Monophyly, divergence times, and evolution of host plant use inferred from a revised phylogeny of the Drosophila repleta species group

Evolution of secondary cell number and position in the Drosophila accessory gland

In animals with internal fertilization, males transfer gametes and seminal fluid during copulation, both of which are required for successful reproduction. In Drosophila and other insects, seminal fluid is produced in the paired accessory gland (AG), the ejaculatory duct, and the ejaculatory bulb. The D. melanogaster AG has emerged as an important model system for this component of male reproductive biology. Seminal fluid proteins produced in the Drosophila AG are required for proper storage and use of sperm by the females, and are also critical for establishing and maintaining a suite of short- and long-term postcopulatory female physiological responses that promote reproductive success. The Drosophila AG is composed of two main cell types. The majority of AG cells, which are referred to as main cells, are responsible for production of many seminal fluid proteins. A minority of cells, about 4%, are referred to as secondary cells. These cells, which are restricted to the distal tip of the D. melanogaster AG, may play an especially important role in the maintenance of the long-term female post-mating response. Many studies of Drosophila AG evolution have suggested that the proteins produced in the gland evolve quickly, as does the transcriptome. Here, we investigate the evolution of secondary cell number and position in the AG in a collection of eight species spanning the entire history of the Drosophila genus. We document a heretofore underappreciated rapid evolutionary rate for both number and position of these specialized AG cells, raising several questions about the developmental, functional, and evolutionary significance of this variation.

Diverse signatures of convergent evolution in cacti-associated yeasts

Many distantly related organisms have convergently evolved traits and lifestyles that enable them to live in similar ecological environments. However, the extent of phenotypic convergence evolving through the same or distinct genetic trajectories remains an open question. Here, we leverage a comprehensive dataset of genomic and phenotypic data from 1,049 yeast species in the subphylum Saccharomycotina (Kingdom Fungi, Phylum Ascomycota) to explore signatures of convergent evolution in cactophilic yeasts, ecological specialists associated with cacti. We inferred that the ecological association of yeasts with cacti arose independently ~17 times. Using machine-learning, we further found that cactophily can be predicted with 76% accuracy from functional genomic and phenotypic data. The most informative feature for predicting cactophily was thermotolerance, which is likely associated with duplication and altered evolutionary rates of genes impacting the cell envelope in several cactophilic lineages. We also identified horizontal gene transfer and duplication events of plant cell wall-degrading enzymes in distantly related cactophilic clades, suggesting that putatively adaptive traits evolved through disparate molecular mechanisms. Remarkably, multiple cactophilic lineages and their close relatives are emerging human opportunistic pathogens, suggesting that the cactophilic lifestyle-and perhaps more generally lifestyles favoring thermotolerance-may preadapt yeasts to cause human disease. This work underscores the potential of a multifaceted approach involving high throughput genomic and phenotypic data to shed light onto ecological adaptation and highlights how convergent evolution to wild environments could facilitate the transition to human pathogenicity.

Genetic variation in disease resistance in Drosophila spp. is mitigated in Drosophila sechellia by specialization to a toxic host

We found that Drosophila species vary in their susceptibility to the broad-spectrum entomopathogen, Metarhizium anisopliae (strain Ma549). Generalist species were generally more resistant than dietary specialists, with the cactophilic Drosophila buzzatii and Drosophila sechellia, a specialist of the Morinda citrifolia (Morinda) fruit, being most susceptible. Morinda fruit is reported to be toxic to most herbivores because it contains Octanoic Acid (OA). We confirmed that OA is toxic to Drosophila spp., other than D. sechellia, and we also found that OA is highly toxic to entomopathogenic fungi including Ma549 and Beauveria bassiana. Drosophila sechellia fed a diet containing OA, even at levels much less than found in Morinda fruit, had greatly reduced susceptibility to Ma549. This suggests that specializing to Morinda may have provided an enemy-free space, reducing adaptive prioritization on a strong immune response. Our results demonstrate that M. anisopliae and Drosophila species with divergent lifestyles provide a versatile model system for understanding the mechanisms of host-pathogen interactions at different scales and in environmental context.

Extended lifespan and sex-specific fertility loss in cold-acclimated flies of the sibling species Drosophila buzzatii and Drosophila koepferae

Survival and reproduction are the core elements of Darwinian fitness. In the context of a fixed energy budget, organisms tend to allocate resources in order to maximize one at the expense of the other, in what has been called the lifespan-reproduction trade-off. Reproductive arrest and extended lifespan are common responses to low temperatures in many insects including fruit flies. In this study, we aim to understand the overwintering strategy of two closely-related Drosophila species with contrasting distribution ranges. We compared survival, lifespan, ovarian maturation, and reproductive output (fecundity and fertility) of virgin and mated adults of both Drosophila buzzatii and Drosophila koepferae after long-term cold exposure at dormancy-inducing conditions (10 °C, 10:14 L:D) and controls (25 °C, 12:12 L:D). Virgin flies of D. buzzatii showed the longest lifespan (averaging 102 days) under dormancy-inducing conditions. Cold-induced reproductive arrest preserves reproductive capacity mainly in virgin females that mated after reproductive dormancy, indicating that males were much more susceptible to fertility loss than females, in both species. Notably, females of D. buzzatii were capable of protecting stored sperm from cold damage and produced viable progeny. Even if, in D. buzzatii, fertility of flies mated after the cold-exposure was extremely low, cold temperature likely sterilized D. koepferae males, indicating that cold carry-over effects are stronger for the species with the shorter lifespan. Such species-specific effects of low temperature over fitness likely contributed to the divergence of these closely-related species and to the spread of D. buzzatii into cooler environments.

Phylogenomics provides insights into the evolution of cactophily and host plant shifts in Drosophila

Cactophilic species of the Drosophila buzzatii cluster (repleta group) comprise an excellent model group to investigate genomic changes underlying adaptation to extreme climate conditions and host plants. In particular, these species form a tractable system to study the transition from chemically simpler breeding sites (like prickly pears of the genus Opuntia) to chemically more complex hosts (columnar cacti). Here, we report four highly contiguous genome assemblies of three species of the buzzatii cluster. Based on this genomic data and inferred phylogenetic relationships, we identified candidate taxonomically restricted genes (TRGs) likely involved in the evolution of cactophily and cactus host specialization. Functional enrichment analyses of TRGs within the buzzatii cluster identified genes involved in detoxification, water preservation, immune system response, anatomical structure development, and morphogenesis. In contrast, processes that regulate responses to stress, as well as the metabolism of nitrogen compounds, transport, and secretion were found in the set of species that are columnar cacti dwellers. These findings are in line with the hypothesis that those genomic changes brought about key mechanisms underlying the adaptation of the buzzatii cluster species to arid regions in South America.

