Biology and ecology of the Oriental flower-breeding Drosophila elegans and related species.

Animals adapt to their environments in the course of evolution. One effective approach to elucidate mechanisms of adaptive evolution is to compare closely related species with model organisms in which knowledge of the molecular and physiological bases of various traits has been accumulated. Drosophila elegans and its close relatives, belonging to the same species group as the model organism D. melanogaster, exhibit various unique characteristics such as flower-breeding habit, courtship display, territoriality, sexual dimorphism, and colour polymorphism. Their ease of culturing and availability of genomic information makes them a useful model for understanding mechanisms of adaptive evolution. Here, we review the morphology, distribution, and phylogenetic relationships of D. elegans and related species, as well as their characteristic flower-dependent biology, food habits, and life-history traits. We also describe their unique mating and territorial behaviours and note their distinctive karyotype and the genetic mechanisms of morphological diversity that have recently been revealed.

Intense browsing by sika deer (Cervus nippon) drives the genetic differentiation of hairy nettle (Urtica thunbergiana) populations.

Many studies have inferred the way in which natural selection, genetic drift and gene flow shape the population genetic structures, but very few have quantified the population differentiation under spatially and temporally varying levels of selection pressure, population fluctuation and gene flow. In Nara Park (6.6 km2), central Japan, where several hundred sika deer (Cervus nippon) have been protected for more than 1,200 years, heavily- or moderately-haired nettle (Urtica thunbergiana) populations have evolved probably in response to intense deer browsing. Here, we analysed the genetic structure of two Nara Park populations and five surrounding populations using amplified fragment length polymorphism markers. A total of 546 marker loci were genotyped from 210 individuals. A Bayesian method estimated 5.5% of these loci to be outliers, which are putatively under natural selection. Neighbour-joining, principal coordinates and Bayesian clustering analyses using all-loci, non-outlier loci and outlier loci datasets showed that the Nara Park populations formed a cluster distinct from the surroundings. These results indicate the genome-wide differentiation of the Nara Park populations from the surroundings. Moreover, these imply the following: (1) gene flow is limited between these populations and thus genetic drift is a major factor causing the differentiation; and (2) natural selection imposed by intense deer browsing has contributed to some extent to the differentiation. In conclusion, sika deer seems to have counteracted genetic drift to drive the genetic differentiation of hairy nettles in Nara Park. This study suggests that a single herbivore species could lead to genetic differentiation among plant populations.

DROP: Molecular voucher database for identification of Drosophila parasitoids.

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here, we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP, genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and six proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyse research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

The parasitoid complex of D. suzukii and other fruit feeding Drosophila species in Asia.

Drosophila suzukii is an invasive fly of East Asian origin that has become a serious fruit pest worldwide. Classical biological control through the introduction of parasitoids from Asia could help reduce populations of D. suzukii in invaded regions. Little is known about the native parasitoids of the fly in Asia. Therefore, surveys for larval parasitoids of D. suzukii were carried out in China and Japan between 2015 and 2017. Parasitoids of D. suzukii and other fruit-inhabiting drosophilids (D. pulchrella and D. subpulchrella) that are probably attacked by the same parasitoid complex were found in four Chinese provinces and four Japanese prefectures. Larval parasitoids were obtained at most sites where D. suzukii was found, with parasitism varying from 0.0 to 75.6%. At least eight parasitoid species were reared. The most abundant and frequent parasitoids were the Figitidae Ganaspis cf. brasiliensis and Leptopilina japonica, but another Leptopilina species and at least five Braconidae species belonging to the genera Areotetes, Asobara and Tanycarpa were obtained in low numbers. Due to its likely restricted host range, the most promising parasitoid for biological control is Ganaspis cf. brasiliensis. However, its exact specificity and taxonomic status require future research.

Variation in lipid synthesis, but genetic homogeneity, among Leptopilina parasitic wasp populations.

