Regulatory evolution tuning pigmentation intensity quantitatively in Drosophila.

Quantitative variation in attributes such as color, texture, or stiffness dominates morphological diversification. It results from combinations of alleles at many Mendelian loci. Here, we identify an additional source of quantitative variation among species, continuous evolution in a gene regulatory region. Specifically, we examined the modulation of wing pigmentation in a group of fly species and showed that inter-species variation correlated with the quantitative expression of the pigmentation gene yellow. This variation results from an enhancer of yellow determining darkness through species-specific activity. We mapped the divergent activities between two sister species and found the changes to be broadly distributed along the enhancer. Our results demonstrate that enhancers can act as dials fueling quantitative morphological diversification by modulating trait properties.

On the taxonomic status of the tenebrionoid genera Falsopedilus Pic, 1924 and Hintonosia Báguena Corella, 1948 (Coleoptera: Mycteridae) with descriptions of new species.

We re-evaluate the taxonomic placement of the genus Hintonosia Báguena Corella, 1948, hitherto placed in Aderidae Csíki, 1909. The assessment of key morphological characters based on the type specimen of the type species of this genus, Hintonosia bismacrocephalus Báguena Corella, 1948 (= Hintonosia macrocephalus Pic, 1935, homonym), demonstrated that it does not possess the synapomorphies of the Aderidae. Instead, its clear position in Mycteridae Blanchard, 1845 is uncovered, leading us to the transfer of Hintonosia to the subfamily Eurypinae Thomson, 1860 of Mycteridae. Moreover, Hintonosia was found congeneric with the mycterid genus Falsopedilus Pic, 1924 and the new synonymy is therefore proposed. Additionally, two African species of Falsopedilus are described, a key to, and a checklist of Falsopedilus species are presented.

Odor-regulated oviposition behavior in an ecological specialist.

Colonization of a novel ecological niche can require, or be driven by, evolution of an animal's behaviors promoting their reproductive success. We investigated the evolution and sensory basis of oviposition in Drosophila sechellia, a close relative of Drosophila melanogaster that exhibits extreme specialism for Morinda citrifolia noni fruit. D. sechellia produces fewer eggs than other drosophilids and lays these almost exclusively on noni substrates. We show that visual, textural and social cues do not explain this species-specific preference. By contrast, we find that loss of olfactory input in D. sechellia, but not D. melanogaster, essentially abolishes egg-laying, suggesting that olfaction gates gustatory-driven noni preference. Noni odors are detected by redundant olfactory pathways, but we discover a role for hexanoic acid and the cognate Ionotropic receptor 75b (Ir75b) in odor-evoked oviposition. Through receptor exchange in D. melanogaster, we provide evidence for a causal contribution of odor-tuning changes in Ir75b to the evolution of D. sechellia's oviposition behavior.

Increased chromatin accessibility promotes the evolution of a transcriptional silencer in Drosophila.

The loss of discrete morphological traits, the most common evolutionary transition, is typically driven by changes in developmental gene expression. Mutations accumulating in regulatory elements of these genes can disrupt DNA binding sites for transcription factors patterning their spatial expression, or delete entire enhancers. Regulatory elements, however, may be silenced through changes in chromatin accessibility or the emergence of repressive elements. Here, we show that increased chromatin accessibility at the gene yellow, combined with the gain of a repressor site, underlies the loss of a wing spot pigmentation pattern in a Drosophila species. The gain of accessibility of this repressive element is regulated by E93, a transcription factor governing the progress of metamorphosis. This convoluted evolutionary scenario contrasts with the parsimonious mutational paths generally envisioned and often documented for morphological losses. It illustrates how evolutionary changes in chromatin accessibility may directly contribute to morphological diversification.

Resolving between novelty and homology in the rapidly evolving phallus of Drosophila.

