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DROP: Molecular voucher database for identification of Drosophila parasitoids
Molecular Ecology Resources
Abstract
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 (http://doi.org/10.5281/zenodo.4519656), 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 6 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 catalyze 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.
Supplementary resource (1)
Data
June 2021
... A major challenge is lack of detailed knowledge on the host preferences and prevalences of particular parasitoid species in different areas and phases of moth population cycles (Klemola et al., 2008(Klemola et al., , 2014Ruohomäki et al., 2000;Tenow, 1972;Vindstad, 2014). In this regard, the first methodological complication arises from difficulties in identifying parasitoids in multi-species communities, which frequently include cryptic species that are difficult or impossible to separate based on morphological traits (Lue et al., 2021;Sigut et al., 2017). The parasitoid communities of autumnal and winter moths are speciesrich and ecologically diverse, involving species from at least 19 genera in five families (Klemola et al., 2007(Klemola et al., , 2014Vindstad, 2014;Vindstad et al., 2010). ...
... Barcoding and metabarcoding approaches also allow obtaining data directly from herbivore larvae, without a need to rear hosts and parasitoids to adults (Kitson et al., 2019;Miller, Aguilera, et al., 2021;Miller, Polaszek, & Evans, 2021;Nakadai & Kawakita, 2017;Sow et al., 2019;Volf et al., 2017). Furthermore, when a reference barcode library for relevant parasitoids is available, their local community structures and abundances can be estimated based on large-scale material obtained through, for example, Malaise trapping (Barsoum et al., 2019;DeWaard et al., 2019;Lue et al., 2021;Roslin et al., 2022). ...
... However, the extreme diversity of insects means that even the most comprehensive global or regional barcode libraries will at best contain only a subset of all species present in nature(Ratnasingham & Hebert, 2007;Roslin et al., 2022), and large-scale databases also frequently include barcodes of misidentified individuals(Meiklejohn et al., 2019). Curated taxon-or system-specific barcode libraries are therefore in many cases necessary for targeting relevant research questions and hypotheses(Lee et al., 2019;Lue et al., 2021;Nisole et al., 2020;Toro- Delgado et al., 2022). Here, by drawing on the combined expertise of taxonomists, ecologists, and geneticists, we constructed a comprehensive DNA barcode library for parasitoids that attack the immature stages of the geometrid moths E. autumnata and O. brumata in their main outbreak range in northern Europe. ...
Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the 10-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined recorded parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.
... A major challenge is lack of detailed knowledge on the host preferences and prevalences of particular parasitoid species in different areas and phases of moth population cycles (Klemola et al., 2008(Klemola et al., , 2014Ruohomäki et al., 2000;Tenow, 1972;Vindstad, 2014). In this regard, the first methodological complication arises from difficulties in identifying parasitoids in multi-species communities, which frequently include cryptic species that are difficult or impossible to separate based on morphological traits (Lue et al., 2021;Sigut et al., 2017). The parasitoid communities of autumnal and winter moths are speciesrich and ecologically diverse, involving species from at least 19 genera in five families (Klemola et al., 2007(Klemola et al., , 2014Vindstad, 2014;Vindstad et al., 2010). ...
... Barcoding and metabarcoding approaches also allow obtaining data directly from herbivore larvae, without a need to rear hosts and parasitoids to adults (Kitson et al., 2019;Miller, Aguilera, et al., 2021;Miller, Polaszek, & Evans, 2021;Nakadai & Kawakita, 2017;Sow et al., 2019;Volf et al., 2017). Furthermore, when a reference barcode library for relevant parasitoids is available, their local community structures and abundances can be estimated based on large-scale material obtained through, for example, Malaise trapping (Barsoum et al., 2019;DeWaard et al., 2019;Lue et al., 2021;Roslin et al., 2022). ...
... However, the extreme diversity of insects means that even the most comprehensive global or regional barcode libraries will at best contain only a subset of all species present in nature(Ratnasingham & Hebert, 2007;Roslin et al., 2022), and large-scale databases also frequently include barcodes of misidentified individuals(Meiklejohn et al., 2019). Curated taxon-or system-specific barcode libraries are therefore in many cases necessary for targeting relevant research questions and hypotheses(Lee et al., 2019;Lue et al., 2021;Nisole et al., 2020;Toro- Delgado et al., 2022). Here, by drawing on the combined expertise of taxonomists, ecologists, and geneticists, we constructed a comprehensive DNA barcode library for parasitoids that attack the immature stages of the geometrid moths E. autumnata and O. brumata in their main outbreak range in northern Europe. ...
Large areas of forests are annually damaged or destroyed by outbreaking insect pests. Understanding the factors that trigger and terminate such population eruptions has become crucially important, as plants, plant-feeding insects, and their natural enemies may respond differentially to the ongoing changes in the global climate. In northernmost Europe, climate-driven range expansions of the geometrid moths Epirrita autumnata and Operophtera brumata have resulted in overlapping and increasingly severe outbreaks. Delayed density-dependent responses of parasitoids are a plausible explanation for the ten-year population cycles of these moth species, but the impact of parasitoids on geometrid outbreak dynamics is unclear due to a lack of knowledge on the host ranges and prevalences of parasitoids attacking the moths in nature. To overcome these problems, we reviewed the literature on parasitism in the focal geometrid species in their outbreak range, and then constructed a DNA barcode reference library for all relevant parasitoid species based on reared specimens and sequences obtained from public databases. The combined parasitoid community of E. autumnata and O. brumata consists of 32 hymenopteran species, all of which can be reliably identified based on their barcode sequences. The curated barcode library presented here opens up new opportunities for estimating the abundance and community composition of parasitoids across populations and ecosystems based on mass barcoding and metabarcoding approaches. Such information can be used for elucidating the role of parasitoids in moth population control, possibly also for devising methods for reducing the extent, intensity, and duration of outbreaks.
... Drosophila parasitoids belong to four superfamilies of Hymenoptera: Chalcidoidea, Cynipoidea, Ichneumonoidea, and Diaprioidea. These groups have independently evolved to parasitize various Drosophila species, employing distinct parasitic strategies (Lue et al., 2021). For over two centuries, it has been established that these parasitoid wasps typically target Drosophila's larval or pupal stages. ...
... Larval parasitoids from the Branconidae (Asobara) and Figitidae (Leptopilina, Ganaspis) families are koinobionts, allowing the host to continue its development while the parasitoid wasp develops within it. In contrast, pupal parasitoids from the Diapriidae (Trichopria), Pteromalidae (Pachycrepoideus), and Encytidae families are idiobionts, which arrest host development immediately after parasitization (Carton et al., 1986;Lue et al., 2021;Prévost, 2009). ...
Parasitoid wasps exert strong selective pressure on their hosts, driving the evolution of diverse defense strategies. Drosophila, a widely studied model organism, hosts a wide range of parasites, including parasitoid wasps, and has evolved immune and behavioral mechanisms to mitigate the risk of parasitization. These defenses range from avoidance and evasion to post-infection immune responses, such as melanotic encapsulation. In response, parasitoid wasps have developed countermeasures, contributing to an ongoing arms race between host and parasite. This article reviews the anti-parasitoid behaviors of Drosophila, focusing on their role in reducing parasitization and enhancing host survival and fitness. It also explores the molecular and neuronal circuit mechanisms that underlie these behaviors, using Drosophila as an ecologically relevant model for studying host-parasitoid interactions. Furthermore, the article discusses the potential applications of these findings in biological pest control and highlights key unresolved questions in the field.
... The use of molecular tools, including species-specific PCR primers, for parasitoid species identification can help alleviate this problem (Gariepy et al. 2005;Traugott et al. 2006;Gariepy et al. 2007Gariepy et al. , 2008Rugman-Jones et al. 2011Gariepy and Messing 2012;Shariff et al. 2014;Furlong 2015;Shimbori et al. 2023). However, their development requires DNA sequences that are tied to authoritatively identified specimens (Lue et al. 2021;Shimbori et al. 2023), which is often not the case, given that many of the world's parasitoid fauna remain undescribed (Forbes et al. 2018). Fortunately, when an economically-important invasive pest is the focus of an importation biological control programme, the specimens and taxonomic knowledge may be available to facilitate the development of molecular diagnostic tools that can be used to document the spread and impact of unintentionally introduced parasitoids. ...
... brasiliensis G1 took place in Oregon in 2022, with the only detections occurring after release. As the DNA barcodes for both adventive and intentionally-released populations are identical Lue et al. 2021), the methods used in the present study cannot distinguish between post-release detections and the spread of already-established adventive populations. Other methods and continued surveys will be needed to tease apart the contribution of released and adventive populations of G. cf. ...
In recent years, there has been an increase in the adventive establishment and spread of parasitoid wasps outside of their native range. However, lack of taxonomic tools can hinder the efficient screening of field-collected samples to document the establishment and range expansion of parasitoids on continent-wide geographic scales. Here we report that Leptopilina japonica (Hymenoptera, Figitidae), a parasitoid of the globally invasive fruit pest Drosophila suzukii (Diptera, Drosophilidae), is now widespread in much of North America despite not having been intentionally introduced. Surveys in 2022 using a variety of methods detected L. japonica in 10 of 11 surveyed USA States and one Canadian Province where it was not previously known to occur. In most surveys, L. japonica was the most common species of D. suzukii parasitoid found. The surveys also resulted in the detection of Ganaspis cf. brasiliensis (Hymenoptera, Figitidae), the recently-released biological control agent of D. suzukii, in six USA States where it had not previously been found. These new detections are likely a result of intentional biological control introductions rather than spread of adventive populations. A species-specific multiplex PCR assay was developed as a rapid, accurate and cost-effective method to distinguish L. japonica, G. cf. brasiliensis, the closely-related cosmopolitan parasitoid Leptopilina heterotoma (Hymenoptera, Figitidae) and other native parasitoid species. This dataset and the associated molecular tools will facilitate future studies of the spread and ecological impacts of these introduced parasitoids on multiple continents.
... To avoid these problems, vouchers represent an essential connection between the molecular data and the taxon and allow verifying and updating the taxonomic identity of the sequenced species (Lue et al. 2021). A DNA sequence will always be linked to a taxon voucher. ...
... A DNA sequence will always be linked to a taxon voucher. Without the voucher, a molecular study cannot be fully confirmed, having to trust the person making the identification (Lue et al. 2021). Vouchers in biology are specimens, preparations, pictures or any part of the specimen that allow other researchers to examine the taxonomic identity assigned to a specimen by the author of a study (Astrin et al. 2013). ...
DNA barcoding is a powerful tool to identify species using nucleotide differences found in the cytochrome oxidase I mitochondrial gene between species. Since it was proposed, several projects are promoting the construction of a DNA barcode library for all eukaryotes. DNA barcoding in conjunction with single-gene species delimitation methods have been used to estimate diversity at species level, allowing a rapid and comprehensive assessment of biodiversity. These methods have been developed with the purpose of clustering data sets of orthologous sequences in molecular operational taxonomic unit (MOTU). The MOTUs obtained by these methods could be compared with the taxonomic data to discover hidden diversity. In this chapter we discuss the main concepts and methodologies on DNA barcoding approach and review the use of species delimitation methods in the Neotropics. The huge biodiversity, lack of taxonomic effort and scarcity of funds are still challenging the broad use of this technology in the Neotropics.KeywordsCOIMOTUBarcode of lifeHidden biodiversity
... Sequences of the CO1 barcode region were obtained from five specimens (Table 1) using standard procedures at Advanced Identification Methods (AIM, Leipzig, Germany, see Morinière et al., 2015) and the Leibniz Institute for the Analysis of Biodiversity Change ward-and the HCO2198-JJ reverse-primer). We combined our CO1 barcode sequences with those of Leptopilina specimens deposited at the DROP Database (Lue et al., 2021), including the sequences published together with the description of L. japonica (Novković et al., 2011). Using Geneious (vers. ...
... We deposited all sequence data in the DROP database (http:// doi.org/10.5281/zenodo.4519656; Lue et al., 2021) and in BOLD (Ratnasingham & Hebert, 2007). ...
Two years after the first European record in Italy, we report the first occurrence of the parasitoid wasp Leptopilina japonica Novković & Kimura, 2011 (Hymenoptera: Figitidae) in Germany. The species is a larval‐pupal parasitoid of Drosophila suzukii (Matsumura, 1931) (Diptera: Drosophilidae), which is a widespread invasive and economically important pest of soft‐skinned fruit. In total, we found 29 specimens of L. japonica in five different locations in southern and western Germany in the years 2021, 2022 and 2023. We examined the specimens morphologically and generated their DNA barcodes for identification. In three of the locations, L. japonica was sampled from raspberries. In two locations, L. japonica was caught in two and three consecutive years, respectively, which indicates adventive establishment. As D. suzukii and L. japonica originate from the same region in Asia, the possible establishment of L. japonica could be a case of unintentional biological control in Germany. In addition to this first record in Germany, we present a diagnosis of L. japonica to distinguish the species from the rest of the European Leptopilina fauna.
... Perry and Heraty, 2019, 2021). However, morphological misidentifications and incorrect DNA barcodes on public databases hinder research assessing the impact of parasitoids (Lue et al., 2021(Lue et al., , 2022. This is an important issue, because validated DNA barcodes can be used by researchers with little taxonomic experience (Darling and Blum, 2007) and can also be applied to immature life stages and cryptic species (Waugh, 2007). ...
... This is an important issue, because validated DNA barcodes can be used by researchers with little taxonomic experience (Darling and Blum, 2007) and can also be applied to immature life stages and cryptic species (Waugh, 2007). Nevertheless, accurate DNA barcodes depend on the use of specimens that have been authoritatively identified (Lue et al., 2021(Lue et al., , 2022. ...
