Genetically Encoded Lizard Color Divergence for Camouflage and Thermoregulation.

Local adaptation is critical in speciation and evolution, yet comprehensive studies on proximate and ultimate causes of local adaptation are generally scarce. Here, we integrated field ecological experiments, genome sequencing, and genetic verification to demonstrate both driving forces and molecular mechanisms governing local adaptation of body coloration in a lizard from the Qinghai-Tibet Plateau. We found dark lizards from the cold meadow population had lower spectrum reflectance but higher melanin contents than light counterparts from the warm dune population. Additionally, the colorations of both dark and light lizards facilitated the camouflage and thermoregulation in their respective microhabitat simultaneously. More importantly, by genome resequencing analysis, we detected a novel mutation in Tyrp1 that underpinned this color adaptation. The allele frequencies at the site of SNP 459# in the gene of Tyrp1 are 22.22% G/C and 77.78% C/C in dark lizards and 100% G/G in light lizards. Model-predicted structure and catalytic activity showed that this mutation increased structure flexibility and catalytic activity in enzyme TYRP1, and thereby facilitated the generation of eumelanin in dark lizards. The function of the mutation in Tyrp1 was further verified by more melanin contents and darker coloration detected in the zebrafish injected with the genotype of Tyrp1 from dark lizards. Therefore, our study demonstrates that a novel mutation of a major melanin-generating gene underpins skin color variation co-selected by camouflage and thermoregulation in a lizard. The resulting strong selection may reinforce adaptive genetic divergence and enable the persistence of adjacent populations with distinct body coloration.

Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation.

Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.

Temperature differently affects body pigmentation of the paper wasp Polistes dominula along an urban and a wider geographical gradient.

In insects, different pigments, such as melanins and pterins, are involved in thermoregulation. The degree of melanisation often varies along geographical gradients, according to the so-called thermal melanism hypothesis, i.e. darker forms are found in colder places because they can warm up more quickly. Similarly, pterins work as heat sinks and thus are expected to be more abundant in colder sites. Cities, which are warmer than surrounding areas (Urban Heat Island (UHI) effect), might also be expected to influence pigmentation, although studies are lacking. Here, we sampled workers of the social paper wasp Polistes dominula (Christ, 1791) (Vespidae) across an urbanisation gradient in an Italian metropolis and used iNaturalist pictures of this species across Italy to study pigmentation patterns at both urban and larger geographical scales. We found a lower yellow intensity of abdominal spots at warmer locations. Scanning Electron Microscopy strongly suggested that yellow colouration is due xanthopterin, known to be the heat sink molecule in other social vespids. Thus, wasps from warmer (i.e., urban) environments are likely to have fewer xanthopterin granules, in line with the lack of need for heat storage due to the local thermal gradient (UHI effect). At the country level, we found that wasps at higher latitudes had smaller yellow spots on the thorax and only two spots instead of four at higher altitudes, in full accordance with the thermal melanism hypothesis. In conclusion, climatic conditions seem to affect insect colour patterns both along urban and wider geographical gradients, although colour changes may affect different body parts and pigments likely according to different needs.

Adaptive and non-adaptive convergent evolution in feather reflectance of California Channel Islands songbirds.

Convergent evolution is widely regarded as a signature of adaptation. However, testing the adaptive consequences of convergent phenotypes is challenging, making it difficult to exclude non-adaptive explanations for convergence. Here, we combined feather reflectance spectra and phenotypic trajectory analyses with visual and thermoregulatory modelling to test the adaptive significance of dark plumage in songbirds of the California Channel Islands. By evolving dark dorsal plumage, island birds are generally less conspicuous to visual-hunting raptors in the island environment than mainland birds. Dark dorsal plumage also reduces the energetic demands associated with maintaining homeothermy in the cool island climate. We also found an unexpected pattern of convergence, wherein the most divergent island populations evolved greater reflectance of near-infrared radiation. However, our heat flux models indicate that elevated near-infrared reflectance is not adaptive. Analysis of feather microstructure suggests that mainland-island differences are related to coloration of feather barbs and barbules rather than their structure. Our results indicate that adaptive and non-adaptive mechanisms interact to drive plumage evolution in this system. This study sheds light on the mechanisms driving the association between dark colour and wet, cold environments across the tree of life, especially in island birds.

ebony underpins Batesian mimicry in melanic stoneflies.