Evolution of the odorant-binding protein gene family in Drosophila

Odorant-binding proteins (OBPs) are encoded by a gene family involved in the perception of olfactory signals in insects. This chemosensory gene family has been advocated as a candidate to mediate host preference and host shifts in insects, although it also participates in other physiological processes. Remarkable differences in the OBP gene repertoire have been described across insect groups, suggesting an accelerated gene turnover rate. The genus Drosophila, is a valuable resource for ecological genomics studies since it comprises groups of ecologically diverse species and there are genome data for many of them. Here, we investigate the molecular evolution of this chemosensory gene family across 19 Drosophila genomes, including the melanogaster and repleta species groups, which are mostly associated with rotting fruit and cacti, respectively. We also compared the OBP repertoire among the closely related species of the repleta group, associated with different subfamilies of Cactaceae that represent disparate chemical challenges for the flies. We found that the gene family size varies widely between species, ranging from 39 to 54 candidate OBPs. Indeed, more than 54% of these genes are organized in clusters and located on chromosomes X, 2, and 5, with a distribution conserved throughout the genus. The family sizes in the repleta group and D. virilis (virilis-repleta radiation) were smaller than in the melanogaster group. We tested alternative evolutionary models for OBP family size and turnover rates based on different ecological scenarios. We found heterogeneous gene turnover rates (GR) in comparisons involving columnar cactus specialists, prickly pear specialists, and fruit dwellers lineages, and signals of rapid molecular evolution compatible with positive selection in specific OBP genes. Taking ours and previous results together, we propose that this chemosensory gene family is involved in host adaptation and hypothesize that the adoption of the cactophilic lifestyle in the repleta group accelerated the evolution of members of the family.

Transcriptional responses are oriented towards different components of the rearing environment in two Drosophila sibling species

Background

The chance to compare patterns of differential gene expression in related ecologically distinct species can be particularly fruitful to investigate the genetics of adaptation and phenotypic plasticity. In this regard, a powerful technique such as RNA-Seq applied to ecologically amenable taxa allows to address issues that are not possible in classic model species. Here, we study gene expression profiles and larval performance of the cactophilic siblings Drosophila buzzatii and D. koepferae reared in media that approximate natural conditions and evaluate both chemical and nutritional components of the diet. These closely related species are complementary in terms of host-plant use since the primary host of one is the secondary of the other. D. koepferae is mainly a columnar cactus dweller while D. buzzatii prefers Opuntia hosts.

Results

Our comparative study shows that D. buzzatii and D. koepferae have different transcriptional strategies to face the challenges posed by their natural resources. The former has greater transcriptional plasticity, and its response is mainly modulated by alkaloids of its secondary host, while the latter has a more canalized genetic response, and its transcriptional plasticity is associated with the cactus species.

Conclusions

Our study unveils a complex pleiotropic genetic landscape in both species, with functional links that relate detox responses and redox mechanisms with developmental and neurobiological processes. These results contribute to deepen our understanding of the role of host plant shifts and natural stress driving ecological specialization.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08745-9.

Ir56b is an atypical ionotropic receptor that underlies appetitive salt response in Drosophila

Salt taste is one of the most ancient of all sensory modalities. However, the molecular basis of salt taste remains unclear in invertebrates. Here, we show that the response to low, appetitive salt concentrations in Drosophila depends on Ir56b, an atypical member of the ionotropic receptor (Ir) family. Ir56b acts in concert with two coreceptors, Ir25a and Ir76b. Mutation of Ir56b virtually eliminates an appetitive behavioral response to salt. Ir56b is expressed in neurons that also sense sugars via members of the Gr (gustatory receptor) family. Misexpression of Ir56b in bitter-sensing neurons confers physiological responses to appetitive doses of salt. Ir56b is unique among tuning Irs in containing virtually no N-terminal region, a feature that is evolutionarily conserved. Moreover, Ir56b is a "pseudo-pseudogene": its coding sequence contains a premature stop codon that can be replaced with a sense codon without loss of function. This stop codon is conserved among many Drosophila species but is absent in a number of species associated with cactus in arid regions. Thus, Ir56b serves the evolutionarily ancient function of salt detection in neurons that underlie both salt and sweet taste modalities.

OUP accepted manuscript

Interspecific hybridization is often seen as a genomic stress that may lead to new gene expression patterns and deregulation of transposable elements (TEs). The understanding of expression changes in hybrids compared with parental species is essential to disentangle their putative role in speciation processes. However, to date we ignore the detailed mechanisms involved in genomic deregulation in hybrids. We studied the ovarian transcriptome and epigenome of the Drosophila buzzatii and Drosophila koepferae species together with their F₁ hybrid females. We found a trend toward underexpression of genes and TE families in hybrids. The epigenome in hybrids was highly similar to the parental epigenomes and showed intermediate histone enrichments between parental species in most cases. Differential gene expression in hybrids was often associated only with changes in H3K4me3 enrichments, whereas differential TE family expression in hybrids may be associated with changes in H3K4me3, H3K9me3, or H3K27me3 enrichments. We identified specific genes and TE families, which their differential expression in comparison with the parental species was explained by their differential chromatin mark combination enrichment. Finally, cis–trans compensatory regulation could also contribute in some way to the hybrid deregulation. This work provides the first study of histone content in Drosophila interspecific hybrids and their effect on gene and TE expression deregulation.

Phylogenomic analyses of the genus Drosophila reveals genomic signals of climate adaptation

Many Drosophila species differ widely in their distributions and climate niches, making them excellent subjects for evolutionary genomic studies. Here, we have developed a database of high‐quality assemblies for 46 Drosophila species and one closely related Zaprionus. Fifteen of the genomes were newly sequenced, and 20 were improved with additional sequencing. New or improved annotations were generated for all 47 species, assisted by new transcriptomes for 19. Phylogenomic analyses of these data resolved several previously ambiguous relationships, especially in the melanogaster species group. However, it also revealed significant phylogenetic incongruence among genes, mainly in the form of incomplete lineage sorting in the subgenus Sophophora but also including asymmetric introgression in the subgenus Drosophila. Using the phylogeny as a framework and taking into account these incongruences, we then screened the data for genome‐wide signals of adaptation to different climatic niches. First, phylostratigraphy revealed relatively high rates of recent novel gene gain in three temperate pseudoobscura and five desert‐adapted cactophilic mulleri subgroup species. Second, we found differing ratios of nonsynonymous to synonymous substitutions in several hundred orthologues between climate generalists and specialists, with trends for significantly higher ratios for those in tropical and lower ratios for those in temperate‐continental specialists respectively than those in the climate generalists. Finally, resequencing natural populations of 13 species revealed tropics‐restricted species generally had smaller population sizes, lower genome diversity and more deleterious mutations than the more widespread species. We conclude that adaptation to different climates in the genus Drosophila has been associated with large‐scale and multifaceted genomic changes.

