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Animal evolution is characterized by frequent turnover of sexually dimorphic traits – new sex- specific characters are gained, and some ancestral sex-specific characters are lost, in many lineages. In insects, sexual differentiation is predominantly cell-autonomous and depends on the expression of the doublesex (dsx) transcription factor. In most cases, cells that transcribe dsx have the potential to undergo sex-specific differentiation, while those that lack dsx expression do not. Consistent with this mode of development, comparative research has shown that the origin of new sex-specific traits can be associated with the origin of new spatial domains of dsx expression. In this report, we examine the opposite situation – a secondary loss of the sex comb, a male-specific grasping structure that develops on the front legs of some drosophilid species. We show that, while the origin of the sex comb is linked to an evolutionary gain of dsx expression in the leg, sex comb loss in a newly identified species of Lordiphosa (Drosophilidae) is associated with a secondary loss of dsx expression. We discuss how the developmental control of sexual dimorphism affects the mechanisms by which sex-specific traits can evolve.

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.

Despite numerous phylogenetic studies on the family Drosophilidae, relationships among some important lineages are still poorly resolved. An example is the equivocal position of the Zygothrica genus group that is mostly comprised of the mycophagous genera Hirtodrosophila, Mycodrosophila, Paramycodrosophila, and Zygothrica. To fill this gap, we conducted a phylogenetic analysis by assembling a dataset of 24 genes from 92 species, including 42 species of the Zygothrica genus group mainly from the Palearctic and Oriental regions. The resulting tree shows that the Zygothrica genus group is monophyletic and places it as the sister to the genus Dichaetophora, and the clade Zygothrica genus group + Dichaetophora is sister to the Siphlodora + Idiomyia/Scaptomyza clade. Within the Zygothrica genus group, the genera Mycodrosophila and Paramycodrosophila are both recognized as monophyletic, while neither the genus Zygothrica nor Hirtodrosophila is monophyletic. We also used this phylogenetic tree to investigate the evolution of mycophagy by reconstructing ancestral food habit in the Drosophilidae. We found that fungus-feeding habit has been gained independently in two lineages. The most recent common ancestor (MRCA) of the subgenus Drosophila was estimated to have acquired mycophagy by expanding its ancestral feeding niche on fermenting fruits to decayed fungi, while the MRCA of the Zygothrica genus group shifted its niche from fruits to fungi as a specialist probably preferring fresh fruiting bodies.

Drosophila prolongata, a member of the rhopaloa subgroup of the melanogaster species group, occurs in Southeast Asia. Drosophila prolongata is known to have unique and prominent sexual dimorphism, with extraordinarily thick and elongated forelegs only in males. Mating behavior of D. prolongata is also characteristic: males perform “leg vibration” in their courtship toward females, in which the elongated forelegs play an important role. Comparisons with closely related species suggest that these morphological and behavioral traits have evolved rapidly after the divergence of D. prolongata. In the present study, variation in morphological and behavioral traits was examined among D. prolongata strains derived from single females collected in their natural habitats. Significant variations were detected in the size of various body parts, aggressiveness of interactions between males, and mating behavior. However, no obvious relationship was observed between morphological and behavioral traits. These results suggested that genetic factors contribute to the variation in morphological and behavioral traits in D. prolongata. The strains characterized in this study are useful for studies on the genetic mechanisms underlying the evolution of characteristic traits in D. prolongata.

A new species of the Drosophila (Drosophila) melanica species group (Diptera: Drosophilidae), Drosophila denruoi Suwito & Watabe, sp. nov., is described from northern Vietnam. It is proved by crossing experiments that reproductive isolation is complete between this species and other morphologically similar species. Larval ganglion cells of D. denruoi possess 2n = 12 chromosomes, comprised of four pairs of acrocentric, one pair of metacentric and one pair of micro-chromosomes. This is the largest number of acrocentric chromosomes in the group and implies that the species has the most primitive chromosomal configuration in the melanica group. Based on the results of crossing experiments and close morphological examination, Drosophila pengi Okada & Kurokawa, 1957 from central Japan, once regarded as a synonym of Drosophila tsigana Burla & Gloor, 1952, is shown to be distinct from D. tsigana. Drosophila pengi is thus resurrected as a member of the melanica group. We synonymize Drosophila bisetata Toda, 1988, described from central Myanmar, with D. pengi. In addition, a population from Guizhou, southwestern China, once regarded as D. tsigana, is also identified as D. pengi. These populations from central Myanmar and southwestern China share the diagnostic characters of D. pengi. At the same time, it is reconfirmed that the Hokkaido population is conspecific with European D. tsigana. Furthermore, another species, Drosophila longiserrata Toda, 1988 described from central Myanmar, is synonymized with Drosophila afer Tan, Hsu & Sheng, 1949 from China, based on their having identical karyotypes and external morphology.