The evolution of Batesian mimicry - whereby harmless species avoid predation through their resemblance to harmful species - has long intrigued biologists. In rare cases, Batesian mimicry is linked to intraspecific colour variation, in which only some individuals within a population resemble a noxious 'model'. Here, we assess intraspecific colour variation within a widespread New Zealand stonefly, wherein highly melanized individuals of Zelandoperla closely resemble a chemically defended aposematic stonefly, Austroperla cyrene. We assess convergence in the colour pattern of these two species, compare their relative palatability to predators, and use genome-wide association mapping to assess the genetic basis of this resemblance. Our analysis reveals that melanized Zelandoperla overlap significantly with Austroperla in colour space but are significantly more palatable to predators, implying that they are indeed Batesian mimics. Analysis of 194,773 genome-wide SNPs reveals an outlier locus (ebony) strongly differentiating melanic versus non-melanic Zelandoperla. Genotyping of 338 specimens from a single Zelandoperla population indicates that ebony explains nearly 70% of the observed variance in melanism. As ebony has a well-documented role in insect melanin biosynthesis, our findings indicate this locus has a conserved function across deeply divergent hexapod lineages. Distributional records suggest a link between the occurrence of melanic Zelandoperla and the forested ecosystems where the model Austroperla is abundant, suggesting the potential for adaptive shifts in this system underpinned by environmental change.

Secondary Sexual Trait Melanization in "Black" Scavenger Flies: Nutritional Plasticity and Its Evolution.

AbstractThe black scavenger fly Sepsis thoracica exhibits polyphenic development resulting in alternate small black and large amber male morphs. Although the behavior, ecology, and physiology of both morphs are being scrutinized, the evolutionary origins of the nutritional polyphenism remain poorly understood. I here use a comparative approach to study variation in the degree of melanization of the forefemur-a secondary sexual trait. Melanization showed nutritional plasticity in all species, and character mapping suggests polyphenic development to represent the ancestral character state that was lost repeatedly. That is, interspecific variation among the studied species is mainly caused by the loss and not the gain of polyphenic development. Coevolution between male melanization and mating system differences further implicates sexual selection in the evolution of male melanization. These findings highlight the usefulness of comparative and natural history data in shedding new light on the evolution of phenotypic variation.

Thermal Costs and Benefits of Replicated Color Evolution in the White Sands Desert Lizard Community.

AbstractTraits often contribute to multiple functions, complicating our understanding of the selective pressures that influence trait evolution. In the Chihuahuan Desert, predation is thought to be the primary driver of cryptic light coloration in three White Sands lizard species relative to the darker coloration of populations on adjacent dark soils. However, coloration also influences radiation absorption and thus animal body temperatures. We combined comparative physiological experiments and biophysical models to test for thermal consequences of evolving different color morphs in White Sands across the three species. While light and dark morphs have not evolved different physiological heat limits within species, differences in radiation absorption between morphs lead to body temperature differences that impact relative overheating risk and activity patterns. Moreover, for all three species, an idealized morph that matches the White Sands substrate would have considerably less activity time, by approximately 1 month, than existing light morphs. Overall, there are both benefits and costs to greater substrate matching, the balance of which may prevent the evolution of optimal crypsis. Our work highlights the importance of color in dictating thermal performance and the complexity inherent in understanding the evolution of coloration.

Colour scales with climate in North American ratsnakes: a test of the thermal melanism hypothesis using community science images.

Animal colour is a complex trait shaped by multiple selection pressures that can vary across geography. The thermal melanism hypothesis predicts that darker coloration is beneficial to animals in colder regions because it allows for more rapid solar absorption. Here, we use community science images of three closely related species of North American ratsnakes (genus Pantherophis) to examine if climate predicts colour variation across range-wide scales. We predicted that darker individuals are found in colder regions and higher elevations, in accordance with the thermal melanism hypothesis. Using an unprecedented dataset of over 8000 images, we found strong support for temperature as a key predictor of darker colour, supporting thermal melanism. We also found that elevation and precipitation are predictive of colour, but the direction and magnitude of these effects were more variable across species. Our study is the first to quantify colour variation in Pantherophis ratsnakes, highlighting the value of community science images for studying range-wide colour variation.

Skin structure, coloration, and habitat utilization in typical and melanistic morphs of the grass snake (Natrix natrix).

