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      patternize : An R package for quantifying colour pattern variation

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          <p id="P1"> <div class="list"> <a class="named-anchor" id="L1"> <!-- named anchor --> </a> <ol style="list-style-type: &#xA;&#x9;&#x9;&#x9;&#x9;&#x9;decimal&#xA;&#x9;&#x9;&#x9;&#x9;"> <li id="d1698518e195"> <div class="so-custom-list-content so-ol"> <p class="first" id="P2">The use of image data to quantify, study and compare variation in the colors and patterns of organisms requires the alignment of images to establish homology, followed by color-based segmentation of images. Here we describe an R package for image alignment and segmentation that has applications to quantify color patterns in a wide range of organisms. </p> </div> </li> <li id="d1698518e198"> <div class="so-custom-list-content so-ol"> <p class="first" id="P3"> <tt>patternize</tt> is an R package that quantifies variation in color patterns obtained from image data. <tt>patternize</tt> first defines homology between pattern positions across specimens either through manually placed homologous landmarks or automated image registration. Pattern identification is performed by categorizing the distribution of colors using an RGB threshold, <i>k</i>-means clustering or watershed transformation. </p> </div> </li> <li id="d1698518e210"> <div class="so-custom-list-content so-ol"> <p class="first" id="P4">We demonstrate that <tt>patternize</tt> can be used for quantification of the color patterns in a variety of organisms by analyzing image data for butterflies, guppies, spiders and salamanders. Image data can be compared between sets of specimens, visualized as heatmaps and analyzed using principal component analysis (PCA). </p> </div> </li> <li id="d1698518e216"> <div class="so-custom-list-content so-ol"> <p class="first" id="P5"> <tt>patternize</tt> has potential applications for fine scale quantification of color pattern phenotypes in population comparisons, genetic association studies and investigating the basis of color pattern variation across a wide range of organisms. </p> </div> </li> </ol> </div> </p>

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          Most cited references 16

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          A single amino acid mutation contributes to adaptive beach mouse color pattern.

          Natural populations of beach mice exhibit a characteristic color pattern, relative to their mainland conspecifics, driven by natural selection for crypsis. We identified a derived, charge-changing amino acid mutation in the melanocortin-1 receptor (Mc1r) in beach mice, which decreases receptor function. In genetic crosses, allelic variation at Mc1r explains 9.8% to 36.4% of the variation in seven pigmentation traits determining color pattern. The derived Mc1r allele is present in Florida's Gulf Coast beach mice but not in Atlantic coast mice with similar light coloration, suggesting that different molecular mechanisms are responsible for convergent phenotypic evolution. Here, we link a single mutation in the coding region of a pigmentation gene to adaptive quantitative variation in the wild.
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            Experimental evidence that predation promotes divergence in adaptive radiation.

            Adaptive radiation is the evolution of ecological and phenotypic diversity within a rapidly multiplying lineage. Recent studies have identified general patterns in adaptive radiation and inferred that resource competition is a primary factor driving phenotypic divergence. The role and importance of other processes, such as predation, remains controversial. Here we use Timema stick insects to show that adaptive radiation can be driven by divergent selection from visual predators. Ecotypes using different host-plant species satisfy criteria for the early stages of adaptive radiation and differ in quantitative aspects of color, color pattern, body size, and body shape. A manipulative field experiment demonstrates that the direction and strength of divergent selection on these traits is strongly positively correlated with the direction and magnitude of their population divergence in nature but only when selection is estimated in the presence of predation. Our results indicate that both competition and predation may commonly serve as mechanisms of adaptive radiation.
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              Complex modular architecture around a simple toolkit of wing pattern genes

              Identifying the genomic changes that control morphological variation and understanding how they generate diversity is a major goal of evolutionary biology. In Heliconius butterflies, a small number of genes control the development of diverse wing color patterns. Here, we used full genome sequencing of individuals across the Heliconius erato radiation and closely related species to characterize genomic variation associated with wing pattern diversity. We show that variation around color pattern genes is highly modular, with narrow genomic intervals associated with specific differences in color and pattern. This modular architecture explains the diversity of color patterns and provides a flexible mechanism for rapid morphological diversification.

                Author and article information

                Methods in Ecology and Evolution
                Methods Ecol Evol
                February 2018
                February 03 2018
                : 9
                : 2
                : 390-398
                © 2018


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