Automated measurement of Drosophila wings

Genetic variation for sexual dimorphism in developmental traits in Drosophila melanogaster

Sexual dimorphism in traits of insects during the developmental stages could potentially be the direct or indirect result of sex-specific selection provided that genetic variation for sexual dimorphism is present. We investigated genetic variation in sexual dimorphism in a set of Drosophila melanogaster inbred lines for 2 traits: egg to adult development time and pupation site preference. We observed considerable genetic variation in sexual dimorphism among lines in both traits. The sexual dimorphic patterns remained relatively consistent across multiple trials, despite both traits being sensitive to environmental conditions. Additionally, we measured 2 sexually dimorphic adult morphological traits in 6 sampled lines and investigated correlations in the sexual dimorphism patterns with the 2 developmental traits. The abundance of genetic variation in sexual dimorphism for D. melanogaster developmental traits demonstrated in this study provides evidence for a high degree of evolvability of sex differences in preadult traits in natural populations.

Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium

What regulates organ size and shape remains one fundamental mystery of modern biology. Research in this area has primarily focused on deciphering the regulation in time and space of growth and cell division, while the contribution of cell death has been overall neglected. This includes studies of the Drosophila wing, one of the best-characterized systems for the study of growth and patterning, undergoing massive growth during larval stage and important morphogenetic remodeling during pupal stage. So far, it has been assumed that cell death was relatively neglectable in this tissue both during larval stage and pupal stage, and as a result, the pattern of growth was usually attributed to the distribution of cell division. Here, using systematic mapping and registration combined with quantitative assessment of clone size and disappearance as well as live imaging, we outline a persistent pattern of cell death and clone elimination emerging in the larval wing disc and persisting during pupal wing morphogenesis. Local variation of cell death is associated with local variation of clone size, pointing to an impact of cell death on local growth that is not fully compensated by proliferation. Using morphometric analyses of adult wing shape and genetic perturbations, we provide evidence that patterned death locally and globally affects adult wing shape and size. This study describes a roadmap for precise assessment of the contribution of cell death to tissue shape and outlines an important instructive role of cell death in modulating quantitatively local growth and morphogenesis of a fast-growing tissue.

Integrating artificial intelligence and wing geometric morphometry to automate mosquito classification

Mosquitoes (Diptera: Culicidae) comprise over 3500 global species, primarily in tropical regions, where the females act as disease vectors. Thus, identifying medically significant species is vital. In this context, Wing Geometric Morphometry (WGM) emerges as a precise and accessible method, excelling in species differentiation through mathematical approaches. Computational technologies and Artificial Intelligence (AI) promise to overcome WGM challenges, supporting mosquito identification. AI explores computers' thinking capacity, originating in the 1950s. Machine Learning (ML) arose in the 1980s as a subfield of AI, and deep Learning (DL) characterizes ML's subcategory, featuring hierarchical data processing layers. DL relies on data volume and layer adjustments. Over the past decade, AI demonstrated potential in mosquito identification. Various studies employed optical sensors, and Convolutional Neural Networks (CNNs) for mosquito identification, achieving average accuracy rates between 84 % and 93 %. Furthermore, larval Aedes identification reached accuracy rates of 92 % to 94 % using CNNs. DL models such as ResNet50 and VGG16 achieved up to 95 % accuracy in mosquito identification. Applying CNNs to georeference mosquito photos showed promising results. AI algorithms automated landmark detection in various insects' wings with repeatability rates exceeding 90 %. Companies have developed wing landmark detection algorithms, marking significant advancements in the field. In this review, we discuss how AI and WGM are being combined to identify mosquito species, offering benefits in monitoring and controlling mosquito populations.

Complexities of recapitulating polygenic effects in natural populations: replication of genetic effects on wing shape in artificially selected and wild-caught populations of Drosophila melanogaster

Identifying the genetic architecture of complex traits is important to many geneticists, including those interested in human disease, plant and animal breeding, and evolutionary genetics. Advances in sequencing technology and statistical methods for genome-wide association studies have allowed for the identification of more variants with smaller effect sizes, however, many of these identified polymorphisms fail to be replicated in subsequent studies. In addition to sampling variation, this failure to replicate reflects the complexities introduced by factors including environmental variation, genetic background, and differences in allele frequencies among populations. Using Drosophila melanogaster wing shape, we ask if we can replicate allelic effects of polymorphisms first identified in a genome-wide association studies in three genes: dachsous, extra-macrochaete, and neuralized, using artificial selection in the lab, and bulk segregant mapping in natural populations. We demonstrate that multivariate wing shape changes associated with these genes are aligned with major axes of phenotypic and genetic variation in natural populations. Following seven generations of artificial selection along the dachsous shape change vector, we observe genetic differentiation of variants in dachsous and genomic regions containing other genes in the hippo signaling pathway. This suggests a shared direction of effects within a developmental network. We also performed artificial selection with the extra-macrochaete shape change vector, which is not a part of the hippo signaling network, but showed a largely shared direction of effects. The response to selection along the emc vector was similar to that of dachsous, suggesting that the available genetic diversity of a population, summarized by the genetic (co)variance matrix (G), influenced alleles captured by selection. Despite the success with artificial selection, bulk segregant analysis using natural populations did not detect these same variants, likely due to the contribution of environmental variation and low minor allele frequencies, coupled with small effect sizes of the contributing variants.

Phenotypic extremes or extreme phenotypes? On the use of large and small-bodied "phenocopied" Drosophila melanogaster males in studies of sexual selection and conflict

In the fruit fly, Drosophila melanogaster, variation in body size is influenced by a number of different factors and may be strongly associated with individual condition, performance and success in reproductive competitions. Consequently, intra-sexual variation in size in this model species has been frequently explored in order to better understand how sexual selection and sexual conflict may operate and shape evolutionary trajectories. However, measuring individual flies can often be logistically complicated and inefficient, which can result in limited sample sizes. Instead, many experiments use large and/or small body sizes that are created by manipulating the developmental conditions experienced during the larval stages, resulting in "phenocopied" flies whose phenotypes resemble what is seen at the extremes of a population's size distribution. While this practice is fairly common, there has been remarkedly few direct tests to empirically compare the behaviour or performance of phenocopied flies to similarly-sized individuals that grew up under typical developmental conditions. Contrary to assumptions that phenocopied flies are reasonable approximations, we found that both large and small-bodied phenocopied males frequently differed from their standard development equivalents in their mating frequencies, their lifetime reproductive successes, and in their effects on the fecundity of the females they interacted with. Our results highlight the complicated contributions of environment and genotype to the expression of body size phenotypes and lead us to strongly urge caution in the interpretation of studies solely replying upon phenocopied individuals.