Melanism is a polymorphic phenotype caused by the number and density of melanocyte cells producing melanin pigment in the skin and widely observed in snakes. The frequency of this coloration in populations is associated with its opposing fitness consequences and can be closely related to species-specific characteristics such as sex, reproduction, and nutrition, as well as environmental factors such as climate and geography. Although melanism is frequently seen in snakes, the skin structure of melanistic individuals has not been studied in detail. Also, the impact of the black phenotype on habitat use has not yet been clarified in this species. Here, we show a comparison of typical and melanistic morphs of the grass snake Natrix natrix population of Anatolia for the first time in terms of skin structure, habitat, and sex. We found that melanistic individuals, in which partial melanism is more abundant than total melanism, comprise 13% of the population. Melanocyte area of the skin is 1.4 times greater in melanistic compared to the typical individuals. The epidermis is thicker in typical morphs by 7.7%. Hinge regions between adjacent scales do not bare melanocytes in both morphs. As for habitat utilization, we revealed that melanistic individuals of the Isikli population tend to occur closer to water bodies than typical ones. Our data provide a new perspective on poorly known aspects of color polymorphism and habitat use of widely distributed, semi-aquatic Natrix natrix.

Climate and body size have differential roles on melanism evolution across workers in a worldwide ant genus.

One of the main aspects associated with the diversity in animal colour is the variation in melanization levels. In ectotherms, melanism can be advantageous in aiding thermoregulation through heat absorption. Darker bodies may also serve as a shield from harmful UV-B radiation. Melanism may also confer protection against parasites and predators through improving immunity responses and camouflage in regions with high precipitation, with complex and shaded vegetations and greater diversity of pathogens and parasites. We studied melanism evolution in the globally distributed ant genus Pheidole under the pressures of temperature, UV-B radiation and precipitation, while considering the effects of body size and nest habit, traits that are commonly overlooked. More importantly, we account for worker caste polymorphism, which is marked by distinct roles and behaviours. We revealed for the first time distinct evolutionary trajectories for each worker subcaste. As expected, major workers from species inhabiting locations with lower temperatures and higher precipitation tend to be more melanised. Curiously, we show a slight trend where minor workers of larger species also tend to have darker bodies when inhabiting regions with higher precipitation. Lastly, we did not find evidence for the effects of UV-B radiation and nest habit in the lightness variation of workers. Our paper explores the evolution of ant melanization considering a marked ant worker polymorphism and a wide range of ecological factors. We discuss our findings under the light of the Thermal Melanism Hypothesis, the Photoprotection Hypothesis and the Gloger's Rule.

Identification of two new recessive MC1R alleles in red-coloured Evolèner cattle and other breeds.

Sequence variations in the melanocortin-1 receptor (MC1R) gene are associated with melanism in different animal species. Six functionally relevant alleles have been described in cattle to date. In a hypothesis-free approach we performed a genome-wide allelic association study with black, red and wild-coloured cattle of three Alpine cattle breeds (Eringer, Evolèner and Valdostana), revealing a single significant association signal close to the MC1R gene. We searched for candidate causative variants by sequencing the entire coding sequence and identified two novel protein-changing variants. We propose designating the mutant alleles at MC1R:c.424C>T as ev1 and at MC1R:c.263G>A as ev2 . Both affect conserved amino acid residues in functionally important transmembrane domains (p.Arg142Cys and p.Ser88Asn). Both alleles segregate predominantly in the Swiss Evolèner breed. They occur in other European cattle breeds such as Abondance and Rotes Höhenvieh as well. We observed almost perfect association between the MC1R genotypes and the coat colour phenotype in a cohort of 513 black, red and wild-coloured cattle. Animals carrying two copies of MC1R loss-of-function alleles or that were compound heterozygous for e, ev1 , or ev2 have a red to dark red (chestnut-like red) coat colour. These findings expand the spectrum of causal MC1R variants causing recessive red in cattle.

Climatic conditions and prevalence of melanistic snakes-contrasting effects of warm springs and mild winters.

Climate change is one of the greatest challenges that wildlife is facing. Rapid shifts in climatic conditions may accelerate evolutionary changes in populations as a result of strong selective pressure. Most studies focus on the impact of climatic conditions on phenologies and annual cycles, whereas there are fewer reports of empirical support for climate-driven changes in the phenotypic variability of free-living populations. We investigated whether climatic variables explain the prevalence of colour polymorphism in a population of the grass snake (Natrix natrix) with two morphotypes, the melanistic and non-melanistic ones, in the period 1981-2013. We found that the prevalence of the black phenotype was negatively related to spring temperature and winter harshness, expressed as the number of snow days. According to the thermal melanism hypothesis, a high predation rate during warmer springs may override relaxed thermal benefits and vice versa, i.e. black individuals may perform better than typical ones when thermal conditions in spring are unfavourable. In turn, because they are smaller, melanistic individuals may be exposed to a higher risk of winter mortality, particularly during longer winters. We highlight the need for more studies on the effects of climatic conditions on temporal variation in melanism prevalence in other populations and species as well as in various geographic regions.

