Natural variation of ebony gene controlling thoracic pigmentation in Drosophila melanogaster

Temporal genomics in Hawaiian crickets reveals compensatory intragenomic coadaptation during adaptive evolution

Theory predicts that compensatory genetic changes reduce negative indirect effects of selected variants during adaptive evolution, but evidence is scarce. Here, we test this in a wild population of Hawaiian crickets using temporal genomics and a high-quality chromosome-level cricket genome. In this population, a mutation, flatwing, silences males and rapidly spread due to an acoustically-orienting parasitoid. Our sampling spanned a social transition during which flatwing fixed and the population went silent. We find long-range linkage disequilibrium around the putative flatwing locus was maintained over time, and hitchhiking genes had functions related to negative flatwing-associated effects. We develop a combinatorial enrichment approach using transcriptome data to test for compensatory, intragenomic coevolution. Temporal changes in genomic selection were distributed genome-wide and functionally associated with the population's transition to silence, particularly behavioural responses to silent environments. Our results demonstrate how 'adaptation begets adaptation'; changes to the sociogenetic environment accompanying rapid trait evolution can generate selection provoking further, compensatory adaptation.

The role of the epidermis enhancer element in positive and negative transcriptional regulation of ebony in Drosophila melanogaster

The spatiotemporal regulation of gene expression is essential to ensure robust phenotypic outcomes. Pigmentation patterns in Drosophila are determined by pigments biosynthesized in the developing epidermis and the cis-regulatory elements of the genes involved in this process are well-characterized. Here, we report that the known primary epidermal enhancer is dispensable for the transcriptional activation of ebony (involved in light-colored pigment synthesis) in the developing epidermis of Drosophila melanogaster. The evidence was obtained by introducing an approximately 1 kbp deletion at the primary epidermal enhancer by genome editing. The effect of the primary epidermal enhancer deletion on pigmentation and on the endogenous expression pattern of a mCherry-fused ebony allele was examined in the abdomen. The expression levels of the mCherry-fused ebony in the primary epidermal enhancer-deleted strains were slightly higher than that of the control strain, indicating that the sequences outside the primary epidermal enhancer have an ability to drive an expression of this gene in the epidermis. Interestingly, the primary epidermal enhancer deletion resulted in a derepression of this gene in the dorsal midline of the abdominal tergites, where dark pigmentation is present in the wild-type individuals. This indicated that the primary epidermal enhancer fragment contains a silencer. Furthermore, the endogenous expression pattern of ebony in the 2 additional strains with partially deleted primary epidermal enhancer revealed that the silencer resides within a 351-bp fragment in the 5' portion of the primary epidermal enhancer. These results demonstrated that deletion assays combined with reporter assays are highly effective in detecting the presence of positively and negatively regulating sequences within and outside the focal cis-regulatory elements.

Attack of the dark clones the genetics of reproductive and color traits of South African honey bees (Apis mellifera spp.)

The traits of two subspecies of western honey bees, Apis mellifera scutellata and A.m. capensis, endemic to the Republic of South Africa (RSA), are of biological and commercial relevance. Nevertheless, the genetic basis of important phenotypes found in these subspecies remains poorly understood. We performed a genome wide association study on three traits of biological relevance in 234 A.m. capensis, 73 A.m. scutellata and 158 hybrid individuals. Thirteen markers were significantly associated to at least one trait (P ≤ 4.28 × 10⁻⁶): one for ovariole number, four for scutellar plate and eight for tergite color. We discovered two possible causative variants associated to the respective phenotypes: a deletion in GB46429 or Ebony (NC_007070.3:g.14101325G>del) (R69Efs*85) and a nonsense on GB54634 (NC_007076.3:g.4492792A>G;p.Tyr128*) causing a premature stop, substantially shortening the predicted protein. The mutant genotypes are significantly associated to phenotypes in A.m. capensis. Loss-of-function of Ebony can cause accumulation of circulating dopamine, and increased dopamine levels correlate to ovary development in queenless workers and pheromone production. Allelic association (P = 1.824 x 10⁻⁵) of NC_007076.3:g.4492792A>G;p.Tyr128* to ovariole number warrants further investigation into function and expression of the GB54634 gene. Our results highlight genetic components of relevant production/conservation behavioral phenotypes in honey bees.