A review of the Drosophila (Drosophila) quadrisetata species group is provided on the basis of samples collected from tropical to warm–temperate areas of the Oriental Region and the collection records so far accumulated for all known species. Three new species, D. (D.) aotsukai Suwito & Watabe sp. nov., D. (D.) rinjaniensis Suwito & Watabe sp. nov. and D. (D.) sundaensis Suwito & Watabe sp. nov., are described, and new distribution records and supplementary, revised descriptions are given for known species. A multiple-entry key, based on a character database, to all species of this species group is constructed and uploaded to the Internet.

On macroevolutionary time scales, the same genes can regulate the development of homologous structures through strikingly different cellular processes. Comparing the development of similar morphological traits in closely related species may help elucidate the evolutionary dissociation between pattern formation and morphogenesis. We address this question by focusing on the interspecific differences in sex comb development in Drosophilids. The sex comb is a recently evolved, male-specific structure composed of modified bristles. Previous work in the obscura and melanogaster species groups (Old World Sophophora) has identified two distinct cellular mechanisms that give rise to nearly identical adult morphologies. Here, we describe sex comb development in a species from a more distantly related lineage, the genus Lordiphosa. Although the expression of key regulatory genes is largely conserved in both clades, the cell behaviors responsible for sex comb formation show major differences between Old World Sophophora and Lordiphosa. We suggest that the many-to-one mapping between development and adult phenotype increases the potential for evolutionary innovations.

Phylogenetic relationships of 26 Phortica species were investigated based on DNA sequence data of two mitochondrial (ND2, COI) and one nuclear (28S rRNA) genes. Five monophyletic groups were recovered in the genus Phortica, of which three were established as new subgenera, Alloparadisa, Ashima, and Shangrila. The subgenus Allophortica was suggested as the most basal lineage in Phortica, followed by the lineage of P. helva + P. sobodo + P. varipes. The remaining Phortica species, most of Oriental distribution, formed a monophyletic group, and were subdivided into three lineages (i.e., the subgenera Ashima, Phortica, and Shangrila). The subgenera Shangrila and Phortica were suggested as sister taxa, and four clades were recovered in the subgenus Ashima. The result of reconstruction of ancestral distribution and estimation of divergence times indicates that, the ancestor of the genus Phortica restricted to Africa, its initial diversification was dated back to ca. 23 Mya (coinciding with the Oligocene/Miocene boundary); sympatric speciation and an Africa-to-Asia dispersal was proposed to account for the current distribution of Allophortica and the rest Phortica; most of the rest diversification of Phortica occurred in southern China, and the divergence between the African clade and its Oriental counterpart was suggested as a result of vicariance following a dispersal of their ancestral species from southern China to Africa.

Six new species of the Drosophila robusta species group are described from Southeast Asian Islands. Kalimantan and Sunda Islands lie east of Bali, from which Drosophila barobusta sp.nov and D. uncinata sp.nov belong to the lacertosa subgroup, and D. sungaicola sp.nov, D. baliensis sp.nov, D. hitam sp.nov and D. subaquatica sp.nov to the okadai subgroup. The robusta group from Southeast Asian tropics exclusively inhabits streamsides in mountainous highlands with an elevation of more than 600 m from the sea level.

A new subgenus Allstegana is established within the genus Parastegana, including two known and two new species from southern China: P. (A.) maculipennis (Okada, 1971), P. (A.) drosophiloides (Toda and Peng, 1992), P. (A.) brevivena Chen and Zhang, sp. nov., and P. (A.) punctalata Chen and Watabe, sp. nov. A key to all known species of Parastegana is provided.

Karyotypes and reproductive isolation were studied in two allopatric populations of Drosophila tsigana, one from Guizhou Province in southern China and the other from Hokkaido in northern Japan, and in one population of a closely related species, D. longiserrata, from Guizhou. In metaphase plates of larval brain cells, both geographic strains of Drosophila tsigana showed 2n=10 chromosomes, with 2 pairs of metacentric (V-shape), 2 pairs of acrocentric (R-shape), and 1 pair of dot-liked (D-shape) chromosomes. Drosophila longiserrata showed the same number, 10 chromosomes, comprising 2V, 1J (sub-metacentric chromosome), 1R, and 1D. X chromosomes of both species were acrocentric, the presumed ancestral form. Premating isolation was complete between D. tsigana and D. longiserrata, and successful mating was also limited in crosses between the two geographic populations of D. tsigana, especially in crosses between Japanese (JP) females and Guizhou (GZ) males. F1 hybrids were obtained only from crosses between GZ females and JP males, and fertilities of both F1 females and males were quite incomplete. The results of morphological observations, karyotypic analyses, and crossing experiments clearly showed that the GZ and JP populations of "D. tsigana" were highly divergent from each other and that each population should be recognized as a biologically valid species. The present morphological observations and chromosomal analyses, together with the original descriptions, strongly suggest that "Guizhou D. tsigana" might be conspecific with D. bisetata Toda, 1988 from Myanmar, and that D. longiserrata might be conspecific with D. afer Tan, Hsu, and Sheng, 1949 from Meitan, Guizhou.