Climate predicts both visible and near-infrared reflectance in butterflies.

Climatic gradients frequently predict large-scale ecogeographical patterns in animal coloration, but the underlying causes are often difficult to disentangle. We examined ecogeographical patterns of reflectance among 343 European butterfly species and isolated the role of selection for thermal benefits by comparing animal-visible and near-infrared (NIR) wavebands. NIR light accounts for ~50% of solar energy but cannot be seen by animals so functions primarily in thermal control. We found that reflectance of both dorsal and ventral surfaces shows thermally adaptive correlations with climatic factors including temperature and precipitation. This adaptive variation was more prominent in NIR than animal-visible wavebands and for body regions (thorax-abdomen and basal wings) that are most important for thermoregulation. Thermal environments also predicted the reflectance difference between dorsal and ventral surfaces, which may be due to modulation between requirements for heating and cooling. These results highlight the importance of climatic gradients in shaping the reflectance properties of butterflies at a continent-wide scale.

Rethinking Gloger's Rule: Climate, Light Environments, and Color in a Large Family of Tropical Birds (Furnariidae).

AbstractEcogeographic rules provide a framework within which to test evolutionary hypotheses of adaptation. Gloger's rule predicts that endothermic animals should have darker colors in warm/rainy climates. This rule also predicts that animals should be more rufous in warm/dry climates, the so-called complex Gloger's rule. Empirical studies frequently demonstrate that animals are darker in cool/wet climates rather than in warm/wet climates. Furthermore, sensory ecology predicts that, to enhance crypsis, animals should be darker in darker light environments. We aimed to disentangle the effects of climate and light environments on plumage color in the large Neotropical passerine family Furnariidae. We found that birds in cooler and rainier climates had darker plumage even after controlling for habitat type. Birds in darker habitats had darker plumage even after controlling for climate. The effects of temperature and precipitation interact so that the negative effect of precipitation on brightness is strongest in cool temperatures. Finally, birds tended to be more rufous in warm/dry habitats but also, surprisingly, in cool/wet locales. We suggest that Gloger's rule results from complementary selective pressures arising from myriad ecological factors, including crypsis, thermoregulation, parasite deterrence, and resistance to feather abrasion.

Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle.

Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle (Chelonia mydas) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq; 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds (n = 158). Our results support genetic divergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation of C. mydas to the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.

The Structure of Causal Explanations in Population Biology.

The scope of this paper can be clarified by means of a well-known phenomenon that is usually called 'industrial melanism': the fact that the melanic form of the peppered moth became dominant in industrial areas in England in the second half of the nineteenth century. Such changes in relative phenotype frequencies are important explananda for population biologists. Apart from trying to explain such changes over time, population biologists also often try to explain differences between populations, e.g. why yellow shell colour is dominant in certain colonies of land snails and almost absent in other colonies. The causal explanations that are given to address such explananda are the objects of analysis in this paper. Our primary aim is to explicate their structure: we want to capture the typical ingredients of causal explanations in population biology, and their organisation. Based on this explication, we discuss how natural selection fits into recent mechanical philosophy of science, and engage in the debate on the nature of evolutionary theory.

Darker ants dominate the canopy: Testing macroecological hypotheses for patterns in colour along a microclimatic gradient.

Gradients in cuticle lightness of ectotherms have been demonstrated across latitudes and elevations. Three key hypotheses have been used to explain these macroecological patterns: the thermal melanism hypothesis (TMH), the melanism-desiccation hypothesis (MDH) and the photo-protection hypothesis (PPH). Yet the broad abiotic measures, such as temperature, humidity and UV-B radiation, typically used to detect these ecogeographical patterns, are a poor indication of the microenvironment experienced by small, cursorial ectotherms like ants. We tested whether these macroecological hypotheses explaining cuticle lightness held at habitat and microclimatic level by using a vertical gradient within a tropical rainforest. We sampled 222 ant species in lowland, tropical rainforest across four vertical strata: subterranean, ground, understory and canopy. We recorded cuticle lightness, abundance and estimated body size for each species and calculated an assemblage-weighted mean for cuticle lightness and body size for each vertical stratum. Abiotic variables (air temperature, vapour pressure deficit and UV-B radiation) were recorded for each vertical stratum. We found that cuticle lightness of ant assemblages was vertically stratified: ant assemblages in the canopy and understory were twice as dark as assemblages in ground and subterranean strata. Cuticle lightness was not correlated with body size, and there was no support for the TMH. Rather, we attribute this cline in cuticle lightness to a combination of the MDH and the PPH. Our findings indicate that broad macroecological patterns can be detected at much smaller spatial scales and that microclimatic gradients can shape trait variation, specifically the cuticle lightness of ants. These results suggest that any changes to microclimate that occur due to land-use change or climate warming could drive selection of ants based on cuticle colour, altering assemblage structure and potentially ecosystem functioning.

