Phylogenetic relationships and macro-evolutionary patterns within the Drosophila tripunctata "radiation" (Diptera: Drosophilidae)

Dietary Variation Effect on Life History Traits and Energy Storage in Neotropical Species of Drosophila (Diptera; Drosophilidae)

The ability of an organism to respond to nutritional stress can be a plastic character under the action of natural selection, affecting several characteristics, including life history and energy storage. The genus Drosophila (Diptera; Drosophilidae) presents high variability regarding natural resource exploration. However, most works on this theme have studied the model species D. melanogaster Meigen, 1830 and little is known about Neotropical drosophilids. Here we evaluate the effects of three diets, with different carbohydrate-to-protein ratios, on life history (viability and development time) and metabolic pools (triglycerides, glycogen, and total soluble protein contents) of three Neotropical species of Drosophila: D. maculifrons Duda, 1927; D. ornatifrons Duda, 1927, both of the subgenus Drosophila Sturtevant, 1939, and D. willistoni Sturtevant, 1916 of the subgenus Sophophora Sturtevant, 1939. Our results showed that only D. willistoni was viable on all diets, D. maculifrons was not viable on the sugary diet, while D. ornatifrons was barely viable on this diet. The sugary diet increased the development time of D. willistoni and D. ornatifrons, and D. willistoni glycogen content. Thus, the viability of D. maculifrons and D. ornatifrons seems to depend on a certain amount of protein and/or a low concentration of carbohydrate in the diet. A more evident effect of the diets on triglyceride and protein pools was detected in D. ornatifrons, which could be related to the adult attraction to dung and carrion baited pitfall as food resource tested in nature. Our results demonstrated that the evolutionary history and differential adaptations to natural macronutrient resources are important to define the amplitude of response that a species can present when faced with dietary variation.

Skeleton phylogeny reconstructed with transcriptomes for the tribe Drosophilini (Diptera: Drosophilidae)

The family Drosophilidae is one of the most important model systems in evolutionary biology. Thanks to advances in high-throughput sequencing technology, a number of molecular phylogenetic analyses have been undertaken by using large data sets of many genes and many species sampled across this family. Especially, recent analyses using genome sequences have depicted the family-wide skeleton phylogeny with high confidence. However, the taxon sampling is still insufficient for minor lineages and non-Drosophila genera. In this study, we carried out phylogenetic analyses using a large number of transcriptome-based nucleotide sequences, focusing on the largest, core tribe Drosophilini in the Drosophilidae. In our analyses, some noise factors against phylogenetic reconstruction were taken into account by removing putative paralogy from the datasets and examining the effects of missing data, i.e. gene occupancy and site coverage, and incomplete lineage sorting. The inferred phylogeny has newly resolved the following phylogenetic positions/relationships at the genomic scale: (i) the monophyly of the subgenus Siphlodora including Zaprionus flavofasciatus to be transferred therein; (ii) the paraphyly of the robusta and melanica species groups within a clade comprised of the robusta, melanica and quadrisetata groups and Z. flavofasciatus; (iii) Drosophila curviceps (representing the curviceps group), D. annulipes (the quadrilineata subgroup of the immigrans group) and D. maculinotata clustered into a clade sister to the Idiomyia + Scaptomyza clade, forming together the expanded Hawaiian drosophilid lineage; (iv) Dichaetophora tenuicauda (representing the lineage comprised of the Zygothrica genus group and Dichaetophora) placed as the sister to the clade of the expanded Hawaiian drosophilid lineage and Siphlodora; and (v) relationships of the subgenus Drosophila and the genus Zaprionus as follows: (Zaprionus, (the quadrilineata subgroup, ((D. sternopleuralis, the immigrans group proper), (the quinaria radiation, the tripunctata radiation)))). These results are to be incorporated into the so-far published phylogenomic tree as a backbone (constraint) tree for grafting much more species based on sequences of a limited number of genes. Such a comprehensive, highly confident phylogenetic tree with extensive and dense taxon sampling will provide an essential framework for comparative studies of the Drosophilidae.

