Why the leopard got its spots: relating pattern development to ecology in felids

Heterozygosity is low where rare color variants in wild carnivores prevail

Coat color and pattern are a distinguished feature in mammalian carnivores, shaped by climatic cycles and habitat type. It can be expressed in various ways, such as gradients, polymorphisms, and rare color variants. Although natural selection explains much of the phenotypic variation found in the wild, genetic drift and heterozygote deficiency, as prominent in small and fragmented populations, may also affect phenotypic variability through the fixation of recessive alleles. The aim of this study was to test whether rare color variants in the wild could relate to a deficiency of heterozygotes, resulting from habitat fragmentation and small population size. We present an overview of all rare color variants in the order Carnivora, and compiled demographic and genetic data of the populations where they did and did not occur, to test for significant correlations. We also tested how phylogeny and body weight influenced the presence of color variants with phylogenetic generalized linear mixed models (PGLMMs). We found 40 color-variable species and 59 rare color variants. In 17 variable phenotypic populations for which genetic diversity was available, the average A R was 4.18, H O = 0.59, and H E = 0.66, and F IS = 0.086. We found that variable populations displayed a significant reduction in heterozygosity and allelic richness compared to non-variable populations across species. We also found a significant negative correlation between population size and inbreeding coefficients. Therefore, it is possible that small effective size had phenotypic consequences on the extant populations. The high frequency of the rare color variants (averaging 20%) also implies that genetic drift is locally overruling natural selection in small effective populations. As such, rare color variants could be added to the list of phenotypic consequences of inbreeding in the wild.

Evolution of Plumage Patterns in a Pattern Morphospace: A Phylogenetic Analysis of Melanerpine Woodpeckers

AbstractPlumage patterns of melanerpine (Melanerpes-Sphyrapicus) woodpeckers are strikingly diverse. Understanding the evolution and function of this diversity is challenging because of the difficulty of quantifying plumage patterns. We use a three-dimensional space to characterize the evolution of melanerpine achromatic plumage patterns. The axes of the space are three pattern features (spatial frequency, orientation, and contrast) quantified using two-dimensional fast Fourier transformation of museum specimen images. Mapping plumage in pattern space reveals differences in how species and subclades occupy the space. To quantify these differences, we derive two new measures of pattern: pattern diversity (diversity across plumage patches within a species) and pattern uniqueness (divergence of patterns from those of other species). We estimate that the melanerpine ancestor had mottled plumage and find that pattern traits across patches and subclades evolve at different rates. We also find that smaller species are more likely to display horizontal face patterning. We promote pattern spaces as powerful tools for investigating animal pattern evolution.

Development shapes the evolutionary diversification of rodent stripe patterns

Vertebrate groups have evolved strikingly diverse color patterns. However, it remains unknown to what extent the diversification of such patterns has been shaped by the proximate, developmental mechanisms that regulate their formation. While these developmental mechanisms have long been inaccessible empirically, here we take advantage of recent insights into rodent pattern formation to investigate the role of development in shaping pattern diversification across rodents. Based on a broad survey of museum specimens, we first establish that various rodents have independently evolved diverse patterns consisting of longitudinal stripes, varying across species in number, color, and relative positioning. We then interrogate this diversity using a simple model that incorporates recent molecular and developmental insights into stripe formation in African striped mice. Our results suggest that, on the one hand, development has facilitated pattern diversification: The diversity of patterns seen across species can be generated by a single developmental process, and small changes in this process suffice to recapitulate observed evolutionary changes in pattern organization. On the other hand, development has constrained diversification: Constraints on stripe positioning limit the scope of evolvable patterns, and although pattern organization appears at first glance phylogenetically unconstrained, development turns out to impose a cryptic constraint. Altogether, this work reveals that pattern diversification in rodents can in part be explained by the underlying development and illustrates how pattern formation models can be leveraged to interpret pattern evolution.

Habitat geometry rather than visual acuity limits the visibility of a ground-nesting bird's clutch to terrestrial predators

The nests of ground-nesting birds rely heavily on camouflage for their survival, and predation risk, often linked to ecological changes from human activity, is a major source of mortality. Numerous ground-nesting bird populations are in decline, so understanding the effects of camouflage on their nesting behavior is relevant to their conservation concerns. Habitat three-dimensional (3D) geometry, together with predator visual abilities, viewing distance, and viewing angle, determine whether a nest is either visible, occluded, or too far away to detect. While this link is intuitive, few studies have investigated how fine-scale geometry is likely to help defend nests from different predator guilds. We quantified nest visibility based on 3D occlusion, camouflage, and predator visual modeling in northern lapwings, Vanellus vanellus, on different land management regimes. Lapwings selected local backgrounds that had a higher 3D complexity at a spatial scale greater than their entire clutches compared to local control sites. Importantly, our findings show that habitat geometry-rather than predator visual acuity-restricts nest visibility for terrestrial predators and that their field habitats, perceived by humans as open, are functionally closed with respect to a terrestrial predator searching for nests on the ground. Taken together with lapwings' careful nest site selection, our findings highlight the importance of considering habitat geometry for understanding the evolutionary ecology and management of conservation sites for ground-nesting birds.