Molecular and morphometric divergence of four species of butterflies (Nymphalidae and Pieridae) from the Western Himalaya, India

Morphometric and molecular divergence among four butterfly species of the families Nymphalidae and Pieridae from the western Himalaya region were investigated using molecular tools, traditional morphometric measures and a truss network system. The considered species were Danaus chrysippus, Vanessa cardui, Pieris brassicae and Pieris canidia. Traditional taxonomy is sometimes unable to discriminate cryptic species or species that have close morphological features. Although taxonomists carefully examine external body features to differentiate the species; however, there is a risk for misidentification during a visual assessment of cryptic species. Therefore, we aimed to use the truss network system of 14 morphological landmarks interconnected to yield 90 variables about molecular taxonomy. Principal component analysis (PCA), discriminant function analysis (DFA) and cluster analysis (CA) were employed to determine morphometric variations. In the traditional analysis, 79, 68, 16 and 5 characters out of 90 were found significant (p < 0.05) for D. chrysippus, V. cardui, P. brassicae and P. canidia, respectively. One to seven principal components were extracted through PCA; they explained 87.5-100% of the total variance in samples. Notably, DFA correctly classified 100% of the original grouped cases and 100% of the cross-validated grouped cases. However, the variations were not the same for the two different methods (truss and traditional) employed for the analysis. We correctly identified all the species; the interspecies sequence divergence was between 0.1034 and 0.1398, and the intra-species sequence divergence range was 0.0001 to 0.0128 using the Cytochrome c oxidase subunit-I (COI) gene. The present study provides useful information about the application and complementary role of traditional with truss morphometric analysis for the precise identification and classification of the selected species.

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.

Enhanced mechanical properties of hBN-ZrO2 composites and their biological activities on Drosophila melanogaster: synthesis and characterization

In this study, six compositions in the system [x(h-BN)-(100 - x)ZrO2] (10 ≤ x ≤ 90) were synthesized by a bottom up approach, i.e., the solid-state reaction technique. XRD results showed the formation of a novel and main phase of zirconium oxynitrate ZrO(NO3)2 and SEM exhibited mixed morphology of layered and stacked h-BN nanosheets with ZrO2 grains. The composite sample 10 wt% h-BN + 90 wt% ZrO2 (10B90Z) showed outstanding mechanical properties for different parameters, i.e., density (3.12 g cm-3), Young's modulus (10.10 GPa), toughness (2.56 MJ m-3), and maximum mechanical strength (227.33 MPa). The current study further checked the in vivo toxicity of composite 10B90Z and composite 90B10Z using Drosophila melanogaster. The composite 10B90Z showed less cytotoxicity in this model, while the composite 90B10Z showed higher toxicity in terms of organ development as well as internal damage of the gut mostly at the lower concentrations of 1, 10, and 25 μg mL-1. Altogether, the current study proposes the composite 10B90Z as an ideal compound for applications in biomedical research. This composite 10B90Z displays remarkable mechanical and biological performances, due to which we recommend this composition for various biomedical applications.

Pleiotropic effects of regulatory variation in tan result in correlation of two pigmentation traits in Drosophila melanogaster

Traits with a common genetic basis frequently display correlated phenotypic responses to selection or environmental conditions. In Drosophila melanogaster, pigmentation of the abdomen and a trident-shaped region on the thorax are genetically correlated. Here, we used a pooled replicated genomewide association approach (Pool-GWAS) to identify the genetic basis of variation in thoracic trident pigmentation in two Drosophila melanogaster populations. We confirmed the previously reported large effect of ebony and the association of the cosmopolitan inversion In(3R)Payne. For the first time, we identified tan as another major locus contributing to variation in trident pigmentation. Intriguingly, the regulatory variants of tan that were most strongly associated with female abdominal pigmentation also showed a strong association with trident pigmentation. We validated this common genetic basis in transgenic assays and found qualitatively similar effects on trident and abdominal pigmentation. Further work is required to determine whether this genetic correlation is favoured by natural selection or reflects a neutral by-product of a shared regulatory architecture.