A method to predict the response to directional selection using a Kalman filter

Predicting evolution remains challenging. The field of quantitative genetics provides predictions for the response to directional selection through the breeder's equation, but these predictions can have errors. The sources of these errors include omission of traits under selection, inaccurate estimates of genetic variance, and nonlinearities in the relationship between genetic and phenotypic variation. Previous research showed that the expected value of these prediction errors is often not zero, so predictions are systematically biased. Here, we propose that this bias, rather than being a nuisance, can be used to improve the predictions. We use this to develop a method to predict evolution, which is built on three key innovations. First, the method predicts change as the breeder's equation plus a bias term. Second, the method combines information from the breeder's equation and from the record of past changes in the mean to predict change using a Kalman filter. Third, the parameters of the filter are fitted in each generation using a learning algorithm on the record of past changes. We compare the method to the breeder's equation in two artificial selection experiments, one using the wing of the fruit fly and another using simulations that include a complex mapping of genotypes to phenotypes. The proposed method outperforms the breeder's equation, particularly when traits under selection are omitted from the analysis, when data are noisy, and when additive genetic variance is estimated inaccurately or not estimated at all. The proposed method is easy to apply, requiring only the trait means over past generations.

MAPPER: An Open-Source, High-Dimensional Image Analysis Pipeline Unmasks Differential Regulation of Drosophila Wing Features

Phenomics requires quantification of large volumes of image data, necessitating high throughput image processing approaches. Existing image processing pipelines for Drosophila wings, a powerful genetic model for studying the underlying genetics for a broad range of cellular and developmental processes, are limited in speed, precision, and functional versatility. To expand on the utility of the wing as a phenotypic screening system, we developed MAPPER, an automated machine learning-based pipeline that quantifies high-dimensional phenotypic signatures, with each dimension quantifying a unique morphological feature of the Drosophila wing. MAPPER magnifies the power of Drosophila phenomics by rapidly quantifying subtle phenotypic differences in sample populations. We benchmarked MAPPER’s accuracy and precision in replicating manual measurements to demonstrate its widespread utility. The morphological features extracted using MAPPER reveal variable sexual dimorphism across Drosophila species and unique underlying sex-specific differences in morphogen signaling in male and female wings. Moreover, the length of the proximal-distal axis across the species and sexes shows a conserved scaling relationship with respect to the wing size. In sum, MAPPER is an open-source tool for rapid, high-dimensional analysis of large imaging datasets. These high-content phenomic capabilities enable rigorous and systematic identification of genotype-to-phenotype relationships in a broad range of screening and drug testing applications and amplify the potential power of multimodal genomic approaches.

Drosophila Wing Integration and Modularity: A Multi-Level Approach to Understand the History of Morphological Structures

Simple Summary

The diverse components of any morphological structure are integrated with respect to each other since they have developed, functioned, and evolved together, a phenomenon known as integration. However, this integration is not absolute but organized in units (i.e., modules) that are relatively independent while participating to generate a structure that acts as a functional whole. Even though most of the studies on modularity and integration have focused on variation among individuals within populations, there are more levels of variation that exhibit modularity and integration, deriving from distinct sources such as genetic variation, phenotypic plasticity, fluctuating asymmetry, evolutionary change, among others. Consequently, the present study focused on analysing the integration and modularity of the wing shape of some of the best-known model organisms, i.e., the genus Drosophila, at the static, developmental, and evolutionary levels to acquire a better insight about how modularity and integration act at different analytical levels. The strong integration and overall similarities observed in the variation pattern at multiple levels suggest a shared mechanism underlying the observed variation in Drosophila’s wing shape and added a new piece of evidence of stasis in the evolutionary history of Drosophila wing.

Abstract

Static, developmental, and evolutionary variation are different sources of morphological variation which can be quantified using morphometrics tools. In the present study we have carried out a comparative multiple level study of integration (i.e., static, developmental, and evolutionary) to acquire insight about the relationships that exist between different integration levels, as well as to better understand their involvement in the evolutionary processes related to the diversification of Drosophila’s wing shape. This approach was applied to analyse wing evolution in 59 species across the whole genus in a large dataset (~10,000 wings were studied). Static integration was analysed using principal component analysis, thus providing an integration measurement for overall wing shape. Developmental integration was studied between wing parts by using a partial least squares method between the anterior and posterior compartments of the wing. Evolutionary integration was analysed using independent contrasts. The present results show that all Drosophila species exhibit strong morphological integration at different levels. The strong integration and overall similarities observed at multiple integration levels suggest a shared mechanism underlying this variation, which could result as consequence of genetic drift acting on the wing shape of Drosophila.

The evolution of larger size in high-altitude Drosophila melanogaster has a variable genetic architecture

Important uncertainties persist regarding the genetic architecture of adaptive trait evolution in natural populations, including the number of genetic variants involved, whether they are drawn from standing genetic variation, and whether directional selection drives them to complete fixation. Here, we take advantage of a unique natural population of Drosophila melanogaster from the Ethiopian highlands, which has evolved larger body size than any other known population of this species. We apply a bulk segregant quantitative trait locus mapping approach to 4 unique crosses between highland Ethiopian and lowland Zambian populations for both thorax length and wing length. Results indicated a persistently variable genetic basis for these evolved traits (with largely distinct sets of quantitative trait loci for each cross), and at least a moderately polygenic architecture with relatively strong effects present. We complemented these mapping experiments with population genetic analyses of quantitative trait locus regions and gene ontology enrichment analysis, generating strong hypotheses for specific genes and functional processes that may have contributed to these adaptive trait changes. Finally, we find that the genetic architectures indicated by our quantitative trait locus mapping results for size traits mirror those from similar experiments on other recently evolved traits in this species. Collectively, these studies suggest a recurring pattern of polygenic adaptation in this species, in which causative variants do not approach fixation and moderately strong effect loci are present.