Neural crest cells as a source of microevolutionary variation

Vertebrates have some of the most complex and diverse features in animals, from varied craniofacial morphologies to colorful pigmentation patterns and elaborate social behaviors. All of these traits have their developmental origins in a multipotent embryonic lineage of neural crest cells. This "fourth germ layer" is a vertebrate innovation and the source of a wide range of adult cell types. While others have discussed the role of neural crest cells in human disease and animal domestication, less is known about their role in contributing to adaptive changes in wild populations. Here, we review how variation in the development of neural crest cells and their derivatives generates considerable phenotypic diversity in nature. We focus on the broad span of traits under natural and sexual selection whose variation may originate in the neural crest, with emphasis on behavioral factors such as intraspecies communication that are often overlooked. In all, we encourage the integration of evolutionary ecology with developmental biology and molecular genetics to gain a more complete understanding of the role of this single cell type in trait covariation, evolutionary trajectories, and vertebrate diversity.

Distance from human settlements favors wild-type appearance of feral cats (Felis catus) in Mediterranean woodland

Camouflage is a common trait enabling animals to avoid detection by predators and prey. Patterns such as spots and stripes are convergent across carnivore families, including felids, and are hypothesized to have adaptive value through camouflage. House cats (Felis catus) were domesticated thousands of years ago, but despite artificial selection for a wide variety of coat colors, the wild-type pattern of tabby cats is very common. We aimed to determine whether this pattern grants an advantage over other morphs in natural environments. We collected cat images taken with camera traps in natural areas near and far from 38 rural settlements in Israel, to compare the habitat use by feral cats of different colors. We tested the effect of proximity to villages and habitat vegetation (normalized difference vegetation index, NDVI) on the probability of space use by the tabby morph compared to the others. NDVI had a positive effect on site use in both morphs, but non-tabby cats had a 2.1 higher probability of using the near sites than the far sites, independent of NDVI. The wild-type tabby cats' probability of site use were equally likely to be unaffected by proximity, or have an interaction of proximity with NDVI whereby the far transects are used with increasing probability in sites of denser vegetation. We hypothesize that the camouflage of tabby cats, more than other colors and patterns, confers an advantage in roaming the woodland habitats for which this pattern evolved. This has both theoretical implications as rare empirical evidence of the adaptive value of fur coloration, and practical implications on managing the ecological impact of feral cats worldwide.

Optimizing the automated recognition of individual animals to support population monitoring

Reliable estimates of population size and demographic rates are central to assessing the status of threatened species. However, obtaining individual-based demographic rates requires long-term data, which is often costly and difficult to collect. Photographic data offer an inexpensive, noninvasive method for individual-based monitoring of species with unique markings, and could therefore increase available demographic data for many species. However, selecting suitable images and identifying individuals from photographic catalogs is prohibitively time-consuming. Automated identification software can significantly speed up this process. Nevertheless, automated methods for selecting suitable images are lacking, as are studies comparing the performance of the most prominent identification software packages. In this study, we develop a framework that automatically selects images suitable for individual identification, and compare the performance of three commonly used identification software packages; Hotspotter, I3S-Pattern, and WildID. As a case study, we consider the African wild dog, Lycaon pictus, a species whose conservation is limited by a lack of cost-effective large-scale monitoring. To evaluate intraspecific variation in the performance of software packages, we compare identification accuracy between two populations (in Kenya and Zimbabwe) that have markedly different coat coloration patterns. The process of selecting suitable images was automated using convolutional neural networks that crop individuals from images, filter out unsuitable images, separate left and right flanks, and remove image backgrounds. Hotspotter had the highest image-matching accuracy for both populations. However, the accuracy was significantly lower for the Kenyan population (62%), compared to the Zimbabwean population (88%). Our automated image preprocessing has immediate application for expanding monitoring based on image matching. However, the difference in accuracy between populations highlights that population-specific detection rates are likely and may influence certainty in derived statistics. For species such as the African wild dog, where monitoring is both challenging and expensive, automated individual recognition could greatly expand and expedite conservation efforts.

First record of the servaline morph in a serval (Leptailurus serval Schreber, 1776) in Akagera National Park, Rwanda

The serval (Leptailurus serval) is a medium-sized felid that is widespread throughout Sub-Saharan Africa. We report on the first scientific record of the servaline morph in a serval in Akagera National Park, Rwanda. Though this morph has been documented in the forested ecosystems of West and Central Africa, the servaline morph has not been recorded in a predominantly savannah ecosystem. Further research into the prevalence of this morph outside of forest ecosystems and the adaptive advantage of the servaline coat pattern in servals is recommended. Our findings highlight the importance of conserving savannah ecosystems to preserve morphological diversity in a species.

Macroevolution of protective coloration across caterpillars reflects relationships with host plants

A critical function of animal coloration is avoiding attack, either by warning predators or reducing detectability. Evolution of these divergent strategies may depend on prey palatability and apparency to predators: conspicuous coloration may be favoured if species are distasteful, or habitats make hiding difficult; by contrast, camouflage may be effective if prey lack defences or environments are visually complex. For insect herbivores, host plants provide both chemical defence and the background against which they are detected or obscured; thus, plant traits may be key to coloration in these foundational terrestrial organisms. We use 1808 species of larval Lepidoptera to explore macroevolution of protective coloration strategy. We find that colour and pattern evolve jointly in caterpillars, similar to an array of species across the animal kingdom, while individual elements of coloration evolve closely with diet ecology. Consistent with key tenets of plant defence and plant-herbivore coevolutionary theory, conspicuous colours are associated with herbaceous host plants-thought to be defended by toxins-while camouflage colours and patterns are associated with woody plants and grasses. Contrary to theory, dietary specialization is not associated with conspicuous coloration. Our results add valuable insights into the evolutionary forces shaping colour and pattern in nature.

