Population genomics of Drosophila suzukii reveal longitudinal population structure and signals of migrations in and out of the continental United States

Genomic Diversity Illuminates the Environmental Adaptation of Drosophila suzukii

Biological invasions carry substantial practical and scientific importance and represent natural evolutionary experiments on contemporary timescales. Here, we investigated genomic diversity and environmental adaptation of the crop pest Drosophila suzukii using whole-genome sequencing data and environmental metadata for 29 population samples from its native and invasive range. Through a multifaceted analysis of this population genomic data, we increase our understanding of the D. suzukii genome, its diversity and its evolution, and we identify an appropriate genotype-environment association pipeline for our dataset. Using this approach, we detect genetic signals of local adaptation associated with nine distinct environmental factors related to altitude, wind speed, precipitation, temperature, and human land use. We uncover unique functional signatures for each environmental variable, such as the prevalence of cuticular genes associated with annual precipitation. We also infer biological commonalities in the adaptation to diverse selective pressures, particularly in terms of the apparent contribution of nervous system evolution to enriched processes (ranging from neuron development to circadian behavior) and to top genes associated with all nine environmental variables. Our findings therefore depict a finer-scale adaptive landscape underlying the rapid invasion success of this agronomically important species.

Dissecting the invasion history of Spotted-Wing Drosophila (Drosophila suzukii) in Portugal using genomic data

BACKGROUND

The invasive pest Spotted-Wing Drosophila, Drosophila suzukii (Matsumura), causes extensive damage and production losses of soft-skinned fruits. Native to Asia, the species has now spread worldwide, with first reports in Portugal in 2012. In this study, we focus on the genomic signatures of the recent Portuguese invasion, in the context of worldwide patterns established in previous works. We analyzed whole genome pool sequencing data from three Portuguese populations (N = 240) sampled in 2019 and 2021.

RESULTS

The correlation of allele frequencies suggested that Portuguese populations are related to South European ones, indicating a Mediterranean invasion route. While two populations exhibited levels of genetic variation comparable to others in the invasive range, a third showed low levels of genetic diversity, which may result from a recent colonization of the region. Genome-wide analyses of natural selection identified ten genes previously associated with D. suzukii's invasive capacity, which may have contributed to the species' success in Portugal. Additionally, we pinpointed six genes evolving under positive selection across Portuguese populations but not in European ones, which is indicative of local adaptation. One of these genes, nAChRalpha7, encodes a nicotinic acetylcholine receptor, which are known targets for insecticides widely used for D. suzukii control, such as neonicotinoids and spinosyns. Although spinosyn resistance has been associated with mutations in the nAChRalpha6 in other Drosophila species, the putative role of nAChRalpha7 in insecticide resistance and local adaptation in Portuguese D. suzukii populations encourages future investigation.

CONCLUSIONS

Our results highlight the complex nature of rapid species invasions and the role of rapid local adaptation in determining the invasive capacity of these species.

Potential of Ocotea indecora Essential Oil for Controlling Drosophila suzukii: Molecular Predictions for Toxicity and Selectivity to Beneficial Arthropods

The protection of soft-skinned fruits against Drosophila suzukii has relied primarily on the efficacy of a few synthetic molecules. Despite their short-term efficacy, these molecules can cause environmental pollution, unintendedly affect non-target organisms, and fail to provide sustainable control. The shortfalls of using synthetic pesticides warrant the search for alternatives, such as essential oils extracted from plants, with greater eco-friendlier properties. Here, we chemically characterized and evaluated the toxicity of the essential oil extracted from leaves of Ocotea indecora (Schott) Mez (Lauraceae) against D. suzukii via two exposure pathways (ingestion and contact). We also assessed the selectivity of the essential oil to two predatory natural enemies, Eriopis connexa and Chrysoperla externa and two pollinator bees, Apis mellifera and Partamona helleri. In addition, we conducted in silico predictions to investigate potential interactions between the major compound of the essential oil and the insects' transient receptor potential (TRP) channels. Our chromatographic analysis revealed sesquirosefuran (87%) as the major compound. Higher toxicity to adults of D. suzukii was observed in contact exposure (LC50 = 0.43 μL mL-1) compared to ingestion (LC50 = 0.72 μL mL-1). However, the essential oil did not cause mortality to the non-target organisms tested here, even when applied at 2.20 μL mL-1. Molecular predictions demonstrated that sesquirosefuran binds more stably to the TRP channels of D. suzukii than to those expressed in beneficial arthropods. Collectively, our findings provide the initial framework for the potential use of O. indecora essential oil as a sustainable alternative for managing D. suzukii infestations.