A new species of the Drosophila tripunctata group (Diptera: Drosophilidae) associated with fallen flowers of six Lecythidaceae species in the Amazon Rainforest

The tripunctata group falls under the subgenus Drosophila Falln, 1823 of the genus Drosophila Falln, 1823, and is composed of four subgroups and 17 species not assigned to subgroups. This group is widely distributed throughout tropical regions and is predominantly found in preserved forest environments. With a predicted high number of cryptic species, the occurrence of intraspecific morphological polymorphisms made it difficult to establish lines in the laboratory. The capture of males for comparison of the terminalia makes it hard to identify and delimit species; however, these difficulties can be overcome through the use of techniques such as searching for species in naturally occurring places, establishing isofemale lines in the laboratory, or using molecular techniques. In this work, we search for imagoes of species of the tripunctata group over present fallen flowers of the Lecythidaceae on the ground of the Amazon rainforest. The collected individuals were morphologically and molecularly analyzed. This species is described here under the binomial Drosophila lecythus sp. nov.

Urban evolution of thermal physiology in a range-expanding, mycophagous fruit fly, Drosophila tripunctata

In Drosophila spp., their often high number of annual generations, large population sizes and large amounts of standing genetic variation should predispose them to undergo contemporary adaptation to climatic warming. However, a number of laboratory experimental evolution studies in this group of organisms suggest strong limits on the rate and magnitude of contemporary thermal adaptation. Here, we explore this discrepancy by examining the potential for rapid evolutionary divergence between wild populations of Drosophila tripunctata Loew, 1862 from rural and urban sites. We performed a multi-generation common garden study and found evidence for the evolution of higher heat tolerance (critical thermal maximum) in flies from urban populations. We also detected evolutionary divergence in cold resistance (chill coma recovery time), with diminished cold resistance in flies from urban populations, although the effect was weaker than the shift in heat tolerance. Our study provides evidence of contemporary urban thermal adaptation, although the magnitude of phenotypic change lagged the magnitude of environmental temperature change across the urbanization gradient, suggesting potential limits on the evolution of urban thermal physiology.

DrosoPhyla: Resources for Drosophilid Phylogeny and Systematics

The vinegar fly Drosophila melanogaster is a pivotal model for invertebrate development, genetics, physiology, neuroscience, and disease. The whole family Drosophilidae, which contains over 4,400 species, offers a plethora of cases for comparative and evolutionary studies. Despite a long history of phylogenetic inference, many relationships remain unresolved among the genera, subgenera, and species groups in the Drosophilidae. To clarify these relationships, we first developed a set of new genomic markers and assembled a multilocus data set of 17 genes from 704 species of Drosophilidae. We then inferred a species tree with highly supported groups for this family. Additionally, we were able to determine the phylogenetic position of some previously unplaced species. These results establish a new framework for investigating the evolution of traits in fruit flies, as well as valuable resources for systematics.

Phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica (Diptera, Drosophilidae), with insights into the evolution of breeding sites usage