Appearance and suppression of Turing patterns under a periodically forced feed

Turing instability is a general and straightforward mechanism of pattern formation in reaction-diffusion systems, and its relevance has been demonstrated in different biological phenomena. Still, there are many open questions, especially on the robustness of the Turing mechanism. Robust patterns must survive some variation in the environmental conditions. Experiments on pattern formation using chemical systems have shown many reaction-diffusion patterns and serve as relatively simple test tools to study general aspects of these phenomena. Here, we present a study of sinusoidal variation of the input feed concentrations on chemical Turing patterns. Our experimental, numerical and theoretical analysis demonstrates that patterns may appear even at significant amplitude variation of the input feed concentrations. Furthermore, using time-dependent feeding opens a way to control pattern formation. The patterns settled at constant feed may disappear, or new patterns may appear from a homogeneous steady state due to the periodic forcing.

Recognition of Coat Pattern Variation and Broken Tail Phenomenon in the Asiatic Golden Cat (Catopuma temminckii)

Simple Summary

A variety of new survey technologies are continuously being developed and used in wildlife monitoring. Rapidly advancing and widely used camera trap survey technology has helped to capture data and gain insights into many species. The Eastern Himalayas is a global biodiversity hotspot with exceptionally high species diversity. The Asian golden cat is widely distributed in the Yarlung Zangbo Grand Canyon National Nature Reserve. It inhabits seasonal rain forests from 100 m above sea level to the Rhododendron forest up to 3500 m above sea level. Coat pattern variation in the Asian golden cat is particularly prominent in this region. The common color type is the most widely distributed, followed by nine other types. We found 10 coat pattern variations and two coat patterns with a broken tail made up 0.32% of independent photos taken during a long-term nine-year monitoring program. The variation in coat patterns is indicative of the geography of the region. Environmental conditions regulate and activate the genetic diversity of Asian golden cat phenotypes. This study further strengthened the understanding of the basic knowledge of golden cat color types and lays the foundation for exploring the diversity of golden cat color types at the molecular level.

Abstract

The Asian golden cat (Catopuma temminckii) is the most varied wild cat species in terms of coat color. Understanding coat pattern variation will help to elucidate the mechanisms behind it as well as its relationship with the environment. We conducted long-term (2013–2021) monitoring of Asian golden cats in the Yarlung Zangbo Grand Canyon National Nature Reserve, Tibet, using camera traps at 283 points over 89,991 camera days. A total of 620 cat photos were recorded, including 344 (55.48%) with recognizable color patterns. Vector graphics of the coat patterns were extracted from the field image data, which revealed 10 color types in the ratio common: cinnamon: reddish-brown long hair: ocelot: blackening: melanistic: gray: brown: brown short hair: pure black = 123:76:57:35:22:8:7:7:5:4. The genes for coat pattern variation are widespread in the Asian golden cat population and are relatively stable. The increase in population size intraspecific competition has led to the tail break phenotype in individual cats. The gene encoding for tail breakage in Asian golden cats remains unknown. This study provides basic information for understanding faunal diversity in the Eastern Himalayan biodiversity hotspot and serves as a reference for studies on the formation mechanisms for feline color pattern diversity.

Molecular tracking and prevalence of the red colour morph restricted to a harvested leopard population in South Africa

The red leopard (Panthera pardus) colour morph is a colour variant that occurs only in South Africa, where it is confined to the Central Bushveld bioregion. Red leopards have been spreading over the past 40 years, which raises the speculation that the prevalence of this phenotype is related to low dispersal of young individuals owing to high off‐take in the region. Intensive selective hunting tends to remove large resident male leopards from the breeding population, which gives young male leopards the chance to mate with resident female leopards that are more likely to be their relatives, eventually increasing the frequency of rare genetic variants. To investigate the genetic mechanisms underlying the red coat colour morph in leopards, and whether its prevalence in South Africa relates to an increase in genetic relatedness in the population, we sequenced exons of six coat colour‐associated genes and 20 microsatellite loci in twenty Wild‐type and four red leopards. The results were combined with demographic data available from our study sites. We found that red leopards own a haplotype in homozygosity identified by two SNPs and a 1 bp deletion that causes a frameshift in the tyrosinase‐related protein 1 (TYRP1), a gene known to be involved in the biosynthesis of melanin. Microsatellite analyses indicate clear signs of a population bottleneck and a relatedness of 0.11 among all pairwise relationships, eventually supporting our hypothesis that a rare colour morph in the wild has increased its local frequency due to low natal dispersal, while subject to high human‐induced mortality rate.