The genitalia present some of the most rapidly evolving anatomical structures in the animal kingdom, possessing a variety of parts that can distinguish recently diverged species. In the Drosophila melanogaster group, the phallus is adorned with several processes, pointed outgrowths, that are similar in size and shape between species. However, the complex three-dimensional nature of the phallus can obscure the exact connection points of each process. Previous descriptions based upon adult morphology have primarily assigned phallic processes by their approximate positions in the phallus and have remained largely agnostic regarding their homology relationships. In the absence of clearly identified homology, it can be challenging to model when each structure first evolved. Here, we employ a comparative developmental analysis of these processes in eight members of the melanogaster species group to precisely identify the tissue from which each process forms. Our results indicate that adult phallic processes arise from three pupal primordia in all species. We found that in some cases the same primordia generate homologous structures whereas in other cases, different primordia produce phenotypically similar but remarkably non-homologous structures. This suggests that the same gene regulatory network may have been redeployed to different primordia to induce phenotypically similar traits. Our results highlight how traits diversify and can be redeployed, even at short evolutionary scales.

The genus Syzeton Blackburn, 1891 (Coleoptera, Aderidae) in the United States of America.

The species of Syzeton Blackburn, 1891 (=Zonantes Casey, 1895, syn. nov.) known from the United States are revised. All species formerly placed under Zonantes Casey, 1895 are transferred to Syzeton Blackburn, 1891: S. ouachitanus (Werner, 1990), comb. nov.; S. fasciatus (Melsheimer, 1846), comb. nov.; S. hubbardi (Casey, 1895), comb. nov.; S. nubifer (LeConte, 1878), comb. nov.; S. ater (LeConte, 1875), comb. nov.; S. pallidus (Werner, 1990), comb. nov.; S. subfasciatus (LeConte, 1875), comb. nov.; S. floridanus (Werner, 1990), comb. nov.; S. signatus (Haldeman, 1848), comb. nov.). Additionally, three new species are described herein: Syzeton gruberi n. sp., Syzeton arizonae n. sp., both from Arizona, and Syzeton belovi n. sp., from Texas, Oklahoma and Florida. Finally, Zonantes mississippiensis Werner, 1990 is considered a junior synonym of Syzeton ouachitanus (Werner, 1990), syn. nov.

A standardized nomenclature and atlas of the female terminalia of Drosophila melanogaster.

The model organism Drosophila melanogaster has become a focal system for investigations of rapidly evolving genital morphology as well as the development and functions of insect reproductive structures. To follow up on a previous paper outlining unifying terminology for the structures of the male terminalia in this species, we offer here a detailed description of the female terminalia of D. melanogaster. Informative diagrams and micrographs are presented to provide a comprehensive overview of the external and internal reproductive structures of females. We propose a collection of terms and definitions to standardize the terminology associated with the female terminalia in D. melanogaster and we provide a correspondence table with the terms previously used. Unifying terminology for both males and females in this species will help to facilitate communication between various disciplines, as well as aid in synthesizing research across publications within a discipline that has historically focused principally on male features. Our efforts to refine and standardize the terminology should expand the utility of this important model system for addressing questions related to the development and evolution of animal genitalia, and morphology in general.

Large-scale analysis of Drosophila core promoter function using synthetic promoters.

The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it "computes" expression remains poorly understood. To dissect its function, we carried out a comprehensive structure-function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture. We then measured synthetic promoters' activities of ~3,000 mutational variants with and without an external stimulus (hormonal activation), at large scale and with high accuracy using robotics and a dual luciferase reporter assay. We observed a strong impact on activity of the different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely accounts for the combinatorial effects on core promoter activity. These findings shed new light on the quantitative assessment of gene expression in metazoans.

New Mixaderus species from the Mascarene Islands (Coleoptera: Aderidae).

Following a previous revision of species of the genus Mixaderus Collado Alonso-Zarazaga, 1996 (Coleoptera: Aderidae) from Madagascar and the Mascarene islands, I describe here six new species from the same genus from La Réunion and Mauritius: Mixaderus reunionensis n. sp.; Mixaderus chassaini n. sp.; Mixaderus lemagneni n. sp.; Mixaderus tamisieri n. sp.; Mixaderus voisini n. sp.; Mixaderus mauritiensis n. sp. I also provide an updated key to the Mixaderus species from the Mascarene archipelago.

Review of Aderidae Csiki, 1909 (Insecta: Coleoptera) of Cabo Verde.

