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.     

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.     

Genetic Architecture of Abdominal Pigmentation in Drosophila melanogaster

Pigmentation varies within and between species and is often adaptive. The amount of pigmentation on the abdomen of Drosophila melanogaster is a relatively simple morphological trait, which serves as a model for mapping the genetic basis of variation in complex phenotypes. Here, we assessed natural variation in female abdominal pigmentation in 175 sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel, derived from the Raleigh, NC population. We quantified the proportion of melanization on the two most posterior abdominal segments, tergites 5 and 6 (T5, T6). We found significant genetic variation in the proportion of melanization and high broad-sense heritabilities for each tergite. Genome-wide association studies identified over 150 DNA variants associated with the proportion of melanization on T5 (84), T6 (34), and the difference between T5 and T6 (35). Several of the top variants associated with variation in pigmentation are in tan, ebony, and bric-a-brac1, genes known to affect D. melanogaster abdominal pigmentation. Mutational analyses and targeted RNAi-knockdown showed that 17 out of 28 (61%) novel candidate genes implicated by the genome-wide association study affected abdominal pigmentation. Several of these genes are involved in developmental and regulatory pathways, chitin production, cuticle structure, and vesicle formation and transport. These findings show that genetic variation may affect multiple steps in pathways involved in tergite development and melanization. Variation in these novel candidates may serve as targets for adaptive evolution and sexual selection in D. melanogaster.     

Abdominal pigmentation in Drosophila melanogaster females from natural Indian populations

Females of Drosophila melanogaster collected from five geographically distant populations in India were analysed for the intensity of pigmentation in the 5th, 6th and 7th segments of the abdomen. In all three segments, this intensity was found to vary among individuals of any given population, and, furthermore, different populations differ with respect to this phenotypic trait. Statistical analysis revealed significant intra- and interpopulational variation. A clinical pattern was detected: females from populations closer to the equator tended to have lighter cuticle, in which case differences between the three segments could not be detected and all three segments responded both independently and jointly to latitudinal variation, as indicated by a statistically significant positive correlation between latitude and pigmentation score. This is the first report on abdominal pigmentation analysis in natural populations of D. melanogaster that provides evidence that phenotypic flexibility reflects temperature differences, as a result of which abdominal pigmentation shows geographic differentiation.     

Wing pigmentation in Calopteryx damselflies: a role in thermoregulation?

Body melanization may show adaptive variation related to thermoregulation ability, and it is to be expected that the degree of melanization will change among populations or closely related species across environmental gradients of solar radiation and/or environmental temperature. Some melanized secondary sexual traits may also play a role in sexual selection, leading to interpopulation variation, which would not be predicted by thermoregulation pressures alone. We studied the relationships between the interpopulation variation in wing pigmentation level (i.e. melanized secondary sexual trait) of two closely related species of Calopteryx damselfly, and both solar radiation and maximum environmental temperature estimates. Wing pigmentation differs between these species, is gender specific and is used in species' discrimination. Only Calopteryx virgo meridionalis males showed a significant negative partial correlation between wing pigmentation degree and temperature. However, C. virgo meridionalis females showed a positive significant partial correlation between wing pigmentation degree and solar radiation. Wing pigmentation in Calopteryx xanthostoma males was not related to solar radiation or temperature. Thus, thermoregulation pressures poorly explained the observed variations in wing pigmentation between populations, although they might have an adaptive significance at the species' level. As wing pigmentation showed important latitudinal variation, several other selection pressures which might act on melanized traits are briefly discussed. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 103 , 36–44.     

Size and sex matter: reproductive biology and determinants of offspring survival in Gazella marica

For prey, many behavioural traits are constrained by the risk of predation. Therefore, shifts between warning and cryptic coloration have been suggested to result in parallel changes in several behaviours. In the present study, we tested whether changes in chromatic contrast among eight populations of the strawberry poison‐dart frog, Dendrobates pumilio, co‐vary with behaviour, as expected if selection is imposed by predators relying on visual detection of prey. These eight populations are geographically isolated on different island in the Bocas del Toro region of Panama and have recently diverged morphologically and genetically. We found that aggression and explorative behaviour were strongly correlated and also that males tended to be more aggressive and explorative if they belonged to populations with conspicuously coloured individuals. We discuss how evolutionary switches between predator avoidance strategies and associated behavioural divergence between populations may affect reproductive isolation. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●● , ●●–●●.     

