DOI: 10.5061/dryad.ksn02v7j9
title: Perch choice and substrate matching to the dorsal patterns of Amphibolurus muricatus lizards

description: The patterns of lizards and backgrounds were analysed using QCPA tools
 available in the MICA Toolbox. The csv files provided in this repository
 represents the output from this analysis and includes cluster information,
 edge information and the result of visual modelling (visual contrast
 analysis, colour adjacency analysis and boundary strength
 analysis.   The backgrounds that cryptic animals choose
 will affect the efficacy of their camouflage. Most animals use a range of
 microhabitats consisting of a variety of substrates, vegetation and
 lighting conditions. As some of these will be better suited to
 facilitating camouflage than others, we expect cryptic animals to consider
 their conspicuousness when choosing a background to occupy. If the
 availability of backgrounds varies between populations of cryptic animals,
 then selective pressure on their colouration may also vary, resulting in
 intraspecific variation and presumably animals being better suited to the
 backgrounds locally available to them than those at other locations. In
 this study we investigate how backgrounds available to Jacky dragons
 (Amphibolurus muricatus) vary across their range, whether these lizards
 are occupying backgrounds that match well to their dorsal patterns, and
 how backgrounds compare to their dorsal patterns. Wild lizards were
 located and photographed along with the background they were found on, and
 other options available nearby. We compared lizards and backgrounds within
 their microhabitat as well as all backgrounds across all microhabitats. We
 found that lizards were not occupying the backgrounds that best matched
 their own patterns, that background options varied between locations, and
 that lizards from certain locations were occupying backgrounds closer
 matching to their own pattern than those from other locations. These
 outcomes provide interesting insight into the variance of local factors
 that influence the pattern phenotype, as well as how the relative need for
 camouflage might vary and be balanced with other needs.
description: # Perch choice and substrate matching to the dorsal patterns of
 Amphibolurus muricatus lizards Dataset DOI:
 [10.5061/dryad.ksn02v7j9](https://doi.org/10.5061/dryad.ksn02v7j9) J
 Salisbury and R Peters La Trobe University, Australia Correspondence:
 [richard.peters@latrobe.edu.au](mailto:richard.peters@latrobe.edu.au)
 **License: CC0** ## **Descriptions of data files available:** Data
 represent the output of image analysis using the MICA Toolbox. See
 [https://www.empiricalimaging.com/knowledge-base/](https://www.empiricalimaging.com/knowledge-base/). Additional details are available in the following reference: * van den Berg, C. P., Troscianko, J., Endler, J. A., Marshall, N. J. J. and Cheney, K. L. (2020). Quantitative Colour Pattern Analysis (QCPA): A comprehensive framework for the analysis of colour patterns in nature. Methods Ecol. Evol. 11, 316–332. --- ### **SalisburyPeters-BackgroundData-LEIA.csv** Results from LEIA analysis, colour adjacency analysis (CAA), visual contrast analysis (VCA) and boundary strength analysis (BSA) using the MICA Toolbox for images of background. Multiple images per lizard but one row per image. Variable name is in bold. * **Lizard** Unique name for each specimen * **Id** Unique number for each specimen * **Location** Categorical variable denoting the location in which the lizard was captured * **Clade** Categorical variable indicating the genetic clade of the lizard * **Image** Number representing the type of substrate. 