The Neotropical region harbors an astonishing diversity of species, but still encompasses the least studied biogeographic region of the world. These properties apply for different taxonomic groups, and can be exemplified by drosophilids. In fact, high levels of cryptic diversity have recently been discovered for Neotropical species of the Zygothrica genus group, but relationships among these species, or them and other Drosophilidae species still remains to be addressed. Therefore, the aim of this study was to evaluate the phylogenetic relationships between fungus-associated Neotropical species of the genera Hirtodrosophila, Mycodrosophila and Zygothrica, which together with Paramycodrosophila and Paraliodrosophila compose the Zygothrica genus group. For this, fragments of the mitochondrial cytochrome oxidase subunits I (COI) and II (COII) genes, and the nuclear alpha methyldopa (Amd) and dopa decarboxylase (Ddc) genes were newly characterized for 43 Neotropical specimens of fungus-associated drosophilids, and analyzed in the context of 51 additional Drosophilinae sequences plus one Steganinae outgroup. Based on the resulting phylogeny, the evolution of breeding sites usage was also evaluated through ancestral character reconstructions. Our results revealed the Zygothrica genus group as a monophyletic lineage of Drosophila that branches after the subgenera Sophophora and Drosophila. Within this lineage, Mycodrosophila species seem to encompass the early offshoot, followed by a grade of Hirtodrosophila species, with derived branches mostly occupied by representatives of Zygothrica. This genus, in particular, was subdivided into five major clades, two of which include species of Hirtodrosophila, whose generic status needs to be reevatuated. According to our results, the use of fungi as breeding sites encompasses a symplesiomorphy for the Zygothrica genus group, since one of the recovered clades is currently specialized in using flowers as breeding sites whereas a sole species presents a reversal to the use of fruits of a plant of Gentianales. So, in general, this study supports the paraphyly of Drosophila in relation to fungus-associated Neotropical species of Drosophilidae, providing the first molecular insights into the phylogenetic patterns related to the evolution of this diverse group of species and some of its characteristic traits.

Evolutionary history and classification of Micropia retroelements in Drosophilidae species

Transposable elements (TEs) have the main role in shaping the evolution of genomes and host species, contributing to the creation of new genes and promoting rearrangements frequently associated with new regulatory networks. Support for these hypotheses frequently results from studies with model species, and Drosophila provides a great model organism to the study of TEs. Micropia belongs to the Ty3/Gypsy group of long terminal repeats (LTR) retroelements and comprises one of the least studied Drosophila transposable elements. In this study, we assessed the evolutionary history of Micropia within Drosophilidae, while trying to assist in the classification of this TE. At first, we performed searches of Micropia presence in the genome of natural populations from several species. Then, based on searches within online genomic databases, we retrieved Micropia-like sequences from the genomes of distinct Drosophilidae species. We expanded the knowledge of Micropia distribution within Drosophila species. The Micropia retroelements we detected consist of an array of divergent sequences, which we subdivided into 20 subfamilies. Even so, a patchy distribution of Micropia sequences within the Drosophilidae phylogeny could be identified, with incongruences between the species phylogeny and the Micropia phylogeny. Comparing the pairwise synonymous distance (dS) values between Micropia and three host nuclear sequences, we found several cases of unexpectedly high levels of similarity between Micropia sequences in divergent species. All these findings provide a hypothesis to the evolution of Micropia within Drosophilidae, which include several events of vertical and horizontal transposon transmission, associated with ancestral polymorphisms and recurrent Micropia sequences diversification.

Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

In this study, Renschler et al. set out to analyze the impact of genomic rearrangements on genome topology using the Drosophila genus and X chromosome dosage compensation as a model. The authors developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. Their data provides unique insights into genome topology evolution. RA

Genome rearrangements that occur during evolution impose major challenges on regulatory mechanisms that rely on three-dimensional genome architecture. Here, we developed a scaffolding algorithm and generated chromosome-length assemblies from Hi-C data for studying genome topology in three distantly related Drosophila species. We observe extensive genome shuffling between these species with one synteny breakpoint after approximately every six genes. A/B compartments, a set of large gene-dense topologically associating domains (TADs), and spatial contacts between high-affinity sites (HAS) located on the X chromosome are maintained over 40 million years, indicating architectural conservation at various hierarchies. Evolutionary conserved genes cluster in the vicinity of HAS, while HAS locations appear evolutionarily flexible, thus uncoupling functional requirement of dosage compensation from individual positions on the linear X chromosome. Therefore, 3D architecture is preserved even in scenarios of thousands of rearrangements highlighting its relevance for essential processes such as dosage compensation of the X chromosome.