Wing plastic response to temperature variation in two distantly related Neotropical Drosophila species (Diptera, Drosophilidae)

Phenotypic plasticity has been described for morphological and life-history traits in many organisms. In Drosophila, temperature drives phenotypic change in several traits, but few Neotropical species have been studied and whether the phenotypic variation associated with plasticity is adaptive remains unclear. Here, we studied the phenotypic response to temperature variation in the distantly related Neotropical species Drosophila mercatorum Patterson and Wheeler, 1942 and Drosophila willistoni Sturtevant, 1916. We evaluate if wing shape variation follows that observed in the Neotropical species Drosophila cardini Sturtevant, 1916: round wings at lower temperatures and narrower wings at higher temperatures. The variation in egg–adult development time and in wing size, shape, and allometry was described using reaction norms and geometric morphometrics. In both species, development time and wing size decreased with increasing temperature and wing allometry showed that size explained ≈10% of the shape variation. Wing shape, however, exhibited contrasting responses. At higher temperatures, D. mercatorum developed slightly slender wings, following the pattern previously found for D. cardini, whereas D. willistoni developed plumper and shorter wings, supporting previous studies on Drosophila melanogaster Meigen, 1830. We conclude that all traits studied here were influenced by temperature, and that wing shape seems also to be influenced by phylogeny.

Conserved and Divergent Aspects of Plasticity and Sexual Dimorphism in Wing Size and Shape in Three Diptera

The ability of powered flight in insects facilitated their great evolutionary success allowing them to occupy various ecological niches. Beyond this primary task, wings are often involved in various premating behaviors, such as the generation of courtship songs and the initiation of mating in flight. These specific functions imply special adaptations of wing morphology, as well as sex-specific wing morphologies. Although wing morphology has been extensively studied in Drosophila melanogaster (Meigen, 1830), a comprehensive understanding of developmental plasticity and the impact of sex on wing size and shape plasticity is missing for other Diptera. Therefore, we raised flies of the three Diptera species Drosophila melanogaster, Ceratitis capitata (Wiedemann, 1824) and Musca domestica (Linnaeus, 1758) at different environmental conditions and applied geometric morphometrics to analyze wing shape. Our data showed extensive interspecific differences in wing shape, as well as a clear sexual wing shape dimorphism in all three species. We revealed an impact of different rearing temperatures on wing shape in all three species, which was mostly explained by plasticity in wing size in D. melanogaster. Rearing densities had significant effects on allometric wing shape in D. melanogaster, while no obvious effects were observed for the other two species. Additionally, we did not find evidence for sex-specific response to different rearing conditions in D. melanogaster and C. capitata, while a male-specific impact of different rearing conditions was observed on non-allometric wing shape in M. domestica. Overall, our data strongly suggests that many aspects of wing morphology underly species-specific adaptations and we discuss potential developmental and functional implications of our results.

Using phenotypic plasticity to understand the structure and evolution of the genotype-phenotype map

Deciphering the genotype-phenotype map necessitates relating variation at the genetic level to variation at the phenotypic level. This endeavour is inherently limited by the availability of standing genetic variation, the rate of spontaneous mutation to novo genetic variants, and possible biases associated with induced mutagenesis. An interesting alternative is to instead rely on the environment as a source of variation. Many phenotypic traits change plastically in response to the environment, and these changes are generally underlain by changes in gene expression. Relating gene expression plasticity to the phenotypic plasticity of more integrated organismal traits thus provides useful information about which genes influence the development and expression of which traits, even in the absence of genetic variation. We here appraise the prospects and limits of such an environment-for-gene substitution for investigating the genotype-phenotype map. We review models of gene regulatory networks, and discuss the different ways in which they can incorporate the environment to mechanistically model phenotypic plasticity and its evolution. We suggest that substantial progress can be made in deciphering this genotype-environment-phenotype map, by connecting theory on gene regulatory network to empirical patterns of gene co-expression, and by more explicitly relating gene expression to the expression and development of phenotypes, both theoretically and empirically.

Using comprehensive machine-learning models to classify complex morphological characters

Recognizing and classifying multiple morphological features, such as patterns, sizes, and textures, can provide a comprehensive understanding of their variability and phenotypic evolution. Yet, quantitatively measuring complex morphological characters remains challenging.We provide a machine learning-based pipeline (SVMorph) to consider and classify complex morphological characters in multiple organisms that have either small or large datasets.Our pipeline integrates two descriptors, histogram of oriented gradient and local binary pattern, to meet various classification needs. We also optimized feature extraction by adding image data augmentation to improve model generalizability.We tested SVMorph on two real-world examples to demonstrate that it can be used with small training datasets and limited computational resources. Comparing with multiple CNN-based methods and traditional techniques, we show that SVMorph is reliable and fast in texture-based individual classification. Thus, SVMorph can be used to efficiently classify multiple morphological characters in distinct nonmodel organisms.

Genomics of altitude-associated wing shape in two tropical butterflies

Understanding how organisms adapt to their local environment is central to evolution. With new whole-genome sequencing technologies and the explosion of data, deciphering the genomic basis of complex traits that are ecologically relevant is becoming increasingly feasible. Here, we studied the genomic basis of wing shape in two Neotropical butterflies that inhabit large geographical ranges. Heliconius butterflies at high elevations have been shown to generally have rounder wings than those in the lowlands. We reared over 1,100 butterflies from 71 broods of H. erato and H. melpomene in common-garden conditions and showed that wing aspect ratio, that is, elongatedness, is highly heritable in both species and that elevation-associated wing aspect ratio differences are maintained. Genome-wide associations with a published data set of 666 whole genomes from across a hybrid zone, uncovered a highly polygenic basis to wing aspect ratio variation in the wild. We identified several genes that have roles in wing morphogenesis or wing aspect ratio variation in Drosophila flies, making them promising candidates for future studies. There was little evidence for molecular parallelism in the two species, with only one shared candidate gene, nor for a role of the four known colour pattern loci, except for optix in H. erato. Thus, we present the first insights into the heritability and genomic basis of within-species wing aspect ratio in two Heliconius species, adding to a growing body of evidence that polygenic adaptation may underlie many ecologically relevant traits.