Three polyphagous pest Liriomyza spp. (Diptera: Agromyzidae) have recently invaded Australia and are damaging horticultural crops. Parasitic wasps are recognized as effective natural enemies of leafmining species globally and are expected to become important biocontrol agents in Australia. However, the hymenopteran parasitoid complex of agromyzids in Australia is poorly known and its use hindered due to taxonomic challenges when based on morphological characters. Here, we identified 14 parasitoid species of leafminers based on molecular and morphological data. We linked DNA barcodes (5' end cytochrome c oxidase subunit I (COI) sequences) to five adventive eulophid wasp species (Chrysocharis pubicornis (Zetterstedt), Diglyphus isaea (Walker), Hemiptarsenus varicornis (Girault), Neochrysocharis formosa (Westwood), and Neochrysocharis okazakii Kamijo) and two braconid species (Dacnusa areolaris (Nees) and Opius cinerariae Fischer). We also provide the first DNA barcodes (5' end COI sequences) with linked morphological characters for seven wasp species, with three identified to species level (Closterocerus mirabilis Edwards & La Salle, Trigonogastrella parasitica (Girault), and Zagrammosoma latilineatum Ubaidillah) and four identified to genus (Aprostocetus sp., Asecodes sp., Opius sp. 1, and Opius sp. 2). Phylogenetic analyses suggest C. pubicornis, D. isaea, H. varicornis, and O. cinerariae are likely cryptic species complexes. Neochrysocharis formosa and Aprostocetus sp. specimens were infected with Rickettsia. Five other species (Cl. mirabilis, D. isaea, H. varicornis, Opius sp. 1, and Opius sp. 2) were infected with Wolbachia, while two endosymbionts (Rickettsia and Wolbachia) co-infected N. okazakii. These findings provide background information about the parasitoid fauna expected to help control the leafminers.
... Therefore, studies on leafminer flies that depend on inexpert morphological identification should be viewed with caution. DNA barcoding provides an exciting tool for biological studies in fields such as ecology, evolution, genetics and biological control through the promise of reliable taxonomic identifications (Lue et al. 2021;Ratnasingham & Hebert 2013). It has aided studies of biodiversity and the establishment of species interactions within food webs. ...
... Our study, however, provides a good example of the challenges and pitfalls of this system, and a caution against relying only on one tool. Many sequences lodged in GenBank and BOLD are not directly linked to an authoritatively identified specimen, or contain errors (Lue et al. 2021). Thus, researchers seeking to identify their specimens through molecular sequencing can find there is no identified species match (as we found with our C. australis specimen), or that there are conflicting or potentially incorrect matches, as with our parasitoid E. messene specimen. ...
The wheat sheath miner, Cerodontha australis , is widespread and abundant in New Zealand and also occurs in eastern Australia. Adult and larval C. australis feed on cereals and grasses, including the economically important perennial ryegrass, Lolium perenne . There is little literature about C. australis , and much of the early work may relate to other species due to its initial misidentification. Morphology‐based identification can be challenging, and the absence of online barcode sequences from voucher specimens for C. australis has precluded diagnosis using molecular techniques. In this study, two individual adult leafminers collected from L. perenne plants in New Zealand were confirmed as C. australis morphologically. One has been retained as a voucher specimen and its mitochondrial barcode sequence submitted to online databases. Comparison with adult and larval specimens previously sequenced by the authors confirmed they were also C. australis . Molecular identification of 20 hymenopteran pupal endoparasitoids, and a subset of the puparia they emerged from, revealed Trichopria sp. (Diapriidae), Eupelmus messene (Eupelmidae) and three haplotypes (or closely related species) of Eulophidae. Sequences for all wasps were submitted to GenBank. All the puparia were visually identified as C. australis , and a subset that included a host pupa of each identified endoparasitoid species were confirmed as C. australis based on comparison with our barcode sequence. This work will aid future studies on C. australis and has allowed identification of unidentified sequences on public databases formerly submitted by other New Zealand researchers. It also provides new records of association between C. australis and its pupal endoparasitoids. More broadly, our study provides an example of the importance of authoritative morphological identification of specimens alongside molecular identification, and highlights the challenges in identifying species for which this has not been done.
... The experiment used cultures of Drosophila species and their associated parasitoids collected from two tropical rainforest locations in North Queensland Australia: Paluma (S18° 59.031' E146° 14.096') and Kirrama Range (S18° 12.134' E145° 53.102') (< 100 m above sea level) . Lue et al. 2021). Drosophila isofemale lines were kept on standard Drosophila medium (corn flour, yeast, sugar, agar and methyl-4-hydroxybenzoate) for approximately 45 to 70 non-overlapping generations. ...
... Cultures of Drosophila simulans and their associated parasitoids collected from two tropical rainforest locations in North Queensland Australia: Paluma (S18° 59.031' E146° 14.096') and Kirrama Range (S18° 12.134' E145° 53.102'; both <100 m above sea level; -21) were used (for more details on the parasitoid strains see Lue et al. 2021). Drosophila simulans isofemale lines were kept on standard Drosophila medium (corn flour, yeast, sugar, agar and methyl-4-hydroxybenzoate) for approximately 45 to 70 non-overlapping generations before the experiments. ...
Ecological communities are composed of a multitude of interacting species, and the outcome of pairwise interactions depends on other co-occurring species within the community. With current global environmental changes, both abiotic and biotic environment are changing, affecting the structure and dynamics of communities. I used a series of laboratory experiments on a set of Drosophila species and their parasitic wasps to investigate the effects of biotic and abiotic factors on interactions and communities. I first compared the outcome of host-parasitoid interactions across community modules commonly found in host-parasitoid communities (i.e., pairwise interaction, exploitative competition, apparent competition, and both exploitative and apparent competition). I found generally higher host suppression with multiple parasitoid species, but species-specific effects for parasitoid performance. I then observed that warming impacts host communities through direct effects on species performance rather than altered competitive interactions and parasitism. Finally, I found that temperature strongly influences the effects of multiple parasitoids on host suppression across different parasitoid assemblages, suggesting a general pattern for the environmental dependence of trophic and non-trophic interactions. My thesis emphasizes the importance of considering environmental factors and different interaction types to better predict community dynamics in a rapidly changing world.
... These strategies enable the parasites to initiate their life cycle in their insect hosts, grow within them, and eventually kill them [1]. Fruit flies of the well-characterized genus Drosophila serve as hosts to over 60 parasitoid wasp species [2]. The flies of some Drosophila species defend themselves by encapsulating and melanizing wasp eggs. ...
Unusual membrane-bound particles are present in the venom of the parasitoid wasps that parasitize Drosophila melanogaster. These venom particles harbor about 400 proteins and suppress the encapsulation of a wasp egg. Whereas the proteins in the particles of Leptopilina boulardi venom modify host hemocyte properties, those in L. heterotoma kill host hemocytes. The mechanisms underlying this differential effect are not well understood. The proteome of the L. heterotoma venom particles has been described before, but that of L. boulardi has not been similarly examined. Using sequence-based programs, we report the presence of conserved proteins in both proteomes with strong enrichment in the endomembrane and exosomal cell components. Extracellular vesicle markers are present in both proteomes, as are numerous toxins. Both proteomes also contain proteins lacking any annotation. Among these, we identified the proteins with structural similarity to the ADP-ribosyltransferase enzymes involved in bacterial virulence. We propose that invertebrate fluids like parasitoid venom contain functional extracellular vesicles that deliver toxins and virulence factors from a parasite to a host. Furthermore, the presence of such vesicles may not be uncommon in the venom of other animals. An experimental verification of the predicted toxin functions will clarify the cellular mechanisms underlying successful parasitism.
... These flies account for one-third of the fly diversity within Cyclorrhapha, with over 55 000 known species [26] and are encountered in all parts of the world in various habitats encompassing leaf-mines, decaying fruits, dung or carcasses [27]. The known diversity of Figitidae is also remarkable knowing the challenge of morphological identification in this clade [28], with more than 1700 species described and 14 000 species currently estimated worldwide [29,30]. Within the Figitidae family, the Eucoilinae subfamily, to which Leptopilina belongs, stands out as the most species rich, with around 1000 described species [31][32][33]. ...
Over the course of evolution, hymenopteran parasitoids have developed a close relationship with heritable viruses, sometimes integrating viral genes into their chromosomes. For example, in Drosophila parasitoids belonging to the Leptopilina genus, 13 viral genes from the Filamentoviridae family have been domesticated to deliver immunosuppressive factors to host immune cells, thereby protecting parasitoid offspring from the host immune response. The present study aims to comprehensively characterize this domestication event in terms of the viral genes involved, the wasp diversity affected by this event and its chronology. Our genomic analysis of 41 Cynipoidea wasps from six subfamilies revealed 18 viral genes that were endogenized during the early radiation of the Eucoilini/Trichoplastini clade around 75 million years ago. Wasps from this highly diverse clade develop not only from Drosophila but also from a variety of Schizophora. This event coincides with the radiation of Schizophora, a highly speciose Diptera clade, suggesting that viral domestication facilitated wasp diversification in response to host diversification. Additionally, in one of the species, at least one viral gene was replaced by another gene derived from a related filamentovirus. This study highlights the impact of viral domestication on the diversification of parasitoid wasps.
... Species identification is best done, initially, by comparing barcode data with that of the Sosa-Calvo et al. (2024) study. Consulting the database of DNA sequence data for parasitoids of Drosophilidae developed by Lue et al. (2021), and the use of the diagnostic polymerase chain reaction primers developed by Gariepy et al. (2024), are also useful pathways to accurate identification. ...
Ganaspis Foerster includes several cryptic species that are important larval parasitoids of the invasive pest Drosophila suzukii (Matsumura), spotted-wing drosophila (SWD). Drosophila suzukii, native to Asia, was first discovered in 2008 in North America and Europe, becoming a devastating pest of soft-skinned fruit crops. Biological control could be among the safest, most environmentally benign, and cost-effective methods for long-term and landscape-level management of this invasive pest. Foreign exploration in East Asia discovered several major larval
D. suzukii parasitoids. One of them was initially described as Ganaspis brasiliensis (Ihering) and consisted of 2 major genetic groups (G1 and G3). The groups are now recognized as 2 different species, Ganaspis kimorum Buffington and Ganaspis lupini Buffington. The more host-specific species G. kimorum was selected and approved for field release in the United States in 2021 and has been widely released since 2022. Here, we provide a comprehensive overview of the parasitoid’s taxonomy, current known distribution, biology, ecology, mass-rearing methods, and
biological control potential.
... Vol.: (0123456789) construct the L. boulardi phylogenetic tree (Lue et al., 2021). Multiple alignments were performed with MUSCLE (Edgar, 2004) and the terminal ambigous parts of the aligned sequences were deleted using Unipro UGENE version 1.26.1 (Okonechnikov et al., 2012). ...
Drosophila suzukii (Matsumura) (Diptera: Drosophilidae) is a serious invasive crop pest native to Asia and currently widespread in many parts of the globe. However, little information is available on its seasonal abundance in southern Italian fruit crops, including Mount Etna (Sicily, Italy). Here, we aimed at investigating i) the pest seasonal flight activity, ii) its population genetics, and iii) the potential occurrence of associated parasitoids. To this end, traps were deployed in five locations of strawberry and cherry districts of East and North-West sides of the Mount Etna for one year. In addition, host-parasitoid interactions with wasp species sampled by sentinel fruit trapping were investigated under laboratory conditions. The East locations were warmer than the North-West ones, and flies were captured all year except in August. In the North-West locations no flies were caught during the winter. Fly captures peaked in late spring and autumn in all locations. Sequencing of a portion of the mithocondrial cytochrome oxidase I (COI) from individuals of D. suzukii indicated a population genetic identity suggesting a single source of invasion. The field trapping revealed the occurrence of one larval parasitoid, Leptopilina boulardi (Barbotin, Carton and Kelner-Pillault) (Hymenoptera: Figitidae), and two pupal parasitoids, Pachycrepoideus vindemiae (Rondani) (Hymenoptera: Pteromalidae) and Trichopria drosophilae Perkins (Hymenoptera: Diapriidae). Nevertheless, only the pupal parasitoids were able to successfully develop on D. suzukii in laboratory bioassays. While obtained results indicate that climatic conditions strongly affect the local fly population and represent the bases for developing sustainable D. suzukii management programs, native parasitoid impact on pest population dynamic should be further investigated in this region-specific context.
... Drosophila fly populations track these changes, increasing rapidly when resources become available and decreasing abruptly once they are depleted (Breitmeyer & Markow, 1998). Worldwide, Drosophila species are hosts for more than 100 parasitoid species (Lue et al., 2021). Trichopria drosophilae and Pachycrepoideus vindemiae are cosmopolitan solitary Drosophilidae pupal parasitoids that coexist in both natural and agricultural ecosystems but have contrasting life histories. ...
Variability in the availability of resources through time is a common attribute in trophic interactions, but its effects on the fitness of different consumer species and on interspecific competition between them are not clearly understood.
To investigate this, we allowed two parasitoid species, Trichopria drosophilae and Pachycrepoideus vindemiae, to exploit Drosophila host pupae under different temporal variability treatments, either on their own or simultaneously.
When tested individually (in the absence of interspecific competition), both parasitoid species had lower fitness when hosts were exposed for a short duration at high density than when exposed for a long duration at low density. When both parasitoid species exploited hosts simultaneously, interspecific competition significantly decreased the number of offspring for both parasitoid species. The outcome of this interspecific competition depended on host temporal variability, with T. drosophilae or P. vindemiae dominating in short and long host exposure treatments, respectively.
These results can be explained by the combination of host availability and egg load of female adult parasitoids. When abundant hosts are provided for a short period, the ample mature eggs of the proovigenic T. drosophilae enable them to exploit hosts more efficiently than P. vindemiae, which is synovigenic. However, P. vindemiae is an intrinsically superior competitor and dominates when multiparasitism occurs. Multiparasitism is more frequent when hosts are at low levels relative to the egg load of the parasitoids.
Our results clearly demonstrate that resource temporal availability can alter the outcome of competition between consumers with different reproductive traits.
... A coordinated methodological approach to sampling and identifying introduced larval parasitoids of D. suzukii has been developed by Canadian and American researchers and is being implemented to delimit the range of adventive G. kimorum and L. japonica, determine whether they attack any species of Drosophila other than D. suzukii, and estimate their impact on D. suzukii populations (Abram et al., 2022b). In addition, a curated database of parasitoids of Drosophila has been developed to aid in conclusive identification of parasitoids collected by future studies (Lue et al., 2021). ...