A holocenic and dynamic hybrid zone between two cactophilic Drosophila species in a coastal lowland plain of the Brazilian Atlantic Forest

Hybridization and introgression are processes that contribute to shaping biological diversity. The factors promoting the formation of these processes are multiples but poorly explored in a biogeographical and ecological context. In the southeast coastal plain of the Brazilian Atlantic Forest, a hybrid zone was described between two closely related cactophilic species, Drosophila antonietae and D. serido. Here, we revisited and analysed specimens from this hybrid zone to evaluate its temporal and spatial dynamic. We examined allopatric and sympatric populations of the flies using independent sources of data such as mitochondrial and nuclear sequences, microsatellite loci, morphometrics of wings and male genitalia, and climatic niche models. We also verified the emergence of the flies from necrotic tissues of collected cacti to verify the role of host association for the population dynamics. Our results support the existence of a hybrid zone due to secondary contact and limited to the localities where the two species are currently in contact. Furthermore, we detected asymmetric bidirectional introgression and the maintenance of the species integrity, ecological association and morphological characters, suggesting selection and limited introgression. Considering our paleomodels, probably this hybrid zone is recent and the contact occurred during the Holocene to the present day, favoured by range expansion of their populations due to expansion of open and dry areas in eastern South America during palaeoclimatic and geomorphological events.

Evolution of male genitalia in the Drosophila repleta species group (Diptera: Drosophilidae)

The Drosophila repleta group comprises more than one hundred species that inhabit several environments in the Neotropics and use different hosts as rearing and feeding resources. Rather homogeneous in their external morphology, they are generally distinguished by the male genitalia, seemingly their fastest evolving morphological trait, constituting an excellent model to study patterns of genital evolution in the context of a continental adaptive radiation. Although much is known about the evolution of animal genitalia at population level, surveys on macroevolutionary scale of this phenomenon are scarce. This study used a suite of phylogenetic comparative methods to elucidate the macroevolutionary patterns of genital evolution through deep time and large continental scales. Our results indicate that male genital size and some aspects of shape have been evolving by speciational evolution, probably due to the microevolutionary processes involved in species mate recognition. In contrast, several features of the aedeagus shape seemed to have evolved in a gradual fashion, with heterogeneous evolutionary phenotypic rates among clades. In general, the tempo of the evolution of aedeagus morphology was constant from the origin of the group until the Pliocene, when it accelerated in some clades that diversified mainly in this period. The incidence of novel ecological conditions in the tempo of aedeagus evolution and the relationship between species mate recognition and speciation in the Drosophila repleta group are discussed.

Structure, Organization, and Evolution of Satellite DNAs: Insights from the Drosophila repleta and D. virilis Species Groups

The fact that satellite DNAs (satDNAs) in eukaryotes are abundant genomic components, can perform functional roles, but can also change rapidly across species while being homogenous within a species, makes them an intriguing and fascinating genomic component to study. It is also becoming clear that satDNAs represent an important piece in genome architecture and that changes in their structure, organization, and abundance can affect the evolution of genomes and species in many ways. Since the discovery of satDNAs more than 50 years ago, species from the Drosophila genus have continuously been used as models to study several aspects of satDNA biology. These studies have been largely concentrated in D. melanogaster and closely related species from the Sophophora subgenus, even though the vast majority of all Drosophila species belong to the Drosophila subgenus. This chapter highlights some studies on the satDNA structure, organization, and evolution in two species groups from the Drosophila subgenus: the repleta and virilis groups. We also discuss and review the classification of other abundant tandem repeats found in these species in the light of the current information available.

Plastic Variation in the Phyletic Lineages of Cactophilic Drosophila meridionalis and Relation to Hosts as Potential for Diversification

The insect/plant interaction is known to be a trigger for diversification and even speciation. Experimental analyses on fitness traits and phenotypic variation using alternative host sites have been performed to understand the process of diversification relative to insect/plant interactions. For cactophilic species of Drosophila, the speciation process is considered an adaptive radiation in response to the exploration of species of the Cactaceae as breeding and feeding sites. In this work, we analyzed life history and morphological traits in individuals from two phyletic lineages (Evolutionarily Significant Units ESU) of the cactophilic species Drosophila meridionalis (Wasserman 1962) (Diptera: Drosophilidae) raised from media prepare. The characters analyzed corresponded to viability, developmental time, and four morphological measurements. The experiments were performed in a semi-natural medium prepared with fermenting tissues of the natural hosts, Cereus hildmaniannus and Opuntia monacantha. Viability, development time, and three morphological measurements were influenced by lineage, suggesting differentiation between the lineages. However, in O. monacantha, the mean viability was greater (~15%) and development time was longer (~336 h) than in C. hildmaniannus (~11% and ~301 h, respectively). Only the developmental time was significantly affected by the host cactus. In general, ESU group A had better values than ESU group BC for the evaluated traits. This finding suggested differentiation between the two lineages and different plastic responsiveness to the contrasting environments of the hosts, and that C. hildmaniannus may be a relatively stressful environment for the larvae, as for other Drosophila species.

Computational Sequence Analysis of Inversion Breakpoint Regions in the Cactophilic Drosophila mojavensis Lineage

We investigated rates of chromosomal evolution in Drosophila mojavensis using whole-genome sequence information from D. mojavensis, Drosophila buzzatii, and Drosophila virilis. Drosophila mojavensis is a cactophilic species of the repleta group living under extreme ecological conditions in the deserts of the Southwestern United States and Northwestern México. The genome of D. buzzatii, another member of the repleta group, was recently sequenced and the largest scaffolds anchored to all chromosomes using diverse procedures. Chromosome organization between D. mojavensis and D. buzzatii was compared using MUMmer and GRIMM software. Our results corroborate previous cytological analyses that indicated chromosome 2 differed between these 2 species by 10 inversions, chromosomes X and 5 differed by one inversion each, and chromosome 4 was homosequential. In contrast, we found that chromosome 3 differed by 5 inversions instead of the expected 2 that were previously inferred by cytological analyses. Thirteen of these inversions occurred in the D. mojavensis lineage: 12 are fixed and one of them is a polymorphic inversion previously described in populations from Sonora and Baja California, México. We previously investigated the breakpoints of chromosome 2 inversions fixed in D. mojavensis. Here we characterized the breakpoint regions of the 5 inversions found in chromosome 3 in order to infer the molecular mechanism that generated each inversion and its putative functional consequences. Overall, our results reveal a number of gene alterations at the inversion breakpoints with putative adaptive consequences that point to natural selection as the cause for fast chromosomal evolution in D. mojavensis.