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.

Pigmentation pattern and developmental constraints: flight muscle attachment sites delimit the thoracic trident of Drosophila melanogaster

In their seminal paper published in 1979, Gould and Lewontin argued that some traits arise as by-products of the development of other structures and not for direct utility in themselves. We show here that this applies to the trident, a pigmentation pattern observed on the thorax of Drosophila melanogaster. Using reporter constructs, we show that the expression domain of several genes encoding pigmentation enzymes follows the trident shape. This domain is complementary to the expression pattern of stripe (sr), which encodes an essential transcription factor specifying flight muscle attachment sites. We demonstrate that sr limits the expression of these pigmentation enzyme genes to the trident by repressing them in its own expression domain, i.e. at the flight muscle attachment sites. We give evidence that repression of not only yellow but also other pigmentation genes, notably tan, is involved in the trident shape. The flight muscle attachment sites and sr expression patterns are remarkably conserved in dipterans reflecting the essential role of sr. Our data suggest that the trident is a by-product of flight muscle attachment site patterning that arose when sr was co-opted for the regulation of pigmentation enzyme coding genes.

The evolutionary origination of a novel expression pattern through an extreme heterochronic shift

The evolutionary origins of morphological structures are thought to often depend upon the redeployment of old genes into new developmental settings. Although many examples of cis-regulatory divergence have shown how pre-existing patterns of gene expression have been altered, only a small number of case studies have traced the origins of cis-regulatory elements that drive new expression domains. Here, we elucidate the evolutionary history of a novel expression pattern of the yellow gene within the Zaprionus genus of fruit flies. We observed a unique pattern of yellow transcript accumulation in the wing disc during the third larval instar, a stage that precedes its typical expression pattern associated with cuticular melanization by about a week. The region of the Zaprionus wing disc that expresses yellow subsequently develops into a portion of the thorax, a tissue for which yellow expression has been reported for several fruit fly species. Tests of GFP reporter transgenes containing the Zaprionus yellow regulatory region revealed that the wing disc pattern arose by changes in the cis-regulatory region of yellow. Moreover, the wing disc enhancer activity of yellow depends upon a short conserved sequence with ancestral thoracic functions, suggesting that the pupal thorax regulatory sequence was genetically reprogrammed to drive expression that commences much earlier during development. These results highlight how novel domains of gene expression may arise by extreme shifts in timing during the origins of novel traits.

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.

Factors underlying natural variation in body pigmentation of Drosophila melanogaster

Molecular mechanisms underlying standing genetic variation of an ecologically relevant trait such as pigmentation trait variation in a model insect, Drosophila melanogaster, are relevant to our understanding of different kinds of intergenomic interactions. In this study, we focused on the association between body pigmentation and stress resistance, and on genotype-by-environment interaction, both of which are likely to contribute to the persistence of phenotypic variation in a natural population. First, we detected a significant association between pigmentation traits in females and starvation resistance (darker strains were weaker) and a weak association between pigmentation and chill coma recovery time (darker strains showed shorter recovery time) among 20 inbred strains from the Drosophila melanogaster Genetic Reference Panel (DGRP), which originated from a natural population in North America. These associations revealed a complex relationship between body pigmentation and physiological traits that may give rise to balanced selective forces acting on the traits under fluctuating environmental conditions. Second, using four of the DGRP strains, a substantial degree of genotype (strain) × environment (rearing temperature) interaction was detected among expression levels of the genes encoding effector enzymes in the melanin biosynthesis pathway. These interactions can potentially reduce the efficiency of purifying selection on the pigmentation traits over a wide range of temperature conditions. Finally, we discuss possible mechanisms that contribute to the maintenance of the standing pigmentation variation in this species.