Spectral phenotyping of embryonic development reveals integrative thermodynamic responses

Background

Energy proxy traits (EPTs) are a novel approach to high dimensional organismal phenotyping that quantify the spectrum of energy levels within different temporal frequencies associated with mean pixel value fluctuations from video. They offer significant potential in addressing the phenotyping bottleneck in biology and are effective at identifying lethal endpoints and measuring specific functional traits, but the extent to which they might contribute additional understanding of the phenotype remains unknown. Consequently, here we test the biological significance of EPTs and their responses relative to fundamental thermodynamic principles. We achieve this using the entire embryonic development of Radix balthica, a freshwater pond snail, at different temperatures (20, 25 & 30 °C) and comparing responses against predictions from Arrhenius’ equation (Q₁₀ = 2).

Results

We find that EPTs are thermally sensitive and their spectra of frequency response enable effective high-dimensional treatment clustering throughout organismal development. Temperature-specific deviation in EPTs from thermodynamic predictions were evident and indicative of physiological mitigation, although they differed markedly in their responses from manual measures. The EPT spectrum was effective in capturing aspects of the phenotype predictive of biological outcomes, and suggest that EPTs themselves may reflect levels of energy turnover.

Conclusions

Whole-organismal biology is incredibly complex, and this contributes to the challenge of developing universal phenotyping approaches. Here, we demonstrate the biological relevance of a new holistic approach to phenotyping that is not constrained by preconceived notions of biological importance. Furthermore, we find that EPTs are an effective approach to measuring even the most dynamic life history stages.

Supplementary information

The online version contains supplementary material available at 10.1186/s12859-021-04152-1.

Computer Vision, Machine Learning, and the Promise of Phenomics in Ecology and Evolutionary Biology

For centuries, ecologists and evolutionary biologists have used images such as drawings, paintings and photographs to record and quantify the shapes and patterns of life. With the advent of digital imaging, biologists continue to collect image data at an ever-increasing rate. This immense body of data provides insight into a wide range of biological phenomena, including phenotypic diversity, population dynamics, mechanisms of divergence and adaptation, and evolutionary change. However, the rate of image acquisition frequently outpaces our capacity to manually extract meaningful information from images. Moreover, manual image analysis is low-throughput, difficult to reproduce, and typically measures only a few traits at a time. This has proven to be an impediment to the growing field of phenomics – the study of many phenotypic dimensions together. Computer vision (CV), the automated extraction and processing of information from digital images, provides the opportunity to alleviate this longstanding analytical bottleneck. In this review, we illustrate the capabilities of CV as an efficient and comprehensive method to collect phenomic data in ecological and evolutionary research. First, we briefly review phenomics, arguing that ecologists and evolutionary biologists can effectively capture phenomic-level data by taking pictures and analyzing them using CV. Next we describe the primary types of image-based data, review CV approaches for extracting them (including techniques that entail machine learning and others that do not), and identify the most common hurdles and pitfalls. Finally, we highlight recent successful implementations and promising future applications of CV in the study of phenotypes. In anticipation that CV will become a basic component of the biologist’s toolkit, our review is intended as an entry point for ecologists and evolutionary biologists that are interested in extracting phenotypic information from digital images.

WingBank: A Wing Image Database of Mosquitoes

Mosquito-borne diseases affect millions of people and cause thousands of deaths yearly. Vaccines have been hitherto insufficient to mitigate them, which makes mosquito control the most viable approach. But vector control depends on correct species identification and geographical assignment, and the taxonomic characters of mosquitoes are often inconspicuous to non-taxonomists, which are restricted to a life stage and/or even damaged. Thus, geometric morphometry, a low cost and precise technique that has proven to be efficient for identifying subtle morphological dissimilarities, may contribute to the resolution of these types of problems. We have been applying this technique for more than 10 years and have accumulated thousands of wing images with their metadata. Therefore, the aims of this work were to develop a prototype of a platform for the storage of biological data related to wing morphometry, by means of a relational database and a web system named “WingBank.” In order to build the WingBank prototype, a multidisciplinary team performed a gathering of requirements, modeled and designed the relational database, and implemented a web platform. WingBank was designed to enforce data completeness, to ease data query, to leverage meta-studies, and to support applications of automatic identification of mosquitoes. Currently, the database of the WingBank contains data referring to 77 species belonging to 15 genera of Culicidae. From the 13,287 wing records currently cataloged in the database, 2,138 were already made available for use by third parties. As far as we know, this is the largest database of Culicidae wings of the world.

Allometry constrains the evolution of sexual dimorphism in Drosophila across 33 million years of divergence

Sexual dimorphism is widely viewed as adaptive, reflecting the evolution of males and females toward divergent fitness optima. Its evolution, however, may often be constrained by the shared genetic architecture of the sexes, and by allometry. Here, we investigated the evolution of sexual size dimorphism, shape dimorphism, and their allometric relationship, in the wings of 82 taxa in the family Drosophilidae that have been diverging for at least 33 million years. Shape dimorphism among species was remarkably similar, with males characterized by longer, thinner wings than females. There was, however, quantitative variation among species in both size and shape dimorphism, with evidence that they have adapted to different evolutionary optima in different clades on timescales of about 10 million years. Within species, shape dimorphism was predicted by size, and among species, there was a strong relationship between size dimorphism and shape dimorphism. Allometry constrained the evolution of shape dimorphism for the two most variable traits we studied, but dimorphism was evolutionary labile in other traits. The keys for disentangling alternative explanations for dimorphism evolution are studies of natural and sexual selection, together with a deeper understanding of how microevolutionary parameters of evolvability relate to macroevolutionary patterns of divergence.

