiting epigenomic signatures of cis-regulatory roles, and aid the interpretation or GWAS variants. The FIREcaller package is implemented in R and freely available at https://yunliweb.its.unc.edu/FIREcaller.Highlights– Frequently Interacting Regions (FIREs) can be used to identify tissue and cell-type-specific cis-regulatory regions.– An R software, FIREcaller, has been developed to identify FIREs and clustered FIREs into super-FIREs.

scholarly journals Scrapie-resistant sheep show certain coat colour characteristics

2009 ◽  
Vol 91 (1) ◽  
pp. 39-46 ◽  
Author(s):  
R. M. SAWALHA ◽  
L. BELL ◽  
S. BROTHERSTONE ◽  
I. WHITE ◽  
A. J. WILSON ◽  
...  
Keyword(s):  
Maximum Likelihood ◽  
Linear Model ◽  
Morphological Diversity ◽  
Coat Colour ◽  
Unintended Consequences ◽  
Colour Pattern ◽  
Reverse Pattern ◽  
Colour Patterns ◽  
Log Linear ◽  
The Relationship

SummarySusceptibility to scrapie is known to be associated with polymorphisms at the prion protein (PrP) gene, and this association is the basis of current selective programmes implemented to control scrapie in many countries. However, these programmes might have unintended consequences for other traits that might be associated withPrPgenotype. The objective of this study was to investigate the relationship betweenPrPgenotype and coat colour characteristics in two UK native sheep breeds valued for their distinctive coat colour patterns. Coat colour pattern, darkness and spotting andPrPgenotype records were available for 11 674 Badgerfaced Welsh Mountain and 2338 Shetland sheep. The data were analysed with a log–linear model using maximum likelihood. Results showed a strong significant association ofPrPgenotype with coat colour pattern in Badgerfaced Welsh Mountain and Shetland sheep and with the presence of white spotting in Shetland sheep. Animals with the ARR/ARR genotype (the most scrapie resistant) had higher odds of having a light dorsum and a dark abdomen than the reverse pattern. The implication of these associations is that selection to increase resistance to scrapie based only onPrPgenotype could result in change in morphological diversity and affect other associated traits such as fitness.

Cautery-induced colour patterns in Precis coenia (Lepidoptera: Nymphalidae)

Development ◽  
1985 ◽  
Vol 86 (1) ◽  
pp. 191-203
Author(s):  
H. F. Nijhout
Keyword(s):  
Computer Simulations ◽  
Hind Wing ◽  
Wing Surface ◽  
Colour Pattern ◽  
Physiological Conditions ◽  
Classical Work ◽  
Pattern Determination ◽  
Colour Patterns ◽  
Experimental Findings ◽  
Precis Coenia

Cautery of the dorsal hind wing in the butterfly, Precis coenia, induces the formation of a concentric colour pattern around the site of injury. The induced pattern is identical in pigmentation to the eyespots that normally develop on this wing surface. This response to cautery also occurs, though much less dramatically, on the ventral forewing. In addition to the peculiar response to cautery, the dorsal hindwing of Precis also develops a series of unique pattern aberrations in response to coldshock. These consist of irregular elongation of the anterior eyespot along the proximodistal axis of the wing. In the most dramatic aberrations the eyespot field covers the entire anterior half of the wing surface. An analysis is presented that attempts to reconcile the effects of cautery on the Precis hindwing with the very different morphological effects of cautery on the colour pattern of Ephestia kühniella, described by Kühn & Von Engelhardt. Computer simulations reveal that the finding presented in this paper, as well as the classical work on Ephestia, can both be explained by assuming that the site of cautery becomes a sink for one of the morphogens involved in colour pattern determination. The experimental findings furthermore indicate that minor perturbations of the wing epidermis can evoke the physiological conditions that attend normal eyespot determination. It is shown that this interpretation also helps to explain the unusual pattern modifications following coldshock.

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