Drosophila suzukii, spotted-wing drosophila, is an invasive pest in Canada that can lay its eggs into fresh fruits,
unlike many of its close relatives. Larval feeding inside fruit causes the fruit to spoil prematurely. Some parasitoids
have been found attacking D. suzukii larvae and pupae in regions that D. suzukii has invaded, including Asobara cf.
rufescens in Canada. A parasitoid from Asia, Ganaspis kimorum, has the narrowest host range of the parasitoids
identified in the native range of D. suzukii and has been approved for release in some countries. In 2019, an adventive population of G. kimorum and of another parasitoid, Leptopilina japonica, was detected in British Columbia, where research is now being conducted to determine if these parasitoids attack native species of Drosophila. The chapter also reviews the predators, pathogens, and use of sterile insect technique for biological control of
D. suzukii.
... While the use of UCE markers coupled with nex-gen sequencing technology has made generating larger amounts of data much easier and more affordable, there is still a place for mitochondrial 'barcode' data with respect to determining these cryptic species. We strongly encourage newly generated barcode data to be only compared to barcode data here in this paper, as well as barcode data in the Drosophila parasitoid database DROP (Lue et al. 2021) where sequences are backed by authoritatively identified voucher specimens. ...
Based on host specificity and distribution data, it has been hypothesized that Ganaspis brasiliensis (Ihering, 1905), a natural enemy of the horticultural pest spotted-wing drosophila, Drosophila suzukii Matsumura, 1931 (SWD), was composed of multiple, cryptic species. Parasitoid wasps assigned to the species name Ganaspis brasiliensis and Ganaspis cf. brasiliensis were investigated using a molecular dataset of ultra-conserved elements (UCEs) and morphology. We report strong evidence for the presence of cryptic species based on the combination of UCE data (1,379 UCE loci), host specificity, ovipositor morphology, and distribution data. We describe these new cryptic species as: Ganaspis lupinisp. nov., and Ganaspis kimorumsp. nov.Ganaspis lupini was formerly recognized as Ganaspis brasiliensis G3, and Ganaspis kimorum as Ganaspis brasiliensis G1. These two new species appear to be restricted to the temperate climates, whereas Ganaspis brasiliensis (formerly recognized as Ganaspis brasiliensis G5) has a more pan-tropical distribution. We investigated the characterization of the ovipositor clip of these species, and hypothesize that G. kimorum, which has a reduced ovipositor clip, has an advantage in ovipositing into fresh fruit, still on the host plant, while attacking SWD; as a corollary, G. brasiliensis and G. lupini, which both have a larger ovipositor clip, are better adapted to attacking hosts in softer, rotting fruit on the ground. As Ganaspis kimorum was authorized for release as a biological control agent against SWD under the name Ganaspis brasiliensis G1, the results here have direct impact on the field of biological control.
... Drosophila larvae and pupae serve as hosts to more than 60 species of such parasitic wasps. 5 The female wasp's sharp ovipositor pierces the first line of host defense-the larval exoskeleton, made of cuticle-to introduce an egg and venom. This step triggers an encapsulation response in which larval blood cells (hemocytes) of the hosts' innate immune system (macrophage-like plasmatocytes-called macrophages here-and their derivatives, lamellocytes) cooperate to recognize, surround, melanize, and destroy the wasp egg. ...
While fruit flies (Drosophila melanogaster) and humans exhibit immune system dysfunction in space, studies examining their immune systems’ interactions with natural parasites in space are lacking. Drosophila parasitoid wasps modify blood cell function to suppress host immunity. In this study, naive and parasitized ground and space flies from a tumor-free control and a blood tumor-bearing mutant strain were examined. Inflammation-related genes were activated in space in both fly strains. Whereas control flies did not develop tumors, tumor burden increased in the space-returned tumor-bearing mutants. Surprisingly, control flies were more sensitive to spaceflight than mutant flies; many of their essential genes were downregulated. Parasitoids appeared more resilient than fly hosts, and spaceflight did not significantly impact wasp survival or the expression of their virulence genes. Previously undocumented mutant wasps with novel wing color and wing shape were isolated post-flight and will be invaluable for host-parasite studies on Earth.
... The amber wasp L. heterotoma belongs to a large guild of parasitoids attacking Drosophila species, with a current count of 108 species belonging to 20 genera (Carton et al., 1986;Lue et al., 2021; Kraaijeveld & Godfray, 1999). D. phalerata is the most abundant fungal-feeding host and is parasitized mainly by L. clavipes (Driessen et al., 1990). ...
The parasitoid Leptopilina heterotoma has been used as a model system for more than 70 years, contributing greatly to diverse research areas in ecology and evolution. Here, we synthesized the large body of work on L. heterotoma with the aim to identify new research avenues that could be of interest also for researchers studying other parasitoids and insects. We start our review with a description of typical L. heterotoma characteristics, as well as that of the higher taxonomic groups to which this species belongs. We then continue discussing host suitability and immunity, foraging behaviors, as well as fat accumulation and life histories. We subsequently shift our focus towards parasitoid‐parasitoid interactions, including L. heterotoma coexistence within the larger guild of Drosophila parasitoids, chemical communication, as well as mating and population structuring. We conclude our review by highlighting the assets of L. heterotoma as a model system, including its intermediate life history syndromes, the ease of observing and collecting natural hosts and wasps, as well as recent genomic advances. The parasitoid Leptopilina heterotoma has been used as a model system in biology for more than 70 years. This review aims to provide a broad and detailed synthesis of the work performed on this system, including immunity, behavioral ecology, endosymbiotic and trophic interactions, as well as physiology. Overall, the scientific literature on L. heterotoma unites research based on field observations and experiments, as well as laboratory studies, highlighting the versatility of this model system.
... Drosophila larvae and pupae are hosts to numerous parasitic wasp (i.e., parasitoid) species 94 . During development, a parasitoid consumes fat from only a single host insect and fat stores are often not replenished during adult life 95,96 . ...
In arthropods, larger individuals tend to have more fat reserves, but data for many taxa are still missing. For the vinegar fly Drosophila melanogaster , only few studies have provided experimental data linking body size to fat content. This is rather surprising considering the widespread use of D. melanogaster as a model system in biology. Here, we hypothesized that fat content in D. melanogaster is positively correlated with body size. To test this, we manipulated the developmental environment of D. melanogaster by decreasing food availability. We then measured pupal size and quantified fat content of laboratory-reared D. melanogaster . We subsequently measured pupal size and fat content of several field-caught Drosophila species. Starvation, crowding, and reduced nutrient content led to smaller laboratory-reared pupae that contained less fat. Pupal size was indeed found to be positively correlated with fat content. The same correlation was found for field-caught Drosophila pupae belonging to different species. As fat reserves are often strongly linked to fitness in insects, further knowledge on the relationship between body size and fat content can provide important information for studies on insect ecology and physiology.
... Kirrama Range (S18°12. USNMENT01557102 and USNMENT01557297, reference sequence BOLD process ID:DROP164-21; for more details on the parasitoid strains used see Lue et al., 2021). We kept Drosophila isofemale lines on standard Drosophila medium (corn flour, yeast, sugar, agar and methyl-4-hydroxybenzoate) for approximately 45 to 70 non-overlapping generations. ...
Ecological communities are composed of many species, forming complex networks of interactions. Current environmental changes are altering the structure and species composition of ecological networks, which could modify interactions, either directly or indirectly. To predict changes in the functioning of communities, we need to understand whether species interactions are primarily driven by network structure (i.e. topology) or the specific identities of species (i.e. nodes). Yet, this partitioning of effects is challenging and thus rarely explored.
Here we disentangled the influence of network structure and the identities of species on the outcome of consumer–resource interactions using a host–parasitoid system.
We used four common community modules in host–parasitoid communities to represent network structure (i.e. host–parasitoid, exploitative competition, alternative host and a combination of exploitative competition and alternative host). We assembled nine different species combinations per community module in a laboratory experiment using a pool of three Drosophila hosts and three larval parasitoid species (Leptopilina sp., Ganaspis sp. and Asobara sp.). We compared host suppression and parasitoid performance across community modules and species assemblages to identify general effects linked to network structure and specific effects due to species community composition.
We found that multiple parasitoid species enhanced host suppression due to sampling effect, weaker interspecific than intraspecific competition between parasitoids, and synergism. However, the effects of network structure on parasitoid performance were species specific and dependent on the identity of co‐occurring species. Consequently, multiple parasitoid species generally strengthen top‐down control, but the performance of the parasitoids depends on the identity of either the co‐occurring parasitoid species, the alternative host species or both.
Our results highlight the importance of preserving parasitoid diversity for ecosystem functioning and show that other effects depend on species community composition, and may therefore be altered by ongoing environmental changes.
... The remaining sequences cover COI barcodes for 44 mainly Nearctic and Palaearctic species and very few ribosomal 18S and 28S sequences (Quicke et al. 2009). In order to facilitate ecological studies with Dusona, a reliable reference barcode library would be needed (Lue et al. 2021). ...
In the present time of biodiversity crisis, assessing species diversity by accurate and accessible taxonomic revisions is more crucial than ever. Parasitoid wasps are considered as both one of the most diverse and under-studied groups in the tree of life. Dusona Cameron, 1901 (Ichneumonidae, Campopleginae) is with 442 species one of the most species - rich genera of Darwin wasps, but despite the existence of recent keys, species identification has proven difficult to impossible to non-specialists. In this study, we examined about 1,500 Dusona specimens from recent and historical collections in Sweden and Switzerland. We provide a photographic guide to diagnostic characters and detailed plates for 57 out of 125 Western Palaearctic Dusona species, facilitating species identification based on existing keys. We add 11 and 3 species to the faunistic records of Sweden and Switzerland, respectively. Furthermore, we reconstruct the phylogeny of European Dusona based on four standard markers (COI, CAD, ITS2, 28S) for 45 species, complemented with a reliable reference barcode library for 46 species. Even though we can identify several morphologically distinct clades, we do not propose any new subgenera due to prevalent homoplasy of characters. While most species are well separated by barcodes, several morphologically distinct species have barely discriminatory barcode sequences (p-distances < 2%) or are even paraphyletic in this marker, indicating limitations in the applicability of barcodes for Darwin wasps. This study reveals severe gaps in the inventories of neglected taxa even for well-studied countries such as Sweden and Switzerland. As this study makes species determination for Western Palaearctic Dusona more accessible, we encourage more people, including non-specialists, to work with this genus.
... One specimen of L. japonica generated a sequence that could be analyzed (92% complementary between forward and reverse). The COI sequence of L. japonica was added to the Leptopilina species sequence matrix that was selected from the DROP project (Lue et al. 2021), a molecular voucher database designed for parasitoids of Drosophila species in which sequences are linked to vouchers and vetted by taxonomists. ...
We report the first known incidence of two parasitoid species of the invasive pest, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), in the United States (US). The discovery of Ganaspis brasiliensis (Ihering) (Hymenoptera: Figitidae) and Leptopilina japonica (Novković & Kimura) (Hymenoptera: Figitidae) in northwestern Washington State (US) was made shortly after their discovery in nearby southwestern British Columbia (Canada), indicating that contiguous populations of these species are established in both countries. The first specimen of L. japonica from Washington was collected in the fall of 2020, when it was found in a rice wine/orange juice trap deployed to survey for Vespa mandarinia Smith (Hymenoptera: Vespidae). Subsequent examination of trap contents from the 2020–2021 seasons indicated the presence of both L. japonica and G. brasiliensis. In September of 2021, live collections of both G. brasiliensis and L. japonica were made, reared from D. suzukii-infested Himalayan blackberry in Whatcom County, WA. Adult parasitoid identifications were based on morphology and COI DNA barcodes. All sequenced specimens to date from Washington and British Columbia belong to the G1 group of G. brasiliensis, the only group approved for release as a classical biological control agent in the US. This study provides an example of how even small changes in the geographic range of a natural enemy, now extending across an international border, may have significant consequences for the future of a biological control program.
... The three larval parasitoid species Asobara sp. [32]). Drosophila simulans isofemale lines were kept on standard Drosophila medium (corn flour, yeast, sugar, agar and methyl-4hydroxybenzoate) for approximately 45-70 non-overlapping generations before the experiments. ...
Current global changes are reshaping ecological communities and modifying environmental conditions. We need to recognize the combined impact of these biotic and abiotic factors on species interactions, community dynamics and ecosystem functioning. Specifically, the strength of predator prey interactions often depends on the presence of other natural enemies: it weakens with competition and interference or strengthens with facilitation. Such effects of multiple predators on prey are likely to be affected by changes in the abiotic environment, altering top-down control, a key structuring force in natural and agricultural ecosystems. Here, we investigated how warming alters the effects of multiple predators on prey suppression using a dynamic model coupled with empirical laboratory experiments with Drosophila-parasitoid communities. While multiple parasi-toids enhanced top-down control under warming, parasitoid performance generally declined when another parasitoid was present owing to competitive interactions. This could reduce top-down control over multiple generations. Our study highlights the importance of accounting for interactive effects between abiotic and biotic factors to better predict community dynamics in a rapidly changing world and thus better preserve ecosystem functioning and services such as biological control.
Drosophila and parasitic wasps in the genus Leptopilina have long been a model for understanding host-parasite interactions. Indeed, parasitic wasps are important drivers of ecological and evolutionary processes broadly, but we are generally lacking information about the diversity, natural history, and evolution of these relationships. We collected insects from the Caribbean Island of Saint Lucia, home to the eastern Caribbean ‘ dunni ’ subgroup of Drosophila : a clade long appreciated for its recent patterns of speciation and adaptation. Here we present an integrative approach that incorporates natural history, taxonomy, physiology, and genomics to describe Leptopilina n. sp. Buffington, Lue, Davis & Tracey sp. nov. (Hymenoptera: Figitidae), a virulent parasitoid of dunni group flies, especially Drosophila antillea. Leptopilina n. sp. is nested within an early-branching clade of Leptopilina , offering insights into the evolution of this important genus of Drosophila parasitoids. We present a high-quality assembly for this wasp’s 1Gbp genome, and for its bacterial endosymbiont: Wolbachia strain “ w Lmal”. Furthermore, we show that w Lmal induces parthenogenesis in the wasp, and that these wasps are reliant upon their Wolbachia infections to produce female offspring. Finally, comparison to historical museum specimens indicate that Leptopilina n. sp. had been collected approximately 40 years prior from the nearby island of Guadeloupe and were also asexually reproducing. This work represents one of only a handful of studies in which field biology, taxonomy, systematics, genomics, and experimental biology are integrated into a species description: showcasing the possibilities for biodiversity research in the genomic era.