Repeatability analysis improves the reliability of behavioral data

Reliability of data has become a major concern in the course of the reproducibility crisis. Especially when studying animal behavior, confounding factors such as novelty of the test apparatus can lead to a wide variability of data which may mask treatment effects and consequently lead to misinterpretation. Habituation to the test situation is a common practice to circumvent novelty induced increases in variance and to improve the reliability of the respective measurements. However, there is a lack of published empirical knowledge regarding reasonable habituation procedures and a method validation seems to be overdue. This study aimed at setting up a simple strategy to increase reliability of behavioral data measured in a familiar test apparatus. Therefore, exemplary data from mice tested in an Open Field (OF) arena were used to elucidate the potential of habituation and how reliability of measures can be confirmed by means of a repeatability analysis using the software R. On seven consecutive days, male C57BL/6J, BALB/cJ and 129S1/SvImJ mice were tested in an OF arena once daily and individual mouse behavior was recorded. A repeatability analysis was conducted with regard to repeated trials of habituation. Our data analysis revealed that monitoring animal behavior during habituation is important to determine when individual differences of the measurements are stable. Repeatability values from distance travelled and average activity increased over the habituation period, revealing that around 60% of the variance of the data can be explained by individual differences between mice. The first day of habituation was significantly different from the following 6 days. A three-day habituation period appeared to be sufficient in this study. Overall, these results emphasize the importance of habituation and in depth analysis of habituation data to define the correct starting point of the experiment for improving the reliability and reproducibility of experimental data.

A Multivariate Genome-Wide Association Study of Wing Shape in Drosophila melanogaster

Due to the complexity of genotype-phenotype relationships, simultaneous analyses of genomic associations with multiple traits will be more powerful and informative than a series of univariate analyses. However, in most cases, studies of genotype-phenotype relationships have been analyzed only one trait at a time. Here, we report the results of a fully integrated multivariate genome-wide association analysis of the shape of the Drosophila melanogaster wing in the Drosophila Genetic Reference Panel. Genotypic effects on wing shape were highly correlated between two different laboratories. We found 2396 significant SNPs using a 5% false discovery rate cutoff in the multivariate analyses, but just four significant SNPs in univariate analyses of scores on the first 20 principal component axes. One quarter of these initially significant SNPs retain their effects in regularized models that take into account population structure and linkage disequilibrium. A key advantage of multivariate analysis is that the direction of the estimated phenotypic effect is much more informative than a univariate one. We exploit this fact to show that the effects of knockdowns of genes implicated in the initial screen were on average more similar than expected under a null model. A subset of SNP effects were replicable in an unrelated panel of inbred lines. Association studies that take a phenomic approach, considering many traits simultaneously, are an important complement to the power of genomics.

A molecular, morphological, and physiological comparison of English and German populations of Calliphora vicina (Diptera: Calliphoridae)

The bluebottle blow fly Calliphora vicina is a common species distributed throughout Europe that can play an important role as forensic evidence in crime investigations. Developmental rates of C. vicina from distinct populations from Germany and England were compared under different temperature regimes to explore the use of growth data from different geographical regions for local case work. Wing morphometrics and molecular analysis between these populations were also studied as indicators for biological differences. One colony each of German and English C. vicina were cultured at the Institute of Legal Medicine in Frankfurt, Germany. Three different temperature regimes were applied, two constant (16°C & 25°C) and one variable (17–26°C, room temperature = RT). At seven time points (600, 850, 1200, 1450, 1800, 2050, and 2400 accumulated degree hours), larval lengths were measured; additionally, the durations of the post feeding stage and intrapuparial metamorphosis were recorded. For the morphometric and molecular study, 184 females and 133 males from each C. vicina population (Germany n = 3, England n = 4) were sampled. Right wings were measured based on 19 landmarks and analyzed using canonical variates analysis and discriminant function analysis. DNA was isolated from three legs per specimen (n = 61) using 5% chelex. A 784 bp long fragment of the mitochondrial cytochrome b gene was sequenced; sequences were aligned and phylogenetically analyzed. Similar larval growth rates of C. vicina were found from different geographic populations at different temperatures during the major part of development. Nevertheless, because minor differences were found a wider range of temperatures and sampling more time points should be analyzed to obtain more information relevant for forensic case work. Wing shape variation showed a difference between the German and English populations (P<0.0001). However, separation between the seven German and English populations at the smaller geographic scale remained ambiguous. Molecular phylogenetic analysis by maximum likelihood method could not unambiguously separate the different geographic populations at a national (Germany vs England) or local level.

Directional selection reduces developmental canalization against genetic and environmental perturbations in Drosophila wings

Natural selection may enhance or weaken the robustness of phenotypes against genetic or environmental perturbations. However, important aspects of the relationship between adaptive evolution and canalization remain unclear. Recent work showed that the evolution of larger wing size in a high altitude natural population of Drosophila melanogaster was accompanied by decanalized wing development--specifically a loss of robustness to genetic perturbation. But this study did not address environmental robustness, and it compared populations that may have numerous biological differences. Here, we perform artificial selection on this same trait in D. melanogaster (larger wing length) and directly test whether this directional selection resulted in decanalization. We find that in general, size-selected replicates show greater frequencies of wing defects than control replicates both after mutagenesis (genetic perturbation) and when subjected to high temperature stress (environmental perturbation), although the increase in defect frequency varies importantly among replicates. These results support the hypothesis that directional selection may result in the loss of both genetic and environmental robustness-offering a rare window into the relationship between adaptation and canalization.

Phenotypic plasticity of Drosophila suzukii wing to developmental temperature: implications for flight

Phenotypic plasticity has been proposed as a mechanism that facilitates the success of biological invasions. In order to test the hypothesis of an adaptive role for plasticity in invasions, particular attention should be paid to the relationship between the focal plastic trait, the environmental stimulus and the functional importance of the trait. The Drosophila wing is particularly amenable to experimental studies of phenotypic plasticity. Wing morphology is known for its plastic variation under different experimental temperatures, but this plasticity has rarely been investigated in a functional context of flight. Here, we investigate the effect of temperature on wing morphology and flight in the invasive pest species Drosophila suzukii Although the rapid invasion of both Europe and North America was most likely facilitated by human activities, D. suzukii is also expected to disperse actively. By quantifying wing morphology and individual flight trajectories of flies raised under different temperatures, we tested whether (1) invasive populations of D. suzukii show higher phenotypic plasticity than their native counterparts, and (2) wing plasticity affects flight parameters. Developmental temperature was found to affect both wing morphology and flight parameters (in particular speed and acceleration), leaving open the possibility of an adaptive value for wing plasticity. Our results show no difference in phenotypic plasticity between invasive and native populations, rejecting a role for wing plasticity in the invasion success.