A Pathway Analysis of Melanin Patterning in a Hemimetabolous Insect

Diversity in insect pigmentation, encompassing a wide range of colors and spatial patterns, is among the most noticeable features distinguishing species, individuals, and body regions within individuals. In holometabolous species, a significant portion of such diversity can be attributed to the melanin synthesis genes, but this has not been formally assessed in more basal insect lineages. Here we provide a comprehensive analysis of how a set of melanin genes (ebony, black, aaNAT, yellow, and tan) contributes to the pigmentation pattern in a hemipteran, Oncopeltus fasciatus For all five genes, RNA interference depletion caused alteration of black patterning in a region-specific fashion. Furthermore, the presence of distinct nonblack regions in forewings and hindwings coincides with the expression of ebony and aaNAT in these appendages. These findings suggest that the region-specific phenotypes arise from regional employment of various combinations of the melanin genes. Based on this insight, we suggest that melanin genes are used in two distinct ways: a "painting" mode, using predominantly melanin-promoting factors in areas that generally lack black coloration, and, alternatively, an "erasing" mode, using mainly melanin-suppressing factors in regions where black is the dominant pigment. Different combinations of these strategies may account for the vast diversity of melanin patterns observed in insects.

Reconciling Differences in Pool-GWAS Between Populations: A Case Study of Female Abdominal Pigmentation in Drosophila melanogaster

The degree of concordance between populations in the genetic architecture of a given trait is an important issue in medical and evolutionary genetics. Here, we address this problem, using a replicated pooled genome-wide association study approach (Pool-GWAS) to compare the genetic basis of variation in abdominal pigmentation in female European and South African Drosophila melanogaster. We find that, in both the European and the South African flies, variants near the tan and bric-à-brac 1 (bab1) genes are most strongly associated with pigmentation. However, the relative contribution of these loci differs: in the European populations, tan outranks bab1, while the converse is true for the South African flies. Using simulations, we show that this result can be explained parsimoniously, without invoking different causal variants between the populations, by a combination of frequency differences between the two populations and dominance for the causal alleles at the bab1 locus. Our results demonstrate the power of cost-effective, replicated Pool-GWAS to shed light on differences in the genetic architecture of a given trait between populations.

Complex patterns of cis-regulatory polymorphisms in ebony underlie standing pigmentation variation in Drosophila melanogaster

Pigmentation traits in adult Drosophila melanogaster were used in this study to investigate how phenotypic variations in continuous ecological traits can be maintained in a natural population. First, pigmentation variation in the adult female was measured at seven different body positions in 20 strains from the Drosophila melanogaster Genetic Reference Panel (DGRP) originating from a natural population in North Carolina. Next, to assess the contributions of cis-regulatory polymorphisms of the genes involved in the melanin biosynthesis pathway, allele-specific expression levels of four genes were quantified by amplicon sequencing using a 454 GS Junior. Among those genes, ebony was significantly associated with pigmentation intensity of the thoracic segment. Detailed sequence analysis of the gene regulatory regions of this gene indicated that many different functional cis-regulatory alleles are segregating in the population and that variations outside the core enhancer element could potentially play important roles in the regulation of gene expression. In addition, a slight enrichment of distantly associated SNP pairs was observed in the ~10 kb cis-regulatory region of ebony, which suggested the presence of interacting elements scattered across the region. In contrast, sequence analysis in the core cis-regulatory region of tan indicated that SNPs within the region are significantly associated with allele-specific expression level of this gene. Collectively, the data suggest that the underlying genetic differences in the cis-regulatory regions that control intraspecific pigmentation variation can be more complex than those of interspecific pigmentation trait differences, where causal genetic changes are typically confined to modular enhancer elements.

Unraveling the Tangled Skein: The Evolution of Transcriptional Regulatory Networks in Development

The molecular and genetic basis for the evolution of anatomical diversity is a major question that has inspired evolutionary and developmental biologists for decades. Because morphology takes form during development, a true comprehension of how anatomical structures evolve requires an understanding of the evolutionary events that alter developmental genetic programs. Vast gene regulatory networks (GRNs) that connect transcription factors to their target regulatory sequences control gene expression in time and space and therefore determine the tissue-specific genetic programs that shape morphological structures. In recent years, many new examples have greatly advanced our understanding of the genetic alterations that modify GRNs to generate newly evolved morphologies. Here, we review several aspects of GRN evolution, including their deep preservation, their mechanisms of alteration, and how they originate to generate novel developmental programs.