Ecological communities face major challenges of biodiversity loss, invasive species, and warming due to human action. Factors that determine the dynamics, stability and functioning of network of interacting species have been debated in ecology since its beginning as discipline. Community complexity and dominant (keystone) species have been proposed as the most relevant factors, however there is lack of knowledge on how these factors will interact with warming and invasion. To determine the effect of complexity, warming or invasion and their combinations on stability and functioning of a food web we performed a microcosm laboratory experiment using Drosophila -parasitoid food webs as a model. During five months, we recorded the dynamics of twelve different food webs (different combinations of flies and parasitoid species with two complexity levels) subjected to two temperature regimes (ambient and warming) and invasion or not by Drosophila suzukii in a factorial design. We did not observe any major effect of complexity or invasion. However, species composition had major effect, as webs with Drosophila simulans present were rapidly dominated by it, reducing diversity, increasing parasitism rate, reducing stability and bringing the community on the verge of collapse. Warming in turn increased diversity, overall fly population and temporal stability, while decreasing parasitism rate. Invasion of D. suzukii was not successful in any of the networks, possibly due to its low competitive ability. Our results imply that dominant species can have very strong effects on dynamics and stability, compared to food web complexity.
Drosophila and its parasitoids provide an ecologically relevant model for studying host-parasitoid biology, focusing on the behavioral and physiological responses involved in host defensive strategies and parasitoid countermeasures. Here, we outline a protocol for rearing Pachycrepoideus, a pupal parasitoid wasp, and a behavioral assay to assess the long-term impact of parasitoid exposure on adult Drosophila. We detail the steps for preparing and cohabiting Drosophila with the wasps, documenting egg-laying, and analyzing reproductive responses and eclosion in fruit flies.
For complete details on the use and execution of this protocol, please refer to Sadanandappa et al.¹
Parasitoid wasps are exceptionally diverse and use specialized adaptations capable of manipulating the physiology and behaviour of host organisms¹. In more than two centuries since the first records of Drosophila-parasitizing wasps, nearly 200 described and provisional parasitoid species of drosophilids have been identified². These include endoparasitoids and ectoparasitoids, as well as species attacking larval and pupal hosts³. Despite a deep history of research attention and remarkable biodiversity, a wasp species that attacks and develops inside the adult stage of a fly host has not been described previously. Here we report the discovery of a wasp species that infects the adult stage of fruit flies in the genus Drosophila, including one of the most deeply studied model organisms in biology, Drosophila melanogaster. Notably, this wasp can be easily collected from backyard fly baits and has a broad geographic distribution throughout the eastern USA. We document its life history and unique host interactions, including egg-laying into and larval emergence from adult flies, and provide protocols to raise wasps from wild-caught host flies. Our results emphasize the need for ongoing research investment in insect biodiversity and systematics. As parasitoid research continues to uncover unusual biology and supports fundamental mechanistic insights into immunity⁴, metabolism⁵, ecology⁶, evolution7–9 and behaviour10–12, we anticipate that this wasp’s association with the laboratory model organism, D. melanogaster, will provide new research opportunities across the life sciences.
Bacteria in the genus Wolbachia have evolved numerous strategies to manipulate arthropod sex, including the conversion of would-be male offspring to asexually reproducing females. This so-called “parthenogenesis induction” phenotype can be found in a number of Wolbachia strains that infect arthropods with haplodiploid sex determination systems, including parasitoid wasps. Despite the discovery of microbe-mediated parthenogenesis more than 30 yr ago, the underlying genetic mechanisms have remained elusive. We used a suite of genomic, computational, and molecular tools to identify and characterize two proteins that are uniquely found in parthenogenesis-inducing Wolbachia and have strong signatures of host-associated bacterial effector proteins. These putative parthenogenesis-inducing proteins have structural homology to eukaryotic protein domains including nucleoporins, the key insect sex determining factor Transformer, and a eukaryotic-like serine–threonine kinase with leucine-rich repeats. Furthermore, these proteins significantly impact eukaryotic cell biology in the model Saccharomyces cerevisiae. We suggest that these proteins are parthenogenesis-inducing factors and our results indicate that this would be made possible by a novel mechanism of bacterial-host interaction.
Variability in the availability of resources through time is a common attribute in trophic interactions, but its effects on the fitness of different consumer species and on interspecific competition between them are not clearly understood.
To investigate this, we allowed two parasitoid species, Trichopria drosophilae and Pachycrepoideus vindemiae , to exploit Drosophila host pupae under three temporal variability treatments, either on their own or simultaneously.
When tested individually (in the absence of interspecific competition), both parasitoid species had lower fitness when hosts were exposed for a short duration at high density than when exposed for a long duration at low density. When both parasitoid species exploited hosts simultaneously, interspecific competition significantly decreased the number of offspring for both parasitoid species. The outcome of this interspecific competition depended on host temporal variability, with T. drosophilae or P. vindemiae dominating in short and long host exposure treatments, respectively.
These results can be explained by the combination of host availability and egg load of female adult parasitoids. When abundant hosts are provided for a short period, the ample mature eggs of the proovigenic T. drosophilae enable them to exploit hosts more efficiently than P. vindemiae , which is synovigenic. However, P. vindemiae is an intrinsically superior competitor and dominates when multiparasitism occurs. Multiparasitism is more frequent when hosts are at low levels relative to the egg load of the parasitoids.
Our results clearly demonstrate that resource temporal availability can alter the outcome of competition between consumers with different reproductive traits.
As mean temperatures increase and heatwaves become more frequent, species are expanding their distributions to colonise new habitats. The resulting novel species interactions will simultaneously shape the temperature‐driven reorganization of resident communities. The interactive effects of climate change and climate change‐facilitated invasion have rarely been studied in multi‐trophic communities, and are likely to differ depending on the nature of the climatic driver (i.e., climate extremes or constant warming). We re‐created under laboratory conditions a host‐parasitoid community typical of high‐elevation rainforest sites in Queensland, Australia, comprising four Drosophila species and two associated parasitoid species. We subjected these communities to an equivalent increase in average temperature in the form of periodic heatwaves or constant warming, in combination with an invasion treatment involving a novel host species from lower‐elevation habitats. The two parasitoid species were sensitive to both warming and heatwaves, while the demographic responses of Drosophila species were highly idiosyncratic, reflecting the combined effects of thermal tolerance, parasitism, competition, and facilitation. After multiple generations, our heatwave treatment promoted the establishment of low‐elevation species in upland communities. Invasion of the low‐elevation species correlated negatively with the abundance of one of the parasitoid species, leading to cascading effects on its hosts and their competitors. Our study, therefore, reveals differing, sometimes contrasting, impacts of extreme temperatures and constant warming on community composition. It also highlights how the scale and direction of climate impacts could be further modified by invading species within a bi‐trophic community network.
As mean temperatures increase and heatwaves become more frequent, species are expanding their distributions to colonise new habitats. The resulting novel species interactions will simultaneously shape the temperature-driven reorganization of resident communities. The interactive effects of climate change and climate change-facilitated invasion have rarely been studied in multi-trophic communities, and are likely to differ depending on the nature of the climatic driver (i.e. climate extremes or constant warming). We recreated under laboratory conditions a host-parasitoid community typical of high-elevation rainforest sites in Queensland, Australia, comprising four Drosophila species and two associated parasitoid species. We subjected these communities to climate change in the form of either heatwaves or constant warming, in combination with an invasion treatment involving a novel host species from lower-elevation habitats. The two parasitoid species were sensitive to both warming and heatwaves, while the demographic responses of Drosophila species were highly idiosyncratic, reflecting the combined effects of thermal tolerance, parasitism, competition, and facilitation. After multiple generations, heatwaves (but not constant warming) promoted the establishment of low-elevation species in upland communities. The introduction of this invading species correlated negatively with the abundance of one of the parasitoid species, leading to cascading effects on its hosts and their competitors. Our study, therefore, reveals differing, sometimes contrasting, impacts of extreme temperatures and constant warming on community composition. It also highlights how the scale and direction of climate impacts could be further modified by range-expanding species within a bi-trophic community network.
Metabarcoding is revolutionizing fundamental research in ecology by enabling large-scale detection of species and producing data that is rich with community context. However, the benefits of metabarcoding have yet to be fully realized in fields of applied ecology, especially those such as classical biological control (CBC) research that involve hyper-diverse taxa. Here, we discuss some of the opportunities that metabarcoding provides CBC and solutions to the main methodological challenges that have limited the integration of metabarcoding in existing CBC workflows. We focus on insect parasitoids, which are popular and effective biological control agents (BCAs) of invasive species and agricultural pests. Accurately identifying native, invasive, and BCA species is paramount, since misidentification can undermine control efforts and lead to large negative socioeconomic impacts. Unfortunately, most existing publicly accessible genetic databases cannot be used to reliably identify parasitoid species, thereby limiting the accuracy of metabarcoding in CBC research. To address this issue, we argue for the establishment of authoritative genetic databases that link metabarcoding data to taxonomically identified specimens. We further suggest using multiple genetic markers to reduce primer bias and increase taxonomic resolution. We also provide suggestions for biological control-specific metabarcoding workflows intended to track the long-term effectiveness of introduced BCAs. Finally, we use the example of the invasive pest, Drosophila suzukii, in a reflective "what if" thought experiment to explore the potential power of community metabarcoding in CBC.
Climate change is altering the relative timing of species interactions by shifting when species first appear in communities and modifying the duration organisms spend in each developmental stage. However, community contexts, such as intraspecific competition and alternative resource species, can prolong shortened windows of availability and may mitigate the effects of phenological shifts on species interactions. Using a combination of laboratory experiments and dynamic simulations, we quantified how the effects of phenological shifts in Drosophila‐parasitoid interactions differed with concurrent changes in temperature, intraspecific competition, and the presence of alternative host species. Our study confirmed that warming shortens the window of host susceptibility. However, the presence of alternative host species sustained interaction persistence across a broader range of phenological shifts than pairwise interactions by increasing the degree of temporal overlap with suitable development stages between hosts and parasitoids. Irrespective of phenological shifts, parasitism rates declined under warming due to reduced parasitoid performance, which limited the ability of community context to manage temporally mismatched interactions. These results demonstrate that the ongoing decline in insect diversity may exacerbate the effects of phenological shifts in ecological communities under future global warming temperatures.
We provide recommendations for sampling and identification of introduced larval parasitoids of spotted-wing drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae). These parasitoids are either under consideration for importation (aka classical) biological control introductions, or their adventive (presumed to
have been accidentally introduced) populations have recently been discovered in North America and Europe. Within the context of the ecology of D. suzukii and its parasitoids, we discuss advantages and disadvantages of estimating larval parasitism levels using different methods, including naturally collected fruit samples and sentinel baits. For most situations, we recommend repeated sampling of naturally occurring fruit rather than using sentinel baits to monitor seasonal dynamics of host plant–Drosophila–parasitoid associations. We describe how to separate Drosophilidae puparia from host fruit material in order to accurately estimate parasitism levels and establish host–parasitoid associations. We provide instructions for identification of emerging parasitoids
and include a key to the common families of parasitoids of D. suzukii. We anticipate that the guidelines for methodology and interpretation of results that we provide here will form the basis for a large, multi-research team sampling effort in the coming years to characterize the biological control and nontarget impacts of accidentally and intentionally introduced larval parasitoids of D. suzukii in several regions of the world.
Climate change is altering the relative timing of species interactions by shifting when species appear in a community and by accelerating developmental rates. However, phenological shifts may be mediated through community contexts, such as intraspecific competition and alternative resource species, which can prolong the otherwise shortened windows of availability. Using a combination of laboratory experiments and dynamic simulations, we quantified how the effects of phenological shifts in Drosophila-parasitoid interactions differed with concurrent changes in temperature, intraspecific competition, and the presence of alternative host species. We found that community context, particularly the presence of alternative host species, supported interaction persistence across a wider range of phenological shifts than pairwise interactions. Parasitism rates declined under warming, which limited the ability of community contexts to manage mismatched interactions. These results demonstrate that ongoing declines in insect diversity may exacerbate the effects of phenological shifts in ecological communities under future global warming temperatures.
The role of natural enemies in promoting coexistence of competing species has generated substantial debate. Modern coexistence theory provides a detailed framework to investigate this topic, but there have been remarkably few empirical applications to the impact of natural enemies.
We tested experimentally the capacity for a generalist enemy to promote coexistence of competing insect species, and the extent to which any impact can be predicted by trade‐offs between reproductive rate and susceptibility to natural enemies.
We used experimental mesocosms to conduct a fully factorial pairwise competition experiment for six rainforest Drosophila species, with and without a generalist pupal parasitoid. We then parameterised models of competition and examined the coexistence of each pair of Drosophila species within the framework of modern coexistence theory.
We found idiosyncratic impacts of parasitism on pairwise coexistence, mediated through changes in fitness differences, not niche differences. There was no evidence of an overall reproductive rate–susceptibility trade‐off. Pairwise reproductive rate–susceptibility relationships were not useful shortcuts for predicting the impact of parasitism on coexistence.
Our results exemplify the value of modern coexistence theory in multi‐trophic contexts and the importance of contextualising the impact of generalist natural enemies to determine their impact. In the set of species investigated, competition was affected by the higher trophic level, but the overall impact on coexistence cannot be easily predicted just from knowledge of relative susceptibility. Methodologically, our Bayesian approach highlights issues with the separability of model parameters within modern coexistence theory and shows how using the full posterior parameter distribution improves inferences. This method should be widely applicable for understanding species coexistence in a range of systems.