Quantitative Morphological Variation in the Developing Drosophila Wing

Quantitative genetic variation in morphology is pervasive in all species and is the basis for the evolution of differences among species. The measurement of morphological form in adults is now beginning to be combined with comparable measurements of form during development. Here we compare the shape of the developing wing to its adult form in a holometabolous insect, Drosophila melanogaster. We used protein expression patterns to measure shape in the developing precursors of the final adult wing. Three developmental stages were studied: late larval third instar, post-pupariation and in the adult fly. We studied wild-type animals in addition to mutants of two genes (shf and ds) that have known effects on adult wing shape and size. Despite experimental noise related to the difficulty of comparing developing structures, we found consistent differences in wing shape and size at each developmental stage between genotypes. Quantitative comparisons of variation arising at different developmental stages with the variation in the final structure enable us to determine when variation arises, and to generate hypotheses about the causes of that variation. In addition we provide linear rules allowing us to link wing morphology in the larva, with wing morphology in the pupa. Our approach provides a framework to analyze quantitative morphological variation in the developing fly wing. This framework should help to characterize the natural variation of the larval and pupal wing shape, and to measure the contribution of the processes occurring during these developmental stages to the natural variation in adult wing morphology.

Mutation predicts 40 million years of fly wing evolution

Mutation enables evolution, but the idea that adaptation is also shaped by mutational variation is controversial. Simple evolutionary hypotheses predict such a relationship if the supply of mutations constrains evolution, but it is not clear that constraints exist, and, even if they do, they may be overcome by long-term natural selection. Quantification of the relationship between mutation and phenotypic divergence among species will help to resolve these issues. Here we use precise data on over 50,000 Drosophilid fly wings to demonstrate unexpectedly strong positive relationships between variation produced by mutation, standing genetic variation, and the rate of evolution over the last 40 million years. Our results are inconsistent with simple constraint hypotheses because the rate of evolution is very low relative to what both mutational and standing variation could allow. In principle, the constraint hypothesis could be rescued if the vast majority of mutations are so deleterious that they cannot contribute to evolution, but this also requires the implausible assumption that deleterious mutations have the same pattern of effects as potentially advantageous ones. Our evidence for a strong relationship between mutation and divergence in a slowly evolving structure challenges the existing models of mutation in evolution.

Semi-automated quantitative Drosophila wings measurements

BACKGROUND

Drosophila melanogaster is an important organism used in many fields of biological research such as genetics and developmental biology. Drosophila wings have been widely used to study the genetics of development, morphometrics and evolution. Therefore there is much interest in quantifying wing structures of Drosophila. Advancement in technology has increased the ease in which images of Drosophila can be acquired. However such studies have been limited by the slow and tedious process of acquiring phenotypic data.

RESULTS

We have developed a system that automatically detects and measures key points and vein segments on a Drosophila wing. Key points are detected by performing image transformations and template matching on Drosophila wing images while vein segments are detected using an Active Contour algorithm. The accuracy of our key point detection was compared against key point annotations of users. We also performed key point detection using different training data sets of Drosophila wing images. We compared our software with an existing automated image analysis system for Drosophila wings and showed that our system performs better than the state of the art. Vein segments were manually measured and compared against the measurements obtained from our system.

CONCLUSION

Our system was able to detect specific key points and vein segments from Drosophila wing images with high accuracy.

Automated Phenotyping Indicates Pupal Size in Drosophila Is a Highly Heritable Trait with an Apparent Polygenic Basis

The intense focus on studying human height has done more than any other genetic analysis to advance our understanding of the heritability of highly complex phenotypes. Here, we describe in detail the properties of a previously unexplored trait in Drosophila melanogaster that shares many salient properties with human height. The total length of the pupal case varies between 2.8 and 3.9 mm among natural variants, and we report that it is among the most heritable traits reported in this species. We have developed a simple semiautomatic phenotyping system with which a single operator can reliably score >5000 individuals in a day. The precision of the automated system is 0.042 mm (± 0.030 SD). All phenotyped individuals are available to be mated in subsequent generations or uniquely archived for future molecular work. We report both broad sense and narrow sense heritability estimates for two biologically distinct data sets. Narrow sense heritability (h²) ranged from 0.44 to 0.50, and broad sense heritability (H²) ranged from 0.58 to 0.61. We present results for mapping the trait in 195 recombinant inbred lines, which suggests that there are no loci with >10% effect size in this panel. We propose that pupal size genetics in Drosophila could represent a model complex trait amenable to deep genetic dissection using the automated system described.

Fifteen years of quantitative trait loci studies in fish: challenges and future directions

Understanding the genetic basis of phenotypic variation is a major challenge in biology. Here, we systematically evaluate 146 quantitative trait loci (QTL) studies on teleost fish over the last 15 years to investigate (i) temporal trends and (ii) factors affecting QTL detection and fine-mapping. The number of fish QTL studies per year increased over the review period and identified a cumulative number of 3632 putative QTLs. Most studies used linkage-based mapping approaches and were conducted on nonmodel species with limited genomic resources. A gradual and moderate increase in the size of the mapping population and a sharp increase in marker density from 2011 onwards were observed; however, the number of QTLs and variance explained by QTLs changed only minimally over the review period. Based on these findings, we discuss the causative factors and outline how larger sample sizes, phenomics, comparative genomics, epigenetics and software development could improve both the quantity and quality of QTLs in future genotype-phenotype studies. Given that the technical limitations on DNA sequencing have mostly been overcome in recent years, a renewed focus on these and other study design factors will likely lead to significant improvements in QTL studies in the future.

