Phylogeny of the gall midges (Diptera, Cecidomyiidae, Cecidomyiinae): Systematics, evolution of feeding modes and diversification rates

Hymenopteran parasitoids reared from European gall midges (Diptera, Cecidomyiidae)

We report the results of investigations 2010 through 2023 of hymenopteran parasitoids associated with gall midges in Europe. A total of 242 collections of gall midges were made, from each of which one to several parasitoid species emerged, resulting in ca. 200 recorded parasitoid species and 267 host-parasitoid interaction records. The parasitoid families involved were Eulophidae (63 species), Platygastridae (56 species), Torymidae (34 species), Pteromalidae (31 species), Ceraphronidae (5 species), Eupelmidae (4 species), Eurytomidae (2 species) and Encyrtidae (1 species). As many as 159 interactions are reported for the first time, significantly enlarging our knowledge of gall midge - parasitoid interactions on the species level. Even more interesting, 51 host records are for parasitoid species for which no host was previously known. Similarly, 28 species of gall midge are reported as host to named parasitoids for the first time. Additionally, 91 parasitoid records were the first for the country in question. Differences between the rearing methods applied and their suitability for recording species with contrasting life histories, are discussed.

Mycobiomes of two distinct clades of ambrosia gall midges (Diptera: Cecidomyiidae) are species-specific in larvae but similar in nutritive mycelia

IMPORTANCE

Ambrosia gall midges are endophagous insect herbivores whose larvae live enclosed within a single gall for their entire development period. They may exhibit phytomycetophagy, a remarkable feeding mode that involves the consumption of plant biomass and mycelia of their cultivated gall symbionts. Thus, AGMs are ideal model organisms for studying the role of microorganisms in the evolution of host specificity in insects. However, compared to other fungus-farming insects, insect-fungus mutualism in AGMs has been neglected. Our study is the first to use DNA metabarcoding to characterize the complete mycobiome of the entire system of the gall-forming insects as we profiled gall surfaces, nutritive mycelia, and larvae. Interestingly, larval mycobiomes were significantly different from their nutritive mycelia, although Botryosphaeria dothidea dominated the nutritive mycelia, regardless of the evolutionary separation of the tribes studied. Therefore, we confirmed a long-time hypothesized paradigm for the important evolutionary association of this fungus with AGMs.

Why put all your eggs in one basket? Evolutionary perspectives on the origins of monogenic reproduction

Sexual reproduction is ubiquitous in eukaryotes, but the mechanisms by which sex is determined are diverse and undergo rapid turnovers in short evolutionary timescales. Usually, an embryo's sex is fated at the moment of fertilisation, but in rare instances it is the maternal genotype that determines the offspring's sex. These systems are often characterised by mothers producing single-sex broods, a phenomenon known as monogeny. Monogenic reproduction is well documented in Hymenoptera (ants, bees and wasps), where it is associated with a eusocial lifestyle. However, it is also known to occur in three families in Diptera (true flies): Sciaridae, Cecidomyiidae and Calliphoridae. Here we review current knowledge of monogenic reproduction in these dipteran clades. We discuss how this strange reproductive strategy might evolve, and we consider the potential contributions of inbreeding, sex ratio distorters, and polygenic control of the sex ratio. Finally, we provide suggestions on future work to elucidate the origins of this unusual reproductive strategy. We propose that studying these systems will contribute to our understanding of the evolution and turnover of sex determination systems.

The genome of the soybean gall midge (Resseliella maxima)

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagné, is a recently discovered insect that feeds on soybean plants in the Midwestern United States. R. maxima larvae feed on soybean stems that may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88× coverage, consisting of 1,009 contigs with an N50 size of 714 kb. The assembly is high quality with a Benchmarking Universal Single-Copy Ortholog (BUSCO) score of 87.8%. Genome-wide GC level is 31.60%, and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae Wood-Mason. The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

Population genetic structure of a recent insect invasion: a gall midge, Asynapta groverae (Diptera: Cecidomyiidae) in South Korea since the first outbreak in 2008

Outbreaks of Asynapta groverae, an invasive mycophagous gall midge, in South Korea have been repeatedly reported since the first occurrence in 2008. This species is a nuisance to residents owing to its mass emergence from newly built and furnished apartments. Here, the levels of genetic diversity, divergence, and structure of invasive A. groverae populations were investigated to understand their ability to survive in novel locations. Population genetic analyses were performed on seven invasive populations, including the first outbreak, sporadically emerged, and two laboratory-isolated (quarantined) populations, using the mitochondrial COI sequences and the ten novel microsatellite markers developed in this study. Non-indigenous A. groverae managed to maintain their populations for 12 years despite decreased genetic polymorphisms resulting from multiple incidences of founder effects by a small number of colonists. Additionally, the advantageous sustainability of A. groverae in the particle boards from which they emerge suggests that human-mediated dispersal is plausible, which may allow for the successful spread or invasion of A. groverae to new locations. This study is one of the few examples to demonstrate that an insect species successfully invaded new regions despite exhibiting decreased genetic diversity that was maintained for a decade. These findings indicate that the high genetic diversity of the initial founding population and asexual reproduction would contribute to the successful invasion of A. groverae in novel environments.

