Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.

Colocasiomyia, a moderate‐sized genus in the subfamily Drosophilinae, comprises seventy (twenty‐six described and forty‐four undescribed) species. Several Colocasiomyia species have evolved intimate mutualisms with specific host plants, especially of the family Araceae: the flies depend throughout the entire life cycle, oviposition, larval growth, pupation, and adult feeding and mating, on inflorescences of their host plants, and in turn act as species‐specific pollinators for their host plants. To understand the evolution of this mutualism between Colocasiomyia flies and their host plants, the phylogenetic relationships of this genus and some possibly related taxa are inferred from a cladistic analysis based on sixty‐two characters of adult morphology. We conclude that Colocasiomyia is polyphyletic, with the C. arenga species group clearly separate. Colocasiomyia without the arenga group (Colocasiomyia proper) is sister to all other studied drosophilines, whereas the arenga group is relatively derived within the Drosophilinae. Within Colocasiomyia proper, four clades are recognized, three of which correspond to previously proposed species groups: the cristata, toshiokai and baechlii groups. The other clade, C. sp.1 aff. nepalensis+C. sp.2 aff. nepalensis, is defined as a new species group. Relationships amongst the four clades and three independent species (C. micheliae, C. gigantea and C. sp.K1) remain almost unresolved, except for a sister group relationship between the toshiokai and baechlii groups. The classification of species groups in Colocasiomyia is revised by erecting two new species groups (crassipes and zeylanica groups) in addition to the three known (baechlii, cristata and toshiokai) groups. Revision of the arenga group, which should be removed from Colocasiomyia, is left for future studies. The evolution of host plant selection in Colocasiomyia is discussed by mapping host plant taxa (families, subfamilies and tribes) on the phylogenetic tree deduced from the cladistic analysis. Cohabitation in the same host inflorescence by a pair of species with microallopatric niche separation on the spadix is hypothesized to have evolved independently at least more than twice in Colocasiomyia.

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Summary The phylogenetic relationships of Lordiphosa and some taxa in Drosophilinae were analysed on the basis of a total of forty‐one selected drosophilid species. These included eighteen species of five Lordiphosa species‐groups as the main target, twenty‐three species representative of the major drosophiline ingroup taxa and four species of Steganinae as outgroup. Sixty‐eight morphological characters of adults were subjected to cladistic analysis. From the results it is concluded that Lordiphosa is polyphyletic; the Lo. tenuicauda species‐group and genus Nesiodrosophila form a single monophyletic group; Lordiphosa proper (i.e. Lordiphosa spp. minus the tenuicauda group) comprises another monophyletic group; within Lordiphosa proper the fenestrarum, nigricolor and denticeps groups are all monophyletic, but monophyly of the miki group is not strongly supported; genera Hirtodrosophila and Scaptomyza and subgenus Sophophora are all monophyletic; and within Drosophilinae, genus Scaptodrosophila is the first to have split from the main lineage, but the branching order of other clades, Chymomyza, Lordiphosa proper, Sophophora, Hirtodrosophila, Nesiodrosophila+ Lo. tenuicauda group, Scaptomyza, Dorsilopha and subgenus Drosophila, remains unresolved. The topology of maximum parsimony cladograms suggests that Lordiphosa proper lies close to Sophophora as proposed previously, although its phylogenetic position could not be determined conclusively. By contrast, bootstrap values tended to contradict another hypothesis that Lordiphosa and Scaptomyza are sister groups.