0 = substrate on which lizard was found while other numbers are randomly selected other substrates in the vicintiy of the lizard * **Descr** Type of substrate * **Name** Details of analysis undertaken in the MICA TOOLBOX  *The following variables are obtained from Local Edge Intensity Analysis* ([http://www.empiricalimaging.com/knowledge-base/local-edge-intensity-analysis-leia/](http://www.empiricalimaging.com/knowledge-base/local-edge-intensity-analysis-leia/)) * **Col mean** The mean chromatic RNL Delta-S values over the entire image * **Col sd** Standard deviation of chromatic Delta-S values * **Col CoV** Chromatic Delta-S Coefficient of variation * **Col skew** Chromatic Delta-S skewness * **Col kurtosis** Chromatic Delta-S kurtosis * **Lum mean** The mean luminance (achromatic) RNL Delta-S values over the entire image * **Lum sd** Standard deviation of luminance Delta-S values * **Lum CoV** Luminance Delta-S Coefficient of variation * **Lum skew** Luminance Delta-S skewness * **Lum kurtosis** Luminance Delta-S kurtosis * **Transform** Specifies which transform was applied to the Delta-S values before the above metrics are calculated (none, square-root, or natural log) * **Col thresh** Specifies the selected chromatic Delta-S threshold, below which all values are set to zero for calculating the above metrics * **Lum thresh** Specifies the selected luminance Delta-S threshold, below which all values are set to zero for calculating the above metrics * **Name2** as per variable 'Name' *The following variables are obtained from Quantiative Colour and Pattern Analysis* ([https://www.empiricalimaging.com/knowledge-base/running-the-qcpa-framework/](https://www.empiricalimaging.com/knowledge-base/running-the-qcpa-framework/))               * **CAA:Sc** Colour Adjacency Analysis: Simpson colour diversity * **CAA:Jc** Colour Adjacency Analysis: Relative Simpson colour diversity * **CAA:St** Colour Adjacency Analysis: Simpson transition diversity * **CAA:Jt** Colour Adjacency Analysis: Relative Simpson transition diversity * **CAA:Hc** Colour Adjacency Analysis: Relative Simpson transition diversity * **CAA:Qc** Colour Adjacency Analysis: Relative Shannon colour diversity * **CAA:Ht** Colour Adjacency Analysis: Shannon transition diversity * **CAA:Qt** Colour Adjacency Analysis: Relative Shannon transition diversity * **CAA:Scpl** Colour Adjacency Analysis: Simpson colour pattern complexity * **CAA:Qcpl** Colour Adjacency Analysis: Shannon colour pattern complexity * **CAA:C** Colour Adjacency Analysis: Pattern Complexity * **CAA:PT** Colour Adjacency Analysis: Average patch size * **CAA:PT** Hrz Colour Adjacency Analysis: Average horizontal patch size * **CAA:PT** Vrt Colour Adjacency Analysis: Average vertical patch size * **CAA:Asp** Colour Adjacency Analysis: Aspect ratio * **VCA:ML** Visual Contrast Analysis: Weighted mean of pattern luminance contrast * **VCA:sL** Visual Contrast Analysis: Weighted standard deviation of pattern luminance contrast * **VCA:CVL** Visual Contrast Analysis: Weighted CoV of pattern luminance contrast * **VCA:MDmax** Visual Contrast Analysis: Weighted mean of pattern Dmax contrast * **VCA:sDmax** Visual Contrast Analysis: Weighted standard deviation of pattern Dmax contrast * **VCA:CVDmax** Visual Contrast Analysis: Weighted CoV of pattern Dmax contrast * **VCA:MSsat** Visual Contrast Analysis: Weighted mean of pattern RNL saturation contrast * **VCA:sSsat** Visual Contrast Analysis: Weighted standard deviation of pattern RNL saturation contrast * **VCA:CVSsat** Visual Contrast Analysis: Weighted CoV of pattern RNL saturation * **VCA:MSL** Visual Contrast Analysis: Weighted mean of RNL luminance pattern contrast * **VCA:sSL** Visual Contrast Analysis: Weighted standard deviation of RNL luminance pattern contrast * **VCA:CVSL** Visual Contrast Analysis: Weighted CoV of RNL luminance pattern contrast * **VCA:MS** Visual Contrast Analysis: Weighted mean of pattern RNL chromaticity contrast * **VCA:sS** Visual Contrast Analysis: Weighted standard deviation of pattern RNL chromaticity contrast * **VCA:CVS** Visual Contrast Analysis: Weighted CoV of pattern RNL chromaticity contrast * **BSA:BML** Boundary Strength Analysis: Weighted mean of luminance boundary strength * **BSA:BsL** Boundary Strength Analysis: Weighted standard deviation of luminance boundary strength * **BSA:BCVL** Boundary Strength Analysis: Weighted CoV of luminance boundary strength * **BSA:BMDmax** Boundary Strength Analysis: Weighted mean of Dmax boundary strength * **BSA:BsDmax** Boundary Strength Analysis: Weighted standard deviation of Dmax boundary strength * **BSA:BCVDmax** Boundary Strength Analysis: Weighted CoV of Dmax boundary strength * **BSA:BMSsat** Boundary Strength Analysis: Weighted mean of RNL saturation boundary strength * **BSA:BsSsat** Boundary Strength Analysis: Weighted standard deviation of RNL saturation boundary strength * **BSA:BCVSsat** Boundary Strength Analysis: Weighted CoV of RNL saturation boundary strength * **BSA:BMSL** Boundary Strength Analysis: Weighted mean of RNL luminance boundary strength * **BSA:BsSL** Boundary Strength Analysis: Weighted standard deviation of RNL luminance boundary strength * **BSA:BCVSL** Boundary Strength Analysis: Weighted CoV of RNL luminance boundary strength * **BSA:BMS** Boundary Strength Analysis: Weighted mean of RNL chromaticity boundary strength * **BSA:BsS** Boundary Strength Analysis: Weighted standard deviation of RNL chromaticity boundary strength * **BSA:BCVS** Boundary Strength Analysis: Weighted CoV of RNL chromaticity boundary strength --- ### **SalisburyPeters-BackgroundData-Clusters.csv** Results from cluster analysis (MICA Toolbox) of backgrounds. Multiple rows per image (one row per count per cluster per background). The variable ‘Image’ indicates if it was the subject used by the lizards when first observed (Image=0) or another option nearby (Image=1:n). Variable name is in bold. * **Lizard** Unique name for each specimen * **Id** Unique number for each specimen * **Location** Categorical variable denoting the location in which the lizard was captured * **Clade** Categorical variable indicating the genetic clade of the lizard * **Image** Number representing the type of substrate. 0 = substrate on which lizard was found while other numbers are randomly selected other substrates in the vicintiy of the lizard *The following variables are obtained from Quantiative Colour and Pattern Analysis* ([https://www.empiricalimaging.com/knowledge-base/running-the-qcpa-framework/](https://www.empiricalimaging.com/knowledge-base/running-the-qcpa-framework/)) * **Cluster** Cluster number (image is segmented into regions of the same appearance referred to as clusters) * **Count** Number of discontiguous regions belonging to the same cluster * **Total Area** Area covered by the cluster * **AverageSize** Average size of the discontiguous regions belonging to the cluster * **PercentArea** Area of the image covered by the cluster * **Perim** perimeter of the cluster * **Major** length of the major axis of the best-fit ellipse around the cluster * **Minor** length of the minor axis of that ellipse * **Angle** orientation of the major axis * **Circ** circularity (closer to 1 is more circular) * **Solidity** ratio of cluster area to the convex hull area (1 = convex, &lt;1 = more concave). * **Feret** longest distance across the cluster * **FeretX** coordinates of the Feret diameter measurement * **FeretY** coordinates of the Feret diameter measurement * **FeretAngle** angle at which the Feret diameter occurs * **MinFeret** shortest distance across * **Name** Details of analysis undertaken in the MICA TOOLBOX * **Pass** Number of segmentation passes * **ClusterID** As per 'Cluster' * **lw_mean** long wavelength cone mean cone-catch value * **lw_sd** long wavelength cone standard deviation of the mean cone-catch value * **mw_mean** medium wavelength cone mean cone-catch value * **mw_sd** medium wavelength cone standard deviation of the mean cone-catch value * **sw_mean** short wavelength cone mean cone-catch value * **sw_sd** short wavelength cone standard deviation of the mean cone-catch value * **uv_mean** UV wavelength cone mean cone-catch value * **uv_sd** UV wavelength cone standard deviation of the mean cone-catch value * **dbl_mean** double cone mean cone-catch value * **dbl_sd** double cone standard deviation of the mean cone-catch value * **Area** As per 'Total Area' * **CoveragePC** Percentage of image covered by cluster * **RNL_X** chromatic contrast value (ΔS) relative to other clusters, in just noticeable differences (JNDs) * **RNL Saturation** saturation measure in RNL colour space * **DmaxChromaticity** maximum chromatic distance between this cluster and others (in JNDs). * **Dmaxchannel** the receptor channel that drives that maximum chromatic contrast --- ### **SalisburyPeters-LizardData-Clusters.csv** Results from cluster analysis (MICA Toolbox) of lizard patterns from the perspective of a Kookaburra observer. Multiple rows per image (one row per count per cluster