Genetic Changes to a Transcriptional Silencer Element Confers Phenotypic Diversity within and between Drosophila Species

The modification of transcriptional regulation has become increasingly appreciated as a major contributor to morphological evolution. However, the role of negative-acting control elements (e.g. silencers) in generating morphological diversity has been generally overlooked relative to positive-acting “enhancer” elements. The highly variable body coloration patterns among Drosophilid insects represents a powerful model system in which the molecular alterations that underlie phenotypic diversity can be defined. In a survey of pigment phenotypes among geographically disparate Japanese populations of Drosophila auraria, we discovered a remarkable degree of variation in male-specific abdominal coloration. In testing the expression patterns of the major pigment-producing enzymes, we found that phenotypes uniquely correlated with differences in the expression of ebony, a gene required for yellow-colored cuticle. Assays of ebony’s transcriptional control region indicated that a lightly pigmented strain harbored cis-regulatory mutations that caused correlated changes in its expression. Through a series of chimeric reporter constructs between light and dark strain alleles, we localized function-altering mutations to a conserved silencer that mediates a male-specific pattern of ebony repression. This suggests that the light allele was derived through the loss of this silencer’s activity. Furthermore, examination of the ebony gene of D. serrata, a close relative of D. auraria which secondarily lost male-specific pigmentation revealed the parallel loss of this silencer element. These results demonstrate how loss-of-function mutations in a silencer element resulted in increased gene expression. We propose that the mutational inactivation of silencer elements may represent a favored path to evolve gene expression, impacting morphological traits

Drosophila suzukii: the genetic footprint of a recent, world-wide invasion

Native to Asia, the soft-skinned fruit pest Drosophila suzukii has recently invaded the United States and Europe. The eastern United States represents the most recent expansion of their range, and presents an opportunity to test alternative models of colonization history. Here we investigate the genetic population structure of this invasive fruit fly, with a focus on the eastern United States. We sequenced six X-linked gene fragments from 246 individuals collected from a total of 12 populations. We examine patterns of genetic diversity within and between populations and explore alternative colonization scenarios using Approximate Bayesian Computation. Our results indicate high levels of nucleotide diversity in this species and suggest that the recent invasions of Europe and the continental United States are independent demographic events. More broadly speaking, our results highlight the importance of integrating population structure into demographic models, particularly when attempting to reconstruct invasion histories. Finally, our simulation results illustrate the general challenge of reconstructing invasion histories using genetic data and suggest that genome-level data are often required to distinguish among alternative demographic scenarios

Highly contiguous assemblies of 101 drosophilid genomes

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

Faunal and seasonal surveys on drosophilid flies by net sweeping in Ehime Prefecture, Shikoku, Japan

A faunal survey on drosophilid flies by net sweeping was carried out in Ehime Prefecture, Shikoku, Japan from October 2009 to October 2010. A total of 11,663 individuals of 54 species belonging to 15 genera were collected by the year-round samplings at two localities, Dogo Park and Mt. Miyukiji, and occasional ones at another site in Matsuyama. The most abundant species was Liodrosophila aerea (49%), followed by Drosophila rufa (17%), D. lutescens (9.6%), D. sternopleuralis (4.0%) and D. bizonata (3.8%). The six dominant species showed more or less similar patterns in seasonal population fluctuation, being abundant in spring and/or fall with some variation between the localities. The observed seasonal patterns of drosophilid flies are discussed in relation to the extraordinary hot weather in the summer of 2010

Taxonomic study of the Drosophila auraria species complex (Diptera: Drosophilidae) with description of a new species

The Drosophila auraria species complex, especially from the Ryukyu archipelago and Taiwan, was reviewed. A new species, D. neoasahinai Watada and Kondo, sp. nov., was described from Okinawa-jima and surrounding islands. Two synonymies were proposed on the basis of the present and previous morphological comparisons and cross experiments; D. yuwanensis Kim and Okada, 1988, as a junior synonym of D. asahinai Okada, 1964, and D. quadraria Bock and Wheeler, 1972, as a junior synonym of D. triauraria Bock and Wheeler, 1972. A laboratory stock (no. 14020-0011.01) maintained in the Drosophila Species Stock Center at the University of California, San Diego and so far designated as D. rufa Kikkawa and Peng, 1938, was identified as D. tani Cheng and Okada, 1985, based on morphology

Raw data for egg hatch rates

Egg hatch rates of all-female and normal lines

Ecological, morphological and molecular studies on Ganaspis individuals (Hymenoptera: Figitidae) attacking Drosophila suzukii (Diptera: Drosophilidae)

Ganaspis individuals parasitizing Drosophila suzukii (Matsumura), a pest of fruit crop, were examined for host use and molecular and morphological differences from those attacking D. lutescens Okada and some other Drosophila species that breed on fermenting fruits. Wild cherry fruits were collected in the suburbs of Tokyo, and drosophilid pupae obtained from these fruits were examined for parasitism. Drosophila suzukii was the only drosophilid species infesting fresh wild cherry fruits, and Ganaspis individuals were the major parasitoids attacking D. suzukii in wild cherry fruits. In parasitism experiments, these Ganaspis individuals parasitized D. suzukii larvae in fresh cherry fruits, but did not parasitize those in Drosophila medium. In addition, they did not parasitize larvae of some other fruit-feeding Drosophila species even when these occurred in fresh cherry fruit. These Ganaspis individuals parasitizing D. suzukii were different from those parasitizing D. lutescens and some other drosophilids in nucleotide sequences of the COI gene, as well as in ITS1 and ITS2. They were also different in the forewing and antenna morphology, although they showed some overlap in morphological traits. They are tentatively assigned as the suzukii- and lutescens-associated types of G. xanthopoda (Ashmead). In the present field survey, Leptopilina japonica Novković & Kimura and some Asobara species were also observed to attack D. suzukii larvae in wild cherry fruit