CamoEvo: An open access toolbox for artificial camouflage evolution experiments

Camouflage research has long shaped our understanding of evolution by natural selection, and elucidating the mechanisms by which camouflage operates remains a key question in visual ecology. However, the vast diversity of color patterns found in animals and their backgrounds, combined with the scope for complex interactions with receiver vision, presents a fundamental challenge for investigating optimal camouflage strategies. Genetic algorithms (GAs) have provided a potential method for accounting for these interactions, but with limited accessibility. Here, we present CamoEvo, an open-access toolbox for investigating camouflage pattern optimization by using tailored GAs, animal and egg maculation theory, and artificial predation experiments. This system allows for camouflage evolution within the span of just 10-30 generations (∼1-2 min per generation), producing patterns that are both significantly harder to detect and that are optimized to their background. CamoEvo was built in ImageJ to allow for integration with an array of existing open access camouflage analysis tools. We provide guides for editing and adjusting the predation experiment and GA as well as an example experiment. The speed and flexibility of this toolbox makes it adaptable for a wide range of computer-based phenotype optimization experiments.

A Multi-Point Identification Approach for the Recognition of Individual Leopards (Panthera pardus kotiya)

Simple Summary

All of the previous research on photography-based leopard identification was conducted based on the assumption that leopard spots and rosette formations do not change in shape or form. We observed 29 instances of changes to spot and rosette formations in continuously observed leopards at Yala National Park, Block 1. Since the previous approaches have flaws and errors, the same leopard may be misdiagnosed and counted numerous times, overestimating leopard populations if the spot and rosette formation of a leopard has changed. To address this issue, we developed the multi-point leopard identification method, which is a novel process for identifying Sri Lankan leopards. The minimum leopard population of Yala National Park, Block 1, on 31 March 2021, was established during the study.

Abstract

Visual leopard identifications performed with camera traps using the capture–recapture method only consider areas of the skin that are visible to the equipment. The method presented here considered the spot or rosette formations of either the two flanks or the face, and the captured images were then compared and matched with available photographs. Leopards were classified as new individuals if no matches were found in the existing set of photos. It was previously assumed that an individual leopard’s spot or rosette pattern would not change. We established that the spot and rosette patterns change over time and that these changes are the result of injuries in certain cases. When compared to the original patterns, the number of spots may be lost or reduced, and some spots or patterns may change in terms of their prominence, shape, and size. We called these changes “obliterate changes” and “rejig changes”, respectively. The implementation of an earlier method resulted in a duplication of leopard counts, achieving an error rate of more than 15% in the population at Yala National Park. The same leopard could be misidentified and counted multiple times, causing overestimated populations. To address this issue, we created a new two-step methodology for identifying Sri Lankan leopards. The multi-point identification method requires the evaluation of at least 9–10 spot areas before a leopard can be identified. Moreover, the minimum leopard population at the YNP 1 comprises at least 77 leopards and has a density of 0.5461 leopards per km².

Irregular spots on body surfaces of vertebrates induced by supercritical pitchfork bifurcations

The classical Turing mechanism containing a long-range inhibition and a short-range self-enhancement provides a type of explanation for the formation of patterns on body surfaces of some vertebrates, e.g., zebras, giraffes, and cheetahs. For other type of patterns (irregular spots) on body surfaces of some vertebrates, e.g., loaches, finless eels, and dalmatian dogs, the classical Turing mechanism no longer applies. Here, we propose a mechanism, i.e., the supercritical pitchfork bifurcation, which may explain the formation of this type of irregular spots, and present a method to quantify the similarity of such patterns. We assume that, under certain conditions, the only stable state of "morphogen" loses its stability and transitions to two newly generated stable states with the influence of external noise, thus producing such ruleless piebald patterns in space. The difference between the competitiveness of these two states may affect the resulting pattern. Moreover, we propose a mathematical model based on this conjecture and obtain this type of irregular patterns by numerical simulation. Furthermore, we also study the influence of parameters in the model on pattern structures and obtain the corresponding pattern structures of some vertebrates in nature, which verifies our conjecture.

Developmental genetics of color pattern establishment in cats

Intricate color patterns are a defining aspect of morphological diversity in the Felidae. We applied morphological and single-cell gene expression analysis to fetal skin of domestic cats to identify when, where, and how, during fetal development, felid color patterns are established. Early in development, we identify stripe-like alterations in epidermal thickness preceded by a gene expression pre-pattern. The secreted Wnt inhibitor encoded by Dickkopf 4 plays a central role in this process, and is mutated in cats with the Ticked pattern type. Our results bring molecular understanding to how the leopard got its spots, suggest that similar mechanisms underlie periodic color pattern and periodic hair follicle spacing, and identify targets for diverse pattern variation in other mammals.

Aposematism in mammals

Aposematic coloration is traditionally considered to signal unpalatability or toxicity. In mammals, most research has focused on just one form of defense, namely, noxious anal secretions, and its black-and-white advertisement as exemplified by skunks. The original formulation of aposematism, however, encompassed a broader range of morphological, physiological, and behavioral defenses, and there are many mammal species with black-and-white contrasting patterns that do not have noxious adaptations. Here, using Bayesian phylogenetic models and data from 1726 terrestrial nonvolant mammals we find that two aspects of conspicuous coloration, black-and-white coloration patterns on the head and body, advertise defenses that are morphological (spines, large body size), behavioral (pugnacity), and physiological (anal secretions), as well as being involved with sexual signaling and environmental factors linked to crypsis. Within Carnivora, defensive anal secretions are associated with complex black-and-white head patterns and longitudinal black-and-white body striping; in primates, larger bodied species exhibit irregular patches of black-and-white pelage; and in rodents, pugnacity is linked to sharp countershading and irregular blocks of white and black pelage. We show that black-and-white coloration in mammals is multifunctional, that it serves to warn predators of several defenses other than noxious anal secretions, and that aposematism in mammals is not restricted to carnivores.