Rapid automated landmarking for morphometric analysis of three-dimensional facial scans

Automated phenotyping is essential for the creation of large, highly standardized datasets from anatomical imaging data. Such datasets can support large-scale studies of complex traits or clinical studies related to precision medicine or clinical trials. We have developed a method that generates three-dimensional landmark data that meet the requirements of standard geometric morphometric analyses. The method is robust and can be implemented without high-performance computing resources. We validated the method using both direct comparison to manual landmarking on the same individuals and also analyses of the variation patterns and outlier patterns in a large dataset of automated and manual landmark data. Direct comparison of manual and automated landmarks reveals that automated landmark data are less variable, but more highly integrated and reproducible. Automated data produce covariation structure that closely resembles that of manual landmarks. We further find that while our method does produce some landmarking errors, they tend to be readily detectable and can be fixed by adjusting parameters used in the registration and control-point steps. Data generated using the method described here have been successfully used to study the genomic architecture of facial shape in two different genome-wide association studies of facial shape.

Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification

BACKGROUND

Global Plants, a collaborative between JSTOR and some 300 herbaria, now contains about 2.48 million high-resolution images of plant specimens, a number that continues to grow, and collections that are digitizing their specimens at high resolution are allocating considerable recourses to the maintenance of computer hardware (e.g., servers) and to acquiring digital storage space. We here apply machine learning, specifically the training of a Support-Vector-Machine, to classify specimen images into categories, ideally at the species level, using the 26 most common tree species in Germany as a test case.

RESULTS

We designed an analysis pipeline and classification system consisting of segmentation, normalization, feature extraction, and classification steps and evaluated the system in two test sets, one with 26 species, the other with 17, in each case using 10 images per species of plants collected between 1820 and 1995, which simulates the empirical situation that most named species are represented in herbaria and databases, such as JSTOR, by few specimens. We achieved 73.21% accuracy of species assignments in the larger test set, and 84.88% in the smaller test set.

CONCLUSIONS

The results of this first application of a computer vision algorithm trained on images of herbarium specimens shows that despite the problem of overlapping leaves, leaf-architectural features can be used to categorize specimens to species with good accuracy. Computer vision is poised to play a significant role in future rapid identification at least for frequently collected genera or species in the European flora.

Cross-Mating Compatibility and Competitiveness among Aedes albopictus Strains from Distinct Geographic Origins - Implications for Future Application of SIT Programs in the South West Indian Ocean Islands

The production of large numbers of males needed for a sustainable sterile insect technique (SIT) control program requires significant developmental and operational costs. This may constitute a significant economic barrier to the installation of large scale rearing facilities in countries that are undergoing a transition from being largely dependent on insecticide use to be in a position to integrate the SIT against Aedes albopictus. Alternative options available for those countries could be to rely on outsourcing of sterile males from a foreign supplier, or for one centralised facility to produce mosquitoes for several countries, thus increasing the efficiency of the mass-rearing effort. However, demonstration of strain compatibility is a prerequisite for the export of mosquitoes for transborder SIT applications. Here, we compared mating compatibility among Ae. albopictus populations originating from three islands of the South Western Indian Ocean, and assessed both insemination rates and egg fertility in all possible cross-mating combinations. Furthermore, competitiveness between irradiated and non-irradiated males from the three studied strains, and the subsequent effect on female fertility were also examined. Although morphometric analysis of wing shapes suggested phenoptypic differences between Ae. albopictus strains, perfect reproductive compatibility between them was observed. Furthermore, irradiated males from the different islands demonstrated similar levels of competitiveness and induced sterility when confronted with fertile males from any of the other island populations tested. In conclusion, despite the evidence of inter-strain differences based on male wing morphology, collectively, our results provide a new set of expectations for the use of a single candidate strain of mass-reared sterile males for area-wide scale application of SIT against Ae. albopictus populations in different islands across the South Western Indian Ocean. Cross-mating competitiveness tests such as those applied here are necessary to assess the quality of mass reared strains for the trans-border application of sterile male release programs.

Disintegrating the fly: A mutational perspective on phenotypic integration and covariation

The structure of environmentally induced phenotypic covariation can influence the effective strength and magnitude of natural selection. Yet our understanding of the factors that contribute to and influence the evolutionary lability of such covariation is poor. Most studies have either examined environmental variation without accounting for covariation, or examined phenotypic and genetic covariation without distinguishing the environmental component. In this study, we examined the effect of mutational perturbations on different properties of environmental covariation, as well as mean shape. We use strains of Drosophila melanogaster bearing well-characterized mutations known to influence wing shape, as well as naturally derived strains, all reared under carefully controlled conditions and with the same genetic background. We find that mean shape changes more freely than the covariance structure, and that different properties of the covariance matrix change independently from each other. The perturbations affect matrix orientation more than they affect matrix eccentricity or total variance. Yet, mutational effects on matrix orientation do not cluster according to the developmental pathway that they target. These results suggest that it might be useful to consider a more general concept of "decanalization," involving all aspects of variation and covariation.

The wing venation patterns to identify single tsetse flies

This is the first study to explore the potential of various geometric morphometrics methods to help the morphological diagnostic of tsetse species, vectors of human and animal trypanosomiases in sub-Saharan Africa. We compared landmarks, semilandmarks and outlines techniques on male and female samples of species, and suggested adapted strategies according to the countries and their own Glossina fauna. We could compare up to 7 taxa belonging to the three main subgenera of the Glossina genus: Nemorhina (5 species), Glossina (1 species) and Austenina (1 species). Our sample included the major vectors of sleeping sickness: G. palpalis palpalis, G. p. gambiensis, G. fuscipes fuscipes and G. f. quanzensis, as well as two important vectors of African animal trypanosomoses: G. tachinoides and Glossina morsitans submorsitans. The average level of correct species recognition by the wing shape was satisfactory, and slightly higher for females than for males. The best scores of correct assignment, in both sexes, were obtained by the contour technique (96% of correct attribution in females, 92% in males), slightly higher than for semilandmarks (95% and 91%) or landmarks (94% and 89%) techniques. We made our images of wings freely available to be used as reference images (http://mome-clic.com), and we describe the conditions and the analytical steps to be followed to identify unknown specimens using external reference images. Under adequate conditions, such use of reference images obtained from a free access server could help species identification of new samples anywhere in Africa.

