The influence of abdominal pigmentation on desiccation and ultraviolet resistance in two species of Drosophila

Sex-Specific Ultraviolet Radiation Tolerance Across Drosophila

The genetic basis of phenotypic differences between species is a longstanding question in evolutionary biology. How new genes form and selection acts to produce differences across species are fundamental to understanding how species evolve. Adaptation and genetic innovation arise in the genome from a variety of sources. Functional genomics requires both genetic discoveries and empirical testing to observe adaptation between lineages. We explore two species of Drosophila from the island of São Tomé and mainland Africa, D. santomea and D. yakuba. These two species have varying distributions based on elevation on São Tomé, with populations of D. yakuba also inhabiting mainland Africa. Genomic/genetic evidence shows genes between species may have a role in adaptation to higher UV tolerance. We conducted empirical UV assays between D. santomea and both D. yakuba populations. Flies were shocked by UVB radiation for 30 min on a transilluminator apparatus. Custom 5-wall acrylic enclosures were constructed for viewing and containment of flies. Island groups show significant differences between fall-time under UV stress and recovery time post-UV stress test between populations and by sex. This study shows evidence that mainland flies are less resistant to UV radiation than their island counterparts. Differential expression analysis also shows potential for new mutations and local adaptation for DNA repair of D. santomea. Understanding the mechanisms and processes that promote adaptation and testing traits within the context of the genome is crucially important to understand evolutionary machinery.

No evidence for the melanin desiccation hypothesis in a larval Lepidopteran

Water regulation is an important physiological challenge for insects due to their small body sizes and large surface area to volume ratios. Adaptations for decreasing cuticular water loss, the largest avenue of loss, are especially important. The melanin desiccation hypothesis states that melanin molecules in the cuticle may help prevent water loss, thus offering protection from desiccation. This hypothesis has much empirical support in Drosophila species, but remains mostly untested in other taxa, including Lepidoptera. Because melanin has many other important functions in insects, its potential role in desiccation prevention is not always clear. In this study we investigated the role of melanin in desiccation prevention in the white-lined Sphinx moth, Hyles lineata (Lepidoptera, Sphingidae), which shows high plasticity in the degree of melanin pigmentation during the late larval instars. We took advantage of this plasticity and used density treatments to induce a wide range of cuticular melanization; solitary conditions induced low melanin pigmentation while crowded conditions induced high melanin pigmentation. We tested whether more melanic larvae from the crowded treatment were better protected from desiccation in three relevant responses: i) total water loss over a desiccation period, ii) change in hemolymph osmolality over a desiccation period, and iii) evaporation rate of water through the cuticle. We did not find support for the melanin desiccation hypothesis in this species. Although treatment influenced total water loss, this effect did not occur via degree of melanization. Interestingly, this implies that crowding, which was used to induce high melanin phenotypes, may have other physiological effects that influence water regulation. There were no differences between treatments in cuticular evaporative water loss or change in hemolymph osmolality. However, we conclude that osmolality may not sufficiently reflect water loss in this case. This study emphasizes the context dependency of melanin's role in desiccation prevention and the importance of considering how it may vary across taxa. In lepidopteran larvae that are constantly feeding phytophagous insects with soft cuticles, melanin may not be necessary for preventing cuticular water loss.

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.

Exposure to ultraviolet-B radiation increases the susceptibility of mosquitoes to infection with dengue virus

By 2100, greenhouse gases are predicted to reduce ozone and cloud cover over the tropics causing increased exposure of organisms to harmful ultraviolet-B radiation (UVBR). UVBR damages DNA and is an important modulator of immune function and disease susceptibility in humans and other vertebrates. The effect of UVBR on invertebrate immune function is largely unknown, but UVBR together with ultraviolet-A radiation impairs an insect immune response that utilizes melanin, a pigment that also protects against UVBR-induced DNA damage. If UVBR weakens insect immunity, then it may make insect disease vectors more susceptible to infection with pathogens of socioeconomic and public health importance. In the tropics, where UVBR is predicted to increase, the mosquito-borne dengue virus (DENV), is prevalent and a growing threat to humans. We therefore examined the effect of UVBR on the mosquito Aedes aegypti, the primary vector for DENV, to better understand the potential implications of increased tropical UVBR for mosquito-borne disease risk. We found that exposure to a UVBR dose that caused significant larval mortality approximately doubled the probability that surviving females would become infected with DENV, despite this UVBR dose having no effect on the expression of an effector gene involved in antiviral immunity. We also found that females exposed to a lower UVBR dose were more likely to have low fecundity even though this UVBR dose had no effect on larval size or activity, pupal cuticular melanin content, or adult mass, metabolic rate, or flight capacity. We conclude that future increases in tropical UVBR associated with anthropogenic global change may have the benefit of reducing mosquito-borne disease risk for humans by reducing mosquito fitness, but this benefit may be eroded if it also makes mosquitoes more likely to be infected with deadly pathogens.