The conserved mitochondrial genomes of Drosophila mercatorum (Diptera: Drosophilidae) with different reproductive modes and phylogenetic implications

Fruit flies (Drosophilidae: Drosophila) are commonly found in daily life and have long been used as model organisms in biology researches. Drosophila mercatorum is one important member of the Drosophila genus and has been used to study centrosome assembly of cells. In this study, we sequenced and analyzed the mitochondrial genome (mitogenome) of D. mercatorum, finding that it contains the typical structure of 37 genes and a control region. The arrangement of mitochondrial genes is in accordance with that in other Drosophila species, which is considered the ancestral organization of insects' mitogenomes. Phylogenetic analyses were performed based on 23 species of Drosophila. Our results supported two monophyletic subgenera, Drosophila and Sophophora, except for D. willistoni which was presented as an early offshoot of Drosophila. The topology ((D. yakuba + D. erecta) + D. melanogaster) was supported. We further compared the mitogenomes of parthenogenesis and sexual reproduction strains of D. mercatorum. However, only one synonymous mutation in COI gene was identified, indicating mitogenomic evolution is not strongly correlated with the different reproductive modes of this species. Taken together, our results demonstrate that mitogenome is an effective molecular marker that can be further used in phylogenetic studies of Drosophila and other organisms.

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.

Phylogeography of the Subgenus Drosophila (Diptera: Drosophilidae): Evolutionary History of Faunal Divergence between the Old and the New Worlds

The current subgenus Drosophila (the traditional immigrans-tripunctata radiation) includes major elements of temperate drosophilid faunas in the northern hemisphere. Despite previous molecular phylogenetic analyses, the phylogeny of the subgenus Drosophila has not fully been resolved: the resulting trees have more or less varied in topology. One possible factor for such ambiguous results is taxon-sampling that has been biased towards New World species in previous studies. In this study, taxon sampling was balanced between Old and New World species, and phylogenetic relationships among 45 ingroup species selected from ten core species groups of the subgenus Drosophila were analyzed using nucleotide sequences of three nuclear and two mitochondrial genes. Based on the resulting phylogenetic tree, ancestral distributions and divergence times were estimated for each clade to test Throckmorton’s hypothesis that there was a primary, early-Oligocene disjunction of tropical faunas and a subsequent mid-Miocene disjunction of temperate faunas between the Old and the New Worlds that occurred in parallel in separate lineages of the Drosophilidae. Our results substantially support Throckmorton’s hypothesis of ancestral migrations via the Bering Land Bridge mainly from the Old to the New World, and subsequent vicariant divergence of descendants between the two Worlds occurred in parallel among different lineages of the subgenus Drosophila. However, our results also indicate that these events took place multiple times over a wider time range than Throckmorton proposed, from the late Oligocene to the Pliocene.

Demographic Structure and Evolutionary History of Drosophila ornatifrons (Diptera, Drosophilidae) from Atlantic Forest of Southern Brazil

Drosoph1la ornatifrons of the guarani group (Diptera: Drosophilidae) is found mainly in humid areas of the Atlantic Forest biome, especially in the southern region of Brazil. Historical and contemporary fragmentation events influenced species diversity and distribution in this biome, although the role of paleoclimatic and paleogeographic events remain to be verified. The objective of the present study was to evaluate the demographic structure of D. ornatifrons from collection sites that are remnants of Atlantic Forest in southern Brazil, in order to contribute to the understanding of the processes that affected the patterns of genetic variability in this species. To achieve this goal, we sequenced 51 individuals from nine localities and 64 individuals from six localities for the mitochondrial genes Cytochrome Oxidase I and II, respectively. Our results indicate that D. ornatifrons may have experienced a demographic expansion event from the southernmost locations of its distribution, most likely from those located next to the coast and in fragments of Atlantic Forest inserted in the Pampa biome (South 2 group), towards the interior (South 1 group). This expansion probably started after the last glacial maximum, between 20,000 and 18,000 years ago, and was intensified near the Pleistocene-Holocene transition, around 12,000 years ago, when temperature started to rise. In this work we discuss how the haplotypes found barriers to gene flow and dispersal, influenced by the biogeographic pattern of Atlantic Forest.