Lipid synthesis can have a major effect on survival and reproduction, yet most insect parasitoids fail to synthesize lipids. For parasitic wasps in the genus Leptopilina, however, studies have suggested that there is intraspecific variation in the ability for lipid synthesis. These studies were performed on only few populations, and a large-scale investigation of both lipogenic ability and population genetic structure is now needed. Here, we first examined lipogenic ability of nine Leptopilina heterotoma populations collected in 2013 and found that five of nine populations synthesized lipids. The 2013 populations could not be used to determine genetic structure; hence, we obtained another 20 populations in 2016 that were tested for lipogenic ability. Thirteen of 20 populations (all Leptopilina heterotoma) were then used to determine the level of genetic differentiation (i.e., haplotype and nucleotide diversity) by sequencing neutral mitochondrial (COI) and nuclear (ITS2) markers. None of the 2016 populations synthesized lipids, and no genetic differentiation was found. Our results did reveal a nearly twofold increase in mean wasp lipid content at emergence in populations obtained in 2016 compared to 2013. We propose that our results can be explained by plasticity in lipid synthesis, where lipogenic ability is determined by environmental factors, such as developmental temperature and/or the amount of lipids carried over from the host.

Related herbivore species show similar temporal dynamics.

Within natural communities, different taxa display different dynamics in time. Why this is the case we do not fully know. This thwarts our ability to predict changes in community structure, which is important for both the conservation of rare species in natural communities and for the prediction of pest outbreaks in agriculture. Species sharing phylogeny, natural enemies and/or life-history traits have been hypothesized to share similar temporal dynamics. We operationalized these concepts into testing whether feeding guild, voltinism, similarity in parasitoid community and/or phylogenetic relatedness explained similarities in temporal dynamics among herbivorous community members. Focusing on two similar datasets from different geographical regions (Finland and Japan), we used asymmetric eigenvector maps as temporal variables to characterize species- and community-level dynamics of specialist insect herbivores on oak (Quercus). We then assessed whether feeding guild, voltinism, similarity in parasitoid community and/or phylogenetic relatedness explained similarities in temporal dynamics among taxa. Species-specific temporal dynamics varied widely, ranging from directional decline or increase to more complex patterns. Phylogeny was a clear predictor of similarity in temporal dynamics at the Finnish site, whereas for the Japanese site, the data were uninformative regarding a phylogenetic imprint. Voltinism, feeding guild and parasitoid overlap explained little variation at either location. Despite the rapid temporal dynamics observed at the level of individual species, these changes did not translate into any consistent temporal changes at the community level in either Finland or Japan. Overall, our findings offer no direct support for the notion that species sharing natural enemies and/or life-history traits would be characterized by similar temporal dynamics, but reveal a strong imprint of phylogenetic relatedness. As this phylogenetic signal cannot be attributed to guild, voltinism or parasitoids, it will likely derive from shared microhabitat, microclimate, anatomy, physiology or behaviour. This has important implications for predicting insect outbreaks and for informing insect conservation. We hope that future studies will assess the generality of our findings across plant-feeding insect communities and beyond, and establish the more precise mechanism(s) underlying the phylogenetic imprint.

Deciphering the Routes of invasion of Drosophila suzukii by Means of ABC Random Forest.

Deciphering invasion routes from molecular data is crucial to understanding biological invasions, including identifying bottlenecks in population size and admixture among distinct populations. Here, we unravel the invasion routes of the invasive pest Drosophila suzukii using a multi-locus microsatellite dataset (25 loci on 23 worldwide sampling locations). To do this, we use approximate Bayesian computation (ABC), which has improved the reconstruction of invasion routes, but can be computationally expensive. We use our study to illustrate the use of a new, more efficient, ABC method, ABC random forest (ABC-RF) and compare it to a standard ABC method (ABC-LDA). We find that Japan emerges as the most probable source of the earliest recorded invasion into Hawaii. Southeast China and Hawaii together are the most probable sources of populations in western North America, which then in turn served as sources for those in eastern North America. European populations are genetically more homogeneous than North American populations, and their most probable source is northeast China, with evidence of limited gene flow from the eastern US as well. All introduced populations passed through bottlenecks, and analyses reveal five distinct admixture events. These findings can inform hypotheses concerning how this species evolved between different and independent source and invasive populations. Methodological comparisons indicate that ABC-RF and ABC-LDA show concordant results if ABC-LDA is based on a large number of simulated datasets but that ABC-RF out-performs ABC-LDA when using a comparable and more manageable number of simulated datasets, especially when analyzing complex introduction scenarios.

Phylogeography, Interaction Patterns and the Evolution of Host Choice in Drosophila-Parasitoid Systems in Ryukyu Archipelago and Taiwan.