Evolution of assortative mating following selective introgression of pigmentation genes between two Drosophila species

Adaptive introgression is ubiquitous in animals, but experimental support for its role in driving speciation remains scarce. In the absence of conscious selection, admixed laboratory strains of Drosophila asymmetrically and progressively lose alleles from one parental species and reproductive isolation against the predominant parent ceases after 10 generations. Here, we selectively introgressed during 1 year light pigmentation genes of D. santomea into the genome of its dark sibling D. yakuba, and vice versa. We found that the pace of phenotypic change differed between the species and the sexes and identified through genome sequencing common as well as distinct introgressed loci in each species. Mating assays showed that assortative mating between introgressed flies and both parental species persisted even after 4 years (~60 generations) from the end of the selection. Those results indicate that selective introgression of as low as 0.5% of the genome can beget morphologically distinct and reproductively isolated strains, two prerequisites for the delimitation of new species. Our findings hence represent a significant step toward understanding the genome-wide dynamics of speciation-through-introgression.

Silencing of Adc and Ebony Causes Abnormal Darkening of Cuticle in Henosepilachna vigintioctopunctata

N-β-alanyldopamine (NBAD) is a precursor of N-acylquinone sclerotin utilized for cross-linking between cuticular proteins for cuticle during insect molting. The importance of NBAD in cuticle tanning has not been well compared among different developing stages of insects. Henosepilachna vigintioctopunctata, a typical polyphagous pest feeding on a large number of Solanaceae and Cucurbitaceae plants in Asian countries, displays diverse cuticle pigmentation patterns among developing stages and body regions. Here, we found that the expression of three genes (Hvadc, Hvebony, and Hvtan) involved in NBAD biosynthesis peaked in the 4-day-old pupae or 0-day-old adults of H. vigintioctopunctata. At the first, second, third, and fourth larval instar and pupal stage, their transcript levels were high just before and/or right after the molting. Moreover, they were more abundantly transcribed at the larval heads than in the bodies. RNA interference (RNAi) of either Hvadc or Hvebony at the third instar larvae selectively deepened the color of the larval head capsules, antennae, mouthpart, scoli, strumae, and legs; and depletion of the two genes blackened the pupal head capsules, antennae, mouthpart, and legs. However, the knockdown of either Hvadc or Hvebony darkened the whole bodies of the adults. Conversely, RNAi of Hvtan at the third instar stage had little influence on the pigmentation in the larvae, pupae, and adults. These findings demonstrated that Adc and Ebony are important in cuticle pigmentation of H. vigintioctopunctata and suggested that larger quantities of NBAD were present in adults and play more important roles in pigmentation than larvae/pupae.

Color lightness of velvet ants (Hymenoptera: Mutillidae) follows an environmental gradient

Color traits are highly influenced by environmental conditions along the distributional range of many species. Studies on the variation of animal coloration across different geographic gradients are, therefore, fundamental for a better understanding of the ecological and evolutionary processes that shape color variation. Here, we address whether color lightness in velvet ants (Hymenoptera: Mutillidae) responds to latitudinal gradients and bioclimatic variations, testing three ecogeographic rules: The Thermal melanism hypothesis; the Photoprotection hypothesis; and Gloger's rule. We test these hypotheses across the New World. We used photographs of 482 specimens (n = 142 species) of female mutillid wasps and extracted data on color lightness (V). We analyzed whether variation in color is determined by bioclimatic factors, using Phylogenetic Generalized Least Square analysis. Our explanatory variables were temperature, ultraviolet radiation, humidity, and forest indicators. Our results were consistent with the Photoprotection hypothesis and Gloger's rule. Species with darker coloration occupied habitats with more vegetation, higher humidity, and UV-B radiation. However, our results refute one of the initial hypotheses suggesting that mutillids do not respond to the predictions of the Thermal melanism hypothesis. The results presented here provide the first evidence that abiotic components of the environment can act as ecological filters and as selective forces driving the body coloration of velvet ants. Finally, we suggest that studies using animals with melanin-based colors as a model for mimetic and aposematic coloration hypotheses consider that this coloration may also be under the influence of climatic factors and not only predators.

