Protas, M. E. & Patel, N. H. Evolution of coloration patterns. Annu. Rev. Cell. Dev. Biol. 24, 425–446 (2008).
Robertson, J. M. & Greene, H. W. Bright colour patterns as social signals in nocturnal frogs. Biol. J. Linn. Soc. 121, 849–857 (2017).
Hill, G. E. et al. (eds) Bird coloration: mechanisms and measurements Vol. 1 (Harvard University Press, Cambridge, 2006).
Hamilton, W. D. & Zuk, M. Heritable true fitness and bright birds—a role for parasites. Science 218, 384–387 (1982).
Lindström, K. & Lundström, J. Male greenfinches (Carduelis chloris) with brighter ornaments have higher virus infection clearance rate. Behav. Ecol. Sociobiol. 48, 44–51 (2000).
Pérez-Rodríguez, L., Jovani, R. & Stevens, M. Shape matters: animal colour patterns as signals of individual quality. Proc. R. Soc. B. 284, 20162446–20162510 (2017).
Stevens, M., Cuthill, I. C., Windsor, A. M. & Walker, H. J. Disruptive contrast in animal camouflage. Proc. R. Soc. B 273, 2433–2438 (2006).
Stevens, M., Winney, I. S., Cantor, A. & Graham, J. Outline and surface disruption in animal camouflage. Proc. R. Soc. B 276, 781–786 (2009).
Allen, W. L., Cuthill, I. C., Scott-Samuel, N. E. & Baddeley, R. Why the leopard got its spots: relating pattern development to ecology in felids. Proc. R. Soc. B 278, 1373–1380 (2010).
Kelley, J. L., Fitzpatrick, J. L. & Merilaita, S. Spots and stripes: ecology and colour pattern evolution in butterflyfishes. Proc. R. Soc. B 280, 20122730–20122739 (2013).
Kondo, S. & Shirota, H. Theoretical analysis of mechanisms that generate the pigmentation pattern of animals. Semin. Cell Dev. Biol. 20, 82–89 (2009).
Theis, A., Salzburger, W. & Egger, B. The function of anal fin egg-spots in the cichlid fish Astatotilapia burtoni. PLoS ONE 7, e29878 (2012).
Palmer, M. E., Calvé, M. R. & Adamo, S. A. Response of female cuttlefish Sepia officinalis (Cephalopoda) to mirrors and conspecifics: evidence for signaling in female cuttlefish. Anim. Cogn. 9, 151–155 (2006).
Gluckman, T. L. & Cardoso, G. C. The dual function of barred plumage in birds; camouflage and communication. J. Evol. Biol. 23, 2501–2506 (2010).
Rowland, H. M. et al. Countershading enhances cryptic protection: an experiment with wild birds and artificial prey. Anim. Behav. 74, 1249–1258 (2007).
Singh, A. P. & Nüsslein-Volhard, C. Zebrafish Stripes as a model for vertebrate review colour pattern formation. Curr. Biol. 25, R81–R92 (2015).
Ruxton, G. D., Sherratt, T. N. & Speed, M. P. Avoiding Attack. Oxford, UK: Oxford University Press. https://doi.org/10.1093/acprof:oso/9780198528609.003.0012 (2004).
Manriquez, K. C., Pardo, L. M., Wells, R. J. D. & Palma, A. T. Crypsis in Paraxanthus barbiger (Decapoda : Brachyura): Mechanisms against visual predators. J. Crustac. Biol. 28, 473–479 (2008).
Nishikawa, H. et al. Molecular basis of wing coloration in a batesian mimic butterfly, Papilio polytes. Sci. Rep. 3, 3184 (2013).
Stevens, M. & Ruxton, G. D. The key role of behaviour in animal camouflage. Biol. Rev. 94, 116–134 (2019).
Wittkopp, P. J., Carroll, S. B. & Kopp, A. Evolution in black and white: genetic control of pigment patterns in Drosophila. Trends Genet. 19, 495–504 (2003).