Rapid evolutionary turnover underlies conserved lncRNA-genome interactions

Many long noncoding RNAs (lncRNAs) can regulate chromatin states, but the evolutionary origin and dynamics driving lncRNA-genome interactions are unclear. We adapted an integrative strategy that identifies lncRNA orthologs in different species despite limited sequence similarity, which is applicable to mammalian and insect lncRNAs. Analysis of the roX lncRNAs, which are essential for dosage compensation of the single X chromosome in Drosophila males, revealed 47 new roX orthologs in diverse Drosophilid species across ∼40 million years of evolution. Genetic rescue by roX orthologs and engineered synthetic lncRNAs showed that altering the number of focal, repetitive RNA structures determines roX ortholog function. Genomic occupancy maps of roX RNAs in four species revealed conserved targeting of X chromosome neighborhoods but rapid turnover of individual binding sites. Many new roX-binding sites evolved from DNA encoding a pre-existing RNA splicing signal, effectively linking dosage compensation to transcribed genes. Thus, dynamic change in lncRNAs and their genomic targets underlies conserved and essential lncRNA-genome interactions.

The Drosophila flavopilosa species group (Diptera, Drosophilidae): an array of exciting questions

The D. flavopilosa group encompasses an ecologically restricted set of species strictly adapted to hosting flowers of Cestrum (Solanaceae). This group presents potential to be used as a model to the study of different questions regarding ecologically restricted species macro and microevolutionary responses, geographical vs. ecological speciation and intra and interspecific competition. This review aims to revisit and reanalyze the patterns and processes that are subjacent to the interesting ecological and evolutionary properties of these species. Biotic and abiotic niche properties of some species were reanalyzed in face of ecological niche modeling approaches in order to get some insights into their ecological evolution. A test of the potential of DNA-Barcoding provided evidences that this technology may be a way of overcoming difficulties related to cryptic species differentiation. The new focus replenishes the scenario with new questions, presenting a case where neither geographical nor ecological speciation may be as yet suggested.

The evolutionary history of mariner-like elements in Neotropical drosophilids

The evolutionary history of mariner-like elements (MLEs) in 49 mainly Neotropical drosophilid species is described. So far, the investigations about the distribution of MLEs were performed mainly using hybridization assays with the Mos1 element (the first mariner active element described) in a widely range of drosophilid species and these sequences were found principally in species that arose in Afrotropical and Sino-Indian regions. Our analysis in mainly Neotropical drosophilid species shows that twenty-three species presented MLEs from three different subfamilies in their genomes: eighteen species had MLEs from subfamily mellifera, fifteen from subfamily mauritiana and three from subfamily irritans. Eleven of these species exhibited elements from more than one subfamily in their genome. In two subfamilies, the analyzed coding region was uninterrupted and contained conserved catalytic motifs. This suggests that these sequences were probably derived from active elements. The species with these putative active elements are Drosophila mediopunctata and D. busckii for the mauritiana subfamily, and D. paramediostriata for the mellifera subfamily. The phylogenetic analysis of MLE, shows a complex evolutionary pattern, exhibiting vertical transfer, stochastic loss and putative events of horizontal transmission occurring between different Drosophilidae species, and even those belonging to more distantly related taxa such as Bactrocera tryoni (Tephritidae family), Sphyracephala europaea (Diopsoidea superfamily) and Buenoa sp. (Hemiptera order). Moreover, our data show that the distribution of MLEs is not restricted to Afrotropical and Sino-Indian species. Conversely, these TEs are also widely distributed in drosophilid species arisen in the Neotropical region.