Examining the molecular basis of coat color in a nocturnal primate family (Lorisidae)

Organisms use color for camouflage, sexual signaling, or as a warning sign of danger. Primates are one of the most vibrantly colored Orders of mammals. However, the genetics underlying their coat color are poorly known, limiting our ability to study molecular aspects of its evolution. The role of the melanocortin 1 receptor (MC1R) in color evolution has been implicated in studies on rocket pocket mice (Chaetodipus intermediusi), toucans (Ramphastidae), and many domesticated animals. From these studies, we know that changes in MC1R result in a yellow/red or a brown/black morphology. Here, we investigate the evolution of MC1R in Lorisidae, a monophyletic nocturnal primate family, with some genera displaying high contrast variation in color patterns and other genera being monochromatic. Even more unique, the Lorisidae family has the only venomous primate: the slow loris (Nycticebus). Research has suggested that the contrasting coat patterns of slow lorises are aposematic signals for their venom. If so, we predict the MC1R in slow lorises will be under positive selection. In our study, we found that Lorisidae MC1R is under purifying selection (ω = 0.0912). In Lorisidae MC1R, there were a total of 75 variable nucleotides, 18 of which were nonsynonymous. Six of these nonsynonymous substitutions were found on the Perodicticus branch, which our reconstructions found to be the only member of Lorisidae that has predominantly lighter coat color; no substitutions were associated with Nycticebus. Our findings generate new insight into the genetics of pelage color and evolution among a unique group of nocturnal mammals and suggest putative underpinnings of monochromatic color evolution in the Perodicticus lineage.

The Camouflage Machine: Optimizing protective coloration using deep learning with genetic algorithms

Evolutionary biologists frequently wish to measure the fitness of alternative phenotypes using behavioral experiments. However, many phenotypes are complex. One example is coloration: camouflage aims to make detection harder, while conspicuous signals (e.g., for warning or mate attraction) require the opposite. Identifying the hardest and easiest to find patterns is essential for understanding the evolutionary forces that shape protective coloration, but the parameter space of potential patterns (colored visual textures) is vast, limiting previous empirical studies to a narrow range of phenotypes. Here, we demonstrate how deep learning combined with genetic algorithms can be used to augment behavioral experiments, identifying both the best camouflage and the most conspicuous signal(s) from an arbitrarily vast array of patterns. To show the generality of our approach, we do so for both trichromatic (e.g., human) and dichromatic (e.g., typical mammalian) visual systems, in two different habitats. The patterns identified were validated using human participants; those identified as the best for camouflage were significantly harder to find than a tried-and-tested military design, while those identified as most conspicuous were significantly easier to find than other patterns. More generally, our method, dubbed the "Camouflage Machine," will be a useful tool for identifying the optimal phenotype in high dimensional state spaces.

Towards an ecology of protective coloration

The strategies underlying different forms of protective coloration are well understood but little attention has been paid to the ecological, life-history and behavioural circumstances under which they evolve. While some comparative studies have investigated the ecological correlates of aposematism, and background matching, the latter particularly in mammals, few have examined the ecological correlates of other types of protective coloration. Here, we first outline which types of defensive coloration strategies may be exhibited by the same individual; concluding that many protective coloration mechanisms can be employed simultaneously, particularly in conjunction with background matching. Second, we review the ecological predictions that have been made for each sort of protective coloration mechanism before systematically surveying phylogenetically controlled comparative studies linking ecological and social variables to antipredator defences that involve coloration. We find that some a priori predictions based on small-scale empirical studies and logical arguments are indeed supported by comparative data, especially in relation to how illumination affects both background matching and self-shadow concealment through countershading; how body size is associated with countershading, motion dazzle, flash coloration and aposematism, although only in selected taxa; how immobility may promote background matching in ambush predators; and how mobility may facilitate motion dazzle. Examination of nearly 120 comparative tests reveals that many focus on ecological variables that have little to do with predictions derived from antipredator defence theory, and that broad-scale ecological studies of defence strategies that incorporate phylogenetics are still very much in their infancy. We close by making recommendations for future evolutionary ecological research.

Genetics and Evolution of Mammalian Coat Pigmentation

The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.

Shifts in the developmental rate of spadefoot toad larvae cause decreased complexity of post-metamorphic pigmentation patterns

Amphibian larvae are plastic organisms that can adjust their growth and developmental rates to local environmental conditions. The consequences of such developmental alterations have been studied in detail, both at the phenotypic and physiological levels. While largely unknown, it is of great importance to assess how developmental alterations affect the pigmentation pattern of the resulting metamorphs, because pigmentation is relevant for communication, mate choice, and camouflage and hence influences the overall fitness of the toads. Here we quantify the variation in several aspects of the pigmentation pattern of juvenile spadefoot toads experimentally induced to accelerate their larval development in response to decreased water level. It is known that induced developmental acceleration comes at the cost of reduced size at metamorphosis, higher metabolic rate, and increased oxidative stress. In this study, we show that spadefoot toads undergoing developmental acceleration metamorphosed with a less complex, more homogeneous, darker dorsal pattern consisting of continuous blotches, compared to the more contrasted pattern with segregated blotches and higher fractal dimension in normally developing individuals, and at a smaller size. We also observed a marked effect of population of origin in the complexity of the pigmentation pattern. Complexity of the post-metamorphic dorsal pigmentation could therefore be linked to pre-metamorphic larval growth and development.