Proteome-wide association studies identify biochemical modules associated with a wing-size phenotype in Drosophila melanogaster

The manner by which genetic diversity within a population generates individual phenotypes is a fundamental question of biology. To advance the understanding of the genotype–phenotype relationships towards the level of biochemical processes, we perform a proteome-wide association study (PWAS) of a complex quantitative phenotype. We quantify the variation of wing imaginal disc proteomes in Drosophila genetic reference panel (DGRP) lines using SWATH mass spectrometry. In spite of the very large genetic variation (1/36 bp) between the lines, proteome variability is surprisingly small, indicating strong molecular resilience of protein expression patterns. Proteins associated with adult wing size form tight co-variation clusters that are enriched in fundamental biochemical processes. Wing size correlates with some basic metabolic functions, positively with glucose metabolism but negatively with mitochondrial respiration and not with ribosome biogenesis. Our study highlights the power of PWAS to filter functional variants from the large genetic variability in natural populations.

How genetic diversity generates complex phenotypes along a continuum remains a fundamental question of biology. Here—applying the emerging SWATH proteomics technology—the authors describe a proteome wide association study (PWAS) of Drosophila wing size and identify functional protein clusters associated with this trait.

Life history evolution and cellular mechanisms associated with increased size in high-altitude Drosophila

Understanding the physiological and genetic basis of growth and body size variation has wide-ranging implications, from cancer and metabolic disease to the genetics of complex traits. We examined the evolution of body and wing size in high-altitude Drosophila melanogaster from Ethiopia, flies with larger size than any previously known population. Specifically, we sought to identify life history characteristics and cellular mechanisms that may have facilitated size evolution. We found that the large-bodied Ethiopian flies laid significantly fewer but larger eggs relative to lowland, smaller-bodied Zambian flies. The highland flies were found to achieve larger size in a similar developmental period, potentially aided by a reproductive strategy favoring greater provisioning of fewer offspring. At the cellular level, cell proliferation was a strong contributor to wing size evolution, but both thorax and wing size increases involved important changes in cell size. Nuclear size measurements were consistent with elevated somatic ploidy as an important mechanism of body size evolution. We discuss the significance of these results for the genetic basis of evolutionary changes in body and wing size in Ethiopian D. melanogaster.

Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster

Organismal size depends on the interplay between genetic and environmental factors. Genome-wide association (GWA) analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment. Genetic analyses in Drosophila have identified conserved signaling pathways controlling size; however, how these pathways control phenotypic diversity is unclear. We performed GWA of size traits using the Drosophila Genetic Reference Panel of inbred, sequenced lines. We find that the top associated variants differ between traits and sexes; do not map to canonical growth pathway genes, but can be linked to these by epistasis analysis; and are enriched for genes and putative enhancers. Performing GWA on well-studied developmental traits under controlled conditions expands our understanding of developmental processes underlying phenotypic diversity.

Genetic studies in Drosophila have elucidated conserved signaling pathways and environmental factors that together control organismal size. In humans, hundreds of genes are associated with height variation, but these associations have not been performed in a controlled environment. As a result we are still lacking an understanding of the mechanisms creating size variability within a species. Here, under carefully controlled environmental conditions, we identify naturally occurring genetic variants that are associated with size diversity in Drosophila. We identify a cluster of associations close to the kek1 locus, a well-characterized growth regulator, but otherwise find that most variants are located in or close to genes that do not belong to the conserved pathways but may interact with these in a biological network. We validate 33 novel growth regulatory genes that participate in diverse cellular processes, most notably cellular metabolism and cell polarity. This study is the first genome-wide association analysis of natural variants underlying size in Drosophila and our results complement the knowledge we have accumulated on this trait from mutational studies of single genes.

Evolutionary stasis in pollen morphogenesis due to natural selection

The contribution of developmental constraints and selective forces to the determination of evolutionary patterns is an important and unsolved question. We test whether the long-term evolutionary stasis observed for pollen morphogenesis (microsporogenesis) in eudicots is due to developmental constraints or to selection on a morphological trait shaped by microsporogenesis: the equatorial aperture pattern. Most eudicots have three equatorial apertures but several taxa have independently lost the equatorial pattern and have microsporogenesis decoupled from aperture pattern determination. If selection on the equatorial pattern limits variation, we expect to see increased variation in microsporogenesis in the nonequatorial clades. Variation of microsporogenesis was studied using phylogenetic comparative analyses in 83 species dispersed throughout eudicots including species with and without equatorial apertures. The species that have lost the equatorial pattern have highly variable microsporogenesis at the intra-individual and inter-specific levels regardless of their pollen morphology, whereas microsporogenesis remains stable in species with the equatorial pattern. The observed burst of variation upon loss of equatorial apertures shows that there are no strong developmental constraints precluding variation in microsporogenesis, and that the stasis is likely to be due principally to selective pressure acting on pollen morphogenesis because of its implication in the determination of the equatorial aperture pattern.

Complex constraints on allometry revealed by artificial selection on the wing of Drosophila melanogaster

Precise exponential scaling with size is a fundamental aspect of phenotypic variation. These allometric power laws are often invariant across taxa and have long been hypothesized to reflect developmental constraints. Here we test this hypothesis by investigating the evolutionary potential of an allometric scaling relationship in drosophilid wing shape that is nearly invariant across 111 species separated by at least 50 million years of evolution. In only 26 generations of artificial selection in a population of Drosophila melanogaster, we were able to drive the allometric slope to the outer range of those found among the 111 sampled species. This response was rapidly lost when selection was suspended. Only a small proportion of this reversal could be explained by breakup of linkage disequilibrium, and direct selection on wing shape is also unlikely to explain the reversal, because the more divergent wing shapes produced by selection on the allometric intercept did not revert. We hypothesize that the reversal was instead caused by internal selection arising from pleiotropic links to unknown traits. Our results also suggest that the observed selection response in the allometric slope was due to a component expressed late in larval development and that variation in earlier development did not respond to selection. Together, these results are consistent with a role for pleiotropic constraints in explaining the remarkable evolutionary stability of allometric scaling.

Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood

We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance-covariance matrices (G). Large-sample theory shows that maximum-likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G. This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G, and of functions of G. We refer to this as the REML-MVN method. This has been implemented in the mixed-model program WOMBAT. Estimates of sampling variances from REML-MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20-dimensional data set for Drosophila wings. REML-MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best-estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML-MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest.