Perch choice and substrate matching to the dorsal patterns of Amphibolurus muricatus lizards
Data files
Oct 06, 2025 version files 2.40 MB
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README.md
19.17 KB
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SalisburyPeters-BackgroundData-Clusters.csv
1.28 MB
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SalisburyPeters-BackgroundData-LEIA.csv
311.34 KB
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SalisburyPeters-LizardData-Clusters.csv
640.74 KB
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SalisburyPeters-LizardData-LEIA.csv
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SalisburyPeters-Xtras.csv
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Abstract
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.
Dataset DOI: 10.5061/dryad.ksn02v7j9
J Salisbury and R Peters
La Trobe University, Australia
Correspondence: 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/. 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/)
- 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/)
- 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/)
- 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, <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, <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/)
- 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/)
- 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