Analog Resonance Computation: A New Model for Human Cognition

Early models of human cognition appeared to posit the brain as a collection of discrete digital computing modules with specific data processing functions. More recent theories such as the Hierarchically Mechanistic Mind characterize the brain as a massive hierarchy of interconnected and adaptive circuits whose primary aim is to reduce entropy. However, studies in high workload/stress situations show that human behavior is often error prone and seemingly irrational. Rather than regarding such behavior to be uncharacteristic, this paper suggest that such "atypical" behavior provides the best information on which to base theories of human cognition. Rather than using a digital paradigm, human cognition should be seen as an analog computer based on resonating circuits whose primary driver is to constantly extract information from the massively complex and rapidly changing world around us to construct an internal model of reality that allows us to rapidly respond to the threats and opportunities.

A "Numerical Evo-Devo" Synthesis for the Identification of Pattern-Forming Factors

Animals display extensive diversity in motifs adorning their coat, yet these patterns have reproducible orientation and periodicity within species or groups. Morphological variation has been traditionally used to dissect the genetic basis of evolutionary change, while pattern conservation and stability in both mathematical and organismal models has served to identify core developmental events. Two patterning theories, namely instruction and self-organisation, emerged from this work. Combined, they provide an appealing explanation for how natural patterns form and evolve, but in vivo factors underlying these mechanisms remain elusive. By bridging developmental biology and mathematics, novel frameworks recently allowed breakthroughs in our understanding of pattern establishment, unveiling how patterning strategies combine in space and time, or the importance of tissue morphogenesis in generating positional information. Adding results from surveys of natural variation to these empirical-modelling dialogues improves model inference, analysis, and in vivo testing. In this evo-devo-numerical synthesis, mathematical models have to reproduce not only given stable patterns but also the dynamics of their emergence, and the extent of inter-species variation in these dynamics through minimal parameter change. This integrative approach can help in disentangling molecular, cellular and mechanical interaction during pattern establishment.

Coloration in Mammals

Mammalian colors and color patterns are some of the most diverse and conspicuous traits found in nature and have been widely studied from genetic/developmental and evolutionary perspectives. In this review we first discuss the proximate causes underlying variation in pigment type (i.e., color) and pigment distribution (i.e., color pattern) and highlight both processes as having a distinct developmental basis. Then, using multiple examples, we discuss ultimate factors that have driven the evolution of coloration differences in mammals, which include background matching, intra- and interspecific signaling, and physiological influences. Throughout, we outline bridges between developmental and functional investigatory approaches that help broaden knowledge of mammals' memorable external appearances, and we point out areas for future interdisciplinary research.

New record on Asiatic Golden Cat Catopuma temminckii Vigors & Horsfield, 1827 (Mammalia: Carnivora: Felidae): photographic evidence of its westernmost distribution in Gaurishankar Conservation Area, Nepal

The Asiatic Golden Cat Catopuma temminckii is poorly known in Nepal and was previously recorded only twice in the eastern part of the country.  We conducted a camera trap survey in the Lapchi Valley (32km2) of Gaurishankar Conservation Area (GCA), a protected area in north-central Nepal, from October 2018 to April 2019. Eleven cameras were deployed to record mammalian diversity in a 2×2 km2 grid across Lapchi block of GCA.  During the study period, four photos and three videos (each of 10 seconds length) of Asiatic Golden Cats were recorded at an elevation of 2,540m at a single camera trap station.  This is the first photographic record of Asiatic Golden Cat in this region of Nepal extending the distribution of the species further west in the Himalaya.  A more detailed study on its distribution, population size and behaviour is warranted in the near future to implement appropriate conservation measures.  

Ecological, behavioral, and phylogenetic influences on the evolution of dorsal color pattern in geckos

The dorsal surfaces of many taxonomic groups often feature repetitive pattern elements consisting of stripes, spots, or bands. Here, we investigate how distinct categories of camouflage pattern work by relating them to ecological and behavioral traits in 439 species of gecko. We use phylogenetic comparative methods to test outstanding hypotheses based on camouflage theory and research in other taxa. We found that bands are associated with nocturnal activity, suggesting bands provide effective camouflage for motionless geckos resting in refugia during the day. A predicted association between stripes and diurnal activity was not supported, suggesting that stripes do not work via dazzle camouflage mechanisms in geckos. This, along with a lack of support for our prediction that plain patterning should be associated with open habitats, suggests that similar camouflage patterns do not work in consistent ways across taxa. We also found that plain and striped lineages frequently switched between using open or closed habitats, whereas spotted lineages rarely transitioned. This suggests that pattern categories differ in how specialized or generalized their camouflage is. This result has ramifications for theory on how camouflage compromises to background heterogeneity and how camouflage pattern might influence evolutionary trajectories.