Pure species discriminate against hybrids in the Drosophila melanogaster species subgroup

Introgression, the exchange of alleles between species, is a common event in nature. This transfer of alleles between species must happen through fertile hybrids. Characterizing the traits that cause defects in hybrids illuminates how and when gene flow is expected to occur. Inviability and sterility are extreme examples of fitness reductions but are not the only type of defects in hybrids. Some traits specific to hybrids are more subtle but are important to determine their fitness. In this report, we study whether F1 hybrids between two species pairs of Drosophila are as attractive as the parental species. We find that in both species pairs, the sexual attractiveness of the F1 hybrids is reduced and that pure species discriminate strongly against them. We also find that the cuticular hydrocarbon (CHC) profile of the female hybrids is intermediate between the parental species. Perfuming experiments show that modifying the CHC profile of the female hybrids to resemble pure species improves their chances of mating. Our results show that behavioral discrimination against hybrids might be an important component of the persistence of species that can hybridize.

Many ways to make darker flies: Intra- and interspecific variation in Drosophila body pigmentation components

Body pigmentation is an evolutionarily diversified and ecologically relevant trait with substantial variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution, including its ecological significance and genetic bases. Pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, and can be under different selective pressures. We decompose Drosophila thorax and abdominal pigmentation, a valuable eco-evo-devo model, into distinct measurable traits related to color and color pattern. We investigate intra- and interspecific variation for those traits and assess its different sources. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate each body part. By focusing on two standard D. melanogaster laboratory populations, we show that pigmentation components vary and covary in distinct manners depending on sex, genetic background, and temperature during development. Studying three natural populations of D. melanogaster along a latitudinal cline and five other Drosophila species, we then show that evolution of lighter or darker bodies can be achieved by changing distinct component traits. Our results paint a much more complex picture of body pigmentation variation than previous studies could uncover, including patterns of sexual dimorphism, thermal plasticity, and interspecific diversity. These findings underscore the value of detailed quantitative phenotyping and analysis of different sources of variation for a better understanding of phenotypic variation and diversification, and the ecological pressures and genetic mechanisms underlying them.

Genetic architecture of a body colour cline in Drosophila americana

Phenotypic variation within a species is often structured geographically in clines. In Drosophila americana, a longitudinal cline for body colour exists within North America that appears to be due to local adaptation. The tan and ebony genes have been hypothesized to contribute to this cline, with alleles of both genes that lighten body colour found in D. americana. These alleles are similar in sequence and function to the allele fixed in D. americana's more lightly pigmented sister species, Drosophila novamexicana. Here, we examine the frequency and geographic distribution of these D. novamexicana-like alleles in D. americana. Among alleles from over 100 strains of D. americana isolated from 21 geographic locations, we failed to identify additional alleles of tan or ebony with as much sequence similarity to D. novamexicana as the D. novamexicana-like alleles previously described. However, using genetic analysis of 51 D. americana strains derived from 20 geographic locations, we identified one new allele of ebony and one new allele of tan segregating in D. americana that are functionally equivalent to the D. novamexicana allele. An additional 5 alleles of tan also showed marginal evidence of functional similarity. Given the rarity of these alleles, however, we conclude that they are unlikely to be driving the pigmentation cline. Indeed, phenotypic distributions of the 51 backcross populations analysed indicate a more complex genetic architecture, with diversity in the number and effects of loci altering pigmentation observed both within and among populations of D. americana. This genetic heterogeneity poses a challenge to association studies and genomic scans for clinal variation, but might be common in natural populations.

Desiccation resistance and pigmentation variation reflects bioclimatic differences in the Drosophila americana species complex

Background

Disentangling the selective factors shaping adaptive trait variation is an important but challenging task. Many studies—especially in Drosophila—have documented trait variation along latitudinal or altitudinal clines, but frequently lack resolution about specific environmental gradients that could be causal selective agents, and often do not investigate covariation between traits simultaneously. Here we examined variation in multiple macroecological factors across geographic space and their associations with variation in three physiological traits (desiccation resistance, UV resistance, and pigmentation) at both population and species scales, to address the role of abiotic environment in shaping trait variation.

Results

Using environmental data from collection locations of three North American Drosophila species—D. americana americana, D. americana texana and D. novamexicana—we identified two primary axes of macroecological variation; these differentiated species habitats and were strongly loaded for precipitation and moisture variables. In nine focal populations (three per species) assayed for each trait, we detected significant species-level variation for both desiccation resistance and pigmentation, but not for UV resistance. Species-level trait variation was consistent with differential natural selection imposed by variation in habitat water availability, although patterns of variation differed between desiccation resistance and pigmentation, and we found little evidence for pleiotropy between traits.

