Maternally transmitted Wolbachia, Spiroplasma, and Cardinium bacteria are common in insects [1], but their interspecific spread is poorly understood. Endosymbionts can spread rapidly within host species by manipulating host reproduction, as typified by the global spread of wRi Wolbachia observed in Drosophila simulans [2, 3]. However, because Wolbachia cannot survive outside host cells, spread between distantly related host species requires horizontal transfers that are presumably rare [4-7]. Here, we document spread of wRi-like Wolbachia among eight highly diverged Drosophila hosts (10-50 million years) over only about 14,000 years (5,000-27,000). Comparing 110 wRi-like genomes, we find ≤0.02% divergence from the wRi variant that spread rapidly through California populations of D. simulans. The hosts include both globally invasive species (D. simulans, D. suzukii, and D. ananassae) and narrowly distributed Australian endemics (D. anomalata and D. pandora) [8]. Phylogenetic analyses that include mtDNA genomes indicate introgressive transfer of wRi-like Wolbachia between closely related species D. ananassae, D. anomalata, and D. pandora but no horizontal transmission within species. Our analyses suggest D. ananassae as the Wolbachia source for the recent wRi invasion of D. simulans and D. suzukii as the source of Wolbachia in its sister species D. subpulchrella. Although six of these wRi-like variants cause strong cytoplasmic incompatibility, two cause no detectable reproductive effects, indicating that pervasive mutualistic effects [9, 10] complement the reproductive manipulations for which Wolbachia are best known. "Super spreader" variants like wRi may be particularly useful for controlling insect pests and vector-borne diseases with Wolbachia transinfections [11].

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.

Background: Species of the Drosophila obscura species group (e.g., D. pseudoobscura, D. subobscura) have served as favorable models in evolutionary studies since the 1930's. Despite numbers of studies conducted with varied types of data, the basal phylogeny in this group is still controversial, presumably owing to not only the hypothetical 'rapid radiation' history of this group, but also limited taxon sampling from the Old World (esp. the Oriental and Afrotropical regions). Here we reconstruct the phylogeny of this group by using sequence data from 6 loci of 21 species (including 16 Old World ones) covering all the 6 subgroups of this group, estimate the divergence times among lineages, and statistically test the 'rapid radiation' hypothesis.

The phylogeny of Colocasiomyia (Drosophilidae) is analysed using data for 70 morphological characters, many of which are re‐evaluated from or added to those used previously, for an expanded taxon sample of 24 Colocasiomyia ingroup species. A special focus is put on three species, of which two have remained unresolved for their relationships to other Colocasiomyia species, and the other is a newly discovered species. The analysis results in a single, most parsimonious cladogram, in which a clade comprising the three focal species is recognized along with other clades recovered for the known species groups of Colocasiomyia. Based on this, a new species group—the gigantea group—is established, including Colocasiomyia gigantea (Okada), C. rhaphidophorae Gao & Toda, n.sp. and C. scindapsae Fartyal & Toda, n.sp. These species of the gigantea group breed on inflorescences/infructescences of the subfamily Monsteroideae (Araceae) exceptionally among Colocasiomyia species, most of which use plants of the subfamily Aroideae as their hosts. Colocasiomyia gigantea uses Epipremnum pinnatum (L.) Engler, C. rhaphidophorae uses Rhaphidophora hookeri Schott and C. scindapsae uses Scindapsus coriaceus Engler as their hosts. The host plants of the gigantea group are epiphytes and differ in the structure of spadix and the fruiting process from those of the Aroideae. To understand how the species of the gigantea group adapt to properties of their host plants, their reproductive ecology—most intensively that of C. gigantea—is investigated. The lifecycle of C. gigantea is characterized by its relatively slow embryonic development (taking approximately 6 days), the very long duration of the full‐grown first instar within the egg capsule (approximately three months) until dehiscence of host infructescence, and its relatively fast larval and pupal development (taking approximately 11 or 12 days). Some morphological adaptations and the reproductive strategy in terms of ‘egg size vs. number’ trade‐off are discussed in relation to their reproductive habits and peculiar lifecycles.

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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 generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of high-quality assemblies for 101 lines of 95 drosophilid species encompassing 14 species groups and 35 sub-groups with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. These assemblies, along with detailed wet lab 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 within this key group.

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