Due to their small size and smooth body, members of the figitid genus Alloxysta can be notoriously difficult to identify based on morphology alone. Moreover, several species are suspected to contain brachypterous variants that previously have been described under separate names. We used gene sequences of the mitochondrial gene cytochrome c oxidase subunit 1 (COI, DNA barcodes) and the internal transcribed spacer (ITS2) to investigate the relationships between species within the genus. Our results show that there is considerably more intraspecific variation in COI than in ITS2, but that both markers can be used to identify potential synonyms of brachypterous and fully winged species. Maximum Likelihood and Bayesian analyses of a concatenated dataset of both markers resulted in similar and fairly well supported phylogenies that indicate genetic divergence not matching morphological species boundaries for some groups. Some of the discrepancies can be explained by infections of the endosymbiont Wolbachia, here reported from the first time in Alloxysta and Charipinae. This study also presents the first records of A. arcuata, A. basimacula, A. brachycera, A. brachyptera, A. brevis, A. citripes, A. consobrina, A. curta, A. fracticornis, A. halterata, A. marshalliana, A. obscurata, A. proxima, A. pusilla, A. ramulifera and A. xanthopa from Norway.
Background: Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior known as galling. Less commonly, cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to usurp other species' galls instead of inducing their own. Using a phylogenomic data set of ultraconserved elements from nearly all lineages of Cynipoidea, we here generate a robust phylogenetic framework and timescale to understand cynipoid systematics and the evolution of these life histories. Results: Our reconstructed evolutionary history for Cynipoidea differs considerably from previous hypotheses. Rooting our analyses with non-cynipoid outgroups, the Paraulacini, a group of inquilines, emerged as sister-group to the rest of Cynipoidea, rendering the gall wasp family Cynipidae paraphyletic. The families Ibaliidae and Liopteridae, long considered archaic and early-branching parasitoid lineages, were found nested well within the Cynipoidea as sister-group to the parasitoid Figitidae. Cynipoidea originated in the early Jurassic around 190 Ma. Either inquilinism or parasitoidism is suggested as the ancestral and dominant strategy throughout the early evolution of cynipoids, depending on whether a simple (three states: parasitoidism, inquilinism and galling) or more complex (seven states: parasitoidism, inquilinism and galling split by host use) model is employed. Conclusions: Our study has significant impact on understanding cynipoid evolution and highlights the importance of adequate outgroup sampling. We discuss the evolutionary timescale of the superfamily in relation to their insect hosts and host plants, and outline how phytophagous galling behavior may have evolved from entomophagous, parasitoid cynipoids. Our study has established the framework for further physiological and comparative genomic work between gall-making, inquiline and parasitoid lineages, which could also have significant implications for the evolution of diverse life histories in other Hymenoptera.
The role of natural enemies in promoting coexistence of competing species has generated substantial debate. Modern coexistence theory provides a detailed framework to investigate this topic, but there have been remarkably few empirical applications to the impact of natural enemies.
We tested experimentally the capacity for a generalist enemy to promote coexistence of competing insect species, and the extent to which any impact can be predicted by trade‐offs between reproductive rate and susceptibility to natural enemies.
We used experimental mesocosms to conduct a fully factorial pairwise competition experiment for six rainforest Drosophila species, with and without a generalist pupal parasitoid. We then parameterised models of competition and examined the coexistence of each pair of Drosophila species within the framework of modern coexistence theory.
We found idiosyncratic impacts of parasitism on pairwise coexistence, mediated through changes in fitness differences, not niche differences. There was no evidence of an overall reproductive rate–susceptibility trade‐off. Pairwise reproductive rate–susceptibility relationships were not useful shortcuts for predicting the impact of parasitism on coexistence.
Our results exemplify the value of modern coexistence theory in multi‐trophic contexts and the importance of contextualising the impact of generalist natural enemies to determine their impact. In the set of species investigated, competition was affected by the higher trophic level, but the overall impact on coexistence cannot be easily predicted just from knowledge of relative susceptibility. Methodologically, our Bayesian approach highlights issues with the separability of model parameters within modern coexistence theory and shows how using the full posterior parameter distribution improves inferences. This method should be widely applicable for understanding species coexistence in a range of systems.
Halting biodiversity decline is one of the most critical challenges for humanity, but biodiversity assessment and monitoring are hampered by taxonomic impediments. We here distinguish between a "dark taxon impediment" caused by a large number of undescribed species and a "superficial description impediment" caused by species descriptions so imprecise that type specimens have to be consulted in order to resolve species identities. Recently, Sharkey et al. (2021) proposed to address the dark taxon impediment for Costa Rican braconid wasps by describing 403 species based on barcode clusters ("BINs") computed by BOLD Systems. The default assumption of the revision is that BIN=Species (e.g., BOLD:ACM9419 becomes Bracon federicomatarritai Sharkey, sp. nov.) and therefore the diagnoses of most species consist only of a consensus barcode. We here argue that this type of "minimalist revision" is unnecessary and undesirable. It is unnecessary because barcode clusters (e.g. BINs) already provide grouping statements that overcome many of the obstacles associated with dark taxon impediments. However, minimalist revisions are also undesirable and problematic because the diagnoses are only based on one character system - that in the case of Sharkey et al. was poorly analyzed. Furthermore, the revision relies on units that violate basic rules of reproducibility because the BINs were delimited by a proprietary algorithm (RESL) that is applied to a mixture of public and private data. Here, we illustrate that many of the BINs described as species are unstable when the available public data are reanalyzed, reiterate that COI mostly measures time of divergence, and that BOLD Systems violates key principles of open science. We conclude by urging authors, reviewers, editors, and grantors to only publish and fund projects that adhere to modern standards of reproducibility.
Global warming is expected to have direct effects on species through their sensitivity to temperature, and also via their biotic interactions, with cascading indirect effects on species, communities, and entire ecosystems. To predict the community-level consequences of global climate change we need to understand the relative roles of both the direct and indirect effects of warming. We used a laboratory experiment to investigate how warming affects a tropical community of three species of Drosophila hosts interacting with two species of parasitoids over a single generation. Our experimental design allowed us to distinguish between the direct effects of temperature on host species performance, and indirect effects through altered biotic interactions (competition among hosts and parasitism by parasitoid wasps). Although experimental warming significantly decreased parasitism for all host-parasitoid pairs, the effects of parasitism and competition on host abundances and host frequencies did not vary across temperatures. Instead, effects on host relative abundances were species-specific, with one host species dominating the community at warmer temperatures, irrespective of parasitism and competition treatments. Our results show that temperature shaped a Drosophila host community directly through differences in species’ thermal performance, and not via its influences on biotic interactions.
Drosophila suzukii (Matsumura) is native to East Asia but has widely established in the Americas and Europe, where it is a devastating pest of soft-skinned fruits. It has a wide host range and these non-crop habitats harbor the fly which then repeatedly reinvades crop fields. Biological control in non-crop habitats could be the cornerstone for sustainable management at the landscape level. Toward this goal, researchers have developed or investigated biological control tactics. We review over 100 studies, conducted in the Americas, Asia and Europe on natural enemies of D. suzukii. Two previous reviews provided an overview of potential natural enemies and detailed accounts on foreign explorations. Here, we provide an up-to-date list of known or evaluated parasitoids, predators and entomopathogens (pathogenic fungi, bacteria, nematodes, and viruses) and summarize research progress to date. We emphasize a systematic approach toward the development of biological control strategies that can stand alone or be combined with more conventional control tools. Finally, we propose a framework for the integrated use of biological control tools, from classical biological control with host-specific Asian parasitoids, to augmentative and conservation biological control with indigenous natural enemies, to the use of entomopathogens. This review provides a roadmap to foster the use of biological control tools in more sustainable D. suzukii control programs. Review Methodology: We searched and reviewed scientific literature on natural enemies and biological controls of Drosophila suzukii from major online databases such as CAB Abstracts, Google Scholar, and ISI Web of Science. The literature has been synthesized by authors working on D. suzukii biological control over the past decade.
The analysis of interaction networks across spatial environmental gradients is a powerful approach to investigate the responses of communities to global change. Using a combination of DNA metabarcoding and traditional molecular methods we built bipartite Drosophila – parasitoid food webs from six Australian rainforest sites across gradients spanning 850 m in elevation and 5°C in mean temperature. Our cost‐effective hierarchical approach to network reconstruction separated the determination of host frequencies from the detection and quantification of interactions. The food webs comprised 5–9 host and 5–11 parasitoid species at each site, and showed a lower incidence of parasitism at high elevation. Despite considerable turnover in the relative abundance of host Drosophila species, and contrary to some previous results, we did not detect significant changes to fundamental metrics of network structure including nestedness and specialisation with elevation. Advances in community ecology depend on data from a combination of methodological approaches. It is therefore especially valuable to develop model study systems for sets of closely‐interacting species that are diverse enough to be representative, yet still amenable to field and laboratory experiments.
Background: Parasitoidism, a specialized life strategy in which a parasite eventually kills its host, is frequently found
within the insect order Hymenoptera (wasps, ants and bees). A parasitoid lifestyle is one of two dominant life strategies
within the hymenopteran superfamily Cynipoidea, with the other being an unusual plant-feeding behavior
known as galling. Less commonly, cynipoid wasps exhibit inquilinism, a strategy where some species have adapted to
usurp other species’ galls instead of inducing their own. Using a phylogenomic data set of ultraconserved elements
from nearly all lineages of Cynipoidea, we here generate a robust phylogenetic framework and timescale to understand
cynipoid systematics and the evolution of these life histories.
Results: Our reconstructed evolutionary history for Cynipoidea differs considerably from previous hypotheses.
Rooting our analyses with non-cynipoid outgroups, the Paraulacini, a group of inquilines, emerged as sister-group to
the rest of Cynipoidea, rendering the gall wasp family Cynipidae paraphyletic. The families Ibaliidae and Liopteridae,
long considered archaic and early-branching parasitoid lineages, were found nested well within the Cynipoidea as
sister-group to the parasitoid Figitidae. Cynipoidea originated in the early Jurassic around 190 Ma. Either inquilinism
or parasitoidism is suggested as the ancestral and dominant strategy throughout the early evolution of cynipoids,
depending on whether a simple (three states: parasitoidism, inquilinism and galling) or more complex (seven states:
parasitoidism, inquilinism and galling split by host use) model is employed.
Conclusions: Our study has significant impact on understanding cynipoid evolution and highlights the importance
of adequate outgroup sampling. We discuss the evolutionary timescale of the superfamily in relation to their insect
hosts and host plants, and outline how phytophagous galling behavior may have evolved from entomophagous,
parasitoid cynipoids. Our study has established the framework for further physiological and comparative genomic
work between gall-making, inquiline and parasitoid lineages, which could also have significant implications for the
evolution of diverse life histories in other Hymenoptera.
African fig fly, Zaprionus indianus Gupta (Diptera: Drosophilidae), is originally from the Afrotropics but has been expanding its geographical range globally, including the United States. It was first reported in Virginia northward in 2012. The current established range of African species is thought to be limited to the southern states in winter, and populations must disperse northward each season. Adults are normally caught in Virginia in mid-summer and later. African fig fly is a competitive invader and affects the dynamics of native drosophilid communities when it invades a new area. While lacking the hardened, serrated ovipositor seen in spotted-wing drosophila, another invasive frugivore, it may come to outnumber that species in commercial plantings. It can lay eggs and develop in many kinds of fruit that have been otherwise injured. However, the ovipositing fly may take advantage of oviposition sites of spotted-wing drosophila, thereby allowing entry of African fig fly larvae, which may outcompete the original inhabitants. Furthermore, African fig fly may be able to infest certain soft-fruit hosts. Biological control in North America and Europe is limited at this time by immunological responses of host larvae; naturally occurring parasitoids have been unable to achieve significant parasitization.
Uncertainty about the taxonomic status and the specificity of a species commonly prevent its consideration as a candidate for biological control of pest organisms. Here we use a combination of molecular analysis and crossing experiments to gather evidence that the parasitoid wasp Ganaspis brasiliensis, a candidate for biological control of the invasive spotted wing drosophila Drosophila suzukii, is a complex of at least two cryptic species. Complementary experiments demonstrate that individuals from one genetic group readily parasitize several drosophila species regardless of their food source while individuals from the other one are almost exclusively specific to larvae feeding in ripening fruits. Because only D. suzukii attacks ripening fruits in its area of invasion, parasitoids from this second group appear to be well suited as a biological control agent. Our study demonstrates the need for a combination of biosystematics with biological and ecological investigations for the development of safe and efficient biological control programs.
We report the presence of two Asian species of larval parasitoids of spotted wing Drosophila, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), in northwestern North America. Leptopilina japonica Novkovic & Kimura and Ganaspis brasiliensis (Ihering) (Hymenoptera: Figitidae) were found foraging near and emerging from fruits infested by D. suzukii at several locations across coastal British Columbia, Canada in the summer and fall of 2019. While G. brasiliensis was found in British Columbia for the first time in 2019, re-inspection of previously collected specimens suggests that L. japonica has been present since at least 2016. Additionally, we found a species of Asobara associated with D. suzukii in British Columbia that is possibly Asobara rufescens (Förster) (known only from the Palearctic Region) based on COI DNA barcode data. These findings add to the list of cases documenting adventive establishment of candidate classical biological control agents outside of their native ranges. The findings also illustrate the need for revisiting species concepts within Asobara, as well as host and geographic distribution data due to cryptic and/or misidentified species.
The role of natural enemies in promoting coexistence of competing species has generated substantial debate. Modern coexistence theory provides a detailed framework to investigate this topic, but there have been remarkably few empirical applications to the impact of natural enemies.
We tested experimentally the capacity for a generalist enemy to promote coexistence of competing insect species, and the extent to which any impact can be predicted by trade-offs between reproductive rate and susceptibility to natural enemies.
We used experimental mesocosms to conduct a fully-factorial pairwise competition experiment for six rainforest Drosophila species, with and without a generalist pupal parasitoid. We then parameterised models of competition and examined the coexistence of each pair of Drosophila species within the framework of modern coexistence theory.