Conclusions

Our multi-faceted approach enabled us to identify potential agents of natural selection and examine how they might influence the evolution of multiple traits at different evolutionary scales. Our findings highlight that environmental factors influence functional trait variation in ways that can be complex, and point to the importance of studies that examine these relationships at both population- and species-levels.

Pleiotropic Effects of ebony and tan on Pigmentation and Cuticular Hydrocarbon Composition in Drosophila melanogaster

Pleiotropic genes are genes that affect more than one trait. For example, many genes required for pigmentation in the fruit fly Drosophila melanogaster also affect traits such as circadian rhythms, vision, and mating behavior. Here, we present evidence that two pigmentation genes, ebony and tan, which encode enzymes catalyzing reciprocal reactions in the melanin biosynthesis pathway, also affect cuticular hydrocarbon (CHC) composition in D. melanogaster females. More specifically, we report that ebony loss-of-function mutants have a CHC profile that is biased toward long (>25C) chain CHCs, whereas tan loss-of-function mutants have a CHC profile that is biased toward short (<25C) chain CHCs. Moreover, pharmacological inhibition of dopamine synthesis, a key step in the melanin synthesis pathway, reversed the changes in CHC composition seen in ebony mutants, making the CHC profiles similar to those seen in tan mutants. These observations suggest that genetic variation affecting ebony and/or tan activity might cause correlated changes in pigmentation and CHC composition in natural populations. We tested this possibility using the Drosophila Genetic Reference Panel (DGRP) and found that CHC composition covaried with pigmentation as well as levels of ebony and tan expression in newly eclosed adults in a manner consistent with the ebony and tan mutant phenotypes. These data suggest that the pleiotropic effects of ebony and tan might contribute to covariation of pigmentation and CHC profiles in Drosophila.

Latitudinal Pigmentation Variation Contradicts Ultraviolet Radiation Exposure: A Case Study in Tropical Indian Drosophila melanogaster

The effects of ultraviolet radiation (UV) on the animal body have been reported in many studies, and melanin has emerged as a protective mechanism. In smaller insects such as Drosophila, replicated patterns of geographical variation in pigmentation have been observed on multiple continents. Such patterns are particularly pronounced on the Indian subcontinent where several species show a parallel cline in pigmentation traits. However, the potential role of UV exposure in generating the observed patterns of pigmentation variation has not been addressed. Here, we examine the association between UV intensity and body pigmentation in D. melanogaster natural populations collected along the latitudinal gradient of the Indian subcontinent. A strong negative relationship was observed between UV intensity and body pigmentation. This analysis clearly indicates that, in the sampled populations, pigmentation variation is independent of UV exposure and related selection pressures. Patterns of pigmentation in natural populations from the Indian subcontinent are better predicted by latitude itself and temperature-related climatic variables.

Morphological and biological characterization of a light-colored mutant in the multicolored Asian lady beetle, Harmonia axyridis

Insect cuticle color formed with melanin pigments has numerous types of mutants which usually cause pleiotropic effects. Melanism has been widely studied, but mutants with light-colored phenotype as well as the consequent fitness changes have rarely been reported.Here, in the laboratory strain of Harmonia axyridis, we found a novel mutant gr and confirmed that the mutation was inherited in a simple Mendelian autosomal recessive manner. This mutant (HAM) continuously displayed a light-colored pigmentation versus dark blackish in the wild phenotype (HAW). L-DOPA and dopamine are melanin precursors, and less L-DOPA was present in the cuticle of larval and adult HAM mutants compared to HAW wild type, but more dopamine was detected in the larval cuticle of HAM (p ≤ 0.0235). For the orange background of elytra, the composition as well as total concentration of carotenoids was different between HAM and HAW, which resulted in significantly lower saturation value but significantly higher hue value in HAM than in HAW (p < 0.0001).Extensive fitness changes were detected in HAM. (a) HAM larvae had similar predation capacity and preimaginal development time as HAW, but the newly emerged adults were much smaller (p < 0.0001). (b) Both fecundity and egg hatch rate in cross ♀(HAM) × ♂(HAM) were significantly lower than those in ♀(HAW) × ♂(HAW) (p ≤ 0.0087), but were not different with those in ♀(HAW) × ♂(HAM).