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.

The genetic architecture of coordinately evolving male wing pigmentation and courtship behavior in Drosophila elegans and Drosophila gunungcola

Many adaptive phenotypes consist of combinations of simpler traits that act synergistically, such as morphological traits and the behaviors that use those traits. Genetic correlations between components of such combinatorial traits, in the form of pleiotropic or tightly linked genes, can in principle promote the evolution and maintenance of these traits. In the Oriental Drosophila melanogaster species group, male wing pigmentation shows phylogenetic correlations with male courtship behavior; species with male-specific apical wing melanin spots also exhibit male visual wing displays, whereas species lacking these spots generally lack the displays. In this study, we investigated the quantitative genetic basis of divergence in male wing spots and displays between D. elegans, which possesses both traits, and its sibling species D. gunungcola, which lacks them. We found that divergence in wing spot size is determined by at least three quantitative trait loci (QTL) and divergence in courtship score is determined by at least four QTL. On the autosomes, QTL locations for pigmentation and behavior were generally separate, but on the X chromosome two clusters of QTL were found affecting both wing pigmentation and courtship behavior. We also examined the genetic basis of divergence in three components of male courtship, wing display, circling, and body shaking. Each of these showed a distinct genetic architecture, with some QTL mapping to similar positions as QTL for overall courtship score. Pairwise tests for interactions between marker loci revealed evidence of epistasis between putative QTL for wing pigmentation but not those for courtship behavior. The clustering of X-linked QTL for male pigmentation and behavior is consistent with the concerted evolution of these traits and motivates fine-scale mapping studies to elucidate the nature of the contributing genetic factors in these intervals.

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.

Transcriptome analysis reveals novel patterning and pigmentation genes underlying Heliconius butterfly wing pattern variation

Background

Heliconius butterfly wing pattern diversity offers a unique opportunity to investigate how natural genetic variation can drive the evolution of complex adaptive phenotypes. Positional cloning and candidate gene studies have identified a handful of regulatory and pigmentation genes implicated in Heliconius wing pattern variation, but little is known about the greater developmental networks within which these genes interact to pattern a wing. Here we took a large-scale transcriptomic approach to identify the network of genes involved in Heliconius wing pattern development and variation. This included applying over 140 transcriptome microarrays to assay gene expression in dissected wing pattern elements across a range of developmental stages and wing pattern morphs of Heliconius erato.

Results

We identified a number of putative early prepattern genes with color-pattern related expression domains. We also identified 51 genes differentially expressed in association with natural color pattern variation. Of these, the previously identified color pattern “switch gene” optix was recovered as the first transcript to show color-specific differential expression. Most differentially expressed genes were transcribed late in pupal development and have roles in cuticle formation or pigment synthesis. These include previously undescribed transporter genes associated with ommochrome pigmentation. Furthermore, we observed upregulation of melanin-repressing genes such as ebony and Dat1 in non-melanic patterns.

Conclusions

This study identifies many new genes implicated in butterfly wing pattern development and provides a glimpse into the number and types of genes affected by variation in genes that drive color pattern evolution.

Cuticular Hydrocarbon Content that Affects Male Mate Preference of Drosophila melanogaster from West Africa

Intraspecific variation in mating signals and preferences can be a potential source of incipient speciation. Variable crossability between Drosophila melanogaster and D. simulans among different strains suggested the abundance of such variations. A particular focus on one combination of D. melanogaster strains, TW1(G23) and Mel6(G59), that showed different crossabilities to D. simulans, revealed that the mating between females from the former and males from the latter occurs at low frequency. The cuticular hydrocarbon transfer experiment indicated that cuticular hydrocarbons of TW1 females have an inhibitory effect on courtship by Mel6 males. A candidate component, a C25 diene, was inferred from the gas chromatography analyses. The intensity of male refusal of TW1 females was variable among different strains of D. melanogaster, which suggested the presence of variation in sensitivity to different chemicals on the cuticle. Such variation could be a potential factor for the establishment of premating isolation under some conditions.