Regardless of the well-documented virilis species group, most groups of the Drosophila virilis section have not been completely studied at molecular level since it was suggested. Therefore, phylogenetic relationships among and within species groups of the virilis section are generally unknown. In present paper, the complete mitochondrial ND2 gene and fragment of COI gene in combination with a nuclear gene, Adh coding region, were used to derive the most extensive molecular phylogeny to date for the Drosophila virilis section. A total of 111 individuals covering 61 species were sampled in this study. Novel phylogenetic findings included (1) support for the paraphyly of the melanica and robusta species group and at least two subgroups of the robusta species group, the lacertosa and okadai subgroups, were distinguished as paraphyletic taxa. In addition, (2) present results revealed the sister relationship between D. moriwakii and the robusta subgroup, conflicting with current taxonomy regarding D. moriwakii, which was shifted from the robusta species group to the melanica group. (3) In contrast to the robusta and melanica species groups, monophyly of the polychaeta species group, the angor group and the virilis group was confirmed, respectively. However, the monophyletic quadrisetata species group was resolved with uncertainty. (4) Our analyses of combined data set suggested close relationship between the quadrisetata species group and the unpublished clefta group, and the okadai subgroup is sister to the clade comprising of the quadrisetata and clefta species groups. Within the virilis section, D. fluvialis and three tropical species groups, the polychaeta group, the angor group and the repleta group, are found to branch off earlier than other ingroup taxa. This suggests that the virilis section might have originated in the Old World tropics. Besides, the derived status of the close affinities of the quadrisetata group, the clefta group, and the melanica and robusta groups is probably the result of their adaptation to forests between subtropical and cool-temperate climate. Based on the consideration of the phylogenetic placement of the species of the virilis section, we suggest that at least five independent migrations occurred from the Old World to the New World.

Drosophila (Sophophora) subpulchrella Takamori and Watabe, sp. nov., of the D. suzukii subgroup in the D. melanogaster species group, is described from Japan and southern China, and compared with its sibling species, D. pulchrella Tan et al. distributed i

A total of 38 Amiota (s. str.) species (about 40% of the world total) are reported from southern China, with descriptions of 23 new species, i.e. sinuata species-group: aculeata Chen and Aotsuka, sp. nov., subsinuata Chen and Aotsuka, sp. nov., xishuangbanna Chen and Aotsuka, sp. nov.; basdeni speciesgroup: brevipartita Chen and Gao, sp. nov., curvispina Chen and Gao, sp. nov., lipingae Chen and Gao, sp. nov., huae Chen and Gao, sp. nov., longispina Chen and Gao, sp. nov.; taurusata speciesgroup: asymmetrica Chen and Takamori, sp. nov.; femorata Chen and Takamori, sp. nov., yixiangensis Chen and Takamori, sp. nov.; alboguttata species-group: ailaoshanensis Chen and Watabe, sp. nov., arcuata Chen and Watabe, sp. nov., dehiscentia Chen and Watabe, sp. nov., jizushanensis Chen and Watabe, sp. nov., latitabula Chen and Watabe, sp. nov., luguhuensis Chen and Watabe, sp. nov., nozawai Chen and Watabe, sp. nov., paraspinata Chen and Watabe, sp. nov., shangrila Chen and Watabe, sp. nov.; and ungrouped: fuscicata Chen and Zhang, sp. nov., wangi Chen and Zhang, sp. nov., wuyishanensis Chen and Zhang, sp. nov. A key to all species from southern China is provided. The Amiota fauna of southern China at the species-group level is compared with that of six geographic regions. The subgenus Amiota is assumed to have originated and produced many species-groups in the Oriental region of East Asia, and then the basdeni, alboguttata and rufescens species-groups might have spread to Europe and North–Central America throughout the Palearctic region of East Asia and both the apodemata, sinuata and nagatai species-groups to tropical regions of South-East Asia.

Three new and two known species of the Drosophila (Sophophora) obscura species-group are reported from Yunnan Province, southern China. The sinobscura species-subgroup is newly established by D. sinobscura, D. hubeiensis and D. luguensis sp. nov. Geographic distribution of the obscura group in and around China is discussed, and a key to 10 Chinese species of the obscura group is provided.