Enhancing Ebony? Common Associations With a cis-Regulatory Haplotype for Drosophila melanogaster Thoracic Pigmentation in a Japanese Population and Australian Populations

The molecular underpinnings of pigmentation diversity in Drosophila have recently emerged as a model for understanding how the evolution of different cis-regulatory variants results in common adaptive phenotypes within species. We compared sequence variation in a 5' regulatory region harboring a modular enhancer containing a ∼0.7-kb core element contributing to abdominal melanisation in African, and a ∼0.5-kb core element contributing to thoracic pigmentation in D. melanogaster from Japan, to tropical and temperate populations from eastern Australia previously shown to be divergent in thoracic pigmentation and ebony expression. The Australian populations exhibited strong association with the core enhancer polymorphism cluster in complete association with Dark and Light phenotypes from Iriomote, Japan. Moreover, the Iriomote Light and Dark core enhancer haplotypes are common to the Australian populations in the direction predicted by pigmentation phenotype. We also confirmed the Japanese patterns of linkage disequilibrium and association of the tropical inversion In(3R)Payne with the Light enhancer haplotype in the Australian tropical light population. A worldwide survey of the ∼0.5-kb ebony control region SNPs and haplotypes in a subset of the Drosophila Genome Nexus (DGN) populations suggest origins in the sub-Saharan ancestral region surrounding Zambia and subsequent invasion following colonization out of Africa. A previous study demonstrated complex within and between population genetic architecture for abdominal pigmentation which is also correlated with thoracic pigmentation in melanized DGN sub-Saharan populations; however, the ∼0.5-kb ebony control region was not associated and both haplotypes are common even in the most intensely pigmented D. melanogaster from high altitude Ethiopia. In the Australian populations, the strong phenotypic association with the enhancer SNPs and haplotypes that at least partly regulates ebony expression in the Iriomote population, our previous work demonstrating opposing clines for thoracic pigmentation and ebony expression, where the expression cline parallels the In(3R)Payne cline, and the concerted evolution of pigmentation intensity and ebony expression under rapid experimental evolution, all point to a common adaptive evolutionary pathway in distinct populations.

Toward Understanding the Repeated Occurrence of Associations between Melanin-Based Coloration and Multiple Phenotypes

Melanin is the most widespread pigment in organisms. Melanin-based coloration has been repeatedly observed to be associated with the same traits and in the same direction in different vertebrate and insect species. However, whether any factors that are common to different taxa account for the repeated evolution of melanin-phenotype associations remains unclear. We propose to approach this question from the perspective of convergent and parallel evolution to clarify to what extent different species have evolved the same associations owing to a shared genetic basis and being subjected to similar selective pressures. Our current understanding of the genetic basis of melanin-phenotype associations allows for both convergent and parallel evolution, but this understanding is still limited. Further research is needed to clarify the generality and interdependencies of the different proposed mechanisms (supergenes, pleiotropy based on hormones, or neural crest cells). The general ecological scenarios whereby melanin-based coloration is under selection-protection from ultraviolet radiation, thermoregulation in cold environments, or as a signal of social status-offer a good opportunity to study how melanin-phenotype associations evolve. Reviewing these scenarios shows that some traits associated with melanin-based coloration might be selected together with coloration by also favoring adaptation but that other associated traits might impede adaptation, which may be indicative of genetic constraints. We therefore encourage further research on the relative roles that selection and genetic constraints play in shaping multiple melanin-phenotype associations. Placed into a phylogenetic context, this will help clarify to what extent these associations result from convergent or parallel evolutionary processes and why melanin-phenotype associations are so common across the tree of life.

The Rate of Evolution of Postmating-Prezygotic Reproductive Isolation in Drosophila

Reproductive isolation is an intrinsic aspect of species formation. For that reason, the identification of the precise isolating traits, and the rates at which they evolve, is crucial to understanding how species originate and persist. Previous work has measured the rates of evolution of prezygotic and postzygotic barriers to gene flow, yet no systematic analysis has studied the rates of evolution of postmating-prezygotic (PMPZ) barriers. We measured the magnitude of two barriers to gene flow that act after mating occurs but before fertilization. We also measured the magnitude of a premating barrier (female mating rate in nonchoice experiments) and two postzygotic barriers (hybrid inviability and hybrid sterility) for all pairwise crosses of all nine known extant species within the melanogaster subgroup. Our results indicate that PMPZ isolation evolves faster than hybrid inviability but slower than premating isolation. Next, we partition postzygotic isolation into different components and find that, as expected, hybrid sterility evolves faster than hybrid inviability. These results lend support for the hypothesis that, in Drosophila, reproductive isolation mechanisms (RIMs) that act early in reproduction (or in development) tend to evolve faster than those that act later in the reproductive cycle. Finally, we tested whether there was evidence for reinforcing selection at any RIM. We found no evidence for generalized evolution of reproductive isolation via reinforcement which indicates that there is no pervasive evidence of this evolutionary process. Our results indicate that PMPZ RIMs might have important evolutionary consequences in initiating speciation and in the persistence of new species.