Detoxification Genes Differ Between Cactus-, Fruit-, and Flower-Feeding Drosophila

We use annotated genomes of 14 Drosophila species covering diverse host use phenotypes to test whether 4 gene families that often have detoxification functions are associated with host shifts among species. Bark, slime flux, flower, and generalist necrotic fruit-feeding species all have similar numbers of carboxyl/cholinesterase, glutathione S-transferase, cytochrome P450, and UDP-glucuronosyltransferase genes. However, species feeding on toxic Morinda citrifolia fruit and the fresh fruit-feeding Drosophila suzukii have about 30 and 60 more, respectively. ABC transporters show a different pattern, with the flower-feeding D. elegans and the generalist necrotic fruit and cactus feeder D. hydei having about 20 and >100 more than the other species, respectively. Surprisingly, despite the complex secondary chemistry we find that 3 cactophilic specialists in the mojavensis species cluster have variably fewer genes than any of the other species across all 4 families. We also find 82 positive selection events across the 4 families, with the terminal D. suzukii and M. citrifolia-feeding D. sechellia branches again having the highest number of such events in proportion to their respective branch lengths. Many of the genes involved in these host-use-specific gene number differences or positive selection events lie in specific clades of the gene families that have been recurrently associated with detoxification. Several genes are also found to be involved in multiple duplication and/or positive selection events across the species studied regardless of their host use phenotypes; the most frequently involved are the ABC transporter CG1718, which is not in a specific clade associated with detoxification, and the α-esterase gene cluster, which is.

Genetic Diversity and Demographic History in the Cactophilic Drosophila repleta Species Group (Diptera: Drosophilidae) in North America Inferred from Mitochondrial DNA Barcodes

Genetic diversity in mitochondrial DNA barcodes, comprising a segment of the cytochrome c oxidase subunit I (COI) gene, was used to infer demographic histories in selected taxa of the cactophilic Drosophila repleta species group in North America. Haplotype and nucleotide diversities were determined in 16 taxa based on both previously published and new sequences. Haplotype diversity (h) differed dramatically in different taxa, varying from h = 0 in Drosophila eremophila, Drosophila hexastigma, and Drosophila bifurca to h = 0.99 in Drosophila hamatofila. Genetic diversity indices and sample sizes were sufficient to infer demographic histories from mismatch distribution analysis and Bayesian skyline plots for 9 taxa: Drosophila mojavensis baja, Drosophila mojavensis sonorensis, Drosophila arizonae, Drosophila aldrichi, D. hamatofila, Drosophila spenceri, Drosophila mainlandi, Drosophila mettleri, and Drosophila nigrospiracula. Evidence was found for both population expansions and relatively stable populations in these species. Demographic history varied dramatically in subspecies of D. mojavensis, showing a relatively stable population size over time in D. m. sonorensis from the mainland Sonoran Desert whereas a large population expansion was evident in D. m. baja from the Baja California Peninsula, providing support for the hypothesis that the split of sister species D. mojavensis and D. arizonae from a common ancestor occurred on the mainland rather than the peninsula as proposed by others. No evidence was found for a causal relationship between a stable or expanding population and host plant shifts from prickly-pear cactus to columnar cacti, which has occurred independently in many taxa of the repleta group.

Genetics and Distribution Modeling: The Demographic History of the Cactophilic Drosophila buzzatii Species Cluster in Open Areas of South America

Biodiversity is the result of historical and recurrent events acting on populations and species. The Drosophila buzzatii species cluster is distributed along a diagonal of open areas in South America. Combining genetic analyses with species distribution models we evaluated the influence of climatic changes in the demography history of this cluster. We performed a Bayesian Skyline analysis and reconstructed the ancestral areas based on mitochondrial cytochrome oxidase I (mtCOI) gene. We modeled the current distribution and projected it to past (mid-Holocene and Last Glacial Maximum) and future. Our results demonstrate that climate change plays a critical role in historical demography and in defining the current and future geographic ranges of these species. The inter-Andean dry valleys and the Chiquitano Seasonally Dry Tropical Forests (SDTF) in Bolivia are considered the ancestral area for the D. buzzatii cluster. From this area, the migration route was through a west-east corridor from central Andes, throughout Bolivia, Paraguay and Argentina toward eastern and northeastern Brazil, along the edges of rain forest. The responses of the species to the climatic changes differ from the dominant assumptions of expansion during dry/cold weather and contraction during wet/warm weather that characterized the glacial cycles. We suggest that the influence of ecology and the potential responsiveness of each taxon to the environmental dynamics should be considered as well. Predictions for the future suggest a decline of suitable areas for the cluster, threatening biodiversity of these habitats. This work showed the importance of an integrative analysis of genetics and geography information to improve the inferences about demographic history hypotheses for the cluster.

Evolution of Reproductive Behavior

Behaviors associated with reproduction are major contributors to the evolutionary success of organisms and are subject to many evolutionary forces, including natural and sexual selection, and sexual conflict. Successful reproduction involves a range of behaviors, from finding an appropriate mate, courting, and copulation, to the successful production and (in oviparous animals) deposition of eggs following mating. As a consequence, behaviors and genes associated with reproduction are often under strong selection and evolve rapidly. Courtship rituals in flies follow a multimodal pattern, mediated through visual, chemical, tactile, and auditory signals. Premating behaviors allow males and females to assess the species identity, reproductive state, and condition of their partners. Conflicts between the "interests" of individual males, and/or between the reproductive strategies of males and females, often drive the evolution of reproductive behaviors. For example, seminal proteins transmitted by males often show evidence of rapid evolution, mediated by positive selection. Postmating behaviors, including the selection of oviposition sites, are highly variable and Drosophila species span the spectrum from generalists to obligate specialists. Chemical recognition features prominently in adaptation to host plants for feeding and oviposition. Selection acting on variation in pre-, peri-, and postmating behaviors can lead to reproductive isolation and incipient speciation. Response to selection at the genetic level can include the expansion of gene families, such as those for detecting pheromonal cues for mating, or changes in the expression of genes leading to visual cues such as wing spots that are assessed during mating. Here, we consider the evolution of reproductive behavior in Drosophila at two distinct, yet complementary, scales. Some studies take a microevolutionary approach, identifying genes and networks involved in reproduction, and then dissecting the genetics underlying complex behaviors in D. melanogaster Other studies take a macroevolutionary approach, comparing reproductive behaviors across the genus Drosophila and how these might correlate with environmental cues. A full synthesis of this field will require unification across these levels.

Evolution of larval segment position across 12 Drosophila species

Many developmental traits that are critical to the survival of the organism are also robust. These robust traits are resistant to phenotypic change in the face of variation. This presents a challenge to evolution. In this article, we asked whether and how a well‐established robust trait, Drosophila segment patterning, changed over the evolutionary history of the genus. We compared segment position scaled to body length at the first‐instar larval stage among 12 Drosophila species. We found that relative segment position has changed many times across the phylogeny. Changes were frequent, but primarily small in magnitude. Phylogenetic analysis demonstrated that rates of change in segment position are variable along the Drosophila phylogenetic tree, and that these changes can occur in short evolutionary timescales. Correlation between position shifts of segments decreased as the distance between two segments increased, suggesting local control of segment position. The posterior‐most abdominal segment showed the highest magnitude of change on average, had the highest rate of evolution between species, and appeared to be evolving more independently as compared to the rest of the segments. This segment was exceptionally elongated in the cactophilic species in our dataset, raising questions as to whether this change may be adaptive.