Hiyama, A., Taira, W. & Otaki, J. M. Color-pattern evolution in response to environmental stress in butterflies. Front. Genet. 3, 15 (2012).
Pérez-Rodríguez, L., Jovani, R. & Mougeot, F. Fractal geometry of a complex plumage trait reveals bird’s quality. Proc. R. Soc. B. 280, 20122783–20122786 (2013).
Jiguet, F. & Bretagnolle, V. Sexy males and choosy females on exploded leks: correlates of male attractiveness in the Little Bustard. Behav. Proc. 103, 246–255 (2014).
Tibbetts, E. A. & Curtis, T. R. Rearing conditions influence quality signals but not individual identity signals in Polistes wasps. Behav. Ecol. 18, 602–607 (2007).
Park, C. J., Kang, H. S. & Gye, M. C. Effects of nonylphenol on early embryonic development, pigmentation and 3,5,3’-triiodothyronine-induced metamorphosis in Bombina orientalis (Amphibia: Anura). Chemosphere 81, 1292–1300 (2010).
Rudh, A. & Qvarnström, A. Adaptive colouration in amphibians. Semin. Cell Dev. Biol. 24, 553–561 (2013).
Rabbani, M., Zacharczenko, B. & Green, D. M. Color pattern variation in a cryptic amphibian, Anaxyrus fowleri. J. Herpetol. 49, 649–654 (2015).
Gomez-Mestre, I., Pyron, R. A. & Wiens, J. J. Phylogenetic analyses reveal unexpected patterns in the evolution of reproductive modes in frogs. Evolution 66, 3687–3700 (2012).
Wells, K. D. The Ecology and Behavior of Amphibians (The University of Chicago Press, USA, 2007).
Haas, A. Phylogeny of frogs as inferred from primarily larval characters (Amphibia: Anura). Cladistics 19, 23–89 (2003).
Wollenberg Valero, K. C. et al. Transcriptomic and macroevolutionary evidence for phenotypic uncoupling between frog life history phases. Nat. Commun. 8, 1–9 (2017).
Van Allen, B. G., Briggs, V. S., McCoy, M. W. & Vonesh, J. R. Carry-over effects of the larval environment on post-metamorphic performance in two hylid frogs. Oecologia 164, 891–898 (2010).
Touchon, J. C., McCoy, M. W., Vonesh, J. R. & Warkentin, K. M. Effects of plastic hatching timing carry over through metamorphosis in red-eyed treefrogs. Ecology 94, 850–860 (2013).
Gomez-Mestre, I. et al. The shape of things to come: linking developmental plasticity to post-metamorphic morphology in anurans. J. Evol. Biol. 23, 1364–1373 (2010).
Thibaudeau, G. & Altig, R. Coloration of Anuran Tadpoles (Amphibia): development, dynamics, function, and hypotheses. ISRN Zoology 1–16 (2012).
Parichy, D. M. & Turner, J. M. Zebrafish puma mutant decouples pigment pattern and somatic metamorphosis. Dev. Biol. 256, 242–257 (2003).
Touchon, J. C., McCoy, M. W., Landberg, T., Vonesh, J. R. & Warkentin, K. M. Putting μ/g in a new light: plasticity in life history switch points reflects fine-scale adaptive responses. Ecology 96, 2192–2202 (2015).
Gomez-Mestre, I., Kulkarni, S. & Buchholz, D. R. Mechanisms and consequences of developmental acceleration in tadpoles responding to pond drying. PLoS ONE 8, e84266 (2013).
Gomez-Mestre, I. & Buchholz, D. R. Developmental plasticity mirrors differences among taxa in spadefoot toads linking plasticity and diversity. PNAS 103, 50 (2006).
Gervasi, S. S. & Foufopoulos, J. Costs of plasticity: responses to desiccation decrease post-metamorphic immune function in a pond-breeding amphibian. Funct. Ecol. 22, 100–108 (2008).