Quantifying Abdominal Pigmentation in Drosophila melanogaster

Pigmentation is a morphologically simple but highly variable trait that often has adaptive significance. It has served extensively as a model for understanding the development and evolution of morphological phenotypes. Abdominal pigmentation in Drosophila melanogaster has been particularly useful, allowing researchers to identify the loci that underlie inter- and intraspecific variations in morphology. Hitherto, however, D. melanogaster abdominal pigmentation has been largely assayed qualitatively, through scoring, rather than quantitatively, which limits the forms of statistical analysis that can be applied to pigmentation data. This work describes a new methodology that allows for the quantification of various aspects of the abdominal pigmentation pattern of adult D. melanogaster. The protocol includes specimen mounting, image capture, data extraction, and analysis. All the software used for image capture and analysis feature macros written for open-source image analysis. The advantage of this approach is the ability to precisely measure pigmentation traits using a methodology that is highly reproducible across different imaging systems. While the technique has been used to measure variation in the tergal pigmentation patterns of adult D. melanogaster, the methodology is flexible and broadly applicable to pigmentation patterns in myriad different organisms.

Sex-biased transcriptome divergence along a latitudinal gradient

Sex-dependent gene expression is likely an important genomic mechanism that allows sex-specific adaptation to environmental changes. Among Drosophila species, sex-biased genes display remarkably consistent evolutionary patterns; male-biased genes evolve faster than unbiased genes in both coding sequence and expression level, suggesting sex differences in selection through time. However, comparatively little is known of the evolutionary process shaping sex-biased expression within species. Latitudinal clines offer an opportunity to examine how changes in key ecological parameters also influence sex-specific selection and the evolution of sex-biased gene expression. We assayed male and female gene expression in Drosophila serrata along a latitudinal gradient in eastern Australia spanning most of its endemic distribution. Analysis of 11 631 genes across eight populations revealed strong sex differences in the frequency, mode and strength of divergence. Divergence was far stronger in males than females and while latitudinal clines were evident in both sexes, male divergence was often population specific, suggesting responses to localized selection pressures that do not covary predictably with latitude. While divergence was enriched for male-biased genes, there was no overrepresentation of X-linked genes in males. By contrast, X-linked divergence was elevated in females, especially for female-biased genes. Many genes that diverged in D. serrata have homologs also showing latitudinal divergence in Drosophila simulans and Drosophila melanogaster on other continents, likely indicating parallel adaptation in these distantly related species. Our results suggest that sex differences in selection play an important role in shaping the evolution of gene expression over macro- and micro-ecological spatial scales.

Using Drosophila pigmentation traits to study the mechanisms of cis-regulatory evolution

One primary agenda of the developmental evolution field is to elucidate molecular mechanisms governing differences in animal form. While mounting evidence has established an important role for mutations in transcription controlling cis-regulatory elements (CREs), the underlying mechanisms that translate these alterations into differences in gene expression are poorly understood. Emerging studies focused on pigmentation differences among closely related Drosophila species have provided many examples of phenotypically relevant CRE changes, and have begun to illuminate how this process works at the level of regulatory sequence function and transcription factor binding. We review recent work in this field and highlight the conceptual and technical challenges that currently await experimental attention.

An Experimental Evolution Test of the Relationship between Melanism and Desiccation Survival in Insects

We used experimental evolution to test the ‘melanism-desiccation’ hypothesis, which proposes that dark cuticle in several Drosophila species is an adaptation for increased desiccation tolerance. We selected for dark and light body pigmentation in replicated populations of D. melanogaster and assayed several traits related to water balance. We also scored pigmentation and desiccation tolerance in populations selected for desiccation survival. Populations in both selection regimes showed large differences in the traits directly under selection. However, after over 40 generations of pigmentation selection, dark-selected populations were not more desiccation-tolerant than light-selected and control populations, nor did we find significant changes in mass or carbohydrate amounts that could affect desiccation resistance. Body pigmentation of desiccation-selected populations did not differ from control populations after over 140 generations of selection, although selected populations lost water less rapidly. Our results do not support an important role for melanization in Drosophila water balance.