Phenotypic variability of thoracic pigmentation in Indian populations of Drosophila melanogaster

Fourteen natural populations of Drosophila melanogaster collected along diverse latitudinal and altitudinal ranges, were analysed for thoracic trident pigmentation at two different breeding temperatures (17 and 25°C) for both sexes. Statistical analyses showed significant intra- as well as interpopulational genetic variations. Clinal patterns for thoracic trident pigmentation along latitude as well as altitude are significantly correlated with thermal amplitude ( T _cv). Crosses between dark (Shimla) and light (Kalka) variants of trident pigmentation produced intermediate phenotypes, and a clear maternal effect was observed in the reciprocal F ₁ crosses. Data suggest that the temperature differences have resulted in phenotypic plasticity of thoracic pigmentation across the Indian subcontinent.     

Correlated changes in circadian clocks in response to selection for faster pre-adult development in fruit flies Drosophila melanogaster

Although, circadian clocks are believed to be involved in the regulation of life-history traits such as pre-adult development time and lifespan in fruit flies Drosophila melanogaster, there is very little unequivocal evidence either to support or refute this. Here we report the results of a long-term study aimed at examining the role of circadian clocks in the temporal regulation of pre-adult development in D. melanogaster. We employed laboratory selection protocol for faster pre-adult development on four large, outbred, random mating populations of Drosophila. We assayed pre-adult development time and circadian period of locomotor activity rhythm of these flies at regular intervals of 5–10 generations. After 50 generations of selection, the overall egg-to-adult duration in the selected stocks was reduced by ~29 h (~12.5 %) relative to controls, with the selected populations showing a concurrent reduction in time taken to hatching, pupation and wing pigmentation, by ~2, ~16, and ~25.2 h, respectively. Furthermore, selected populations showed a concomitant reduction in the circadian period of locomotor activity rhythm, implying that circadian clocks and development time are correlated. Thus, our study provides the first ever unequivocal evidence for the evolution of circadian clocks as a correlated response to selection for faster pre-adult development, suggesting that circadian clocks and development are linked in fruit flies D. melanogaster.     

Genetic basis of natural variation in body pigmentation in Drosophila melanogaster

Body pigmentation in insects and other organisms is typically variable within and between species and is often associated with fitness. Regulatory variants with large effects at bab1, t and e affect variation in abdominal pigmentation in several populations of Drosophila melanogaster. Recently, we performed a genome wide association (GWA) analysis of variation in abdominal pigmentation using the inbred, sequenced lines of the Drosophila Genetic Reference Panel (DGRP). We confirmed the large effects of regulatory variants in bab1, t and e; identified 81 additional candidate genes; and validated 17 candidate genes (out of 28 tested) using RNAi knockdown of gene expression and mutant alleles. However, these analyses are imperfect proxies for the effects of segregating variants. Here, we describe the results of an extreme quantitative trait locus (xQTL) GWA analysis of female body pigmentation in an outbred population derived from light and dark DGRP lines. We replicated the effects on pigmentation of 28 genes implicated by the DGRP GWA study, including bab1, t and e and 7 genes previously validated by RNAi and/or mutant analyses. We also identified many additional loci. The genetic architecture of Drosophila pigmentation is complex, with a few major genes and many other loci with smaller effects.     

A Genome-Wide,Fine-Scale Map of Natural Pigmentation Variation in Drosophila melanogaster

Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome.     

GROWTH TEMPERATURE AND ADULT PIGMENTATION IN TWO DROSOPHILA SIBLING SPECIES: AN ADAPTIVE CONVERGENCE OF REACTION NORMS IN SYMPATRIC POPULATIONS?

Phenotypic plasticity of abdomen pigmentation was investigated in populations of the sibling species Drosophila melanogaster and D. simulans, living in sympatry in two French localities. Ten isofemale lines of each population and species were grown at different constant temperatures spanning their complete thermal range from 12 to 31°C. Genetic variability between isofemale lines was not affected by growth temperature, but was consistently less in D. simulans. For all traits, the dark pigmentation of the abdominal segments decreased according to growth temperature, in agreement with the thermal budget adaptive hypothesis. The shapes of the response curves were different between the abdominal segments, but for a given segment, quite similar in the two species. On average D. simulans was lighter than D. melanogaster, but the difference was mainly expressed at higher temperatures. An interesting result was the difference observed between the two localities: flies from the colder locality (Villeurbanne) were found to be darker than flies from the warmer locality (Bordeaux). Interestingly, this difference was expressed only at low temperatures, 21°C and below, that is, at temperatures encountered in natural conditions. This suggests an adaptive response resulting in a change of the shape of reaction norm and involving genotype-environment interactions. When comparing the genetic structure of geographic populations for quantitative traits, several laboratory environments should be preferred to a single one.     

Annotating ebony on the fly

The distinctive black phenotype of ebony mutants has made it one of the most widely used phenotypic markers in Drosophila genetics. Without doubt, ebony showcases the fruits of the fly community's labours to annotate gene function. As of this writing, FlyBase lists 142 references, 1277 fly stocks, 15 phenotypes and 44 alleles. In addition to its namesake pigmentation phenotype, ebony mutants affect other traits, including phototaxis and courtship. With phenotypic consequences of ebony variants readily apparent in the laboratory, does natural selection also see them in the wild? In this issue of Molecular Ecology, Pool & Aquadro investigate this question and found signs of natural selection on the ebony gene that appear to have resulted from selection for darker pigmentation at higher elevations in sub‐Saharan populations of Drosophila melanogaster. Such findings from population genomic analysis of wild‐derived strains should be included in gene annotations to provide a more holistic view of a gene's function. The evolutionary annotation of ebony added by Pool & Aquadro substantiates that pigmentation can be adaptive and implicates elevation as an important selective factor. This is important progress because the selective factors seem to differ between populations and species. In addition, the study raises issues to consider when extrapolating from selection at the molecular level to selection at the phenotypic level.     

Quantitative morphometrical analysis of a North African population of <Emphasis Type="Italic">Drosophila melanogaster</Emphasis>: sexual dimorphism,and comparison with European populations

Genetic variability of quantitative traits was investigated in aMoroccan population of Drosophila melanogaster, with an isofemale line design. Results were compared with data previously obtained from French populations. Although the environmental and thermal conditions are very different in France and Morocco, only two significant differences were observed: a shorter wing and a lighter abdomen pigmentation in Morocco. It is, therefore, concluded that Moroccan D. melanogaster are quite typical temperate flies, belonging to the Palaearctic region, and very different from the ancestral Afrotropical populations. Almost all traits were genetically variable, as shown by significant intraclass correlations among lines. Genetic correlations were highly significant among three size-related traits, while much lower between size and bristle numbers. Fluctuating asymmetry was greater for abdominal bristles than for sternopleural bristles. Sex dimorphism, analysed as a female/male ratio, was identical in French and Moroccan populations. Examination of the thorax length/thorax width ratio showed that the thorax is more elongated in females. Sexual dimorphism of wing length was significantly more correlated to thorax width than to thorax length. The results illustrate the value of measuring numerous quantitative traits on the same flies for characterizing the genetic architecture of a natural population. In several cases, and especially for genetic correlations, some interesting suggestions could be made, which should be confirmed, or invalidated, by more extensive investigations.     

Latitudinal Adh allozymic variation and ethanol tolerance in Indian populations of Drosophila melanogaster

Ten Indian geographical populations of D. melanogaster were assayed electrophoretically for Adh genic variation. The Indian geographical populations of D. melanogaster revealed significant clinal variation (3 % for 1 d? latitude) at Adh locus and Adh^F allelic frequency correlated significantly with increase in latitude. It was suggested that the abundance of secondary alcohols in the southern Indian tropical and humid environment might exert selective pressure favouring higher frequency of Adh^S allele. Patterns of ethanol utilization as well as ethanol tolerance were analyzed in larval and adult individuals of six geographical populations of D. melanogaster. Latitudinal variation in ethanol tolerance was observed in D. melanogaster populations from India. The parallel occurrence of latitudinal variation it Adh locus as well as ethanol tolerance in Indian geographical populations of D. melanogaster could be maintained by balancing natural selection varying spatially along the north-south axis of the Indian sub-continent.     

Impact of body melanisation on desiccation resistance in montane populations of D. melanogaster: Analysis of seasonal variation

In the montane localities of subtropical regions, winter is the dry season and ectothermic drosophilids are expected to evolve desiccation resistance to cope with drier climatic conditions. An analysis of six montane populations (600–2226 m) of D. melanogaster showed variations for body melanisation (i.e. pigmentation) and desiccation resistance across seasons as well as along altitude. During winter season, plastic changes for melanisation of three posterior abdominal segments (5th + 6th + 7th) correspond with higher desiccation resistance. Thus, we analyzed genetic and plastic effects for these ecophysiological traits by comparing wild-caught and laboratory reared individuals of D. melanogaster for autumn as well as winter season. A ratio of slope values in wild vs. laboratory populations has shown a 1.64-fold plastic effect during autumn; and a two-fold effect during winter. For body melanisation and desiccation resistance, evolutionary response to altitudinal environmental gradient is similar to the phenotypic response across seasons. Thus, our observations are in agreement with the co-gradient hypothesis. Further, we tested the hypothesis whether a thicker cuticle (either due to melanisation or cuticular lipids) leads to lesser cuticular water loss and higher desiccation resistance across seasons as well as according to altitude. Based on within and between population analyses, body melanisation was found to be positively correlated with desiccation resistance but negatively with cuticular water loss. Interestingly, there were no changes in the amount of cuticular lipids per fly across seasons as well as along altitude; and therefore cuticular lipids did not account for desiccation resistance. Cuticular water loss exhibited negative correlation with body melanisation but not with cuticular lipids as well as with changes in body size across seasons. Thus, our data suggest that seasonal changes in body melanisation confer desiccation resistance in montane populations of D. melanogaster.     

Population differences in density and resource allocation of ornamental tail feathers in the barn swallow

Many organisms show well‐defined latitudinal clines in morphology, which appear to be caused by spatially varying natural selection, resulting in different optimal phenotypes in each location. Such spatial variability raises an interesting question, with different prospects for the action of sexual selection on characters that have a dual purpose, such as locomotion and sexual attraction. The outermost tail feathers of barn swallows (Hirundo rustica) represent one such character, and their evolution has been a classic model subject to intense debate. In the present study, we examined individuals from four European populations to analyze geographical variation in the length and mass of tail feathers in relation to body size and wing size. Tail feather length differed between sexes and populations, and such variation was a result of the effects of natural selection, acting through differences in body size and wing size, as well as the effects of sexual selection that favours longer tails. The extra enlargement of the tail promoted by sexual selection (i.e. beyond the natural selection optimum) could be achieved by increasing investment in ornaments, and by modifying feather structure to produce longer feathers of lower density. These two separate processes accounting for the production of longer and more costly tail feathers and less dense feathers, respectively, are consistent with the hypothesis that both Zahavian and Fisherian mechanisms may be involved in the evolution of the long tails of male barn swallows. We hypothesize that the strength of sexual selection increases with latitude because of the need for rapid mating as a result of the short duration of the breeding season at high latitudes. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105 , 925–936.     

Genetic footprints of habitat fragmentation in the extant populations of Sinojackia (Styracaceae): implications for conservation

Sinojackia, a member of the family Styracaceae, is an endangered genus endemic to China. The number of populations and population size of Sinojackia have decreased sharply because of habitat fragmentation and destruction. We studied the genetic diversity of extant populations in two different cohorts (adult and seedling) using eight microsatellite markers to investigate the genetic footprints of habitat fragmentation in four recognized Sinojackia spp. and to develop appropriate conservation measures. Data on intrapopulational genetic diversity suggest that Sinojackia populations have maintained relatively high levels of genetic diversity and low levels of genetic differentiation despite severe fragmentation. The high genetic diversity may be explained by the outcrossing mating system and high longevity of Sinojackia spp. The amount of genetic variation is not associated with population size, which was also supported by bottleneck analysis. In the species studied, there was no significant difference in the genetic diversity between the two cohorts analysed. However, inbreeding increased from adult trees to seedling populations, suggesting that the higher proportion of biparental inbreeding in the recent generations of seedlings is the result of restricted current genetic flow caused by habitat fragmentation. Average seed set per population was not significantly correlated with either population size or genetic diversity. Conservation management should aim to monitor inbreeding and outbreeding depression carefully to ensure the in situ and ex situ conservation of Sinojackia spp. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ?? , ??–??.     

Population genetic structure and a possible role for selection in driving phenotypic divergence in a rainbowfish (Melanotaeniidae)

Quantitative genetic divergence may be driven by drift or selection. The rainbowfish Melanotaenia australis exhibits phenotypic divergence among populations in Western Australia, although the mechanisms driving this divergence are unknown. We used microsatellites to assess neutral genetic divergence (F_ST), and found a hierarchical pattern of subdivision consistent with low divergence between upstream and downstream populations (within drainages), moderate divergence between drainages (within regions), and high divergence between regions. Using a common‐garden approach, we measured quantitative genetic divergence in phenotypic traits (Q_ST). By comparing this to expectations from neutral processes (F_ST), we concluded that the effect of selection varies depending on the spatial scale considered. Within drainages, selection may be causing divergence between upstream and downstream phenotypes but, between regions, selection appears to homogenize phenotypes. This highlights the importance of spatial scale in studies of this kind, and suggests that, because variance in selection pressures can drive speciation, polymorphism in M. australis may represent speciation in action. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102 , 144–160.     

Comparative copulation anatomy of the Drosophila melanogaster species complex (Diptera: Drosophilidae)

The Drosophila melanogaster species complex consists of four species: D. melanogaster, D. simulans, D. sechellia and D. mauritiana. To identify these closely related species, researchers often examine the male genitalia, especially species‐specific shapes of the posterior process, as the most reliable and easily observable character. However, compared to genetic aspects, the evolutionary significance of the posterior process and other genital parts remains largely unexplained. By comparing genital coupling among these species, we revealed that the posterior processes, which are hidden under the female abdominal tergite VII when genital coupling is established, mesh with different parts of the intersegmental membrane between the tergite VIII and the oviscapts and that this membrane region broadens in a species‐specific manner. Furthermore, in D. simulans and D. sechellia, this membrane region is likely to incur wounds from the sharply pointed tip of the posterior process. On the basis of the use and functions of these and other genital parts, we discuss possible evolutionary forces underlying the diversification of genitalia in this group.