Schloerke, B. GGally: Extension to ‘ggplot2’. R package version 2.0.0. https://CRAN.R-project.org/package=GGally (2020).
Covarrubias-Pazaran, G. Genome-assisted prediction of quantitative traits using the R package sommer. PLoS ONE 11, e0156744 (2016).
Lynch, M. & Walsh, B. Genetics and Analysis of Quantitative Traits Vol. 1, 535–557 (Sinauer, Sunderland, MA, 1998).
Burraco, P., Valdés, A. E., Johansson, F. & Gomez-Mestre, I. Physiological mechanisms of adaptive developmental plasticity in Rana temporaria island populations. BMC Evol. Biol. 17, 164 (2017).
Kulkarni, S. S., Denver, R. J., Gomez-Mestre, I. & Buchholz, D. R. Genetic accommodation via modified endocrine signalling explains phenotypic divergence among spadefoot toad species. Nat. Commun. 8, 993 (2017).
Bagnara, J. T. & Fernandez, P. J. Hormonal influences on the development of amphibian pigmentation patterns. Zool. Sci. 10, 733–748 (1993).
Frieden, E. & Just, J. J. Hormonal responses in amphibian metamorphosis. Biochem. Actions Hormon. 1, 1–52 (2012).
Noriega, N. C. & Hayes, T. B. DDT congener effects on secondary sex coloration in the reed frog Hyperolius argus: a partial evaluation of the Hyperolius argus endocrine screen. Comp. Biochem. Physiol. B Biochem. Mol. Biol. 126, 231–237 (2000).
Hayes, T. B. et al. Hermaphroditic, demasculinized frogs after exposure to the herbicide atrazine at low ecologically relevant doses. Proc. Natl. Acad. Sci. 99, 5476–5480 (2002).
Bagnara, J. T. & Matsumoto, J. Comparative anatomy and physiology of pigment cells in nonmammalian tissues. In The Pigmentary System: Physiology and Pathophysiology (2nd edition), (Nordlund, J. J. et al. eds.), 11–59 (Oxford Univ. Press, UK, 2006).
Schanz, T. S., Bensch, S., Grahn, M., Hasselquist, D. & Wittzell, H. Good genes, oxidative stress and condition-dependent sexual signals. Proc. R. Soc. B 266, 1–12 (1999).
Cabrera-Guzmán, E., Díaz-Paniagua, C. & Gomez-Mestre, I. Differential effect of natural and pigment-supplemented diets on larval development and phenotype of anurans. J. Zool. https://doi.org/10.1111/jzo.12827 (2020).
Isaksson, C., Örnborg, J., Stephensen, E. & Andersson, S. Plasma glutathione and carotenoid coloration as potential biomarkers of environmental stress in great tits. EcoHealth 2, 138–146 (2005).
Summers, K. & Clough, M. E. The Evolution of coloration and toxicity in the poison frog family (Dendrobatidae). PNAS 98, 6227–6232 (2001).
Vences, M. et al. Convergent evolution of aposematic coloration in Neotropical poison frogs: a molecular phylogenetic perspective. Org. Divers. Evol. 3, 215–226 (2003).
Sköld, H. N., Aspengren, S. & Wallin, M. Rapid color change in fish and amphibians—function, regulation, and emerging applications. Pigment Cell Melanoma Res. 26, 29–38 (2012).
Gallant, N. & Teather, K. Differences in size, pigmentation, and fluctuating asymmetry in stressed and nonstressed northern leopard frogs (Rana pipiens). Ecoscience 8, 430–436 (2001).
Garcia, T. S. & Sih, A. Color change and color-dependent behavior is response to predation risk in the salamander sister species Ambystoma barbouri and Ambystoma texanum. Oecologia 137, 131–139 (2003).
Polo-Cavia, N. & Gomez-Mestre, I. Pigmentation plasticity enhances crypsis in larval newts: associated metabolic cost and background choice behaviour. Sci. Rep. 7, 39739 (2017).
Blaustein, A. R. & Belden, L. K. Amphibian defenses against ultraviolet-B radiation. Evol. Dev. 5, 89–97 (2003).