Convergent, modular expression of ebony and tan in the mimetic wing patterns of Heliconius butterflies

The evolution of pigmentation in vertebrates and flies has involved repeated divergence at a small number of genes related to melanin synthesis. Here, we study insect melanin synthesis genes in Heliconius butterflies, a group characterised by its diversity of wing patterns consisting of black (melanin), and yellow and red (ommochrome) pigmented scales. Consistent with their respective biochemical roles in Drosophila melanogaster, ebony is upregulated in non-melanic wing regions destined to be pigmented red whilst tan is upregulated in melanic regions. Wing regions destined to be pigmented yellow, however, are downregulated for both genes. This pattern is conserved across multiple divergent and convergent phenotypes within the Heliconii, suggesting a conserved mechanism for the development of black, red and yellow pattern elements across the genus. Linkage mapping of five melanin biosynthesis genes showed that, in contrast to other organisms, these genes do not control pattern polymorphism. Thus, the pigmentation genes themselves are not the locus of evolutionary change but lie downstream of a wing pattern regulatory factor. The results suggest a modular system in which particular combinations of genes are switched on whenever red, yellow or black pattern elements are favoured by natural selection for diverse and mimetic wing patterns.

Divergent enhancer haplotype of ebony on inversion In(3R)Payne associated with pigmentation variation in a tropical population of Drosophila melanogaster

The pattern and intensity of pigmentation have direct impact on individual fitness through various ecological factors. In a Drosophila melanogaster population from southern Japan, thoracic trident pigmentation intensity of most of the strains could be classified into Dark or Light-type. The expression level variation of the ebony gene correlated well with this phenotype and the allelic differences in expression indicated that the variation is partly due to cis-regulatory changes. In the ∼13 kb gene region, we identified 17 nucleotide sites and 2 indels that were in complete association with the thoracic trident pigmentation intensity. Interestingly, 11 out of 19 sites located within ∼0.5 kb of the core epidermis enhancer. These sites had no obvious association with the abdominal pigmentation intensity in the previously analysed African populations from Uganda and Kenya, which suggested that multiple potential mutational pathways in the cis-regulatory control region of a single gene could lead to similar phenotypic variation within this species. We also found that the Light-type enhancer haplotype is strongly linked to a cosmopolitan inversion, In(3R)Payne, which is predominant in warmer climatic regions in both hemispheres. The sequence pattern suggested that the strong linkage may be due to selective forces related to thermal adaptation. The inferred selection for lighter pigmentation in the Japanese population is in the opposite direction of the previously reported case of selection for darker individuals in African populations. Nevertheless, both adaptive changes involved cis-regulatory changes of ebony, which shows that this gene is likely to be a common target of natural selection.

The molecular genetics of clinal variation: a case study of ebony and thoracic trident pigmentation in Drosophila melanogaster from eastern Australia

Widespread pigmentation diversity coupled with a well-defined genetic system of melanin synthesis and patterning in Drosophila provides an excellent opportunity to study phenotypes undergoing evolutionary change. Pigmentation variation is highly correlated with different ecological variables and is thought to reflect adaptations to different environments. Several studies have linked candidate genes from Drosophila melanogaster to intra-population variation and interspecific morphological divergence, but less clearly to variation among populations forming pigmentation clines. We characterized a new thoracic trident pigmentation cline in D. melanogaster populations from eastern Australia, and applied a candidate gene approach to explain the majority of the geographically structured phenotypic variation. More melanized populations from higher latitudes tended to express less ebony than their tropical counterparts, and an independent artificial selection experiment confirmed this association. By partitioning temperature dependent effects, we showed that the genetic differences underlying clinal patterns for trident variation at 25 °C do not explain the patterns observed at 16 °C. Changes in thoracic trident pigmentation could be a common evolutionary response to climatically mediated environmental pressures. On the Australian east coast most of the changes appear to be associated with regulatory divergence of the ebony gene but this depends on temperature.