The Genome of the Soybean Gall Midge ( Resseliella maxima )

The cecidomyiid fly, soybean gall midge, Resseliella maxima Gagné, is a recently discovered insect that feeds on soybean plants in the Midwest US. Resseliella maxima larvae feed on soybean stems which may induce plant death and can cause considerable yield losses, making it an important agricultural pest. From three pools of 50 adults each, we used long-read nanopore sequencing to assemble a R. maxima reference genome. The final genome assembly is 206 Mb with 64.88X coverage, consisting of 1009 contigs with an N50 size of 714 kb. The assembly is high quality with a BUSCO score of 87.8%. Genome-wide GC level is 31.60% and DNA methylation was measured at 1.07%. The R. maxima genome is comprised of 21.73% repetitive DNA, which is in line with other cecidomyiids. Protein prediction annotated 14,798 coding genes with 89.9% protein BUSCO score. Mitogenome analysis indicated that R. maxima assembly is a single circular contig of 15,301 bp and shares highest identity to the mitogenome of the Asian rice gall midge, Orseolia oryzae (Wood-Mason). The R. maxima genome has one of the highest completeness levels for a cecidomyiid and will provide a resource for research focused on the biology, genetics, and evolution of cecidomyiids, as well as plant-insect interactions in this important agricultural pest.

A chromosome-level genome assembly of the orange wheat blossom midge, Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae) provides insights into the evolution of a detoxification system

The orange wheat blossom midge Sitodiplosis mosellana Géhin (Diptera: Cecidomyiidae), an economically important pest, has caused serious yield losses in most wheat-growing areas worldwide in the past half-century. A high-quality chromosome-level genome for S. mosellana was assembled using PacBio long read, Illumina short read, and Hi-C sequencing technologies. The final genome assembly was 180.69 Mb, with contig and scaffold N50 sizes of 998.71 kb and 44.56 Mb, respectively. Hi-C scaffolding reliably anchored 4 pseudochromosomes, accounting for 99.67% of the assembled genome. In total, 12,269 protein-coding genes were predicted, of which 91% were functionally annotated. Phylogenetic analysis indicated that S. mosellana and its close relative, the swede midge Contarinia nasturtii, diverged about 32.7 MYA. The S. mosellana genome showed high chromosomal synteny with the genome of Drosophila melanogaster and Anopheles gambiae. The key gene families involved in the detoxification of plant secondary chemistry were analyzed. The high-quality S. mosellana genome data will provide an invaluable resource for research in a broad range of areas, including the biology, ecology, genetics, and evolution of midges, as well as insect–plant interactions and coevolution.

A LAMP Assay for the Detection of Thecodiplosis japonensis, an Alien Gall Midge Species Pest of Pine Trees

Simple Summary

Thecodiplosis japonensis is considered the most harmful pest to pines in South Korea. T. japonensis is a native species of Japan. Recently, T. japonensis was discovered in China and has caused serious damage to local pine trees. Due to the small size and little morphological difference with its related species, it is difficult to accurately identify T. japonensis by morphological methods. Accurate and efficient molecular identification methods are urgently needed to detect this invasive gall midge pest, yet there was no molecular identification method for T. japonensis. In this study, we developed a LAMP assay to detect T. japonensis based on the COI gene sequence. The LAMP assay could detect as little as 300 fg of gDNA. Using colorimetric amplification and a crude gDNA extraction method, the total procedure could be processed in 75 min. The method established in the study can be easily used in both laboratory and field conditions, enabling rapid molecular identification of T. japonensis.

Abstract

Pine needle gall midge (T. japonensis), native to Japan, has become a serious invasive pest in South Korea and, more recently in 2006, in China. It was first discovered in Qingdao, Shandong Province, and has caused serious damage to local Pinus thunbergii. The insect’s small size makes morphological-based identification difficult; therefore, molecular detection techniques are urgently needed for monitoring and preventing its further spread. At present, there is no simple and accurate field molecular identification tool. To solve this problem, a LAMP-based molecular diagnosis technology of T. japonensis was developed. Four LAMP primers were designed to specifically amplify T. japonensis DNA. Positive LAMP reactions usually produce amplification in one hour. The optimal incubation conditions for LAMP detection were determined with 4 LAMP primers for 60 min at 61 °C. The LAMP detection range of gDNA concentrations is wide, with a minimum detectable gDNA concentration of 300 fg. A non-destructive DNA-releasing procedure, HotSHOT “HS6”, which could extract “crude DNA” for LAMP assay in 10 min, was used for larval and adult samples. Therefore, we established a LAMP-based rapid molecular identification method that can be applied in the monitoring and management of T. japonensis.