Melanism evolution in the cat family is influenced by intraspecific communication under low visibility

Melanism in the cat family has been associated with functions including camouflage, thermoregulation and parasite resistance. Here we investigate a new hypothesis proposing that the evolution of melanism in cats has additionally been influenced by communication functions of body markings. To evaluate this hypothesis, we assembled a species-level data set of morphological (body marks: white marks on the backs of ears) and ecological (circadian activity: arrhythmic/nocturnal, and environmental preference: open/closed) characteristics that could be associated with communication via body markings, and combined these data with a dated molecular phylogeny. Next, we tested the association between melanism and communication, first by relating species’ body marks with their ecological conditions, using a Bayesian implementation of the threshold model. Second, to explore the evolution of characteristics potentially influencing melanism in cat species, we modeled their evolution relative to melanism using models of coordinated vs. independent character changes. Our results suggest that white marks are associated with intraspecific communication between individuals that have non-melanistic phenotypes, as well as towards melanistic individuals (without white marks). The absence of white marks in a melanistic individual tends to be a limiting condition for intraspecific visual communication at night, resulting in an evolutionary dilemma for these species, i.e. to be almost invisible at night, but not to communicate visually. The comparative analysis of several evolutionary models indicated more support for the evolution of melanism being coordinated with the evolution of arrhythmic activity and white marks on the backs of ears.

Optimizing colour for camouflage and visibility using deep learning: the effects of the environment and the observer's visual system

Avoiding detection can provide significant survival advantages for prey, predators, or the military; conversely, maximizing visibility would be useful for signalling. One simple determinant of detectability is an animal's colour relative to its environment. But identifying the optimal colour to minimize (or maximize) detectability in a given natural environment is complex, partly because of the nature of the perceptual space. Here for the first time, using image processing techniques to embed targets into realistic environments together with psychophysics to estimate detectability and deep neural networks to interpolate between sampled colours, we propose a method to identify the optimal colour that either minimizes or maximizes visibility. We apply our approach in two natural environments (temperate forest and semi-arid desert) and show how a comparatively small number of samples can be used to predict robustly the most and least effective colours for camouflage. To illustrate how our approach can be generalized to other non-human visual systems, we also identify the optimum colours for concealment and visibility when viewed by simulated red-green colour-blind dichromats, typical for non-human mammals. Contrasting the results from these visual systems sheds light on why some predators seem, at least to humans, to have colouring that would appear detrimental to ambush hunting. We found that for simulated dichromatic observers, colour strongly affected detection time for both environments. In contrast, trichromatic observers were more effective at breaking camouflage.

Isolating and quantifying the role of developmental noise in generating phenotypic variation

Genotypic variation, environmental variation, and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals. Developmental noise, which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fixed, also contributes to phenotypic variation. While evolutionary biology has long focused on teasing apart the relative contribution of genes and environment to phenotypic variation, our understanding of the role of developmental noise has lagged due to technical difficulties in directly measuring the contribution of developmental noise. The influence of developmental noise is likely underestimated in studies of phenotypic variation due to intrinsic mechanisms within organisms that stabilize phenotypes and decrease variation. Since we are just beginning to appreciate the extent to which phenotypic variation due to stochasticity is potentially adaptive, the contribution of developmental noise to phenotypic variation must be separated and measured to fully understand its role in evolution. Here, we show that variation in the component of the developmental process corresponding to environmental and genetic factors (here treated together as a unit called the LALI-type) versus the contribution of developmental noise, can be distinguished for leopard gecko (Eublepharis macularius) head color patterns using mathematical simulations that model the role of random variation (corresponding to developmental noise) in patterning. Specifically, we modified the parameters of simulations corresponding to variation in the LALI-type to generate the full range of phenotypic variation in color pattern seen on the heads of eight leopard geckos. We observed that over the range of these parameters, variation in color pattern due to LALI-type variation exceeds that due to developmental noise in the studied gecko cohort. However, the effect of developmental noise on patterning is also substantial. Our approach addresses one of the major goals of evolutionary biology: to quantify the role of stochasticity in shaping phenotypic variation.

Extending the Mathematical Palette for Developmental Pattern Formation: Piebaldism

Here, we present a theoretical investigation with potential insights on developmental mechanisms. Three biological factors, consisting of two diffusing factors and a cell-autonomous immobile transcription factor are combined with different feedback mechanisms. This results in four different situations or fur patterns. Two of them reproduce classical Turing patterns: (1) regularly spaced spots, (2) labyrinth patterns or straight lines with an initial slope in the activation of the transcription factor. The third situation does not lead to patterns, but results in different homogeneous color tones. Finally, the fourth one sheds new light on the possible mechanisms leading to the formation of piebald patterns exemplified by the random patterns on the fur of some cows' strains and Dalmatian dogs. Piebaldism is usually manifested as white areas of fur, hair, or skin due to the absence of pigment-producing cells in those regions. The distribution of the white and colored zones does not reflect the classical Turing patterns. We demonstrate that these piebald patterns are of transient nature, developing from random initial conditions and relying on a system's bistability. We show numerically that the presence of a cell-autonomous factor not only expands the range of reaction diffusion parameters in which a pattern may arise, but also extends the pattern-forming abilities of the reaction-diffusion equations.