Fitness surfaces and local thermal adaptation in Drosophila along a latitudinal gradient

Local adaptation is commonly cited to explain species distribution, but how fitness varies along continuous geographical gradients is not well understood. Here, we combine thermal biology and life-history theory to demonstrate that Drosophila populations along a 2500 km latitudinal cline are adapted to local conditions. We measured how heat tolerance and viability rate across eight populations varied with temperature in the laboratory and then simulated their expected cumulative Darwinian fitness employing high-resolution temperature data from their eight collection sites. Simulations indicate a trade-off between annual survival and cumulative viability, as both mortality and the recruitment of new flies are predicted to increase in warmer regions. Importantly, populations are locally adapted and exhibit the optimal combination of both traits to maximize fitness where they live. In conclusion, our method is able to reconstruct fitness surfaces employing empirical life-history estimates and reconstructs peaks representing locally adapted populations, allowing us to study geographic adaptation in silico.

Current stewardship practices in invasion biology limit the value and secondary use of genomic data

Invasive species threaten native biota, putting fragile ecosystems at risk and having a large-scale impact on primary industries. Growing trade networks and the popularity of personal travel make incursions a more frequent risk, one only compounded by global climate change. With increasing publication of whole-genome sequences lies an opportunity for cross-species assessment of invasive potential. However, the degree to which published sequences are accompanied by satisfactory spatiotemporal data is unclear. We assessed the metadata associated with 199 whole-genome assemblies of 89 invasive terrestrial invertebrate species and found that only 38% of these were derived from field-collected samples. Seventy-six assemblies (38%) reported an 'undescribed' sample origin and, while further examination of associated literature closed this gap to 23.6%, an absence of spatial data remained for 47 of the total assemblies. Of the 76 assemblies that were ultimately determined to be field-collected, associated metadata relevant for invasion studies was predominantly lacking: only 35% (27 assemblies) provided granular location data, and 33% (n = 25) lacked sufficient collection date information. Our results support recent calls for standardized metadata in genome sequencing data submissions, highlighting the impact of missing metadata on current research in invasion biology (and likely other fields). Notably, large-scale consortia tended to provide the most complete metadata submissions in our analysis-such cross-institutional collaborations can foster a culture of increased adherence to improved metadata submission standards and a standard of metadata stewardship that enables reuse of genomes in invasion science.

Characterization of Field-Derived Drosophila suzukii (Diptera: Drosophilidae) Resistance to Pyrethroids in California Berry Production

The spotted-wing drosophila, Drosophila suzukii (Matsumura), is a global economic pest of berry crops and stone fruit. Since management of this pest primarily relies on calendar insecticide applications, and field-derived resistance to spinosad has already been documented in California caneberry production, there is significant concern for development of resistance to other insecticides. In this study, susceptibility of D. suzukii populations collected from caneberry and strawberry fields to two pyrethroids, zeta-cypermethrin, and bifenthrin, was assessed in 2019 and 2020. Resistance to both pyrethroids were observed in flies from all sampling sites. For flies collected from caneberries in 2019, the LC50 values ranged from 4.5 to 5.2 mg liter-1 with RR50s ranging from 7.5- to 8.7-fold. Our 2020 assays showed that susceptibility of flies to the discriminating dose of zeta-cypermethrin decreased significantly as the season progressed. For flies collected from strawberries in 2020, the LC50s ranged from 19.0 to 36.1 mg liter-1 and from 30.3 to 90.7 mg liter-1 for zeta-cypermethrin and bifenthrin, respectively. The RR50 values varied from 19.0- to 36.1-fold for zeta-cypermethrin and from 15.9- to 47.7-fold for bifenthrin. This study is the first report of field-derived pyrethroid resistance in D. suzukii from two major California berry production areas. Adoption of informed insecticide resistance management practices would be essential to prolong the efficacy of products available to control D. suzukii. Future molecular work is needed to unravel the underlying genetic mechanisms conferring the observed pyrethroid resistance and to develop robust diagnostics that can inform integrated pest management of this pest.