Melanism, body size, and sex ratio in snakes-new data on the grass snake (Natrix natrix) and synthesis.

It is postulated that melanism in ectotherms is adaptive by enhancing thermoregulation, subsequent resource acquisition, and growth. Such effects may differ between the sexes as a result of the differential costs of self-maintenance and reproduction, but empirical support for the sex-specific consequences of melanism remains inconsistent. We studied the effects of melanism on body size and sex ratio in a population of the European grass snake (Natrix natrix) in SE Poland and also carried out a systematic review of the literature on the consequences of melanism in terrestrial snakes. Melanistic grass snakes of both sexes appeared to be smaller than the typical phenotype, which indicates higher predation pressure and minimal thermal benefits for black individuals. A female-biased sex ratio was observed in the typical phenotype, but not in melanistic snakes, suggesting that the costs for females and/or benefits for males are higher in melanistic individuals. In conjunction with earlier studies, our data indicate that the consequences of melanism may be related to the reproductive mode of species. In viviparous species, melanism tends to improve growth and/or body size and is more frequent in females, whereas the opposite holds for oviparous snakes. Further studies on melanism should examine a wider array of species with different reproductive strategies and traits beyond the usual thermal benefits.

Benefits of insect colours: a review from social insect studies.

Insect colours assist in body protection, signalling, and physiological adaptations. Colours also convey multiple channels of information. These channels are valuable for species identification, distinguishing individual quality, and revealing ecological or evolutionary aspects of animals' life. During recent years, the emerging interest in colour research has been raised in social hymenopterans such as ants, wasps, and bees. These insects provide important ecosystem services and many of those are model research organisms. Here we review benefits that various colour types give to social insects, summarize practical applications, and highlight further directions. Ants might use colours principally for camouflage, however the evolutionary function of colour in ants needs more attention; in case of melanin colouration there is evidence for its interrelation with thermoregulation and pathogen resistance. Colours in wasps and bees have confirmed linkages to thermoregulation, which is increasingly important in face of global climate change. Besides wasps use colours for various types of signalling. Colour variations of well chemically defended social insects are the mimetic model for unprotected organisms. Despite recent progress in molecular identification of species, colour variations are still widely in use for species identification. Therefore, further studies on variability is encouraged. Being closely interconnected with physiological and biochemical processes, insect colouration is a great source for finding new ecological indicators and biomarkers. Due to novel digital imaging techniques, software, and artificial intelligence there are emerging possibilities for new advances in this topic. Further colour research in social insects should consider specific features of sociality.

Double-stranded RNA targeting vATPase B reveals a potential target for pest management of Henosepilachna vigintioctopunctata.

The development of genetic based techniques, specifically RNA interference (RNAi), has emerged as a powerful tool in novel pest management strategies for pestiferous coleoptera. The 28-spotted ladybird beetle, Henosepilachna vigintioctopunctata, is a dynamic foliar pest of solenaceous plants, primarily potato plants, and has quickly become one of the most important pests attacking many crops in Asian countries. In this study, we demonstrate the efficacy of dietary RNAi targeting vATPase B, which led to significant gene silencing. Downstream effects of vATPase B silencing appeared to be both time- and partial dose-dependent. Our results indicate that silencing of vATPase B caused a significant decrease in survival rate, as well as reduced the food stuffs consumption and inhibited the overall development of H. vigintioctopunctata. Furthermore, results demonstrate expression of insect melanism related genes, TH and DDC, was significantly up regulated under the dsvATPase B (RNAi molecule designed against vATPase B) treatment. The impact of oral dsvATPase B delivery on the survival of 1st, 3rd instars, and adults was investigated through bacterially expressed dsRNA. The effectiveness of RNAi-based gene silencing in H. vigintioctopunctata provides a powerful reverse genetic tool for the functional annotation of its genes. This study demonstrates that vATPase B may represent a candidate gene for RNAi-based control of H. vigintioctopunctata.