Evolutionary genomics of host plant adaptation: insights from Drosophila

Variation in gene expression in response to the use of alternate host plants can reveal genetic and physiological mechanisms explaining why insect-host relationships vary from host specialism to generalism. Interpreting transcriptome variation relies on well-annotated genomes, making drosophilids valuable model systems, particularly those species with tractable ecological associations. Patterns of whole genome expression and alternate gene splicing in response to growth on different hosts have revealed expression of gene networks of known detoxification genes as well as novel functionally enriched genes of diverse metabolic and structural functions. Integrating trancriptomic responses with fitness differences and levels of phenotypic plasticity in response to alternate hosts will help to reveal the general nature of genotype-phenotype relationships.

What does mitogenomics tell us about the evolutionary history of the Drosophila buzzatii cluster (repleta group)?

The Drosophila repleta group is an array of more than 100 species endemic to the “New World”, many of which are cactophilic. The ability to utilize decaying cactus tissues as breeding and feeding sites is a key aspect that allowed the successful diversification of the repleta group in American deserts and arid lands. Within this group, the Drosophila buzzatii cluster is a South American clade of seven closely related species in different stages of divergence, making them a valuable model system for evolutionary research. Substantial effort has been devoted to elucidating the phylogenetic relationships among members of the D. buzzatii cluster, including molecular phylogenetic studies that have generated ambiguous results where different tree topologies have resulted dependent on the kinds of molecular marker used. Even though mitochondrial DNA regions have become useful markers in evolutionary biology and population genetics, none of the more than twenty Drosophila mitogenomes assembled so far includes this cluster. Here, we report the assembly of six complete mitogenomes of five species: D. antonietae, D. borborema, D. buzzatii, two strains of D. koepferae and D. seriema, with the aim of revisiting phylogenetic relationships and divergence times by means of mitogenomic analyses. Our recovered topology using complete mitogenomes supports the hypothesis of monophyly of the D. buzzatii cluster and shows two main clades, one including D. buzzatii and D. koepferae (both strains), and the other containing the remaining species. These results are in agreement with previous reports based on a few mitochondrial and/or nuclear genes, but conflict with the results of a recent large-scale nuclear phylogeny, indicating that nuclear and mitochondrial genomes depict different evolutionary histories.

Repeated evolution of asymmetric genitalia and right-sided mating behavior in the Drosophila nannoptera species group

BACKGROUND

Male genitals have repeatedly evolved left-right asymmetries, and the causes of such evolution remain unclear. The Drosophila nannoptera group contains four species, among which three exhibit left-right asymmetries of distinct genital organs. In the most studied species, Drosophila pachea, males display asymmetric genital lobes and they mate right-sided on top of the female. Copulation position of the other species is unknown.

RESULTS

To assess whether the evolution of genital asymmetry could be linked to the evolution of one-sided mating, we examined phallus morphology and copulation position in D. pachea and closely related species. The phallus was found to be symmetric in all investigated species except D. pachea, which displays an asymmetric phallus with a right-sided gonopore, and D. acanthoptera, which harbors an asymmetrically bent phallus. In all examined species, males were found to position themselves symmetrically on top of the female, except in D. pachea and D. nannoptera, where males mated right-sided, in distinctive, species-specific positions. In addition, the copulation duration was found to be increased in the nannoptera group species compared to closely related outgroup species.

CONCLUSION

Our study shows that gains, and possibly losses, of asymmetry in genital morphology and mating position have evolved repeatedly in the nannoptera group. Current data does not allow us to conclude whether genital asymmetry has evolved in response to changes in mating position, or vice versa.

Host use and host shifts in Drosophila

Over a thousand Drosophila species have radiated onto a wide range of feeding and breeding sites. These radiations involve adaptations for locating, accepting, and growing in hosts with highly differing characteristics. In a number of species, owing to the availability of sequenced genomes, particular steps in host specialization and genes that control them, are being identified. Many cases of specialization involve the ability to detoxify some component of the host. Examples include Drosophila sechellia and the octanoic acid in Morinda citrifolia, alpha-amanitin in mycophagous drosophilids, and the alkaloids in cactophilic species. Owing to the known ecologies of many species for which genomes exist, the Drosophila model system provides an unprecedented opportunity to simultaneously examine the genes underlying HOST LOCATION, HOST ACCEPTANCE and HOST USE, the types of selection acting upon them and any coevolutionary interactions among the genes underlying these steps.

Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species

BACKGROUND

Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adaptations in the past. Here we investigate the genetic changes associated with adaptation to arid environments, specifically climatic extremes and new cactus hosts, through such an analysis of five repleta group Drosophila species.

RESULTS

We find disproportionately high rates of gene gains in internal branches in the species' phylogeny where cactus use and subsequently cactus specialisation and high heat and desiccation tolerance evolved. The terminal branch leading to the most heat and desiccation resistant species, Drosophila aldrichi, also shows disproportionately high rates of both gene gains and positive selection. Several Gene Ontology terms related to metabolism were enriched in gene gain events in lineages where cactus use was evolving, while some regulatory and developmental genes were strongly selected in the Drosophila aldrichi branch. Transcriptomic analysis of flies subjected to sublethal heat shocks showed many more downregulation responses to the stress in a heat sensitive versus heat resistant species, confirming the existence of widespread regulatory as well as structural changes in the species' differing adaptations. Gene Ontology terms related to metabolism were enriched in the differentially expressed genes in the resistant species while terms related to stress response were over-represented in the sensitive one.

CONCLUSION

Adaptations to new cactus hosts and hot desiccating environments were associated with periods of accelerated evolutionary change in diverse biochemistries. The hundreds of genes involved suggest adaptations of this sort would be difficult to achieve in the timeframes projected for anthropogenic climate change.

An Improved Genome Assembly for Drosophila navojoa, the Basal Species in the mojavensis Cluster

Three North American cactophilic Drosophila species, D. mojavensis, D. arizonae, and D. navojoa, are of considerable evolutionary interest owing to the shift from breeding in Opuntia cacti to columnar species. The 3 species form the "mojavensis cluster" of Drosophila. The genome of D. mojavensis was sequenced in 2007 and the genomes of D. navojoa and D. arizonae were sequenced together in 2016 using the same technology (Illumina) and assembly software (AllPaths-LG). Yet, unfortunately, the D. navojoa genome was considerably more fragmented and incomplete than its sister species, rendering it less useful for evolutionary genetic studies. The D. navojoa read dataset does not fully meet the strict insert size required by the assembler used (AllPaths-LG) and this incompatibility might explain its assembly problems. Accordingly, when we re-assembled the genome of D. navojoa with the SPAdes assembler, which does not have the strict AllPaths-LG requirements, we obtained a substantial improvement in all quality indicators such as N50 (from 84 kb to 389 kb) and BUSCO coverage (from 77% to 97%). Here we share a new, improved reference assembly for D. navojoa genome, along with a RNAseq transcriptome. Given the basal relationship of the Opuntia breeding D. navojoa to the columnar breeding D. arizonae and D. mojavensis, the improved assembly and annotation will allow researchers to address a range of questions associated with the genomics of host shifts, chromosomal rearrangements and speciation in this group.