Adaptation to local ultraviolet radiation conditions among neighbouring Daphnia populations

Understanding the historical processes that generated current patterns of phenotypic diversity in nature is particularly challenging in subdivided populations. Populations often exhibit heritable genetic differences that correlate with environmental variables, but the non-independence among neighbouring populations complicates statistical inference of adaptation. To understand the relative influence of adaptive and non-adaptive processes in generating phenotypes requires joint evaluation of genetic and phenotypic divergence in an integrated and statistically appropriate analysis. We investigated phenotypic divergence, population-genetic structure and potential fitness trade-offs in populations of Daphnia melanica inhabiting neighbouring subalpine ponds of widely differing transparency to ultraviolet radiation (UVR). Using a combination of experimental, population-genetic and statistical techniques, we separated the effects of shared population ancestry and environmental variables in predicting phenotypic divergence among populations. We found that native water transparency significantly predicted divergence in phenotypes among populations even after accounting for significant population structure. This result demonstrates that environmental factors such as UVR can at least partially account for phenotypic divergence. However, a lack of evidence for a hypothesized trade-off between UVR tolerance and growth rates in the absence of UVR prevents us from ruling out the possibility that non-adaptive processes are partially responsible for phenotypic differentiation in this system.

The genetic, morphological, and physiological characterization of a dark larval cuticle mutation in the butterfly, Bicyclus anynana

Studies on insect melanism have greatly contributed to our understanding of natural selection and the ultimate factors influencing the evolution of darkly pigmented phenotypes. Research on several species of melanic lepidopteran larvae have found that low levels of circulating juvenile hormone (JH) titers are associated with a melanic phenotype, suggesting that genetic changes in the JH biosynthetic pathway give rise to increased deposition of melanin granules in the cuticle in this group. But does melanism arise through different molecular mechanisms in different species? The present study reports on a Bicyclus anynana (Lepidoptera: Nymphalidae) dark larvae single locus mutation, in which larvae exhibit a darker cuticle relative to wild type. Unlike other lepidopteran melanic larvae mutations, this one is autosomal recessive and does not appear to involve a deficiency in JH titers. Unlike JH deficiency mutants, dark larvae mutants display similar growth rates and sexual behaviors as wild type, and topical application of a JH analogue failed to rescue the wild type cuticular coloration. Finally, transmission electron microscopy showed that sclerotization or deposition of diffuse melanin, rather than deposition of melanin granules, produces the dark coloration found in the cuticle of this species. We conclude that different molecular mechanisms underlie larval melanism in different species of Lepidoptera.

Industrial melanism in the peppered moth is not associated with genetic variation in canonical melanisation gene candidates

Industrial melanism in the peppered moth (Biston betularia) is an iconic case study of ecological genetics but the molecular identity of the gene determining the difference between the typical and melanic (carbonaria) morphs is entirely unknown. We applied the candidate gene approach to look for associations between genetic polymorphisms within sixteen a priori melanisation gene candidates and the carbonaria morph. The genes were isolated and sequence characterised in B. betularia using degenerate PCR and from whole-transcriptome sequence. The list of candidates contains all the genes previously implicated in melanisation pattern differences in other insects, including aaNAT, DOPA-decarboxylase, ebony, tan, tyrosine hydroxylase, yellow and yellow2 (yellow-fa). Co-segregation of candidate gene alleles and carbonaria morph was tested in 73 offspring of a carbonaria male-typical female backcross. Surprisingly, none of the sixteen candidate genes was in close linkage with the locus controlling the carbonaria-typical polymorphism. Our study demonstrates that the 'carbonaria gene' is not a structural variant of a canonical melanisation pathway gene, neither is it a cis-regulatory element of these enzyme-coding genes. The implication is either that we have failed to characterize an unknown enzyme-coding gene in the melanisation pathway, or more likely, that the 'carbonaria gene' is a higher level trans-acting factor which regulates the spatial expression of one or more of the melanisation candidates in this study to alter the pattern of melanin production.

Metamodels and phylogenetic replication: a systematic approach to the evolution of developmental pathways

Molecular genetic analysis of phenotypic variation has revealed many examples of evolutionary change in the developmental pathways that control plant and animal morphology. A major challenge is to integrate the information from diverse organisms and traits to understand the general patterns of developmental evolution. This integration can be facilitated by evolutionary metamodels-traits that have undergone multiple independent changes in different species and whose development is controlled by well-studied regulatory pathways. The metamodel approach provides the comparative equivalent of experimental replication, allowing us to test whether the evolution of each developmental pathway follows a consistent pattern, and whether different pathways are predisposed to different modes of evolution by their intrinsic organization. A review of several metamodels suggests that the structure of developmental pathways may bias the genetic basis of phenotypic evolution, and highlights phylogenetic replication as a value-added approach that produces deeper insights into the mechanisms of evolution than single-species analyses.

yellow and ebony are the responsible genes for the larval color mutants of the silkworm Bombyx mori

Many larval color mutants have been obtained in the silkworm Bombyx mori. Mapping of melanin-synthesis genes on the Bombyx linkage map revealed that yellow and ebony genes were located near the chocolate (ch) and sooty (so) loci, respectively. In the ch mutants, body color of neonate larvae and the body markings of elder instar larvae are reddish brown instead of normal black. Mutations at the so locus produce smoky larvae and black pupae. F(2) linkage analyses showed that sequence polymorphisms of yellow and ebony genes perfectly cosegregated with the ch and so mutant phenotypes, respectively. Both yellow and ebony were expressed in the epidermis during the molting period when cuticular pigmentation occurred. The spatial expression pattern of yellow transcripts coincided with the larval black markings. In the ch mutants, nonsense mutations of the yellow gene were detected, whereas large deletions of the ebony ORF were detected in the so mutants. These results indicate that yellow and ebony are the responsible genes for the ch and so loci, respectively. Our findings suggest that Yellow promotes melanization, whereas Ebony inhibits melanization in Lepidoptera and that melanin-synthesis enzymes play a critical role in the lepidopteran larval color pattern.

Genetic basis of sex-specific color pattern variation in Drosophila malerkotliana

Pigmentation is a rapidly evolving trait that can play important roles in mimicry, sexual selection, thermoregulation, and other adaptive processes in many groups of animals. In Drosophila, pigmentation can differ dramatically among closely related taxa, presenting a good opportunity to dissect the genetic changes underlying species divergence. In this report, we investigate the genetic basis of color pattern variation between two allopatric subspecies of Drosophila malerkotliana, a widespread member of the ananassae species subgroup. In D. malerkotliana malerkotliana, the last three abdominal segments are darkly pigmented in males but not in females, while in D. malerkotliana pallens both sexes lack dark pigmentation. Composite interval mapping in F2 hybrid progeny shows that this difference is largely controlled by three quantitative trait loci (QTL) located on the 2L chromosome arm, which is homologous to the 3R of D. melanogaster (Muller element E). Using highly recombinant introgression strains produced by repeated backcrossing and phenotypic selection, we show that these QTL do not correspond to any of the candidate genes known to be involved in pigment patterning and synthesis in Drosophila. These results, in combination with similar analyses in other Drosophila species, indicate that different genetic and molecular changes are responsible for the evolution of similar phenotypic traits in different lineages. This feature makes Drosophila color patterns a powerful model for investigating how the genetic basis of trait evolution is influenced by the intrinsic organization of regulatory pathways controlling the development of these traits.

The evolution of gene regulation underlies a morphological difference between two Drosophila sister species

Understanding the mechanisms underlying the morphological divergence of species is one of the central goals of evolutionary biology. Here, we analyze the genetic and molecular bases of the divergence of body pigmentation patterns between Drosophila yakuba and its sister species Drosophila santomea. We found that loss of pigmentation in D. santomea involved the selective loss of expression of the tan and yellow pigmentation genes. We demonstrate that tan gene expression was eliminated through the mutational inactivation of one specific tan cis-regulatory element (CRE) whereas the Tan protein sequence remained unchanged. Surprisingly, we identify three independent loss-of-function alleles of the tan CRE in the young D. santomea lineage. We submit that there is sufficient empirical evidence to support the general prediction that functional evolutionary changes at pleiotropic loci will most often involve mutations in their discrete, modular cis-regulatory elements.