per lizard). Variable names are in bold. * **Image** Unique name for each specimen * **Id** Unique number for each specimen * **Location** Categorical variable denoting the location in which the lizard was captured * **Clade** Categorical variable indicating the genetic clade of the lizard * **Distance** Viewing distance (m) * **ClusterID** Cluster number (image is segmented into regions of the same appearance referred to as clusters) * **Count** Number of discontiguous regions belonging to the same cluster * **Total Area** Area covered by the cluster * **Average Size** Average size of the discontiguous regions belonging to the cluster * **PercentArea** Area of the image covered by the cluster * **Perimeter** perimeter of the cluster * **Major** length of the major axis of the best-fit ellipse around the cluster * **Minor** length of the minor axis of that ellipse * **Angle** orientation of the major axis * **Circ** circularity (closer to 1 is more circular) * **Solidity** ratio of cluster area to the convex hull area (1 = convex, &lt;1 = more concave). * **Feret** longest distance across the cluster * **FeretX** coordinates of the Feret diameter measurement * **FeretY** coordinates of the Feret diameter measurement * **FeretAngle** angle at which the Feret diameter occurs * **MinFeret** shortest distance across * **Pass** Number of segmentation passes * **lw_mean** long wavelength cone mean cone-catch value * **lw_sd** long wavelength cone standard deviation of the mean cone-catch value * **mw_mean** medium wavelength cone mean cone-catch value * **mw_sd** medium wavelength cone standard deviation of the mean cone-catch value * **sw_mean** short wavelength cone mean cone-catch value * **sw_sd** short wavelength cone standard deviation of the mean cone-catch value * **uv_mean** UV wavelength cone mean cone-catch value * **uv_sd** UV wavelength cone standard deviation of the mean cone-catch value * **dbl_mean** double cone mean cone-catch value * **dbl_sd** double cone standard deviation of the mean cone-catch value * **Area** Area covered by the cluster * **AreaProp** Proportion of image covered by cluster * **RNL X** Chromatic contrast value (ΔS) relative to other clusters, in just noticeable differences (JNDs) * **RNL Saturation** RNL Saturation * **Dmax Chromaticity** DmaxChromaticity * **Dmax channel** Dmaxchannel ---   ### **SalisburyPeters-LizardData-LEIA.csv** Results from LEIA analysis, colour adjacency analysis (CAA), visual contrast analysis (VCA) and boundary strength analysis (BSA) using the MICA Toolbox for images of lizard patterns from the perspective of a kookaburra observer. * **Observer** Avian species visual system used in the analysis * **Image** Unique name for each specimen * **Id** Unique number for each specimen * **Location** Categorical variable denoting the location in which the lizard was captured * **Clade** Categorical variable indicating the genetic clade of the lizard * **Distance** Viewing distance (m) *The following variables are obtained from Local Edge Intensity Analysis* ([http://www.empiricalimaging.com/knowledge-base/local-edge-intensity-analysis-leia/](http://www.empiricalimaging.com/knowledge-base/local-edge-intensity-analysis-leia/)) * **Col mean** The mean chromatic RNL Delta-S values over the entire image * **Col sd** Standard deviation of chromatic Delta-S values * **Col CoV** Chromatic Delta-S Coefficient of variation * **Col skew** Chromatic Delta-S skewness * **Col kurtosis** Chromatic Delta-S kurtosis * **Lum mean** The mean luminance (achromatic) RNL Delta-S values over the entire image * **Lum sd** Standard deviation of luminance Delta-S values * **Lum CoV** Luminance Delta-S Coefficient of variation * **Lum skew** Luminance Delta-S skewness * **Lum kurtosis** Luminance Delta-S kurtosis *The following variables are obtained from Quantiative Colour and Pattern Analysis* ([https://www.empiricalimaging.com/knowledge-base/running-the-qcpa-framework/](https://www.empiricalimaging.com/knowledge-base/running-the-qcpa-framework/)) * **CAA:Sc** Colour Adjacency Analysis: Simpson colour diversity * **CAA:Jc** Colour Adjacency Analysis: Relative Simpson colour diversity * **CAA:St** Colour Adjacency Analysis: Simpson transition diversity * **CAA:Jt** Colour Adjacency Analysis: Relative Simpson transition diversity * **CAA:Hc** Colour Adjacency Analysis: Relative Simpson transition diversity * **CAA:Qc** Colour Adjacency Analysis: Relative Shannon colour diversity * **CAA:Ht** Colour Adjacency Analysis: Shannon transition diversity * **CAA:Qt** Colour Adjacency Analysis: Relative Shannon transition diversity * **CAA:Scpl** Colour Adjacency Analysis: Simpson colour pattern complexity * **CAA:Qcpl** Colour Adjacency Analysis: Shannon colour pattern complexity * **CAA:C** Colour Adjacency Analysis: Pattern Complexity * **CAA:PT** Colour Adjacency Analysis: Average patch size * **CAA:PT Hrz** Colour Adjacency Analysis: Average horizontal patch size * **CAA:PT Vrt** Colour Adjacency Analysis: Average vertical patch size * **CAA:Asp** Colour Adjacency Analysis: Aspect ratio * **VCA:ML** Visual Contrast Analysis: Weighted mean of pattern luminance contrast * **VCA:sL** Visual Contrast Analysis: Weighted standard deviation of pattern luminance contrast * **VCA:CVL** Visual Contrast Analysis: Weighted CoV of pattern luminance contrast * **VCA:MDmax** Visual Contrast Analysis: Weighted mean of pattern Dmax contrast * **VCA:sDmax** Visual Contrast Analysis: Weighted standard deviation of pattern Dmax contrast * **VCA:CVDmax** Visual Contrast Analysis: Weighted CoV of pattern Dmax contrast * **VCA:MSsat** Visual Contrast Analysis: Weighted mean of pattern RNL saturation contrast * **VCA:sSsat** Visual Contrast Analysis: Weighted standard deviation of pattern RNL saturation contrast * **VCA:CVSsat** Visual Contrast Analysis: Weighted CoV of pattern RNL saturation * **VCA:MSL** Visual Contrast Analysis: Weighted mean of RNL luminance pattern contrast * **VCA:sSL** Visual Contrast Analysis: Weighted standard deviation of RNL luminance pattern contrast * **VCA:CVSL** Visual Contrast Analysis: Weighted CoV of RNL luminance pattern contrast * **VCA:MS** Visual Contrast Analysis: Weighted mean of pattern RNL chromaticity contrast * **VCA:sS** Visual Contrast Analysis: Weighted standard deviation of pattern RNL chromaticity contrast * **VCA:CVS** Visual Contrast Analysis: Weighted CoV of pattern RNL chromaticity contrast * **BSA:BML** Boundary Strength Analysis: Weighted mean of luminance boundary strength * **BSA:BsL** Boundary Strength Analysis: Weighted standard deviation of luminance boundary strength * **BSA:BCVL** Boundary Strength Analysis: Weighted CoV of luminance boundary strength * **BSA:BMDmax** Boundary Strength Analysis: Weighted mean of Dmax boundary strength * **BSA:BsDmax** Boundary Strength Analysis: Weighted standard deviation of Dmax boundary strength * **BSA:BCVDmax** Boundary Strength Analysis: Weighted CoV of Dmax boundary strength * **BSA:BMSsat** Boundary Strength Analysis: Weighted mean of RNL saturation boundary strength * **BSA:BsSsat** Boundary Strength Analysis: Weighted standard deviation of RNL saturation boundary strength * **BSA:BCVSsat** Boundary Strength Analysis: Weighted CoV of RNL saturation boundary strength * **BSA:BMSL** Boundary Strength Analysis: Weighted mean of RNL luminance boundary strength * **BSA:BsSL** Boundary Strength Analysis: Weighted standard deviation of RNL luminance boundary strength * **BSA:BCVSL** Boundary Strength Analysis: Weighted CoV of RNL luminance boundary strength * **BSA:BMS** Boundary Strength Analysis: Weighted mean of RNL chromaticity boundary strength * **BSA:BsS** Boundary Strength Analysis: Weighted standard deviation of RNL chromaticity boundary strength * **BSA:BCVS** Boundary Strength Analysis: Weighted CoV of RNL chromaticity boundary strength * **Sex** Sex of lizard (1 = Female) * **SVL** Snout-vent length (mm) * **Weight** Weight (g) * **Habitat** Habitat category (3 levels) * **Habitat2** Habitat category (2 levels) --- ### **SalisburyPeters-Xtras.csv** Provides information about the Sex, SVL, Weight, Genetic Clade, Habitat of focal lizards * **Id** Unique number for each specimen * **Sex** Sex of lizard (1 = Female) * **SVL** Snout-vent length (mm) * **Weight** Weight (g) * **Clade** Categorical variable indicating the genetic clade of the lizard * **Habitat** Habitat category (3 levels) * **Habitat2** Habitat category (2 levels) * **Image** Unique name for each specimen