Genome-Wide Patterns of Sequence Divergence of Protein-Coding Genes Between Drosophila buzzatii and D. mojavensis

Evolutionary rates for protein-coding genes are determined not only by natural selection but also by multiple genomic factors including mutation rates, recombination, gene expression levels, and chromosomal location. To investigate the joint effects of different genomic determinants on protein evolution, we compared the coding sequences of 9017 single-copy orthologs between 2 cactophilic species from the Drosophila subgenus, Drosophila mojavensis and D. buzzatii, whose genomes have been previously sequenced. We assessed the impact of 7 genomic determinants, that is, chromosome type, recombination, chromosomal inversions, expression breadth, expression level, gene length, and the number of exons, on divergence rates of protein-coding genes to understand patterns of evolutionary variation. Integrative analysis of these factors revealed that 1) X-linked and autosomal genes evolve at significantly different rates in agreement with the faster-X hypothesis, 2) genes located on the dot chromosome and pericentromeric regions have higher divergence rates, 3) genes located at chromosomes with more fixed inversions have higher pairwise divergence than those located at nearly collinear chromosomes, and 4) gene expression patterns can be considered the strongest determinant of protein evolution. In addition, the number of exons and protein length had a significant effect on pairwise divergence at synonymous sites. All in all, our results show the relative importance of each genomic factor on the rates of protein evolution and functional constraint in these 2 cactophilic Drosophila species.

Pupal emergence pattern in cactophilic Drosophila and the effect of host plants

Drosophila buzzatii and D. koepferae are sibling cactophilic species. The former breeds primarily on prickly pears (genus Opuntia) whereas the latter breeds on columnar cacti of the genera Cereus and Trichocereus, although with certain degree of niche overlapping. We examined the interspecific differences in diurnal temporal patterns of adult emergence from puparia and evaluated whether this behavior is affected by rearing in the different cactus hosts available in nature. We detected important host-dependent genetic variation for this trait differentially affecting the emergence schedule of these species. Diurnal pattern of emergence time was directly correlated with developmental time and negatively correlated with adult wing size, suggesting that early emergences are at least indirectly correlated with increased fitness. We discussed our results in terms of their putative effects on fitness and the genetic-metabolic pathways that would be presumably affected by host's nutritional-chemical differences.

An investigation of Y chromosome incorporations in 400 species of Drosophila and related genera

Y chromosomes are widely believed to evolve from a normal autosome through a process of massive gene loss (with preservation of some male genes), shaped by sex-antagonistic selection and complemented by occasional gains of male-related genes. The net result of these processes is a male-specialized chromosome. This might be expected to be an irreversible process, but it was found in 2005 that the Drosophila pseudoobscura Y chromosome was incorporated into an autosome. Y chromosome incorporations have important consequences: a formerly male-restricted chromosome reverts to autosomal inheritance, and the species may shift from an XY/XX to X0/XX sex-chromosome system. In order to assess the frequency and causes of this phenomenon we searched for Y chromosome incorporations in 400 species from Drosophila and related genera. We found one additional large scale event of Y chromosome incorporation, affecting the whole montium subgroup (40 species in our sample); overall 13% of the sampled species (52/400) have Y incorporations. While previous data indicated that after the Y incorporation the ancestral Y disappeared as a free chromosome, the much larger data set analyzed here indicates that a copy of the Y survived as a free chromosome both in montium and pseudoobscura species, and that the current Y of the pseudoobscura lineage results from a fusion between this free Y and the neoY. The 400 species sample also showed that the previously suggested causal connection between X-autosome fusions and Y incorporations is, at best, weak: the new case of Y incorporation (montium) does not have X-autosome fusion, whereas nine independent cases of X-autosome fusions were not followed by Y incorporations. Y incorporation is an underappreciated mechanism affecting Y chromosome evolution; our results show that at least in Drosophila it plays a relevant role and highlight the need of similar studies in other groups.

In contrast to other chromosomes (X and autosomes), which are present in males and females, Y chromosomes spend all time in males. Hence it is not surprising that along evolution they became male specialized, e.g., containing a disproportionate amount of male-fertility genes. Interestingly it was found in 2005 that in Drosophila pseudoobscura the Y chromosome reverted to "male-female existence", being incorporated into an autosome. These "Y chromosome incorporations" have important consequences on sex-chromosome evolution, and allow the study of the evolutionary forces that shaped Y chromosomes as they act backwards. As D. pseudoobscura was the second Drosophila species investigated in this respect, it is likely that other cases exist, and that perhaps it is a common phenomenon. In order to answer this question we studied 400 Drosophila species. We found one additional case of Y incorporation, which occurred in the ancestor of Drosophila montium, and currently affects a large number of species; overall 13% of the species we sampled (52/400) have Y incorporations. We also found that a previously suggested cause of Y incorporations (X-autosome fusions) is not a general explanation. Our results show that in Drosophila Y incorporations play a relevant role and highlight the need of similar studies in other groups.

Phylogeny of the Genus Drosophila

Understanding phylogenetic relationships among taxa is key to designing and implementing comparative analyses. The genus Drosophila, which contains over 1600 species, is one of the most important model systems in the biological sciences. For over a century, one species in this group, Drosophila melanogaster, has been key to studies of animal development and genetics, genome organization and evolution, and human disease. As whole-genome sequencing becomes more cost-effective, there is increasing interest in other members of this morphologically, ecologically, and behaviorally diverse genus. Phylogenetic relationships within Drosophila are complicated, and the goal of this paper is to provide a review of the recent taxonomic changes and phylogenetic relationships in this genus to aid in further comparative studies.