The Genetic Basis of Pigmentation Differences Within and Between Drosophila Species

In Drosophila, as well as in many other plants and animals, pigmentation is highly variable both within and between species. This variability, combined with powerful genetic and transgenic tools as well as knowledge of how pigment patterns are formed biochemically and developmentally, has made Drosophila pigmentation a premier system for investigating the genetic and molecular mechanisms responsible for phenotypic evolution. In this chapter, we review and synthesize findings from a rapidly growing body of case studies examining the genetic basis of pigmentation differences in the abdomen, thorax, wings, and pupal cases within and between Drosophila species. A core set of genes, including genes required for pigment synthesis (eg, yellow, ebony, tan, Dat) as well as developmental regulators of these genes (eg, bab1, bab2, omb, Dll, and wg), emerge as the primary sources of this variation, with most genes having been shown to contribute to pigmentation differences both within and between species. In cases where specific genetic changes contributing to pigmentation divergence were identified in these genes, the changes were always located in noncoding sequences and affected cis-regulatory activity. We conclude this chapter by discussing these and other lessons learned from evolutionary genetic studies of Drosophila pigmentation and identify topics we think should be the focus of future work with this model system.

Revisiting classic clines in Drosophila melanogaster in the age of genomics

Adaptation to spatially varying environments has been studied for decades, but advances in sequencing technology are now enabling researchers to investigate the landscape of genetic variation underlying this adaptation genome wide. In this review we highlight some of the decades-long research on local adaptation in Drosophila melanogaster from well-studied clines in North America and Australia. We explore the evidence for parallel adaptation and identify commonalities in the genes responding to clinal selection across continents as well as discussing instances where patterns differ among clines. We also investigate recent studies utilizing whole-genome data to identify clines in D. melanogaster and several other systems. Although connecting segregating genomic variation to variation in phenotypes and fitness remains challenging, clinal genomics is poised to increase our understanding of local adaptation and the selective pressures that drive the extensive phenotypic diversity observed in nature.

Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and between Drosophila Species

The modification of transcriptional regulation has become increasingly appreciated as a major contributor to morphological evolution. However, the role of negative-acting control elements (e.g. silencers) in generating morphological diversity has been generally overlooked relative to positive-acting “enhancer” elements. The highly variable body coloration patterns among Drosophilid insects represents a powerful model system in which the molecular alterations that underlie phenotypic diversity can be defined. In a survey of pigment phenotypes among geographically disparate Japanese populations of Drosophila auraria, we discovered a remarkable degree of variation in male-specific abdominal coloration. In testing the expression patterns of the major pigment-producing enzymes, we found that phenotypes uniquely correlated with differences in the expression of ebony, a gene required for yellow-colored cuticle. Assays of ebony’s transcriptional control region indicated that a lightly pigmented strain harbored cis-regulatory mutations that caused correlated changes in its expression. Through a series of chimeric reporter constructs between light and dark strain alleles, we localized function-altering mutations to a conserved silencer that mediates a male-specific pattern of ebony repression. This suggests that the light allele was derived through the loss of this silencer’s activity. Furthermore, examination of the ebony gene of D. serrata, a close relative of D. auraria which secondarily lost male-specific pigmentation revealed the parallel loss of this silencer element. These results demonstrate how loss-of-function mutations in a silencer element resulted in increased gene expression. We propose that the mutational inactivation of silencer elements may represent a favored path to evolve gene expression, impacting morphological traits.

One of the greatest challenges in understanding the relationship between genotype and phenotype is to discern how changes in DNA affect the normal functioning of genes. Mutations may generate a new function for a gene, yet it is frequently observed that they inactivate some aspect of a gene’s normal capacity. Investigations focused on understanding the developmental basis for the evolution of anatomical structures has found a prevalent role for mutations that alter developmental gene regulation. In animals, genes are transcriptionally activated in specific tissues during development by regulatory sequences distributed across their expansive non-protein coding regions. Regulatory elements known as silencers act to prevent genes from being expressed in certain tissues, providing a mechanism for precise control. Here, we show how a silencer that prevents expression of a pigment-producing enzyme in certain Drosophila species has repeatedly been subject to inactivating mutations that increased this gene’s expression. This example illustrates how such negative-acting regulatory sequences can represent a convenient target for increasing gene expression through the loss of a genetic element.

A single gene causes an interspecific difference in pigmentation in Drosophila

The genetic basis of species differences remains understudied. Studies in insects have contributed significantly to our understanding of morphological evolution. Pigmentation traits in particular have received a great deal of attention and several genes in the insect pigmentation pathway have been implicated in inter- and intraspecific differences. Nonetheless, much remains unknown about many of the genes in this pathway and their potential role in understudied taxa. Here we genetically analyze the puparium color difference between members of the virilis group of Drosophila. The puparium of Drosophila virilis is black, while those of D. americana, D. novamexicana, and D. lummei are brown. We used a series of backcross hybrid populations between D. americana and D. virilis to map the genomic interval responsible for the difference between this species pair. First, we show that the pupal case color difference is caused by a single Mendelizing factor, which we ultimately map to an ∼11-kb region on chromosome 5. The mapped interval includes only the first exon and regulatory region(s) of the dopamine N-acetyltransferase gene (Dat). This gene encodes an enzyme that is known to play a part in the insect pigmentation pathway. Second, we show that this gene is highly expressed at the onset of pupation in light brown taxa (D. americana and D. novamexicana) relative to D. virilis, but not in the dark brown D. lummei. Finally, we examine the role of Dat in adult pigmentation between D. americana (heavily melanized) and D. novamexicana (lightly melanized) and find no discernible effect of this gene in adults. Our results demonstrate that a single gene is entirely or almost entirely responsible for a morphological difference between species.