The Aderidae (Coleoptera: Tenebrionoidea) of Cabo Verde (or Cape Verde in English transcription) Archipelago in the Central Atlantic Ocean is revised based on an examination of types and additional material. Four species are confirmed for the archipelago, three of the genus Cobososia Collado et Alonso-Zarazaga, 1996 and one of the genus Aderus Stephens, 1829. We also propose to transfer Anthicus reductus Wollaston, 1867 (Anthicidae: Anthicinae: Anthicini) to the genus Cobososia (Aderidae), as Cobososia reducta (Wollaston, 1867) comb. nov. and demonstrate, that Cobososia angulithorax (Desbrochers des Loges, 1881) is conspecific with Cobososia reducta (Wollaston, 1867) syn. nov. Finally, we present new records and an illustrated identification key to the ant-like leaf beetles of Cabo Verde.

Regulatory encoding of quantitative variation in spatial activity of a Drosophila enhancer.

Developmental enhancers control the expression of genes prefiguring morphological patterns. The activity of an enhancer varies among cells of a tissue, but collectively, expression levels in individual cells constitute a spatial pattern of gene expression. How the spatial and quantitative regulatory information is encoded in an enhancer sequence is elusive. To link spatial pattern and activity levels of an enhancer, we used systematic mutations of the yellow spot enhancer, active in developing Drosophila wings, and tested their effect in a reporter assay. Moreover, we developed an analytic framework based on the comprehensive quantification of spatial reporter activity. We show that the quantitative enhancer activity results from densely packed regulatory information along the sequence, and that a complex interplay between activators and multiple tiers of repressors carves the spatial pattern. Our results shed light on how an enhancer reads and integrates trans-regulatory landscape information to encode a spatial quantitative pattern.

A sensitive mNeonGreen reporter system to measure transcriptional dynamics in Drosophila development.

The gene regulatory network governing anterior-posterior axis formation in Drosophila is a well-established paradigm to study transcription in developmental biology. The rapid temporal dynamics of gene expression during early stages of development, however, are difficult to track with standard techniques. We optimized the bright and fast-maturing fluorescent protein mNeonGreen as a real-time, quantitative reporter of enhancer expression. We derive enhancer activity from the reporter fluorescence dynamics with high spatial and temporal resolution, using a robust reconstruction algorithm. By comparing our results with data obtained with the established MS2-MCP system, we demonstrate the higher detection sensitivity of our reporter. We used the reporter to quantify the activity of variants of a simple synthetic enhancer, and observe increased activity upon reduction of enhancer-promoter distance or addition of binding sites for the pioneer transcription factor Zelda. Our reporter system constitutes a powerful tool to study spatio-temporal gene expression dynamics in live embryos.

Synopsis of the Asian species in the genus Zarcosia Collado amp; Alonso-Zarazaga, 1996 with new combinations and descriptions of fourteen new species.