Behavioral evolution accompanying host shifts in cactophilic Drosophila larvae

For plant utilizing insects, the shift to a novel host is generally accompanied by a complex set of phenotypic adaptations. Many such adaptations arise in response to differences in plant chemistry, competitive environment, or abiotic conditions. One less well-understood factor in the evolution of phytophagous insects is the selective environment provided by plant shape and volume. Does the physical structure of a new plant host favor certain phenotypes? Here, we use cactophilic Drosophila, which have colonized the necrotic tissues of cacti with dramatically different shapes and volumes, to examine this question. Specifically, we analyzed two behavioral traits in larvae, pupation height, and activity that we predicted might be related to the ability to utilize variably shaped hosts. We found that populations of D. mojavensis living on lengthy columnar or barrel cactus hosts have greater activity and pupate higher in a laboratory environment than populations living on small and flat prickly pear cactus cladodes. Crosses between the most phenotypically extreme populations suggest that the genetic architectures of these behaviors are distinct. A comparison of activity in additional cactophilic species that are specialized on small and large cactus hosts shows a consistent trend. Thus, we suggest that greater motility and an associated tendency to pupate higher in the laboratory are potential larval adaptations for life on a large plant where space is more abundant and resources may be more sparsely distributed.

Transposable Element Misregulation Is Linked to the Divergence between Parental piRNA Pathways in Drosophila Hybrids

Interspecific hybridization is a genomic stress condition that leads to the activation of transposable elements (TEs) in both animals and plants. In hybrids between Drosophila buzzatii and Drosophila koepferae, mobilization of at least 28 TEs has been described. However, the molecular mechanisms underlying this TE release remain poorly understood. To give insight on the causes of this TE activation, we performed a TE transcriptomic analysis in ovaries (notorious for playing a major role in TE silencing) of parental species and their F1 and backcrossed (BC) hybrids. We find that 15.2% and 10.6% of the expressed TEs are deregulated in F1 and BC1 ovaries, respectively, with a bias toward overexpression in both cases. Although differences between parental piRNA (Piwi-interacting RNA) populations explain only partially these results, we demonstrate that piRNA pathway proteins have divergent sequences and are differentially expressed between parental species. Thus, a functional divergence of the piRNA pathway between parental species, together with some differences between their piRNA pools, might be at the origin of hybrid instabilities and ultimately cause TE misregulation in ovaries. These analyses were complemented with the study of F1 testes, where TEs tend to be less expressed than in D. buzzatii. This can be explained by an increase in piRNA production, which probably acts as a defence mechanism against TE instability in the male germline. Hence, we describe a differential impact of interspecific hybridization in testes and ovaries, which reveals that TE expression and regulation are sex-biased.

Evolution of Trichobaris (Curculionidae) in relation to host plants: Geometric morphometrics, phylogeny and phylogeography

The family Curculionidae (Coleoptera), the "true" weevils, have diversified tightly linked to the evolution of flowering plants. Here, we aim to assess diversification at a lower taxonomic level. We analyze the evolution of the genus Trichobaris in association with their host plants. Trichobaris comprises eight to thirteen species; their larvae feed inside the fruits of Datura spp. or inside the stem of wild and cultivated species of Solanaceae, such as potato, tobacco and tomato. We ask the following questions: (1) does the rostrum of Trichobaris species evolve according to the plant tissue used to oviposit, i.e., shorter rostrum to dig in stems and longer to dig in fruits? and (2) does Trichobaris diversify mainly in relation to the use of Datura species? For the first question, we estimated the phylogeny of Trichobaris based on four gene sequences (nuclear 18S and 28S rRNA genes and mitochondrial 16S rRNA and COI genes). Then, we carried out morphogeometric analyses of the Trichobaris species using 75 landmarks. For the second question, we calibrated a COI haplotype phylogeny using a constant rate of divergence to infer the diversification time of Trichobaris species, and we traced the host plant species on the haplotype network. We performed an ancestral state reconstruction analysis to infer recent colonization events and conserved associations with host plant species. We found that ancestral species in the Trichobaris phylogeny use the stem of Solanum plants for oviposition and display weak sexual dimorphism of rostrum size, whereas other, more recent species of Trichobaris display sexual dimorphism in rostrum size and use the fruits of Datura species, and a possible reversion to use the stem of Solanaceae was detected in one Trichobaris species. The use of Datura species by Trichobaris species is widely distributed on haplotype networks and restricted to Trichobaris species that originated ca. 5 ± 1.5 Ma. Given that the origin of Trichobaris is estimated to be ca. 6 ± 1.5 Ma, it is likely that Datura has played a role in its diversification.

Genomics of parallel adaptation at two timescales in Drosophila

Two interesting unanswered questions are the extent to which both the broad patterns and genetic details of adaptive divergence are repeatable across species, and the timescales over which parallel adaptation may be observed. Drosophila melanogaster is a key model system for population and evolutionary genomics. Findings from genetics and genomics suggest that recent adaptation to latitudinal environmental variation (on the timescale of hundreds or thousands of years) associated with Out-of-Africa colonization plays an important role in maintaining biological variation in the species. Additionally, studies of interspecific differences between D. melanogaster and its sister species D. simulans have revealed that a substantial proportion of proteins and amino acid residues exhibit adaptive divergence on a roughly few million years long timescale. Here we use population genomic approaches to attack the problem of parallelism between D. melanogaster and a highly diverged conger, D. hydei, on two timescales. D. hydei, a member of the repleta group of Drosophila, is similar to D. melanogaster, in that it too appears to be a recently cosmopolitan species and recent colonizer of high latitude environments. We observed parallelism both for genes exhibiting latitudinal allele frequency differentiation within species and for genes exhibiting recurrent adaptive protein divergence between species. Greater parallelism was observed for long-term adaptive protein evolution and this parallelism includes not only the specific genes/proteins that exhibit adaptive evolution, but extends even to the magnitudes of the selective effects on interspecific protein differences. Thus, despite the roughly 50 million years of time separating D. melanogaster and D. hydei, and despite their considerably divergent biology, they exhibit substantial parallelism, suggesting the existence of a fundamental predictability of adaptive evolution in the genus.

Both local adaptation on short timescales and the long-term accumulation of adaptive differences between species have recently been investigated using comparative genomic and population genomic approaches in several species. However, the repeatability of adaptive evolution at the genetic level is poorly understood. Here we attack this problem by comparing patterns of long and short-term adaptation in Drosophila melanogaster to patterns of adaptation on two timescales in a highly diverged congener, Drosophila hydei. We found, despite the fact that these species diverged from a common ancestor roughly 50 million years ago, the population genomics of latitudinal allele frequency differentiation shows that there is a substantial shared set of genes likely playing a role in the short term adaptive divergence of populations in both species. Analyses of longer-term adaptive protein divergence for the D. hydei-D. mojavensis and D. melanogaster-D. simulans clades reveal a striking level of parallel adaptation. This parallelism includes not only the specific genes/proteins that exhibit adaptive evolution, but extends even to the magnitudes of the selective effects on interspecific protein differences.

