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 dataset 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.

23Changes in cis-regulatory modules (CRMs) that control developmental gene expression 24 patterns have been implicated in the evolution of animal morphology 1-6 . However, the 25 genetic mechanisms underlying complex morphological traits remain largely unknown. 26 Here we investigated the molecular mechanisms that induce the pigmentation gene yellow 27 (y) in a complex spot and shade pattern on the abdomen of the quinaria group species 28 Drosophila guttifera. We show that the y expression pattern is controlled by only one CRM, 29 which contains a stripe-inducing CRM at its core. We identified several developmental 30 genes that may collectively interact with the CRM to orchestrate the patterning in the 31 pupal abdomen of D. guttifera. We further show that the core CRM is conserved among D. 32 guttifera and the closely related quinaria group species Drosophila deflecta, which displays 33 a similarly spotted abdominal pigment pattern. Our data suggest that besides direct 34 activation of patterns in distinct spots, abdominal spot patterns in Drosophila species may 35 have evolved through partial repression of an ancestral stripe pattern, leaving isolated 36 spots behind. Abdominal pigment patterns of extant quinaria group species support the 37 partial repression hypothesis and further emphasize the modularity of the D. guttifera 38 pattern. 39 40 How complex morphological features develop and evolve is a question of foremost importance 41 in biology. To address this question, we identified genes underlying abdominal pigmentation 42 pattern development in Drosophila guttifera (D. guttifera). The abdomen is decorated with six 43 rows of black spots that run along the anterior-posterior axis, divided by a dark dorsal midline 44shade. This color pattern shows four sub-patterns: a dorsal, median, and lateral pair of spot rows, 45 plus the dorsal midline shade (Fig. 1a, b). D. guttifera belongs to the quinaria species group, 46 whose members display highly diverse abdominal pigmentation patterns 7,8 . While D. guttifera 47 dorsal midline (Extended Data Fig. 2c). Similarly, wg foreshadowed all six rows of spots, while 126 dpp expression matched all but the lateral spot rows (Extended Data Fig. 3b, c). In contrast to the 127 D. guttifera results, abd-A, hh, and zen were absent along the dorsal midline, which is in 128 agreement with the lack of pigment in D. deflecta adults (Extended Data Fig. 3d, e, f, g). 129However, abd-A expression was not detectable where the lateral spot rows will form (Extended 130 Data Fig. 3d), suggesting that these particular spots are controlled differently in D. deflecta. We 131 next cloned the 938 bp orthologous def y spot CRM and transformed it into D. guttifera, using 132 the DsRed reporter assay. The def y spot CRM drove faint dorsal spot row and stripe expression, 133 especially along the dorsal spots (Extended Data Fig. 4). We further subdivided the def y spot 134 CRM into 8 sub-fragments and identified a minimal def y core stripe CRM (288 bp) (#7, 135 Extended Data Fig. 4). This...

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The adult Drosophila eye is a powerful model system for phototransduction and neurodegeneration research. However, single cell resolution transcriptomic data are lacking for this tissue. We present single cell RNA-seq data on 1-day male and female, 3-day and 7-day old male adult eyes, covering early to mature adult eyes. All major cell types, including photoreceptors, cone and pigment cells in the adult eye were captured and identified. Our data sets identified novel cell type specific marker genes, some of which were validated in vivo. R7 and R8 photoreceptors form clusters that reflect their specific Rhodopsin expression and the specific Rhodopsin expression by each R7 and R8 cluster is the major determinant to their clustering. The transcriptomic data presented in this report will facilitate a deeper mechanistic understanding of the adult fly eye as a model system.

Novel species of fungi described in this study include those from various countries as follows: Argentina, Colletotrichum araujiae on leaves, stems and fruits of Araujia hortorum. Australia, Agaricus pateritonsus on soil, Curvularia fraserae on dying leaf of Bothriochloa insculpta, Curvularia millisiae from yellowing leaf tips of Cyperus aromaticus, Marasmius brunneolorobustus on well-rotted wood, Nigrospora cooperae from necrotic leaf of Heteropogon contortus, Penicillium tealii from the body of a dead spider, Pseudocercospora robertsiorum from leaf spots of Senna tora, Talaromyces atkinsoniae from gills of Marasmius crinis-equi and Zasmidium pearceae from leaf spots of Smilax glyciphylla. Brazil, Preussia bezerrensis from air. Chile, Paraconiothyrium kelleni from the rhizosphere of Fragaria chiloensis subsp. chiloensis f. chiloensis. Finland, Inocybe udicola on soil in mixed forest with Betula pendula, Populus tremula, Picea abies and Alnus incana. France, Myrmecridium normannianum on dead culm of unidentified Poaceae. Germany, Vexillomyces fraxinicola from symptomless stem wood of Fraxinus excelsior. India, Diaporthe limoniae on infected fruit of Limonia acidissima, Didymella naikii on leaves of Cajanus cajan, and Fulvifomes mangroviensis on basal trunk of Aegiceras corniculatum. Indonesia, Penicillium ezekielii from Zea mays kernels. Namibia, Neocamarosporium calicoremae and Neocladosporium calicoremae on stems of Calicorema capitata, and Pleiochaeta adenolobi on symptomatic leaves of Adenolobus pechuelii. Netherlands, Chalara pteridii on stems of Pteridium aquilinum, Neomackenziella juncicola (incl. Neomackenziella gen. nov.) and Sporidesmiella junci from dead culms of Juncus effusus. Pakistan, Inocybe longistipitata on soil in a Quercus forest. Poland, Phytophthora viadrina from rhizosphere soil of Quercus robur, and Septoria krystynae on leaf spots of Viscum album. Portugal (Azores), Acrogenospora stellata on dead wood or bark. South Africa, Phyllactinia greyiae on leaves of Greyia sutherlandii and Punctelia anae on bark of Vachellia karroo. Spain, Anteaglonium lusitanicum on decaying wood of Prunus lusitanica subsp. lusitanica, Hawksworthiomyces riparius from fluvial sediments, Lophiostoma carabassense endophytic in roots of Limbarda crithmoides, and Tuber mohedanoi from calcareus soils. Spain (Canary Islands), Mycena laurisilvae on stumps and woody debris. Sweden, Elaphomyces geminus from soil under Quercus robur. Thailand, Lactifluus chiangraiensis on soil under Pinus merkusii, Lactifluus nakhonphanomensis and Xerocomus sisongkhramensis on soil under Dipterocarpus trees. Ukraine, Valsonectria robiniae on dead twigs of Robinia hispida. USA, Spiralomyces americanus (incl. Spiralomyces gen. nov.) from office air. Morphological and culture characteristics are supported by DNA barcodes.