This work represents a provisional inventory of Asian species placed in the genus Zarcosia Collado Alonso-Zarazaga, 1996. Most of these species had not been reassigned since their original description under now obsolete genera, in spite of the morphological homogeneity of the genus Zarcosia Collado Alonso-Zarazaga, 1996. The present work includes the following transfers resulting in 34 new combinations: Z. armipes (Fairmaire, 1896), comb. nov.; Z. batuensis (Werner, 1962), comb. nov.; Z. bipartita (Pic, 1901), comb. nov.; Z. capitalis (Pic, 1901), comb. nov.; Z. cephalica (Werner, 1962), comb. nov.; Z. dentatifemur (Pic, 1912), comb. nov.; Z. discoidalis (Pic, 1902), comb. nov.; Z. genjiensis (Pic, 1917), comb. nov.; Z. glaucescens (Champion, 1920), comb. nov.; Z. grandiceps (Pic, 1899), comb. nov.; Z. holosericea (Champion, 1916), comb. nov.; Z. javana (Pic, 1894), comb. nov.; Z. kempi (Blair, 1924), comb. nov.; Z. longithorax (Pic, 1899), comb. nov.; Z. lucifuga (Heberdey, 1931), comb. nov.; Z. luteitarsis (Champion, 1924), comb. nov.; Z. malayana (Werner, 1962), comb. nov.; Zarcosia nathani (Pic, 1943), comb. nov.; Z. nigrofasciata (Pic, 1899), comb. nov.; Z. obscuricornis (Pic, 1927), comb. nov.; Z. palliditarsis (Pic, 1912), comb. nov.; Z. patucki (Champion, 1924), comb. nov.; Z. picina (Fairmaire, 1893), comb. nov.; Z. plumbea (Champion, 1916), comb. nov.; Z. proprior (Pic, 1920), comb. nov.; Z. rubrobasalis (Pic, 1921), comb. nov.; Z. rufotestacea (Pic, 1901), comb. nov.; Z. sellata (Champion, 1916), comb. nov.; Z. sexdentata (Champion, 1924), comb. nov.; Z. subrobusta (Pic, 1943), comb. nov.; Z. subrufa (Champion, 1924), comb. nov.; Z. testaceitarsis (Pic, 1926), comb. nov.; Z. troglodytes (Champion, 1916), comb. nov.; Z. uncifer (Champion, 1916), comb. nov. In addition, based on the study of over 200 Asian specimens, the geographical distribution of each species is outlined. The study of numerous collections lead me to recognize 14 new species, distinguishable, at least by male genitalia, that I describe here: Zarcosia barlayi n. sp., Zarcosia bedosae n. sp., Zarcosia brunnea n. sp., Zarcosia deharvengi n. sp., Zarcosia gerstmeieri n. sp., Zarcosia ilonae n. sp., Zarcosia intermedia n. sp., Zarcosia lemairei n. sp., Zarcosia schawalleri n. sp., Zarcosia sinuata n. sp., Zarcosia spinifemur n. sp. Zarcosia srilankaensis n. sp., Zarcosia sumatrensis n. sp. and Zarcosia weigeli n. sp. Finally, I propose a new synonymy for Hylophilus picinus var. rufescens Pic, 1905 = Zarcosia picina (Fairmaire, 1893), syn. nov. and design two lectotypes, for Xylophilus picinus, Fairmaire, 1893, pres. design. and for Zarcosia subglaber Pic, 1952 pres. design.

Enhancer evolutionary co-option through shared chromatin accessibility input.

The diversity of forms in multicellular organisms originates largely from the spatial redeployment of developmental genes [S. B. Carroll, Cell 134, 25-36 (2008)]. Several scenarios can explain the emergence of cis-regulatory elements that govern novel aspects of a gene expression pattern [M. Rebeiz, M. Tsiantis, Curr. Opin. Genet. Dev. 45, 115-123 (2017)]. One scenario, enhancer co-option, holds that a DNA sequence producing an ancestral regulatory activity also becomes the template for a new regulatory activity, sharing regulatory information. While enhancer co-option might fuel morphological diversification, it has rarely been documented [W. J. Glassford et al., Dev. Cell 34, 520-531 (2015)]. Moreover, if two regulatory activities are borne from the same sequence, their modularity, considered a defining feature of enhancers [J. Banerji, L. Olson, W. Schaffner, Cell 33, 729-740 (1983)], might be affected by pleiotropy. Sequence overlap may thereby play a determinant role in enhancer function and evolution. Here, we investigated this problem with two regulatory activities of the Drosophila gene yellow, the novel spot enhancer and the ancestral wing blade enhancer. We used precise and comprehensive quantification of each activity in Drosophila wings to systematically map their sequences along the locus. We show that the spot enhancer has co-opted the sequences of the wing blade enhancer. We also identified a pleiotropic site necessary for DNA accessibility of a shared regulatory region. While the evolutionary steps leading to the derived activity are still unknown, such pleiotropy suggests that enhancer accessibility could be one of the molecular mechanisms seeding evolutionary co-option.

Near-chromosome level genome assembly of the fruit pest Drosophila suzukii using long-read sequencing.

Over the past decade, the spotted wing Drosophila, Drosophila suzukii, has invaded Europe and America and has become a major agricultural pest in these areas, thereby prompting intense research activities to better understand its biology. Two draft genome assemblies already exist for this species but contain pervasive assembly errors and are highly fragmented, which limits their values. Our purpose here was to improve the assembly of the D. suzukii genome and to annotate it in a way that facilitates comparisons with D. melanogaster. For this, we generated PacBio long-read sequencing data and assembled a novel, high-quality D. suzukii genome assembly. It is one of the largest Drosophila genomes, notably because of the expansion of its repeatome. We found that despite 16 rounds of full-sib crossings the D. suzukii strain that we sequenced has maintained high levels of polymorphism in some regions of its genome. As a consequence, the quality of the assembly of these regions was reduced. We explored possible origins of this high residual diversity, including the presence of structural variants and a possible heterogeneous admixture pattern of North American and Asian ancestry. Overall, our assembly and annotation constitute a high-quality genomic resource that can be used for both high-throughput sequencing approaches, as well as manipulative genetic technologies to study D. suzukii.