HUGE pipeline to measure temporal genetic variation in Drosophila suzukii populations for genetic biocontrol applications

Understanding the fine-scale genome sequence diversity that exists within natural populations is important for developing models of species migration, temporal stability, and range expansion. For invasive species, agricultural pests, and disease vectors, sequence diversity at specific loci in the genome can impact the efficacy of next-generation genetic biocontrol strategies. Here we describe a pipeline for haplotype-resolution genetic variant discovery and quantification from thousands of Spotted Wing Drosophila (Drosophila suzukii, SWD) isolated at two field sites in the North-Central United States (Minnesota) across two seasons. We observed highly similar single nucleotide polymorphism (SNP) frequencies at each genomic location at each field site and year. This supports the hypotheses that SWD overwinters in Minnesota, is annually populated by the same source populations or a combination of both theories. Also, the stable genetic structure of SWD populations allows for the rational design of genetic biocontrol technologies for population suppression.

Intra- and interspecific comparison of protein polymorphism to establish genetic differentiation in two sympatric species of Drosophila: D. bipectinata and D. malerkotliana

Drosophila bipectinata species complex includes four monophyletic closely related sympatric species with perfect reproductive isolation in natural conditions. Among these, two species, i.e., D. bipectinata and D. malerkotliana are known to be more prevalent in their occurrence all along their distribution area of Oriental-Australian regions. Genetic characteristics of these two species have been studied by earlier researchers mainly by focusing on their chromosomal polymorphism to gain knowledge pertaining to their evolutionary trend. The present work is one step farther, as we considered isozyme variants of three polymorphic enzymes to envisage genetic differentiation among the different natural populations of these two species, along with, a comparative perusal of their certain population genetic parameters. Natural populations of these two species were sampled from eight places aligned on the north-south axis of India and were subjected to isozyme analysis. The collection of both species and the geographical locations were kept same to avoid the effect of temporal or seasonal factors on the distribution of their allelic frequency. The results of this study clearly indicate that there is intraspecific genetic structuring among the populations of both the species with a distinct steady increase in the level of heterozygosity from north to south. The evolutionary tree in the form of dendrogram depicts two genetically differentiated groups of natural populations, one for north and other for South India. Most essential aspect that has been noticed through this study is the evolutionary trend of these two sympatric species being largely similar all along the north-south axis of India.

Spatio-temporal Variation of Spinosad Susceptibility in Drosophila suzukii (Diptera: Drosophilidae), a Three-year Study in California's Monterey Bay Region

Spinosyn insecticides are widely used in conventional berry production, and spinosad is regarded as the most effective insecticide for managing Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), spotted-wing drosophila, in organic berry crops. Following the 2017 identification of spinosad resistance in caneberry fields in the Watsonville area, Santa Cruz Co., California, we conducted a study to examine the seasonal and annual susceptibility of D. suzukii over a three-year period. Adult flies were collected from two conventional and two organic caneberry fields in the Monterey Bay region, California, at 'early', 'middle', and 'late' time points during the 2018-2020 growing seasons, and their susceptibility to spinosad was assessed. Results demonstrated that spinosad susceptibility in the D. suzukii field populations generally decreased during the fruit production season (from June through November), and over consecutive seasons. LC50 values of adults from the conventional sites were determined to be as high as 228.7 mg l-1 in 2018, 665.6 mg l-1 in 2019, and 2700.8 mg l-1 in 2020. For the organically managed fields, LC50s of adults were as great as 300.0 mg l-1 in 2018, 1291.5 mg l-1 in 2019, and 2547.1 mg l-1 in 2020. Resistance ratios based on the LC50 values were as high as 10.7-, 13.2-, and 16.9-fold in 2018, 2019, and 2020, respectively. These results should serve as a caution for growers in other production areas, facilitate informed choice of insecticides used in D. suzukii management, and emphasize the need to develop effective insecticide resistance management strategies for this insect.