The Calibrated Phylogeny of the Drosophila fasciola Subgroup (D. repleta Group Wasserman) Indicates Neogene Diversification of Its Internal Branches

The species of the Drosophila fasciola subgroup Wasserman represent the dominant section of the Drosophila repleta group Wasserman in the American rainforests and have a broad geographical distribution in the New World. However, despite of its wide range, the D. fasciola subgroup is one of the most overlooked D. repleta subgroups. Here, we report a molecular phylogenetic analysis focused on the D. fasciola subgroup using two mitochondrial [cytochrome oxidase subunit I (COI), cytochrome oxidase subunit II (COII)] and two nuclear [elongation factor-1alpha F1 (EF-alphaF1) and transformer (tra)] genes. Overall, we found that this subgroup is a monophyletic taxon, subdivided into two main internal branches: named Fas1 and Fas2 clades. The diversification of these clades is estimated to have begun in the middle Miocene, around 12 Ma [95% high posterior density (HPD) 9.0-15 Ma], and might be associated with the colonization of South America by Central America populations after the closure of Isthmus of Panama due to the temporal congruence between these events. The terminal branches had their origins estimated to be in the Pliocene or the Plio-Pleistocene transition. For the later estimates, both the geomorphological influences and the climatic oscillations of the Pleistocene may have played a role in shaping the diversification of the D. fasciola group.

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.

Dissecting the Satellite DNA Landscape in Three Cactophilic Drosophila Sequenced Genomes

Eukaryote genomes are replete with repetitive DNAs. This class includes tandemly repeated satellite DNAs (satDNA) which are among the most abundant, fast evolving (yet poorly studied) genomic components. Here, we used high-throughput sequencing data from three cactophilic Drosophila species, D. buzzatii, D. seriema, and D. mojavensis, to access and study their whole satDNA landscape. In total, the RepeatExplorer software identified five satDNAs, three previously described (pBuM, DBC-150 and CDSTR198) and two novel ones (CDSTR138 and CDSTR130). Only pBuM is shared among all three species. The satDNA repeat length falls within only two classes, between 130 and 200 bp or between 340 and 390 bp. FISH on metaphase and polytene chromosomes revealed the presence of satDNA arrays in at least one of the following genomic compartments: centromeric, telomeric, subtelomeric, or dispersed along euchromatin. The chromosomal distribution ranges from a single chromosome to almost all chromosomes of the complement. Fiber-FISH and sequence analysis of contigs revealed interspersion between pBuM and CDSTR130 in the microchromosomes of D. mojavensis Phylogenetic analyses showed that the pBuM satDNA underwent concerted evolution at both interspecific and intraspecific levels. Based on RNA-seq data, we found transcription activity for pBuM (in D. mojavensis) and CDSTR198 (in D. buzzatii) in all five analyzed developmental stages, most notably in pupae and adult males. Our data revealed that cactophilic Drosophila present the lowest amount of satDNAs (1.9-2.9%) within the Drosophila genus reported so far. We discuss how our findings on the satDNA location, abundance, organization, and transcription activity may be related to functional aspects.

The role of courtship song in female mate choice in South American Cactophilic Drosophila

Courtship songs have undergone a spectacular diversification in the Drosophila buzzatii cluster. Accordingly, it has been suggested that sexual selection has played a significant role in promoting rapid diversification, reproductive isolation and speciation. However, there is no direct evidence (i.e., song playback experiments with wingless males) supporting this tenet. Moreover, several studies have showed that the courtship song in the genus Drosophila is not always used in female mate choice decisions, nor plays the same role when it is taken into account. In this vein, we use an approach that combines manipulative and playback experiments to explore the importance and the role of courtship song in female mate choice in four species of the D. buzzatii cluster and one species of the closely related D. martensis cluster for outgroup comparison. We also investigate the importance of courtship song in sexual isolation in sympatry between the only semi-cosmopolitan species, D. buzzatii, and the other species of the D. buzzatii cluster. Our study revealed that the courtship song is used by females of the D. buzzatii cluster as a criterion for male acceptance or influences the speed with which males are chosen. In contrast, we showed that this characteristic is not shared by D. venezolana, the representative species of the D. martensis cluster. We also found that the studied species of the D. buzzatii cluster differ in the role that conspecific and heterospecific songs have in female mate choice and in sexual isolation. Our findings support the hypothesis that divergence in female preferences for courtship songs has played a significant role in promoting rapid diversification and reproductive isolation in the D. buzzatii cluster. However, evidence from D. venezolana suggests that the use of the courtship song in female mate choice is not a conserved feature in the D. buzzatii complex.

Enhanced fertility and chill tolerance after cold-induced reproductive arrest in females of temperate species of the Drosophila buzzatii complex

Long-term exposure to low temperatures during adult maturation might decrease fertility after cold recovery as a consequence of carry-over effects on reproductive tissues. This pattern should be more pronounced in tropical than in temperate species as protective mechanisms against chilling injuries are expected to be more effective in the latter. We initially determined the lower thermal thresholds to induce ovarian maturation in four closely related Drosophila species, two inhabiting temperate regions and the other two tropical areas of South America. As expected, only temperate species regularly experience cold-inducing conditions for reproductive arrest during winter in their natural environment. Subsequently, we exposed reproductively arrested and mature females to cold-inducing conditions for reproductive arrest over a long period. Following cold exposure, tropical species exhibited a dramatic fertility decline, irrespective of reproductive status. In contrast, not only were temperate females fecund and fertile but also fertility was superior in females that underwent cold-induced reproductive arrest, suggesting that it might act as a protecting mechanism ensuring fertility after cold recovery. Based on these findings, we decided to evaluate the extent to which reproductive status affects cold tolerance and energy metabolism at low temperature. We found a lower metabolic rate and a higher cold tolerance in reproductively arrested females, although only temperate species attained high levels of chill tolerance. These findings highlight the role of cold-induced reproductive arrest as part of an integrated mechanism of cold adaptation that could potentially contribute to the spread of temperate species into higher latitudes or altitudes.

Contributions of Dryland Forest (Caatinga) to Species Composition, Richness and Diversity of Drosophilidae

In this study, semi-arid environments were tested to see if they support insect diversity. This was evaluated through the structure of the composition of assemblies of drosophilids in three conservation units placed in three different ecoregions in the dryland forests, Caatinga. This is a unique biome in northeast Brazil, comprising approximately 10% of the country. Species richness was investigated over 2 years during a prolonged drought, considered the worst affliction the Caatinga ecosystem had experienced in the last 50 years. Alpha diversity indices and the ecological similarity between the samples were calculated to determine how the environments drive the composition of Drosophilidae in such semi-arid places. A total of 7352 specimens were sampled. They were classified into 20 species belonging to four genera: Drosophila, Rhinoleucophenga, Scaptodrosophila, and Zaprionus. Drosophila nebulosa Sturtevant (44.5%) and Drosophila cardini Sturtevant (12.5%) were the most abundant species. The occurrences and abundances of all the species differed greatly between sites. These results and other ecological analyses indicate that although placed in the same biome, there are great variability in the drosophilid species and abundance among the three protected and conserved dryland environments.