Current State of DNA Barcoding of Sciaroidea (Diptera)-Highlighting the Need to Build the Reference Library

DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.

Hidden Diversity—A New Speciose Gall Midge Genus (Diptera: Cecidomyiidae) Associated with Succulent Aizoaceae in South Africa

Simple Summary

Succulent Aizoaceae (often called “mesembs” or ice plants) form a dominant component of the Succulent Karoo in southern Africa, constituting one of the most species-rich families within the Greater Cape Floristic Region (GCFR). Despite the diversity and abundance of these plants, the diversity of insects specialized on them has never been surveyed methodically prior to this study. In a three-year study of the galling insects associated with succulent Aizoaceae in South Africa, we found that they support a rich community of gall midges (Diptera: Cecidomyiidae), virtually all of which are new to science. This is not surprising, given that knowledge of the Afrotropical fauna of gall midges is scarce, with most species described in the 1900s. Here, we describe the new genus Ruschiola with ten species from succulent Aizoaceae in Namaqualand, the Knersvlakte and the Cedarberg regions of South Africa based on morphological, molecular and life history data. The genetic data were particularly important in this study for differentiating taxa, given that Ruschiola species are very similar morphologically. Members of this genus develop in leaf galls or in plant tissues without visible gall formation, and are highly host specific.

Abstract

Aizoaceae (Caryophyllales) constitute one of the major floral components of the unique Greater Cape Floristic Region (GCFR), with more than 1700 species and 70% endemism. Within succulent Aizoaceae, the subfamily Ruschioideae is the most speciose and rapidly diversifying clade, offering potential niches for the diversification of specialized herbivorous insects. Nevertheless, insect diversity on these plants has not been studied to date, and knowledge of gall-inducing insects in the Afrotropics is generally scarce. Our recent observations indicate that succulent Aizoaceae in the GCFR support a rich and largely unstudied community of gall midges (Diptera: Cecidomyiidae). Here, we provide a first report of their diversity with a description of a new genus, Ruschiola Dorchin, and ten new species, based on morphological and molecular analyses of material collected during a three-year targeted survey across major GCFR vegetation types. A high degree of morphological uniformity in Ruschiola suggests recent diversification and necessitated the use of molecular data and laboratory rearing from host plants to verify species boundaries and host ranges.

Ecological and Molecular Interactions between Insects and Fungi

Insects and fungi represent two of the most widespread groupings of organisms in nature, occurring in every kind of ecological context and impacting agriculture and other human activities in various ways. Moreover, they can be observed to reciprocally interact, establishing a wide range of symbiotic relationships, from mutualism to antagonism. The outcome of these relationships can in turn affect the extent at which species of both organisms can exert their noxious effects, as well as the management practices which are to be adopted to counter them. In conjunction with the launch of a Special Issue of Microorganisms with the same title, this article offers a general overview of the manifold aspects related to such interactions from the perspective of implementing our capacity to regulate them in a direction more favorable for the environment, crop production and human health.

Reclassification of Gall Midges (Diptera: Cecidomyiidae: Cecidomyiini) from Amaranthaceae, with Description of Ten New Species Based on an Integrative Taxonomic Study

The genus Halodiplosis includes 99 species restricted to host-plants of the Amaranthaceae, virtually all of which are from Central Asia. The discovery of numerous undescribed species putatively belonging to this genus in Israel instigated an exhaustive review of the original descriptions of all known species in this genus. This study revealed that the generic concept of Halodiplosis and some of the genera synonymized under it should be redefined based on morphological and life-history attributes, such that Halodiplosis is limited to only 13 species developing in plant tissues without obvious gall formation or as inquilines in galls of other cecidomyiids. Revised status were proposed for Asiodiplosis, Onodiplosis, and Desertomyia, all species of which are gall inducers. A detailed morphological study of the Israeli species combined with data on their life history and an analysis of mitochondrial COI and 16S gene sequences revealed nine gall-inducing species belonging to Asiodiplosis and one inquilinous species belonging to Halodiplosis. All ten species (Asiodiplosis admirabilis n.sp., A. bimoda n.sp., A. delicatula n.sp., A. largifica n.sp., A. mohicana n.sp., A. mucronata n.sp., A. paradoxa n.sp., A. pillosaeconspicua n.sp., A. stellata n.sp., and Halodiplosis fugax n.sp.) are described here as new to science, including the first descriptions of larvae and pupae for these genera.