Summers, K., Symula, R., Clough, M. & Cronin, T. Visual mate choice in poison frogs. Proc. R. Soc. Lond. B. 266, 2141–2145 (1999).
Wollenberg, K. C. & Measey, G. J. Why colour in subterranean vertebrates? Exploring the evolution of colour patterns in caecilian amphibians. J. Evol. Biol. 22, 1046–1056 (2009).
Stevens, M. & Merilaita, S. Animal Camouflage: Mechanisms and Function (eds. Stevens, M. & Merilaita, S.) (Cambridge Univ. Press, UK, 2011).
Spicer, J. I. & Burggren, W. W. Development of physiological regulatory systems: altering the timing of crucial events. Zoology 106, 91–99 (2003).
Rundle, S. D. & Spicer, J. I. Heterokairy: a significant form of developmental plasticity?. Biol. Lett. 12, 20160509 (2016).
Kulkarni, S. S., Gomez-Mestre, I., Moskalik, C. L., Storz, B. L. & Buchholz, D. R. Evolutionary reduction of developmental plasticity in desert spadefoot toads. J. Evol. Biol. 24, 2445–2455 (2011).
Gosner, K. L. A simplified table for staging anuran embryos and larvae with notes on identification. Herpetologica 16, 183–190 (1960).
Tuceryan, M. & Jain, A. K. Chapter 2.1 Texture Analysis, The Handbook of Pattern Recognition and Computer Vision (2nd edition), (eds. Chen, C. H. et al.), 207–248 (World Scientific Publishing Co., Singapore, 1998).
Di Cataldo, S. & Ficarra, E. Mining textural knowledge in biological images: applications, methods, and trends. Comput. Struct. Biotech. 15, 56–67 (2017).
Haralick, R. M., Shanmugam, K., & Dinstein, I. Textural features for image classification. IEEE T. SYST. MAN. CY. B. SMC-3, 610–621 (1973).
Haralick, R. M. Statistical and structural approaches to texture. Proc. IEEE 67, 786–804 (1979).
Conners, R. W., Trivedi, M. M. & Harlow, C. A. Segmentation of a high-resolution urban scene using texture operators. Comput. Gr. Image Process. 25, 273–310 (1984).
Albregtsen, F. Statistical texture measures computed from gray level cooccurrence matrices. Image processing laboratory, Department of Informatics, University of Oslo, Norway (2008).
Cabrera, J. Texture analyzer. https://rsb.info.nih.gov/ij/plugins/texture.html (Accessed December, 2019) (2005).
Sarkar, N. & Chaudhuri, B. B. An efficient differential box-counting approach to compute fractal dimension of image. IEEE T. SYST. MAN CY B. 24, 115–120 (1994).
Karperien, A. FracLac for ImageJ, https://rsb.info.nih.gov/ij/plugins/fraclac/FLHelp/Introduction.htm (accessed December, 2019) (1999–2013).
Mandelbrot, B. B. The Fractal Geometry of Nature (W. H. Freeman and Company, USA, 1982).
Smith, T. G. Jr., Lange, G. D. & Marks, W. B. Fractal methods and results in cellular morphology—dimensions, lacunarity, and multifractals. J. Neurosci. Methods 69, 123–136 (1996).
Lopes, R. & Betrouni, N. Fractal and multifractal analysis: a review. Med. Image Anal. 13, 634–649 (2009).
Tolle, C. R., McJunkin, T. R., Rohrbaugh, D. T. & LaViolette, R. A. Lacunarity definition for ramified data sets based on optimal cover. Phys. D 179, 129–152 (2003).
Peterson, R. A. & Cavanaugh, J. E. Ordered quantile normalization: a semiparametric transformation built for the cross-validation era. J. Appl. Stat. 0, 1–16 (2019).
Buerkner, P. C. brms: an R package for Bayesian multi-level models using Stan. J. Stat. Softw. 80, 1–28 (2016).
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