How do complex animal signals evolve?

Animal signals-involving combinations of acoustic, chemical, visual, and behavioral cues-are among the most diverse traits in nature. Testing hypotheses about signal evolution has been hampered by difficulties with comparing highly divergent signals among species. In this Primer, I describe recent advances in capturing signals and studying their evolution. I highlight new findings using an information theory-based approach to quantifying signal variation in the diverse birds-of-paradise. Growing access to signal databases in tandem with development of new analytical tools will open up new avenues for studying the proximate mechanisms and ultimate evolutionary causes of signal variation, both within and among species.

Seeing spots: quantifying mother-offspring similarity and assessing fitness consequences of coat pattern traits in a wild population of giraffes (Giraffa camelopardalis)

Polymorphic phenotypes of mammalian coat coloration have been important to the study of genetics and evolution, but less is known about the inheritance and fitness consequences of individual variation in complex coat pattern traits such as spots and stripes. Giraffe coat markings are highly complex and variable and it has been hypothesized that variation in coat patterns most likely affects fitness by camouflaging neonates against visually hunting predators. We quantified complex coat pattern traits of wild Masai giraffes using image analysis software, determined the similarity of spot pattern traits between mother and offspring, and assessed whether variation in spot pattern traits was related to fitness as measured by juvenile survival. The methods we described could comprise a framework for objective quantification of complex mammal coat pattern traits based on photographic coat pattern data. We demonstrated that some characteristics of giraffe coat spot shape were likely to be heritable, as measured by mother-offspring regression. We found significant variation in juvenile survival among phenotypic groups of neonates defined by multivariate clustering based on spot trait measurement variables. We also found significant variation in neonatal survival associated with spot size and shape covariates. Larger spots (smaller number of spots) and irregularly shaped or rounder spots (smaller aspect ratio) were correlated with increased survival. These findings will inform investigations into developmental and genetic architecture of complex mammal coat patterns and their adaptive value.

Cultural evolution of military camouflage

While one has evolved and the other been consciously created, animal and military camouflage are expected to show many similar design principles. Using a unique database of calibrated photographs of camouflage uniform patterns, processed using texture and colour analysis methods from computer vision, we show that the parallels with biology are deeper than design for effective concealment. Using two case studies we show that, like many animal colour patterns, military camouflage can serve multiple functions. Following the dissolution of the Warsaw Pact, countries that became more Western-facing in political terms converged on NATO patterns in camouflage texture and colour. Following the break-up of the former Yugoslavia, the resulting states diverged in design, becoming more similar to neighbouring countries than the ancestral design. None of these insights would have been obtained using extant military approaches to camouflage design, which focus solely on concealment. Moreover, our computational techniques for quantifying pattern offer new tools for comparative biologists studying animal coloration.This article is part of the themed issue 'Animal coloration: production, perception, function and application'.

Shape matters: animal colour patterns as signals of individual quality

Colour patterns (e.g. irregular, spotted or barred forms) are widespread in the animal kingdom, yet their potential role as signals of quality has been mostly neglected. However, a review of the published literature reveals that pattern itself (irrespective of its size or colour intensity) is a promising signal of individual quality across species of many different taxa. We propose at least four main pathways whereby patterns may reliably reflect individual quality: (i) as conventional signals of status, (ii) as indices of developmental homeostasis, (iii) by amplifying cues of somatic integrity and (iv) by amplifying individual investment in maintenance activities. Methodological constraints have traditionally hampered research on the signalling potential of colour patterns. To overcome this, we report a series of tools (e.g. colour adjacency and pattern regularity analyses, Fourier and granularity approaches, fractal geometry, geometric morphometrics) that allow objective quantification of pattern variability. We discuss how information provided by these methods should consider the visual system of the model species and behavioural responses to pattern metrics, in order to allow biologically meaningful conclusions. Finally, we propose future challenges in this research area that will require a multidisciplinary approach, bringing together inputs from genetics, physiology, behavioural ecology and evolutionary-developmental biology.

Mapping black panthers: Macroecological modeling of melanism in leopards (Panthera pardus)

The geographic distribution and habitat association of most mammalian polymorphic phenotypes are still poorly known, hampering assessments of their adaptive significance. Even in the case of the black panther, an iconic melanistic variant of the leopard (Panthera pardus), no map exists describing its distribution. We constructed a large database of verified records sampled across the species’ range, and used it to map the geographic occurrence of melanism. We then estimated the potential distribution of melanistic and non-melanistic leopards using niche-modeling algorithms. The overall frequency of melanism was ca. 11%, with a significantly non-random spatial distribution. Distinct habitat types presented significantly different frequencies of melanism, which increased in Asian moist forests and approached zero across most open/dry biomes. Niche modeling indicated that the potential distributions of the two phenotypes were distinct, with significant differences in habitat suitability and rejection of niche equivalency between them. We conclude that melanism in leopards is strongly affected by natural selection, likely driven by efficacy of camouflage and/or thermoregulation in different habitats, along with an effect of moisture that goes beyond its influence on vegetation type. Our results support classical hypotheses of adaptive coloration in animals (e.g. Gloger’s rule), and open up new avenues for in-depth evolutionary analyses of melanism in mammals.