We found idiosyncratic impacts of parasitism on pairwise coexistence, mediated through changes in fitness differences, not niche differences. There was no evidence of an overall reproductive rate – susceptibility trade-off. Pairwise reproductive rate – susceptibility relationships were not useful shortcuts for predicting the impact of parasitism on coexistence.
Our results exemplify the value of modern coexistence theory in multi-trophic contexts and the importance of contextualising the impact of natural enemies. In the set of species investigated, competition was affected by the higher trophic level, but the overall impact on coexistence cannot be easily predicted just from knowledge of relative susceptibility. Methodologically, our Bayesian approach highlights issues with the separability of model parameters within modern coexistence theory and shows how using the full posterior parameter distribution improves inferences. This method should be widely applicable for understanding species coexistence in a range of systems.
To assess the potential of Asobara japonica Belokobylskij (Hymenoptera: Braconidae) as a biological control agent for the invasive Drosophila suzukii (Matsumura) (Diptera: Drosophilidae), key biological traits were evaluated: preference and suitability of different host ages, relative performance on two host species (D. suzukii and Drosophila melanogaster Meigen), female life-time fecundity and egg maturation on the two host species, and parasitism levels on D. suzukii larvae infesting different host fruits (blackberry, cherry and strawberry). Asobara japonica preferred young over old hosts, and although host age did not affect offspring survival, parasitoid offspring developed faster in older than younger hosts but had a reduced body size. There was higher A. japonica offspring survival, longer developmental time, and larger body when reared from D. suzukii than D. melanogaster. Female wasps emerged with around one third of their lifetime egg load and matured eggs rapidly with mature egg load reaching a peak 2-3 d post-emergence. Large females (typically reared from D. suzukii) contained more mature eggs than small females (typically from D. melanogaster). During their lifetime, A. japonica females produced 117.4 and 92.5 progeny on D. suzukii and D. melanogaster, respectively, with a corresponding intrinsic rate of increase of 0.217 and 0.210, respectively. Progeny were strongly female-biased (> 90% females), regardless of host age or species. This larval parasitoid was able to develop from D. suzukii infesting cherry, blackberry or strawberry. This information may help improve protocols for the rearing and future evaluations of this parasitoid for a potential biological control program against D. suzukii.
Applications of biological knowledge, such as forensics, often require the determination of biological materials to a species level. As such, DNA-based approaches to identification, particularly DNA barcoding, are attracting increased interest. The capacity of DNA barcodes to assign newly encountered specimens to a species relies upon access to informatics platforms, such as BOLD and GenBank, which host libraries of reference sequences and support the comparison of new sequences to them. As parameterization of these libraries expands, DNA barcoding has the potential to make valuable contributions in diverse applied contexts. However, a recent publication called for caution after finding that both platforms performed poorly in identifying specimens of 17 common insect species. This study follows up on this concern by asking if the misidentifications reflected problems in the reference libraries or in the query sequences used to test them. Because this reanalysis revealed that missteps in acquiring and analyzing the query sequences were responsible for most misidentifications, a workflow is described to minimize such errors in future investigations. The present study also revealed the limitations imposed by the lack of a polished species-level taxonomy for many groups. In such cases, applications can be strengthened by mapping the geographic distributions of sequence-based species proxies rather than waiting for the maturation of formal taxonomic systems based on morphology.
For more than two centuries, biodiversity collections have served as the foundation for scientific investigation of and education about life on Earth (Melber and Abraham 2002, Cook et al. 2014, Funk 2018). The collections that have been assembled in the past and continue to grow today are a cornerstone of our national heritage that have been treated as such since the founding of the United States (e.g., Jefferson 1799, Goode 1901a, 1901b, Meisel 1926). A diverse array of institutions throughout the United States, from museums and botanical gardens to universities and government agencies, maintain our biodiversity collections as part of their research and education missions. Collectively, these institutions and their staff are stewards for at least 1 billion biodiversity specimens that include such diverse objects as dinosaur bones, pressed plants, dried mushrooms, fish preserved in alcohol, pinned insects, articulated skeletons, eggshells, and microscopic pollen grains. In turn, these collections are a premier resource for exploring life, its forms, interactions, and functions, across evolutionary, temporal, and spatial scales (Bebber et al. 2010, Monfils et al. 2017, Schindel and Cook 2018).
Biodiversity collections have historically consisted of physical objects and the infrastructure to support those objects (Bradley et al. 2014). However, the last two decades have witnessed a remarkable wave of digitization that has reshaped the collections paradigm to include digital data and infrastructure (Nelson and Ellis 2018), opening vast new areas for integrative biological research (e.g., a single plant specimen mounted on an herbarium sheet may be analyzed in multitude ways to yield data on flower morphology, DNA for applications from systematic studies to genome sequences, and isotopes for analyses of nitrogen to understand the mechanisms of phenology in relation to nitrogen uptake). In the United States, investment by the federal government through the National Science Foundation's (NSF) Advancing Digitization of Biodiversity Collections (ADBC) program has facilitated the digitization of approximately 62 million US biodiversity specimens since 2011 through 24 thematic collection networks connecting over 700 collections. These networks have helped to develop a collaborative infrastructure connecting specimen data, human resources, research, and education among institutions. The ADBC program has also provided support to iDigBio (the Integrated Digitized Biocollections), which is the central coordinating unit for the digitization effort. The final ADBC grants will be awarded in 2021.
During the last several years, the Biodiversity Collections Network has led an effort to gather input from primary stakeholder communities regarding future directions for collections and their use in research and education. The effort culminated in a workshop held from 30 October through 1 November 2018 at Oak Spring Garden in Upperville, Virginia, during which a strategy was developed to maximize the value of collections for future research and education that builds on and leverages the accomplishments of the ADBC program. The strategy that was informed by stakeholders, refined by workshop participants, and vetted through public comment from scientific community is presented in the present article.
Drosophila suzukii has become a key invasive pest of soft- and thin-skinned fruit crops in its invaded regions in Europe and Americas, where naturally occurring natural enemies are generally not effective for the suppression of this pest or largely absent such as larval-attacking parasitoids. As a part of systematic evaluations of candidate agents for classical biological control of this invasive pest, we evaluated the functional responses of three Asian-native larval hymenopteran parasitoids, Asobara japonica (Braconidae), Ganaspis brasiliensis, and Leptopilina japonica (both Figitidae) to D. suzukii or Drosophila melanogaster (A. japonica only) larvae. Host larval densities were 5, 10, 15, 20, 25, 30, 35, or 40 larvae per test for A. japonica and 3, 6, 9, 12, 18, 24, 30, 36, or 42 larvae per test for G. brasiliensis or L. japonica. Host larvae were provided in standard artificial diet in tubes for a 24-h exposure to individual female parasitoids under the quarantine conditions (23°C). All three parasitoids showed a linear (type I) functional response to the tested host densities. Host species (for A. japonica only) did not affect the number of hosts parasitized or the functional response. Asobara japonica was more efficient than either figitid in terms of the searching efficiency while L. japonica preformed slightly better than G. brasiliensis under the tested conditions. The results are discussed with respect to the selection of parasitoid species to be released in North America and Europe to suppress D. suzukii.
Taxonomic identification of biological materials can be achieved through DNA barcoding, where an unknown “barcode” sequence is compared to a reference database. In many disciplines, obtaining accurate taxonomic identifications can be imperative (e.g., evolutionary biology, food regulatory compliance, forensics). The Barcode of Life DataSystems (BOLD) and GenBank are the main public repositories of DNA barcode sequences. In this study, an assessment of the accuracy and reliability of sequences in these databases was performed. To achieve this, 1) curated reference materials for plants, macro-fungi and insects were obtained from national collections, 2) relevant barcode sequences (rbcL, matK, trnH-psbA, ITS and COI) from these reference samples were generated and used for searching against both databases, and 3) optimal search parameters were determined that ensure the best match to the known species in either database. While GenBank outperformed BOLD for species-level identification of insect taxa (53% and 35%, respectively), both databases performed comparably for plants and macro-fungi (~81% and ~57%, respectively). Results illustrated that using a multi-locus barcode approach increased identification success. This study outlines the utility of the BLAST search tool in GenBank and the BOLD identification engine for taxonomic identifications and identifies some precautions needed when using public sequence repositories in applied scientific disciplines.
Host-parasitoid interactions are among the most studied interactions between invertebrates because of their fundamental interest-the evolution of original traits in parasitoids-and applied, parasitoids being widely used in biological control. Immunity, and in particular cellular immunity, is central in these interactions, the host encapsulation response being specific for large foreign bodies such as parasitoid eggs. Although already well studied in this species, recent data on Drosophila melanogaster have unquestionably improved knowledge of invertebrate cellular immunity. At the same time, the venomics of parasitoids has expanded, notably those of Drosophila. Here, we summarize and discuss these advances, with a focus on an emerging "time-dependent" view of interactions outcome at the intra-and interspecific level. We also present issues still in debate and prospects for study. Data on the Drosophila-parasitoid model paves the way to new concepts in insect immunity as well as parasitoid wasp strategies to overcome it.
Effective identification of species using short DNA fragments (DNA barcoding and DNA metabarcoding)requires reliable sequence reference libraries of known taxa. Both taxonomically comprehensive coverage and content quality are important for sufficient accuracy. For aquatic ecosystems in Europe, reliable barcode reference libraries are particularly important if molecular identification tools are to be implemented in biomonitoring and reports in the context of the EU Water Framework Directive (WFD)and the Marine Strategy Framework Directive (MSFD). We analysed gaps in the two most important reference databases, Barcode of Life Data Systems (BOLD)and NCBI GenBank, with a focus on the taxa most frequently used in WFD and MSFD. Our analyses show that coverage varies strongly among taxonomic groups, and among geographic regions. In general, groups that were actively targeted in barcode projects (e.g. fish, true bugs, caddisflies and vascular plants)are well represented in the barcode libraries, while others have fewer records (e.g. marine molluscs, ascidians, and freshwater diatoms). We also found that species monitored in several countries often are represented by barcodes in reference libraries, while species monitored in a single country frequently lack sequence records. A large proportion of species (up to 50%)in several taxonomic groups are only represented by private data in BOLD. Our results have implications for the future strategy to fill existing gaps in barcode libraries, especially if DNA metabarcoding is to be used in the monitoring of European aquatic biota under the WFD and MSFD. For example, missing species relevant to monitoring in multiple countries should be prioritized for future collaborative programs. We also discuss why a strategy for quality control and quality assurance of barcode reference libraries is needed and recommend future steps to ensure full utilisation of metabarcoding in aquatic biomonitoring.
Invasive species, and their impacts on natural and agricultural resources, are a growing, multi-billion dollar problem worldwide. For insect species, this is particularly true, as many are small and hard to detect; they can hitchhike on rapid modes of transportation, facilitating survival; and some have the potential to reproduce quickly when accidentally introduced into new areas, assisting their establishment. Responding to these invaders is a three-fold endeavor, involving detection or interception (e.g., port identifiers, surveys), accurate and fast identification (taxonomy), and thorough ecological investigations in native ranges and associated natural enemy complexes (i.e., biological control agents). We use a current project of investigating natural enemies of the brown marmorated stink bug, Halyomorpha halys (Stål) (Heteroptera: Pentatomidae), as an example of how taxonomy and biological control projects are mutually informative, stimulating joint research and shortening the time lag between field observation, publishing data, and using that data for management decisions. We make the case that taxonomic preparedness is critical to this success.
Due to their small size and smooth body, members of the figitid genus Alloxysta can be notoriously difficult to identify based on
morphology alone. Moreover, several species are suspected to contain brachypterous variants that previously have been described under
separate names. We used gene sequences of the mitochondrial gene cytochrome c oxidase subunit 1 (COI, DNA barcodes) and the internal
transcribed spacer (ITS2) to investigate the relationships between species within the genus. Our results show that there is considerably
more intraspecific variation in COI than in ITS2, but that both markers can be used to identify potential synonyms of brachypterous and
fully winged species. Maximum Likelihood and Bayesian analyses of a concatenated dataset of both markers resulted in similar and fairly
well supported phylogenies that indicate genetic divergence not matching morphological species boundaries for some groups. Some of the
discrepancies can be explained by infections of the endosymbiont Wolbachia, here reported from the first time in Alloxysta and Charipinae.
This study also presents the first records of A. arcuata, A. basimacula, A. brachycera, A. brachyptera, A. brevis, A. citripes, A. consobrina,
A. curta, A. fracticornis, A. halterata, A. marshalliana, A. obscurata, A. proxima, A. pusilla, A. ramulifera and A. xanthopa from Norway.
Drosophila suzukii is native to East Asia and an invasive pest of fruit crops widely established in the Americas and Europe. The lack of effective indigenous parasitoids of D. suzukii in the invaded regions prompted surveys for co-evolved parasitoids in Yunnan Province, China, from 2013-2016. From banana-baited traps (2013-2015) 458 parasitoids of drosophilids were reared, comprised of Braconidae (49.56%), Figitidae (37.55%), Diapriidae (7.42%), and Pteromalidae (5.46%). Larval parasitoids included seven braconid species, all Asobara and primarily Asobara mesocauda , and five figitid species, primarily Leptopilina japonica japonica. Pupal parasitoids 34 were the diapriid Trichopria drosophilae and the pteromalid Pachycrepoideus vindemiae. Collections from wild fruits (2016) provided more interesting results. From the puparia of drosophilids collected, comprised of D. suzukii and Drosophila pulchrella, emerged 1,3 parasitoids. The larval parasitoids Ganaspis brasiliensis and L. j. japonica were the prevalent species, reaching a fairly high percentage parasitism of fly puparia collected from berries of Rubus foliosus (22.35%), R. niveus (18.81%), Fragaria moupinensis (19.75%), and Sambucus adnata (63.46%). Ganaspis brasiliensis was the dominant species and was collected only from D. suzukii and D. pulchrella-infested fruits and never from banana-baited traps. Molecular analysis showed two G. brasiliensis lineages, which are discussed with respect to previous Japanese collections. Quarantine tests showed that G. brasiliensis developed from D. suzukii and two closely related hosts (Drosophila melanogaster and Drosophila simulans) but did not develop from seven non-target drosophilid species. Our results suggest that G. brasiliensis is a promising classical biocontrol agent for release in invaded regions.