The karyotypes of the Drosophila robusta species-group, especially its species-subgroup okadai, were studied by using brain cell-Giemsa staining method. Drosophila gani possessed a diploid number of 12 chromosomes, comprising 4 pairs of metacentric, 2 pairs of acrocentric chromosomes, and both D. okadai and D. neokadai did 2n = 12, with 3 pairs of metacentrics, 2 pairs of acrocentrics and 1 pair of microchromosomes. The okadai subgroup characteristically retained a middle-sized acrocentric X chromosome, which implies that this subgroup may occupy an ancestral position for the robusta group.

Compiling all the previous and new records, the most recent list of drosophilid species from East Siberia (56 spp.) and Russian Far East (120 spp.) is provided along with descriptions of five new species, supplementary descriptions of two known species, some nomenclatural changes (five new synonymies, a new homonymy, and a change in status of a taxon from the specific to the subspecific rank), and a key to all the species. Drosophilid faunas of these two regions are compared with those of surrounding six regions in the Northern Hemisphere. Russian Far East constitutes the northeastern Asiatic realm in drosophilid biogeography together with northeastern China and Hokkaido, northern Japan. On the other hand, East Siberia belongs to the northern Palearctic realm extending to northern Europe. The border between these two biogeographic realms lies on the Stanovoy Mts.

On macroevolutionary time scales, the same genes can regulate the development of homologous structures through strikingly different cellular processes. Comparing the development of similar morphological traits in closely related species may help elucidate the evolutionary dissociation between pattern formation and morphogenesis. We address this question by focusing on the interspecific differences in sex comb development in Drosophilids. The sex comb is a recently evolved, male-specific structure composed of modified bristles. Previous work in the obscura and melanogaster species groups (Old World Sophophora) has identified two distinct cellular mechanisms that give rise to nearly identical adult morphologies. Here, we describe sex comb development in a species from a more distantly related lineage, the genus Lordiphosa. Although the expression of key regulatory genes is largely conserved in both clades, the cell behaviors responsible for sex comb formation show major differences between Old World Sophophora and Lordiphosa. We suggest that the many-to-one mapping between development and adult phenotype increases the potential for evolutionary innovations.

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. Results Phylogenetic analyses indicate that each of the subobscura, sinobscura, affinis, and pseudoobscura subgroups is monophyletic. The subobscura and microlabis subgroups form the basal clade in the obscura group. Partial species of the obscura subgroup (the D. ambigua/D. obscura/D. tristis triad plus the D. subsilvestris/D. dianensis pair) forms a monophyletic group which appears to be most closely related to the sinobscura subgroup. The remaining basal relationships in the obscura group are not resolved by the present study. Divergence times on a ML tree based on mtDNA data are estimated with a calibration of 30–35 Mya for the divergence between the obscura and melanogaster groups. The result suggests that at least half of the current major lineages of the obscura group originated by the mid-Miocene time (~15 Mya), a time of the last developing and fragmentation of the temperate forest in North Hemisphere. Conclusion The obscura group began to diversify rapidly before invading into the New World. The subobscura and microlabis subgroups form the basal clade in this group. The obscura subgroup is paraphyletic. Partial members of this subgroup (D. ambigua, D. obscura, D. tristis, D. subsilvestris, and D. dianensis) form a monophyletic group which appears to be most closely related to the sinobscura subgroup.

Drosophila lacertosa, an Oriental member of the robusta species group in the virilis-repleta radiation, has a wide distribution from northern India throughout China to the Far East. Phylogenetic analyses of mitochondrial ND2 gene sequences revealed two genetically significantly diverged lineages with 2.1% DNA sequence divergence. These two lineages are largely allopatric: one is mainly found in southwest China (lineage A), whereas the other ranges central and east of China to northeast Asia (lineage B). The geographic distributions of these two clades narrowly overlap near the provincial boundaries of Yunnan and Guizhou or Guangxi, probably as a consequence of population expansion and secondary contact. These two lineages were estimated to have diverged about 0.56 Mya, and the estimated time of expansion was approximately 70,000 years ago for lineage A population, and 110,000 years ago for lineage B population. The present molecular analysis, together with nearly complete reproductive isolation between those two lineages, strongly suggests that the two lineages might be incipient species.

Interspecific crossability between Drosophila kanekoi and other members of the D. virilis group was studied by using no choice and female choice methods. Asymmetric mating preference was observed in every cross. Females of D. kanekoi more frequently mated to males of D. virilis, D. lummei and of D. montana montana than in the reciprocal crosses. A complete sexual isolation was found between two sympatric species, D. kanekoi and D. ezoana.