Surveys of Drosophila suzukii (Diptera: Drosophilidae) and Its Host Fruits and Associated Parasitoids in Northeastern China

Spotted-wing drosophila, Drosophila suzukii (Matsumura), is a worldwide quarantine pest that is currently undergoing a rapid range expansion in the Americas, Europe, and parts of Africa. It feeds and breeds on soft-skinned fruits such as raspberries, blueberries, and cherries, and can cause significant economic losses to fruit production. This study investigated the occurrence of D. suzukii and its wild host fruits and parasitoids in Liaoning, Northeast China for the first time. Sentinel traps were used to monitor D. suzukii adults, and suspected fruits were collected weekly in four different locations (Wafangdian, Faku, Fengcheng, and Shenyang). The results showed that D. suzukii were distributed in the sweet soft-skinned fruit-production areas of Liaoning, and raspberry was the most infested fruit. During the field survey, four species of wild berries from non-crop habitats were found infested by D. suzukii, and two species of parasitoids (Leptopilina japonica and Asobara japonica) were collected. D. suzukii adult-population dynamics throughout the survey period (June to October) were similar in different survey locations; adult fly populations increased and peaked in August, and then declined until the fly was no longer detectable in October.

Evaluation of Additional Drosophila suzukii Male-Only Strains Generated Through Remobilization of an FL19 Transgene

Drosophila suzukii (D. suzukii) (Matsumura, 1931; Diptera: Drosophilidae), also known as spotted wing Drosophila, is a worldwide pest of fruits with soft skins such as blueberries and cherries. Originally from Asia, D. suzukii is now present in the Americas and Europe and has become a significant economic pest. Growers largely rely on insecticides for the control of D. suzukii. Genetic strategies offer a species-specific environmentally friendly way for suppression of D. suzukii populations. We previously developed a transgenic strain of D. suzukii that produced only males on a diet that did not contain tetracycline. The strain carried a single copy of the FL19 construct on chromosome 3. Repeated releases of an excess of FL19 males led to suppression of D. suzukii populations in laboratory cage trials. Females died as a consequence of overexpression of the tetracycline transactivator (tTA) and tTA-activated expression of the head involution defective proapoptotic gene. The aim of this study was to generate additional male-only strains that carried two copies of the FL19 transgene through crossing the original line with a piggyBac jumpstarter strain. Males that carried either two chromosome 3 or a singleX-linked transgene were identified through stronger expression of the red fluorescent protein marker gene. The brighter fluorescence of the X-linked lines was likely due to dosage compensation of the red fluorescent protein gene. In total, four X-linked lines and eleven lines with two copies on chromosome 3 were obtained, of which five were further examined. All but one of the strains produced only males on a diet without tetracycline. When crossed with wild type virgin females, all of the five two copy autosomal strains examined produced only males. However, the single copy X-linked lines did not show dominant female lethality. Five of the autosomal lines were further evaluated for productivity (egg to adult) and male competition. Based on these results, the most promising lines have been selected for future population suppression experiments with strains from different geographical locations.

Diet Hierarchies Guide Temporal-Spatial Variation in Drosophila suzukii Resource Use

Among insects, female oviposition preferences are critical to understanding the evolutionary dynamics between herbivores and hosts. Previous studies have shown Drosophila resource use has a strong genetic basis, although there is evidence that preferences are adaptable given isolation from ancestral hosts. Given the high degree of adaptability and behavioral plasticity of invasive species, we were interested in the mechanisms affecting host preferences of the invasive fruit fly, Drosophila suzukii, which in recent years has developed a nearly global range infesting small fruit crops. We studied the diet hierarchies of D. suzukii using a combination of laboratory and field assays designed to assess how female oviposition host choice differs given the availability of, and experience with, different fruit and non-fruit hosts. We found that host preferences did not shift over time and flies reared on two differential isolated diets up to F5 behaved and performed similarly regardless of diet lineage. Rather, female host choice appeared guided by a fixed hierarchical system of host preferences. Raspberry was more preferred to mushroom, which was more preferred to goose manure. However, if preferred resources were absent, the use of less-preferred resources was compensatory. We suggest that among niche specialists, such as D. suzukii, these hierarchies may support a bet-hedging strategy, rather than multiple-niche polymorphism, allowing for niche separation during periods of increased competition, while maintaining more diverse, ancestral feeding behaviors when preferred resources are scarce.