Since two decades the richness and potential of natural history collections (NHC) were rediscovered and emphasized, promoting a revolution in the access on data of species occurrence, and fostering the development of several disciplines. Nevertheless, due to their inherent erratic nature, NHC data are plagued by several biases. Understanding these biases is a major issue, particularly because ecological niche models (ENMs) are based on the assumption that data are not biased. Based on it, a recent body of research have focused on searching adequate methods for dealing with biased data and proposed the use of filters in geographical and environmental space. Although the strength of filtering in environmental space has been shown with virtual species, nothing has yet been tested with a real dataset including field validation. In order to contribute to this task, we explore this issue by comparing a dataset from NHC to a recent targeted sampling of the cockroach genus Monastria Saussure, 1864 in the Brazilian Atlantic forest. We showed that, despite strong similarities, the area modeled with NHC data was much smaller. These differences were due to strong climate biases, which increased model’s specificity and reduced sensitivity. By applying two forms of rarefaction in the environmental space, we showed that deleting points at random in the most biased climate class is a powerful way for increasing model’s sensitivity, so making predictions more suitable to the reality.
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.
Background:
We challenge the oft-repeated claim that the beetles (Coleoptera) are the most species-rich order of animals. Instead, we assert that another order of insects, the Hymenoptera, is more speciose, due in large part to the massively diverse but relatively poorly known parasitoid wasps. The idea that the beetles have more species than other orders is primarily based on their respective collection histories and the relative availability of taxonomic resources, which both disfavor parasitoid wasps. Though it is unreasonable to directly compare numbers of described species in each order, the ecology of parasitic wasps-specifically, their intimate interactions with their hosts-allows for estimation of relative richness.
Results:
We present a simple logical model that shows how the specialization of many parasitic wasps on their hosts suggests few scenarios in which there would be more beetle species than parasitic wasp species. We couple this model with an accounting of what we call the "genus-specific parasitoid-host ratio" from four well-studied genera of insect hosts, a metric by which to generate extremely conservative estimates of the average number of parasitic wasp species attacking a given beetle or other insect host species.
Conclusions:
Synthesis of our model with data from real host systems suggests that the Hymenoptera may have 2.5-3.2× more species than the Coleoptera. While there are more described species of beetles than all other animals, the Hymenoptera are almost certainly the larger order.
The Asian spotted wing drosophila, Drosophila suzukii, has recently become a serious pest of soft fruits in Europe. Classical biological control through the introduction of larval parasitoids from its native range in Asia is presently being considered. However, host specificity of potential biological control agents has to be determined to avoid releasing species that may have unintended non-target impacts. Larvae of six different European non-target fly species and the target D. suzukii were exposed either on diet or blueberries to three Asian larval parasitoids, Asobara japonica, Leptopilina japonica, and Ganaspis cf. brasiliensis, and one European species, Leptopilina heterotoma. Asobara japonica showed the lowest specificity, attacking and developing in all Drosophilidae. Leptopilina japonica successfully parasitized two non-target Drosophilidae, D. melanogaster and D. subobscura, with one singly progeny emerging from D. immigrans. Ganaspis cf. brasiliensis had the highest level of specificity but variations occurred between two geographical populations tested. A Japanese population was strictly specific to D. suzukii, whereas another population from China parasitized D. suzukii, D. melanogaster and sporadically D. subobscura. The European L. heterotoma successfully developed in D. melanogaster, D. subobscura and occasionally in D. immigrans, but nearly all eggs and larvae in D. suzukii were encapsulated. These results show that Ganaspis cf. brasiliensis is the species with the highest potential for biological control, but more studies are needed on its taxonomic status and the existence of biotypes or cryptic species varying in their specificity before field releases can be conducted in Europe.
Electronic supplementary material
The online version of this article (10.1007/s10340-018-1003-z) contains supplementary material, which is available to authorized users.
Understanding phylogenetic relationships among taxa is key to designing and implementing comparative analyses. The genus Drosophila, which contains over 1600 species, is one of the most important model systems in the biological sciences. For over a century, one species in this group, Drosophila melanogaster, has been key to studies of animal development and genetics, genome organization and evolution, and human disease. As whole-genome sequencing becomes more cost-effective, there is increasing interest in other members of this morphologically, ecologically, and behaviorally diverse genus. Phylogenetic relationships within Drosophila are complicated, and the goal of this paper is to provide a review of the recent taxonomic changes and phylogenetic relationships in this genus to aid in further comparative studies.
Stored-product psocids (Psocoptera: Liposcelididae) are cosmopolitan storage pests that can damage stored products and cause serious economic loss. However, because of the body size (~1 mm) of eggs, nymphs, and adults, morphological identification of most stored-product psocids is difficult and hampers effective identification. In this study, 10 economically important stored-product Liposcelis spp. psocids (Liposcelis brunnea, L. entomophila, L. decolor, L. pearmani, L. rufa, L.mendax, L. bostrychophila, L. corrodens, L. paeta, and L. tricolor) were collected from 25 geographic locations in 3 countries (China, Czech Republic, and the United States). Ten species-specific probes for identifying these 10 psocid species were designed based on ITS2 sequences. The microarray method and reaction system were optimized. Specificity of each of the ten probes was tested, and all probes were found suitable for use in identification of the respective10 Liposcelis spp. psocids at 66 °C. This method was also used to identify an unknown psocid species collected in Taian, China. This work has contributed to the development of a molecular identification method for stored-product psocids, and can provide technical support not only to facilitate identification of intercepted samples in relation to plant quarantine, but also for use in insect pest monitoring.
Banded iron formations (BIFs) in Archean cratons provide important "geologic barcodes" for the global correlation of Precambrian sedimentary records. Here we report the first finding of late Archean BIFs from the Yangtze Craton, one of largest Precambrian blocks in East Asia with an evolutionary history of over 3.3 Ga. The Yingshan iron deposit at the northeastern margin of the Yangtze Craton, displays typical features of BIF, including: (i) alternating Si-rich and Fe-rich bands at sub-mm to meter scales; (ii) high SiO2 + Fe2O3total contents (average 90.6 wt.%) and Fe/Ti ratios (average 489); (iii) relative enrichment of heavy rare earth elements and positive Eu anomalies (average 1.42); (iv) and sedimentary Fe isotope compositions (δ⁵⁶FeIRMM-014 as low as -0.36‰). The depositional age of the BIF is constrained at ~2464 ± 24 Ma based on U-Pb dating of zircon grains from a migmatite sample of a volcanic protolith that conformably overlied the Yingshan BIF. The BIF was intruded by Neoproterozoic (805.9 ± 4.7 Ma) granitoids that are unique in the Yangtze Craton but absent in the North China Craton to the north. The discovery of the Yingshan BIF provides new constraints for the tectonic evolution of the Yangtze Craton and has important implications in the reconstruction of Pre-Nuna/Columbia supercontinent configurations.
A pressing challenge for ecologists is predicting how human-driven environmental changes will affect the complex pattern of interactions among species in a community. Weighted networks are an important tool for studying changes in interspecific interactions because they record interaction frequencies in addition to presence or absence at a field site. Here we show that changes in weighted network structure following habitat modification are, in principle, predictable. Our approach combines field data with mathematical models: the models separate changes in relative species abundance from changes in interaction preferences (which describe how interaction frequencies deviate from random encounters). The models with the best predictive ability compared to data requirement are those that capture systematic changes in interaction preferences between different habitat types. Our results suggest a viable approach for predicting the consequences of rapid environmental change for the structure of complex ecological networks, even in the absence of detailed, system-specific empirical data.
Molecular approaches are increasingly being used to analyse host-parasitoid food webs as they overcome several hurdles inherent to conventional approaches. However, such studies have focused primarily on the detection and identification of aphids and their aphidiid primary parasitoids, largely ignoring primary parasitoid-hyperparasitoid interactions or limiting these to a few common species within a small geographical area. Furthermore, the detection of bacterial secondary endosymbionts has not been considered in such assays despite the fact that endosymbionts may alter aphid-parasitoid interactions, as they can confer protection against parasitoids. Here we present a novel two-step multiplex PCR (MP-PCR) protocol to assess cereal aphid-primary parasitoid-hyperparasitoid-endosymbiont interactions. The first step of the assay allows detection of parasitoid DNA at a general level (24 primary and 16 hyperparasitoid species) as well as the species-specific detection of endosymbionts (3 species) and cereal aphids (3 species). The second step of the MP-PCR assay targets seven primary and six hyperparasitoid species that commonly occur in Central Europe. Additional parasitoid species not covered by the second-step of the assay can be identified via sequencing 16S rRNA amplicons generated in the first step of the assay. The approach presented here provides an efficient, highly sensitive, and cost-effective (~consumable costs of 1.3 € per sample) tool for assessing cereal aphid-parasitoid-endosymbiont interactions.
Te genus Leptopilina has historically been a poorly understood group. However, some species of Leptopilina are among the best-known model organisms for studying host-parasitoid interactions. As there is no identifcation system for Leptopilina in any part of the United States, we review species that were collected throughout their range in Eastern North America and those commonly used in laboratories. We provide a key for seven species, L. boulardi, L. heterotoma, L. clavipes, L. victoriae, L. decem?agella sp. n., L. maia sp. n. and L. leipsi sp. n., the last three of which are newly described here. Tis study is the frst of its kind for Leptopilina species in North America, as our review and key were developed by examining a large number of specimens collected across broad chronological and geographic scales. Tis allowed us to account for the phenotypic variation within species, and helped us discover diagnostic characters. Te geographic distribution and taxonomic information from this review provides a solid foundation for future research on Leptopilina.
This study records the occurrence of eucoilines (Hymenoptera: Figitidae), parasitoids of the African fig fly Zaprionus indianus Gupta (Diptera: Drosophilidae), in the Brazilian semi-arid Caatinga biome. We obtained from mango (Mangifera indica L.) and guava (Psidium guajava L.) fruits Drosophilidae pupae, which developed into Z. indianus and two species of Eucoilinae parasitoids, Dicerataspis grenadensis Ashmead and Leptopilina boulardi (Barbotin, Carlton & Kelner-Pillaut). This is the first record of the parasitoids D. grenadensis and L. boulardi in the Caatinga biome.
Society faces the complex challenge of supporting biodiversity and ecosystem functioning, while ensuring food security by providing safe traceable food through an ever-more-complex global food chain. The increase in human mobility brings the added threat of pests, parasites, and invaders that further complicate our agro-industrial efforts. DNA barcoding technologies allow researchers to identify both individual species, and, when combined with universal primers and high-throughput sequencing techniques, the diversity within mixed samples (metabarcoding). These tools are already being employed to detect market substitutions, trace pests through the forensic evaluation of trace "environmental DNA", and to track parasitic infections in livestock. The potential of DNA barcoding to contribute to increased security of the food chain is clear, but challenges remain in regulation and the need for validation of experimental analysis. Here, we present an overview of the current uses and challenges of applied DNA barcoding in agriculture, from agro-ecosystems within farmland to the kitchen table.
We use three examples—field and ecology-based inventories in Costa Rica and Papua New Guinea and a museum and taxonomic-based inventory of the moth family Geometridae—to demonstrate the use of DNA barcoding (a short sequence of the mitochondrial COI gene) in biodiversity inventories, from facilitating workflows of identification of freshly collected specimens from the field, to describing the overall diversity of megadiverse taxa from museum collections, and most importantly linking the fresh specimens, the general museum collections and historic type specimens. The process also flushes out unexpected sibling species hiding under long-applied scientific names, thereby clarifying and parsing previously mixed collateral data. The Barcode of Life Database has matured to an essential interactive platform for the multi-authored and multi-process collaboration. The BIN system of creating and tracking DNA sequence-based clusters as proxies for species has become a powerful way around some parts of the ‘taxonomic impediment’, especially in entomology, by providing fast but testable and tractable species hypotheses, tools for visualizing the distribution of those in time and space and an interim naming system for communication.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
DNA barcoding and metabarcoding methods have been invaluable in the study of interactions between host organisms and their symbiotic communities. Barcodes can help identify individual symbionts that are difficult to distinguish using morphological characters, and provide a way to classify undescribed species. Entire symbiont communities can be characterized rapidly using barcoding and especially metabarcoding methods, which is often crucial for isolating ecological signal from the substantial variation among individual hosts. Furthermore, barcodes allow the evolutionary histories of symbionts and their hosts to be assessed simultaneously and in reference to one another. Here, we describe three projects illustrating the utility of barcodes for studying symbiotic interactions: first, we consider communities of arthropods found in the ant-occupied domatia of the East African ant-plant Vachellia (Acacia) drepanolobium; second, we examine communities of arthropod and protozoan inquilines in three species of Nepenthes pitcher plant in South East Asia; third, we investigate communities of gut bacteria of South American ants in the genus Cephalotes. Advances in sequencing and computation, and greater database connectivity, will continue to expand the utility of barcoding methods for the study of species interactions, especially if barcoding can be approached flexibly by making use of alternative genetic loci, metagenomes and whole-genome data.
This article is part of the themed issue ‘From DNA barcodes to biomes’.
The new combination of Ganaspis brasiliensis (Ihering, 1905) is proposed, and the species is redescribed from historical specimens taken in the Neotropical Region as well as more recent specimens reared from Drosophila suzukii Matsumura, 1931 in South Korea. Drosophila suzukii, otherwise known as the spotted-wing Drosophila, is a major pest of soft fruits the world over, and the search for effective natural enemies of this fly are ongoing. Though not parasitoids of D. suzukii, we also propose the following new combinations: Dieucoila brasiliensis (Kieffer, 1909), new combination, and Dieucoila brasiliana (Weld, 1952), new combination. After summarizing all known species of Eucoilinae with the specific epithet ‘brasiliensis’, we encourage future researchers to avoid this name in order prevent nomenclatural confusion.