Trait-specific consequences of inbreeding on adaptive phenotypic plasticity

Environmental changes may stress organisms and stimulate an adaptive phenotypic response. Effects of inbreeding often interact with the environment and can decrease fitness of inbred individuals exposed to stress more so than that of outbred individuals. Such an interaction may stem from a reduced ability of inbred individuals to respond plastically to environmental stress; however, this hypothesis has rarely been tested. In this study, we mimicked the genetic constitution of natural inbred populations by rearing replicate Drosophila melanogaster populations for 25 generations at a reduced population size (10 individuals). The replicate inbred populations, as well as control populations reared at a population size of 500, were exposed to a benign developmental temperature and two developmental temperatures at the lower and upper margins of their viable range. Flies developed at the three temperatures were assessed for traits known to vary across temperatures, namely abdominal pigmentation, wing size, and wing shape. We found no significant difference in phenotypic plasticity in pigmentation or in wing size between inbred and control populations, but a significantly higher plasticity in wing shape across temperatures in inbred compared to control populations. Given that the norms of reaction for the noninbred control populations are adaptive, we conclude that a reduced ability to induce an adaptive phenotypic response to temperature changes is not a general consequence of inbreeding and thus not a general explanation of inbreeding–environment interaction effects on fitness components.

Pigmentation in Drosophila melanogaster reaches its maximum in Ethiopia and correlates most strongly with ultra-violet radiation in sub-Saharan Africa

Background

Pigmentation has a long history of investigation in evolutionary biology. In Drosophila melanogaster, latitudinal and altitudinal clines have been found but their underlying causes remain unclear. Moreover, most studies were conducted on cosmopolitan populations which have a relatively low level of genetic structure and diversity compared to sub-Saharan African populations. We investigated: 1) the correlation between pigmentation traits within and between the thorax and the fourth abdominal segment, and 2) their associations with different geographical and ecological variables, using 710 lines belonging to 30 sub-Saharan and cosmopolitan populations.

Results

Pigmentation clines substantially differed between sub-Saharan and cosmopolitan populations. While positive correlations with latitude have previously been described in Europe, India and Australia, in agreement with Bogert's rule or the thermal melanism hypothesis, we found a significant negative correlation in Africa. This correlation persisted even after correction for altitude, which in its turn showed a positive correlation with pigmentation independently from latitude. More importantly, we found that thoracic pigmentation reaches its maximal values in this species in high-altitude populations of Ethiopia (1,600-3,100 m). Ethiopian flies have a diffuse wide thoracic trident making the mesonotum and the head almost black, a phenotype that is absent from all other sub-Saharan or cosmopolitan populations including high-altitude flies from Peru (~3,400 m). Ecological analyses indicated that the variable most predictive of pigmentation in Africa, especially for the thorax, was ultra-violet (UV) intensity, consistent with the so-called Gloger's rule invoking a role of melanin in UV protection.

Conclusion

Our data suggest that different environmental factors may shape clinal variation in tropical and temperate regions, and may lead to the evolution of different degrees of melanism in different high altitude populations in the tropics.

Pigmentation and behavior: potential association through pleiotropic genes in Drosophila

The molecular basis of pigmentation variation within and among Drosophila species is largely attributed to genes in melanin biosynthesis pathway, which involves dopamine metabolism. Most of the genetic changes underlying pigmentation variations reported to date are changes at the expression levels of the structural genes in the pathway. Within D. melanogaster, changes in cis-regulatory regions of a gene, ebony, are responsible for the naturally occurring variation of the body pigmentation intensity. This gene is also known to be expressed in glia, and many visual and behavioral abnormalities of its mutants have been reported. This implies that the gene has pleiotropic functions in the nervous systems. In this review, current knowledge on pigmentation variation and melanin biosynthesis pathway are summarized, with some focus on pleiotropic features of ebony and other genes in the pathway. A potential association between pigmentation and behavior through such pleiotropic genes is discussed in light of cis-regulatory structure and pleiotropic mutations.