A strawberry accession with elevated methyl anthranilate fruit concentration is naturally resistant to the pest fly Drosophila suzukii.

During the past decade, Drosophila suzukii has established itself as a global invasive fruit pest, enabled by its ability to lay eggs into fresh, ripening fruit. In a previous study, we investigated the impact of different strawberry accessions on the development of D. suzukii eggs, in the search of natural resistance. We identified several accessions that significantly reduced adult fly emergence from infested fruit. In the present study, we aimed at understanding the chemical basis of this effect. We first noted that one of the more resistant accessions showed an unusual enrichment of methyl anthranilate within its fruit, prompting us to investigate this fruit compound as a possible cause limiting fly development. We found that methyl anthranilate alone triggers embryo lethality in a concentration-dependent manner, unlike another comparable organic fruit compound. We also showed that a chemical fraction of the resistant strawberry accession that contains methyl anthranilate carries some activity toward the egg hatching rate. Surprisingly, in spite of the lethal effect of this compound to their eggs, adult females are not only attracted to methyl anthranilate at certain concentrations, but they also display a concentration-dependent preference to lay on substrates enriched in methyl anthranilate. This study demonstrates that methyl anthranilate is a potent agonist molecule against D. suzukii egg development. Its elevated concentration in a specific strawberry accession proven to reduce the fly development may explain, at least in part the fruit resistance. It further illustrates how a single, natural compound, non-toxic to humans could be exploited for biological control of a pest species.

Sensory Evolution: Making Sense of the Noni Scent.

A recent study identifies the neuronal and molecular underpinnings of a key ecological difference between two Drosophila species using a remarkable genetic toolbox for a non-model species.

Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity.

Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. While the open structure as such is not a specific indicator of enhancer activity, active enhancers display a higher degree of accessibility than the primed and repressed states. Molecular mechanisms that may account for these quantitative differences are discussed. A model that relates molecular events at an enhancer to changes in its activity and accessibility in a developing tissue is also proposed.

Evolution: Remodelling Animal Body Plans, Gene by Gene.

Changes in Homeotic (Hox) gene regulation have long been thought to drive the evolution of animal body plans. Direct genetic evidence of their evolutionary role has, however, remained limited. A new study reveals how several mutations distributed across a gene network mask the phenotypic effects of a Hox gene's evolution.

Evolution of Ovipositor Length in Drosophila suzukii Is Driven by Enhanced Cell Size Expansion and Anisotropic Tissue Reorganization.

Morphological diversity is dominated by variation in body proportion [1], which can be described with scaling relationships and mathematical equations, following the pioneering work of D'Arcy Thompson [2] and Julian Huxley [3]. Yet, the cellular processes underlying divergence in size and shape of morphological traits between species remain largely unknown [4-8]. Here, we compare the ovipositors of two related species, Drosophila melanogaster and D. suzukii. D. suzukii has switched its egg-laying niche from rotting to ripe fruit [9]. Along with this shift, the D. suzukii ovipositor has undergone a significant change in size and shape [10]. Using an allometric approach, we find that, while adult ovipositor width has hardly changed between the species, D. suzukii ovipositor length is almost double that of D. melanogaster. We show that this difference mostly arises in a 6-h time window during pupal development. We observe that the developing ovipositors of the two species comprise an almost identical number of cells, with a similar profile of cell shapes and orientations. After cell division stops, we find that the ovipositor area continues to grow in both species through the isotropic expansion of cell apical area and the anisotropic cellular reorganization of the tissue. Remarkably, we find that the lengthening of the D. suzukii ovipositor compared to that of D. melanogaster results from the combination of the accelerated expansion of apical cell size and the enhanced anisotropic rearrangement of cells in the tissue. Therefore, the quantitative fine-tuning of morphogenetic processes can drive evolutionary changes in organ size and shape.