The genetic basis of adaptive pigmentation variation in Drosophila melanogaster

In a broad survey of Drosophila melanogaster population samples, levels of abdominal pigmentation were found to be highly variable and geographically differentiated. A strong positive correlation was found between dark pigmentation and high altitude, suggesting adaptation to specific environments. DNA sequence polymorphism at the candidate gene ebony revealed a clear association with the pigmentation of homozygous third chromosome lines. The darkest lines sequenced had nearly identical haplotypes spanning 14.5 kb upstream of the protein-coding exons of ebony. Thus, natural selection may have elevated the frequency of an allele that confers dark abdominal pigmentation by influencing the regulation of ebony.     

Pleiotropic Effects of methoprene-tolerant(Met), a Gene Involved in Juvenile Hormone Metabolism, on Life History Traits in Drosophila melanogaster

Life history theory assumes that there are alleles with pleiotropic effects on fitness components. Although quantitative genetic data are often consistent with pleiotropy, there are few explicit examples of pleiotropic loci. The Drosophila melanogaster gene Methoprene-tolerant (Met) may be such a locus. The Met gene product, a putative juvenile hormone receptor, facilitates the action of juvenile hormone (JH) and JH analogs; JH affects many life history traits in arthropods. Here we use quantitative complementation to investigate effects of Met mutant and wildtype alleles on female developmental time, onset of reproduction, and fecundity. Whereas the alleles did not differ in their effects on developmental time, we detected allelic variation for the onset of reproduction and for age-specific fecundity. Alleles influenced phenotypic co-variances among traits (developmental time and onset of reproduction; onset of reproduction and both early and late fecundity; early and late fecundity), suggesting that alleles of Met vary in their pleiotropic effects upon life history. Furthermore, the genetic covariance between developmental time and early fecundity attributed to alleles of Met was negative, indicating consistent pleiotropic effects among alleles on these traits. The allelic effects of Met support genetic models where pleiotropy at genes associated with hormone regulation can contribute to the evolution of life history traits.     

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.     

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.     

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.     

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.     

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.     

Phenotypic plasticity in morphological traits in two populations of Drosophila melanogaster

Isofemale lines of two populations of Drosophila melanogaster, originating from France and Tanzania, were examined over a range of temperatures. Morphological traits showed distinct patterns in phenotypic plasticity; flies of the two populations differed in shape. Genotype-by-Environment (G*E) interactions were frequently found in the Tanzania population, but were hardly present in the France population. If G*E interaction was present over temperature, estimates of additive genetic variance and additive genetic covariance were made to compare theoretical models with our data. The conclusion is that in France Drosophila melanogaster has been selected over a wider range of temperatures, resulting in parallel reaction norms of more optimal slope. In contrast, selection must have taken place over a narrower temperature range in Tanzanian flies, and will have exerted no direct influence on the slope of the reaction norm.     

Distinct cold tolerance traits independently vary across genotypes in Drosophila melanogaster

Cold tolerance, the ability to cope with low temperature stress, is a critical adaptation in thermally variable environments. An individual's cold tolerance comprises several traits including minimum temperatures for growth and activity, ability to survive severe cold, and ability to resume normal function after cold subsides. Across species, these traits are correlated, suggesting they were shaped by shared evolutionary processes or possibly share physiological mechanisms. However, the extent to which cold tolerance traits and their associated mechanisms covary within populations has not been assessed. We measured five cold tolerance traits—critical thermal minimum, chill coma recovery, short- and long-term cold tolerance, and cold-induced changes in locomotor behavior—along with cold-induced expression of two genes with possible roles in cold tolerance (heat shock protein 70 and frost)—across 12 lines of Drosophila melanogaster derived from a single population. We observed significant genetic variation in all traits, but few were correlated across genotypes, and these correlations were sex-specific. Further, cold-induced gene expression varied by genotype, but there was no evidence supporting our hypothesis that cold-hardy lines would have either higher baseline expression or induction of stress genes. These results suggest cold tolerance traits possess unique mechanisms and have the capacity to evolve independently.     

Genetic constraints on wing pattern variation in Lycaeides butterflies: A case study on mapping complex,multifaceted traits in structured populations

Patterns of phenotypic variation within and among species can be shaped and constrained by trait genetic architecture. This is particularly true for complex traits, such as butterfly wing patterns, that consist of multiple elements. Understanding the genetics of complex trait variation across species boundaries is difficult, as it necessitates mapping in structured populations and can involve many loci with small or variable phenotypic effects. Here, we investigate the genetic architecture of complex wing pattern variation in Lycaeides butterflies as a case study of mapping multivariate traits in wild populations that include multiple nominal species or groups. We identify conserved modules of integrated wing pattern elements within populations and species. We show that trait covariances within modules have a genetic basis and thus represent genetic constraints that can channel evolution. Consistent with this, we find evidence that evolutionary changes in wing patterns among populations and species occur in the directions of genetic covariances within these groups. Thus, we show that genetic constraints affect patterns of biological diversity (wing pattern) in Lycaeides, and we provide an analytical template for similar work in other systems.     

Pupal period and adult size in Drosophila melanogaster: a cautionary tale of contrasting correlations between two sexually dimorphic traits

Sexual dimorphism (SD) is widespread, reflecting a resolution of genetic conflicts arising from sex-specific differences in selection. However, genetic correlations among traits may constrain the evolution of SD. Drosophila melanogaster exhibits SD for pupal period (males longer) and adult weight (females heavier). This negative inter-sex covariance between the traits contrasts with a significant intra-sex positive genetic correlation (r(g) = 0.95) estimated using lines selected for fast larval development. Path analysis indicated that within sexes the selection regime indirectly reduced adult weight which in turn reduced pupal period. A hypothesis is proposed for the evolution of SD whereby the trait 'pupal period' is divided into 'intrinsic' (correlated with body size) and 'ecological' (uncorrelated with body size) components, and (the larger) females eclose earlier than males size via a shortening of the ecological component, thus achieving the advantage of provisioning eggs prior to sexual maturity. This hypothesis avoids invoking successful 'incompatible antagonistic selection'.     

Autosomal variation for male body size and sperm competition phenotypes is uncorrelated in Drosophila melanogaster

Correlations between male body size and phenotypes impacting post-copulatory sexual selection are commonly observed during the manipulation of male body size by environmental rearing conditions. Here, we control for environmental influences and test for genetic correlations between natural variation in male body size and phenotypes affecting post-copulatory sexual selection in Drosophila melanogaster. Dry weights of virgin males from 90 second-chromosome and 88 third-chromosome substitution lines were measured. Highly significant line effects (p<0.001) documented a genetic basis to variation in male body size. No significant correlations were identified between male body size and the components of sperm competitive ability. These results suggest that natural autosomal variation for male body size has little impact on post-copulatory sexual selection. If genetic correlations exist between male body size and post-copulatory sexual selection then variation in the sex chromosomes are likely candidates, as might be expected if sexually antagonistic coevolution was responsible.     

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.     

Quantitative genetics of learning ability and resistance to stress in Drosophila melanogaster

Even though laboratory evolution experiments have demonstrated genetic variation for learning ability, we know little about the underlying genetic architecture and genetic relationships with other ecologically relevant traits. With a full diallel cross among twelve inbred lines of Drosophila melanogaster originating from a natural population (0.75 < F < 0.93), we investigated the genetic architecture of olfactory learning ability and compared it to that for another behavioral trait (unconditional preference for odors), as well as three traits quantifying the ability to deal with environmental challenges: egg‐to‐adult survival and developmental rate on a low‐quality food, and resistance to a bacterial pathogen. Substantial additive genetic variation was detected for each trait, highlighting their potential to evolve. Genetic effects contributed more than nongenetic parental effects to variation in traits measured at the adult stage: learning, odorant perception, and resistance to infection. In contrast, the two traits quantifying larval tolerance to low‐quality food were more strongly affected by parental effects. We found no evidence for genetic correlations between traits, suggesting that these traits could evolve at least to some degree independently of one another. Finally, inbreeding adversely affected all traits.     

Evolutionary responses of Drosophila melanogaster to selection at different larval densities: changes in genetic variation,specialization and phenotypic plasticity

Abstract We studied the evolutionary response to novel environments by applying artificial selection for total progeny biomass in populations of Drosophila melanogaster maintained at three different larval population densities. We found the relative amount of genetic variability for characters related with biomass to be lower and the correlation between them more negative at the intermediate density, and that selection resulted in changes in phenotypic plasticity and in patterns of resource allocation between traits. We found some evidence for tradeoffs between densities, which suggests that populations living at heterogeneous densities might be subject to disruptive selection. Our results show that adaptation to new environments may be a complex process, involving not only changes in trait means, but also in correlations between traits and between environments.     

Heritability estimates of life history traits in small white butterflyPieris rapae crucivora

Heritabilities and genetic correlations of life history characters (pupal weight, age-specific fecundities, and egg weight) of small white butterfly Pieris rapae crucivora are estimated by a quantitative genetic method (sib analysis). The results indicate moderate or high heritabilities and a largely negative genetic correaltion in age-specific fecundities.     

A multivariate test of evolutionary constraints for thermal tolerance in Drosophila melanogaster

Exposure to extreme temperatures is increasingly likely to impose strong selection on many organisms in their natural environments. The ability of organisms to adapt to such selective pressures will be determined by patterns of genetic variation and covariation. Despite increasing interest in thermal adaptation, few studies have examined the extent to which the genetic covariance between traits might constrain thermal responses. Furthermore, it remains unknown whether sex‐specific genetic architectures will constrain responses to climatic selection. We used a paternal half‐sibling breeding design to examine whether sex‐specific genetic architectures and genetic covariances between traits might constrain evolutionary responses to warming climates in a population of Drosophila melanogaster. Our results suggest that the sexes share a common genetic underpinning for heat tolerance as indicated by a strong positive inter‐sexual genetic correlation. Further, we found no evidence in either of the sexes that genetic trade‐offs between heat tolerance and fitness will constrain responses to thermal selection. Our results suggest that neither trade‐offs, nor sex‐specific genetics, will significantly constrain an evolutionary response to climatic warming, at least in this population of D. melanogaster.     

Latitudinal variation in wild populations of Drosophila melanogaster: heritabilities and reaction norms

Large amounts of genetic variation for wing length and wing area were demonstrated both within and between Drosophila melanogaster populations along a latitudinal gradient in South America. Wing length and wing area showed a strong positive correlation with latitude in both wild flies and laboratory-raised descendants. Large population differences were observed for heritability and coefficient of variation of these two traits, whereas relatively small population differences were found for development time, viability, pupal mortality, sex ratio and their norms of reaction to four developmental temperatures. No clear-cut latitudinal clines were established for these life-history characters. These results are discussed in the light of Bergmann's Rule and the relation between larval development and adult body size.     

Hsp90 and the quantitative variation of wing shape in Drosophila melanogaster

The molecular chaperone protein Hsp90 has been widely discussed as a candidate gene for developmental buffering. We used the methods of geometric morphometrics to analyze its effects on the variation among individuals and fluctuating asymmetry of wing shape in Drosophila melanogaster. Three different experimental approaches were used to reduce Hsp90 activity. In the first experiment, developing larvae were reared in food containing a specific inhibitor of Hsp90, geldanamycin, but neither individual variation nor fluctuating asymmetry was altered. Two further experiments generated lines of genetically identical flies carrying mutations of Hsp83, the gene encoding the Hsp90 protein, in heterozygous condition in nine different genetic backgrounds. The first of these, introducing entire chromosomes carrying either of two Hsp83 mutations, did not increase shape variation or asymmetry over a wild-type control in any of the nine genetic backgrounds. In contrast, the third experiment, in which one of these Hsp83 alleles was introgressed into the wild-type background that served as the control, induced an increase in both individual variation and fluctuating asymmetry within each of the nine genetic backgrounds. No effect of Hsp90 on the difference among lines was detected, pro,iding no evidence for cryptic genetic variation of wing shape. Overall, these results suggest that Hsp90 contributes to, but is not controlling, the buffering of phenotypic variation in wing shape.