The invasive spotted wing drosophila, Drosophila suzukii Matsumura (Dipt.: Drosophilidae), a native of East Asia, has widely established in North America and Europe, where it is a serious pest of small and stone fruit crops. The lack of effective indigenous parasitoids of D. suzukii in the recently colonized regions prompted the first foreign exploration for co-evolved parasitoids in South Korea during 2013 and 2014. We collected the larval parasitoids Asobara japonica Belokobylskij, A. leveri (Nixon) and A.
brevicauda Guerrieri & van Achterberg (Hym.: Braconidae), Ganaspis
brasiliensis (Ihering), Leptopilina japonica japonica Novković & Kimura and L. j. formosana Novković & Kimura (Hym.: Figitidae); and the pupal parasitoids Pachycrepoideus vindemiae (Rondani) (Hym.: Pteromalidae) and Trichopria drosophilae Perkins (Hym.: Diapriidae). From UC Berkeley quarantine records, percentage parasitism ranged from 0 to 17.1 % and varied by geography, season, and collection methods. Asobara japonica was the most common parasitoid species. Higher numbers of parasitoids were reared from field-picked fruit as opposed to traps baited with uninfested fruit. Quarantine bioassays confirmed that A. japonica, G. brasiliensis, L. j. japonica, P. vindemiae, and T. drosophilae developed from D. suzukii. Female individuals of the endoparasitoid, A. japonica, were larger when reared on the larger D. suzukii larvae compared with those reared on the smaller larvae of D. melanogaster Meigen. Larger parasitoid size was associated with longer developmental time. Several of the South Korean parasitoid species have the potential for use in classical biological control and may contribute to the suppression of D. suzukii in the newly invaded regions.
The Drosophila parasitoid system is an excellent model for the study of biological and ecological interactions. In Japan, extensive studies have been carried out on Drosophila parasitoids since the early 2000s. Here we provide up‐to‐date information on their diversity, distributions, host use and reproductive mode. Until now, 45 wasp species have been recorded. In addition, four genetically distinct groups (tentatively assigned as “races”) have been found in Ganaspis brasiliensis (Figitidae). Most of them are larvo‐pupal parasitoids belonging to the families Figitidae and Braconidae, and some are pupal parasitoids of the families Pteromalidae and Diapriidae. A species of Encyrtidae was also recorded. Their major hosts are indicated with information on the host's breeding sites. Except Ganaspis xanthopoda and two races of G. brasiliensis that are distributed both in tropical and temperate regions, they are divided into tropical and temperate species. The tropical species are mainly distributed in Southeast Asia, and their distributions in Japan are restricted to the Ryukyu islands, particularly Iriomote‐jima. The temperate species have been recorded from the main islands of Japan and surrounding islands but not from the Ryukyu islands, except two braconid species, Asobara japonica and Phaenocarpa sp. TK1. Some of the temperate species have also been recorded from Korea, China, Europe and/or North America. Among the 45 Japanese parasitoid species, at least seven are assumed to be thelytokous.
Biodiversity studies greatly benefit from molecular tools, such as DNA metabarcoding, which provides an effective identification tool in biomonitoring and conservation programmes. The accuracy of species‐level assignment, and consequent taxonomic coverage, relies on comprehensive DNA barcode reference libraries. The role of these libraries is to support species identification, but accidental errors in the generation of the barcodes may compromise their accuracy. Here we present an R‐based application, BAGS (Barcode, Audit & Grade System; https://github.com/tadeu95/BAGS), that performs automated auditing and annotation of cytochrome c oxidase subunit I (COI) sequences libraries, for a given taxonomic group of animals, available in the Barcode of Life Data System (BOLD). This is followed by implementing a qualitative ranking system that assigns one of five grades (A to E) to each species in the reference library, according to the attributes of the data and congruency of species names with sequences clustered in Barcode Index Numbers (BINs). Our goal is to allow researchers to obtain the most useful and reliable data, highlighting and segregating records according to their congruency. Different tests were performed to perceive its usefulness and limitations. BAGS fulfils a significant gap in the current landscape of DNA barcoding research tools by quickly screening reference libraries to gauge the congruence status of data and facilitate the triage of ambiguous data for posterior review. Thereby, BAGS has the potential to become a valuable addition in forthcoming DNA metabarcoding studies, in the long term contributing to globally improve the quality and reliability of the public reference libraries.
High‐throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: 1) to provide a comprehensive overview about the state‐of‐the‐art high‐throughput quantification and molecular identification methods used to address population dynamics, community ecology and host‐associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; 2) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and 3) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state‐of‐the‐art and still evolving methods for diagnostics and population‐ and community‐level ecological research of pathogens and pests.
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The establishment of invasive Halyomorpha halys (Stål) outside of its native range may impact native species assemblages, including other pentatomids and their scelionid parasitoids. This has generated interest in defining species diversity and host‐parasitoid associations in this system to better understand the impact of invasive alien species on trophic interactions in invaded regions. Information on scelionid‐pentatomid associations in natural habitats is lacking, and species‐level identification of these associations can be tenuous using rearing and dissection techniques. Naturally occurring pentatomid eggs were collected in areas where H. halys has established in Canada and were analysed using a modified DNA barcoding approach to define species‐level trophic interactions. Identification was possible for >90% of egg masses. Eleven pentatomid and five scelionid species were identified, and trophic links were established. Approximately 70% of egg masses were parasitized; parasitism and parasitoid species composition were described for each species. Telenomus podisi Ashmead was the dominant parasitoid and was detected in all host species. Trissolcus euschisti Ashmead was detected in several host species, but was significantly more prevalent in Chinavia hilaris (Say) and Brochymena quadripustulata (Fabricius). Trissolcus brochymenae Ashmead and Tr. thyantae Ashmead were recorded sporadically. Parasitism of H. halys was 55%, and this species was significantly less likely to be parasitized than native pentatomids. The scelionid species composition of H. halys consisted of Te. podisi, Tr. euschisti, and Tr. thyantae. Although these species cannot develop in fresh H. halys eggs, we demonstrate that parasitoids attempt to exploit this host under field conditions.
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Many studies have investigated species diversity patterns across space and time, but few have explored patterns of coexistence of tightly interacting species. We documented species diversity patterns in a host-parasitoid system across broad geographic location and seasons. We calculated species diversity (H and eH ') and compared the relationship between community similarity and geographic distances of frugivorous Drosophila host (Diptera: Drosophilidae) and Leptopilina parasitoid (Hymenoptera: Figitidae) communities across Eastern North America, from New Hampshire to Florida, at two time points during the breeding season. We also analyzed the influence of environmental factors on species assemblages via constrained correspondence analysis and lastly calculated cluster dendrograms to identify potential host-parasitoid interactions. We found that the composition of Drosophila-Leptopilina communities varied significantly with latitude. Interestingly, diversity increased with increasing latitude, a trend counter to latitudinal patterns of diversity observed in many other taxa. We also found seasonal effects of monthly temperature range and precipitation on host biodiversity patterns across geographic locations. Cluster dendrograms nominated potential parasitoid-hosts and competitive interactions to be validated in the future studies. The present study fills an important gap of knowledge in North American Drosophila-Leptopilina species diversity patterns and lays the groundwork for future ecological and evolutionary studies in this system.
Primary biodiversity data represent the fundamental elements of any study in systematics and evolution. They are, however, no longer gathered as they used to be and the mass-production of observation-based occurrences is overthrowing the collection of specimen-based occurrences. Although this change in practice is a major upheaval with significant consequences in the study of biodiversity, it remains understudied and has not attracted yet the attention it deserves. Analyzing 536 million occurrences from the Global Biodiversity Information Facility (GBIF) mediated data, we show that this spectacular change affects the 24 eukaryote taxonomic classes we targeted: from 1970 to 2016 the proportion of occurrences marked as traceable to tangible material (i.e. specimen-based occurrences) fell from 68 to 18%; moreover, most of those specimen based-occurrences cannot be readily traced back to a specimen because the necessary information is missing. Ethical, practical or legal reasons responsible for this shift are known, and this situation appears unlikely to be reversed. Still, we urge scholars to acknowledge this dramatic change, embrace it and actively deal with it. Specifically, we emphasize why specimen-based occurrences must be gathered, as a warrant to allow both repeating evolutionary studies and conducting rich and diverse investigations. When impossible to secure, voucher specimens must be replaced with observation-based occurrences combined with ancillary data (e.g. pictures, recordings, samples, DNA sequences). Ancillary data are instrumental for the usefulness of biodiversity occurrences and we show that, despite improving technologies to collate them, they remain rarely shared. The consequences of such a change are not yet clear but we advocate collecting material evidence or ancillary data to ensure that primary biodiversity data collected lately do not partly become obsolete when doubtful.
The Microgastrinae are a hugely diverse subfamily of endoparasitoid wasps of lepidopteran caterpillars. They are important in agriculture as biological control agents, and play a significant ecological role in the regulation of caterpillar populations. Whilst the group has been the focus of intensive rearing and DNA barcoding studies in the Northern Hemisphere, the Australian fauna has received little attention. In total, 100 species have been described from or have been introduced into Australia, but the real species diversity for the region is clearly much larger than this. In this study, museum ethanol samples and recent field collections were mined for hundreds of specimens of microgastrine wasps, which were then barcoded for the COI region, ITS2 ribosomal spacer and the wingless nuclear genes, using a pooled sequencing approach on an Illumina Miseq system. Full COI sequences were obtained for 525 individuals which, when combined with 162 publicly available sequences, represented 417 haplotypes and a total of 236 species were delimited using a consensus approach. By more than doubling the number of known microgastrine wasp species in Australia, our study highlights the value of DNA barcoding in the context of employing high‐throughput sequencing methods of bulk ethanol museum collections for biodiversity assessment.
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Discoveries from collections‐based science change the way we perceive ourselves, our environment, and our place in the universe. The 18th Century saw the beginning of formal classification with Linnaeus proposing a system to classify all of life. The 19th Century ushered in the age of exploration as naturalists undertook large‐scale collecting expeditions leading to major scientific advances (the founding of Physical Geography, Meteorology, Ecology, Biogeography, and Evolution) and challenging long held beliefs about nature. In the 20th Century collections were central to paradigm shifts, including theories of Continental Drift and Phylogenetic Systematics; Molecular Phylogenetics added testable hypotheses, and computerized specimen records gave rise to the field of Biodiversity. In the first 15 years of the 21st Century we have seen tree‐thinking pervade the life sciences, leading to the emergence of Evolutionary Medicine, Evolutionary Ecology, and new Food Safety methods. More advances are on the way: 1) Open access to large amounts of specimen data & images, 2) Linking of collections and climate data to phylogenies on a global scale, and 3) Production of vast quantities of genomic data allowing us to address big evolutionary questions. As a result of collections‐based science people see themselves not as the center of all things but rather as part of a complex universe. It is essential that we integrate new discoveries with knowledge from the past (e.g., collections) in order to understand this planet, we all inhabit. To ensure the health of collections‐based science we must come together and plan for the future.
Ganaspis brasiliensis (Ihering) (Hymenoptera: Figitidae: Eucoilinae) is a Drosophila parasitoid that has often been misidentified as G. xanthopoda (Ashmead) in recent studies. This study aims to clarify genetic differentiation of G. brasiliensis based on the nucleotide sequences of the mitochondrial cytochrome oxidase subunit 1 (CO1) gene and three nuclear DNA regions, the inter-transcribed spacers 1 and 2 (ITS1 and ITS2) and putative 60S ribosomal protein L37 (RpL37), as well as crossing experiments. Four lineages are recognized in individuals assigned as G. basiliensis by morphology, (1) individuals occurring in Japan and probably South Korea, (2) individuals from a small subtropical island of Japan, Iriomote-jima, (3) individuals from temperate lowlands of Japan and high altitude areas of Southeast Asia, and (4) individuals occurring widely in Asia, America, Hawaii and Africa. The first lineage is a specialist of Drosophila suzukii (Matsumura), a pest of fresh fruit, and also the fourth lineage has a capacity to parasitize this pest species. The first, third and fourth lineages occur sympatrically at least in Tokyo. The third and fourth lineages differed in mate choice and host use to some extent, but post-mating isolation between them was almost absent.
It is essential that any DNA barcode reference library be based upon correctly identified specimens. The Barcode of Life Data Systems (BOLD) requires information such as images, geo-referencing, and details on the museum holding the voucher specimen for each barcode record to aid recognition of potential misidentifications. Nevertheless, there are misidentifications and incomplete identifications (e.g., to a genus or family) on BOLD, mainly for species from tropical regions. Unfortunately, experts are often unavailable to correct taxonomic assignments due to time constraints and the lack of specialists for many groups and regions. However, considerable progress could be made if barcode records were available for all type specimens. As a result of recent improvements in analytical protocols, it is now possible to recover barcode sequences from museum specimens that date to the start of taxonomic work in the 18th century. The present study discusses success in the recovery of DNA barcode sequences from 2805 type specimens of geometrid moths which represent 1965 species, corresponding to about 9% of the 23 000 described species in this family worldwide and including 1875 taxa represented by name-bearing types. Sequencing success was high (73% of specimens), even for specimens that were more than a century old. Several case studies are discussed to show the efficiency, reliability, and sustainability of this approach.
Molecular species delimitation has the potential to speed up both discovery and description rates for new species. However, several studies have shown a limited performance of the standard DNA barcoding approach which relies on a single mitochondrial gene, cytochrome oxidase 1 (COI). Besides incomplete lineage sorting or a low substitution rate, distortion of mitochondrial inheritance patterns by bacterial endosymbionts could explain the failure of barcoding. Numerous reviews have discussed this phenomenon, but only few empirical examples exist. In the present study, we examine the effect of Wolbachia bacteria on barcoding in the parasitoid wasp genus Diplazon. Although integrative taxonomy recognizes 16 species, COI only recovers up to ten. Adding multivariate morphometrics, genotyping a fast-evolving nuclear gene (ITS2) and screening the Diplazon species for Wolbachia, we show that the failure of DNA barcoding coincides with the presence of the endosymbiont. Two species even share identical COI haplotypes and Wolbachia strains, even though ITS2 suggests that they are not closely related. This is one of very few examples of mitochondrial DNA introgression between well-established insect species, facilitated by Wolbachia. We review similar reports, provide a list of criteria to identify endosymbiont-mediated introgression, and discuss the prevalence and impact of this phenomenon on insect systematics and evolution.