An Integrative Study on Asphondylia spp. (Diptera: Cecidomyiidae), Causing Flower Galls on Lamiaceae, with Description, Phenology, and Associated Fungi of Two New Species

An integrative study on some species of Asphondylia was carried out. Two species of gall midges from Italy, Asphondylia rivelloi sp. nov. and Asphondylia micromeriae sp. nov. (Diptera: Cecidomyiidae), causing flower galls respectively on Clinopodium vulgare and Micromeria graeca (Lamiaceae), are described and illustrated. The characteristics of each developmental stage and induced galls are described, which allowed the discrimination of these new species in the complex of Asphondylia developing on Lamiaceae plants. Molecular data based on sequencing both nuclear (ITS2 and 28S-D2) and mitochondrial (COI) genes are also provided in support of this discrimination. Phylogeny based on nuclear markers is consistent with the new species, whereas COI phylogeny suggests introgression occurring between the two species. However, these species can also be easily identified using a morphological approach. Phenology of host plants and gall midges are described, and some peculiar characteristics allow the complete and confident discrimination and revision of the treated species. Gall-associated fungi were identified as Botryosphaeria dothidea,Alternaria spp., and Cladosporium spp.

Horizontal Transfer of Microbial Toxin Genes to Gall Midge Genomes

A growing body of evidence has underscored the role of horizontal gene transfer (HGT) in animal evolution. Previously, we discovered the horizontal transfer of the gene encoding the eukaryotic genotoxin cytolethal distending toxin B (cdtB) from the pea aphid Acyrthosiphon pisum secondary endosymbiont (APSE) phages to drosophilid and aphid nuclear genomes. Here, we report cdtB in the nuclear genome of the gall-forming "swede midge" Contarinia nasturtii (Diptera: Cecidomyiidae) via HGT. We searched all available gall midge genome sequences for evidence of APSE-to-insect HGT events and found five toxin genes (aip56, cdtB, lysozyme, rhs, and sltxB) transferred horizontally to cecidomyiid nuclear genomes. Surprisingly, phylogenetic analyses of HGT candidates indicated APSE phages were often not the ancestral donor lineage of the toxin gene to cecidomyiids. We used a phylogenetic signal statistic to test a transfer-by-proximity hypothesis for animal HGT, which suggested that microbe-to-insect HGT was more likely between taxa that share environments than those from different environments. Many of the toxins we found in midge genomes target eukaryotic cells, and catalytic residues important for toxin function are conserved in insect copies. This class of horizontally transferred, eukaryotic cell-targeting genes is potentially important in insect adaptation.

Ecological and biogeographic drivers of biodiversity cannot be resolved using clade age-richness data

Estimates of evolutionary diversification rates - speciation and extinction - have been used extensively to explain global biodiversity patterns. Many studies have analyzed diversification rates derived from just two pieces of information: a clade's age and its extant species richness. This "age-richness rate" (ARR) estimator provides a convenient shortcut for comparative studies, but makes strong assumptions about the dynamics of species richness through time. Here we demonstrate that use of the ARR estimator in comparative studies is problematic on both theoretical and empirical grounds. We prove mathematically that ARR estimates are non-identifiable: there is no information in the data for a single clade that can distinguish a process with positive net diversification from one where net diversification is zero. Using paleontological time series, we demonstrate that the ARR estimator has no predictive ability for real datasets. These pathologies arise because the ARR inference procedure yields "point estimates" that have been computed under a saturated statistical model with zero degrees of freedom. Although ARR estimates remain useful in some contexts, they should be avoided for comparative studies of diversification and species richness.

Cladistic analysis of the genus Bruggmanniella Tavares (Diptera, Cecicomyiidae, Asphondyliini) with evolutionary inferences on the gall inducer-host plant association and description of a new Brazilian species

In this study, we present a phylogenetic analysis of the genus Bruggmanniella Tavares based on morphological features. Cladistic analyses were conducted using 57 characters from 26 species. All species of Bruggmanniella except for B. byrsonimae were selected as ingroup and the genera Asphondylia Loew, Bruggmannia Tavares, Illiciomyia Tokuda, Parazalepidota Maia, Pseudasphondylia Monzen, Schizomyia Kieffer, and Lopesia Rübsaamen as outgroup. We used characters from larvae, pupae, adults, and galls. The results of this study supported Bruggmanniella as the sister group of Pseudasphondylia. Bruggmanniella actinodaphnes Tokuda and Yukawa and B. cinnamomi Tokuda and Yukawa have been moved to genus Pseudasphondylia (Pseudasphondylia actinodaphnes (Tokuda and Yukawa) comb. nov. and Pseudasphondylia cinnamomi (Tokuda and Yukawa) comb. nov.). The new genus Odontokeros gen. nov. has been erected for the single species Odontokeros brevipes (Lin, Yang & Tokuda) comb. nov. In addition, we described a new Brazilian species, Bruggmanniella miconia Garcia, Lamas and Urso-Guimarães sp. nov. Identification keys to the New World species of Bruggmanniella are presented.