Island biotas provide a great opportunity to study not only the phylogeographic patterns of a group of species, but also to explore the differentiation in their coevolutionary interactions. Drosophila and their parasitoids are exemplary systems for studying complex interaction patterns. However, there is a lack of studies combining interaction-based and molecular marker-based methods. We applied an integrated approach combining phylogeography, interaction, and host-choice behavior studies, with the aim to understand how coevolutionary interactions evolve in Drosophila-parasitoid island populations. The study focused on the three most abundant Drosophila species in Ryukyu archipelago and Taiwan: D. albomicans, D. bipectinata, and D. takahashii, and the Drosophila-parasitoid Leptopilina ryukyuensis. We determined mitochondrial COI haplotypes for samples representing five island populations of Drosophila and four island populations of L. ryukyuensis. We additionally sequenced parts of the autosomal Gpdh for Drosophila samples, and the ITS2 for parasitoid samples. Phylogenetic and coalescent analyses were used to test for demographic events and to place them in a temporal framework. Geographical differences in Drosophila-parasitoid interactions were studied in host-acceptance, host-suitability, and host-choice experiments. All four species showed species-specific phylogeographic patterns. A general trend of the haplotype diversity increasing towards the south was observed. D. albomicans showed very high COI haplotype diversity, and had the most phylogeographically structured populations, with differentiation into the northern and the southern population-group, divided by the Kerama gap. Differentiation in host suitability was observed only between highly structured populations of D. albomicans, possibly facilitated by restricted gene flow. Differentiation in host-acceptance in D. takahashii, and host-acceptance and host-choice in L. ryukyuensis was found, despite there being no differentiation in these two species according to molecular markers. Host choice assays show that L. ryukyuensis populations that have had more time to coevolve adapt their behavior to exploit the most suitable host - D. albomicans. L. ryukyuensis parasitoids on border ranges may, on the other hand, benefit from broader host-acceptance, that may facilitate adaptation to uncertain and variable environments. All results indicate that Drosophila-parasitoid populations in the Ryukyu archipelago and Taiwan have different evolutionary trajectories, and coevolve in a dynamic, complex, and local-specific way.

Genetic analyses of resistance against Leptopilina victoriae in Drosophila bipectinata.

Drosophila bipectinata from Iriomote-jima (IR) is susceptible to the endoparasitoid Leptopilina victoriae from Kota Kinabalu (L. victoriae KK), but D. bipectinata from Kota Kinabalu (KK) and Bogor (BG) is resistant. The cross experiments between the resistant (KK) and susceptible (IR) populations of D. bipectinata suggested that the resistance to this parasitoid is a dominant trait and controlled by a single locus or few linked loci on an autosome. In the AFLP analysis using the IR, KK and BG populations of D. bipectinata and the resistant and susceptible populations derived from a mixed population of these three geographic populations, a DNA fragment almost specific to susceptible flies was detected. It also revealed that genes from the IR population were more frequently maintained in the mixed population compared with those from the KK and BG populations, suggesting that at least a number of genes from the IR population are more advantageous under the laboratory conditions. This explains our previous results that the resistance was lowered in the mixed population although the resistance itself is suggested to incur only low costs; i.e., the resistance gene(s) from the KK and BG populations would have been linked with some genes that are disadvantageous under the laboratory conditions.

What determines host acceptance and suitability in tropical Asian Drosophila parasitoids?

For successful parasitism, parasitoid females must oviposit and the progeny must develop in individual hosts. Here, we investigated the determinants of host acceptance for oviposition and host suitability for larval development of Drosophila parasitoids from Bogor and Kota Kinabalu (≍1,800 km northeast of Bogor), Indonesia, in tropical Asia. Asobara pleuralis (Ashmead) from both localities oviposited frequently (>60%) in all of the drosophilid species tested, except the strain from Kota Kinabalu oviposited rarely (10%) in Drosophila eugracilis Bock & Wheeler. Leptopilina victoriae Nordlander from both localities only oviposited frequently (>77%) in species from the Drosophila melanogaster species group except D. eugracilis (<3.7%), whereas Leptopilina pacifica Novkovic & Kimura from Bogor oviposited frequently (>85%) only in species from the Drosophila immigrans species group. Thus, host acceptance appeared to be affected by host taxonomy, at least in Leptopilina species. Host suitability varied considerably, even among closely related drosophilid species, which suggests that the host suitability is at least in part independent of host taxonomy and that it has been determined via parasitoid-host coevolutionary interactions (i.e., arms race). Host acceptance did not always coincide with host suitability, i.e., parasitoids sometimes oviposited in unsuitable host species. Geographic origin strongly affected the host acceptance and suitability in the A. pleuralis-D. eugracilis parasitoid-host pair, whereas it only weakly affected the acceptability and suitability in other parasitoid-host combinations.