Phylogenomics of braconid wasps (Hymenoptera, Braconidae) sheds light on classification and the evolution of parasitoid life history traits

UCE-based phylogenomics of the lepidopteran endoparasitoid wasp subfamily Rogadinae (Hymenoptera: Braconidae) unveils a new Neotropical tribe

During the past two decades, the phylogenetic relationships and higher-level classification of the subfamily Rogadinae have received relevant contributions based on Sanger, mitogenome and genome-wide nuclear DNA sequence data. These studies have helped to update the circumscription and tribal classification of this subfamily, with six tribes currently recognised (Aleiodini, Betylobraconini, Clinocentrini, Rogadini, Stiropiini and Yeliconini). The tribal relationships within Rogadinae, however, are yet to be fully resolved, including the status of tribe Facitorini, previously regarded as betylobraconine, with respect to the members of Yeliconini. We conducted a phylogenomic analysis among the tribes of Rogadinae based on genomic ultraconserved element (UCE) data and extensive taxon sampling including three undescribed genera of uncertain tribal placement. Our almost fully supported estimate of phylogeny confirmed the basal position of Rogadini within the subfamily and a Facitorini clade (Yeliconini+Aleiodini) that led us to propose the former group as a valid rogadine tribe (Facitorini stat. res.). Stiropiini, however, was recovered for the first time as sister to the remaining rogadine tribes except Rogadini, and Clinocentrini as sister to a clade with Betylobraconini+the three undescribed genera. The relationships recovered and morphological examination of the material included led us to place the latter three new genera and recently described genus Gondwanocentrus within a new rogadine tribe, Gondwanocentrini Shimbori & Zaldívar-Riverón trib. nov. We described these genera (Ghibli Shimbori & Zaldívar-Riverón gen. nov., Racionais Shimbori & Zaldívar-Riverón gen. nov. and Soraya Shimbori gen. nov.) with two or three new species each (G. miyazakii Shimbori & Zaldívar-Riverón sp. nov., G. totoro Shimbori & Zaldívar-Riverón sp. nov., R. brunus Shimbori & Zaldívar-Riverón sp. nov., R. kaelejay Shimbori & Zaldívar-Riverón sp. nov., R. superstes Shimbori & Zaldívar-Riverón sp. nov., S. alencarae Shimbori sp. nov. and S. venus Shimbori & Zaldívar-Riverón sp. nov.). A new species of Facitorini, Jannya pasargadae Gadelha & Shimbori sp. nov., is also described. Our newly proposed classification expands the number of tribes and genera within Rogadinae to 8 and 66 respectively. ZooBank: urn:lsid:zoobank.org:pub:51951C78-069A-4D8B-B5F0-7EBD4D9D21CE.

Review of the genus Paradelius De Saeger, 1942 of East Asia (Hymenoptera, Braconidae, Cheloninae, Adeliini) with the description of a new species from South Korea

The East Palaearctic species of the adeliine genus Paradelius De Saeger, 1942 are reviewed. The genus Sculptomyriola Belokobylskij, 1988 is synonymised with Paradelius and treated as its subgenus. The following species are transferred to subgenus Paradelius (Sculptomyriola): P. (Sc.) extremiorientalis (Belokobylskij, 1988), comb. nov.; P. (Sc.) ghilarovi (Belokobylskij, 1988), comb. nov.; P. (Sc.) neotropicalis Shimbori & Shaw, 2019; P. (Sc.) nigrus Whitfield, 1988; P. (Sc.) rubrus Whitfield, 1988; P. (Sc.) sinevi (Belokobylskij, 1998), comb. nov. A new species Paradelius (Sculptomyriola) koreanussp. nov. from Korean Peninsula is described. The genus Sinadelius He & Chen, 2000 is synonymised with Paradelius De Saeger and also treated as its subgenus. The species Sinadeliusguangxiensis He & Chen, 2000 and S.nigricans He & Chen, 2000 are transferred to Paradelius (Sinadelius) (comb. nov.). A key for determination of the World known Paradelius species from three its subgenera, Paradelius s.str., Sculptomyriola Belokobylskij and Sinadelius He & Chen, and illustrated redescriptions of the type of genus and its Asian species are provided.

Mitogenome architecture supports the non-monophyly of the cosmopolitan parasitoid wasp subfamily Doryctinae (Hymenoptera: Braconidae) recovered by nuclear and mitochondrial phylogenomics

Mitochondrial DNA gene organisation is an important source of phylogenetic information for various metazoan taxa at different evolutionary timescales, though this has not been broadly tested for all insect groups nor within a phylogenetic context. The cosmopolitan subfamily Doryctinae is a highly diverse group of braconid wasps mainly represented by ectoparasitoids of xylophagous beetle larvae. Previous molecular studies based on Sanger and genome-wide (ultraconserved elements, UCE; and mitochondrial genomes) sequence data have recovered a non-monophyletic Doryctinae, though the relationships involved have always been weakly supported. We characterised doryctine mitogenomes and conducted separate phylogenetic analyses based on mitogenome and UCE sequence data of ~100 representative doryctine genera to assess the monophyly and higher-level classification of the subfamily. We identified rearrangements of mitochondrial transfer RNAs (tRNAs) that support a non-monophyletic Doryctinae consisting of two separate non-related clades with strong geographic structure ('New World' and 'Old World' clades). This geographic structure was also consistently supported by the phylogenetic analyses preformed with mitogenome and UCE sequence data. These results highlight the utility of the mitogenome gene rearrangements as a potential source of phylogenetic information at different evolutionary timescales.

The complete mitochondrial genome of Aphidius colemani (Hymenoptera: Braconidae: Aphidiinae)

The genome-level features are crucial genetic resources for species identification and phylogenetic analysis. Here, the complete mitochondrial genome of Aphidius colemani Viereck 1912 (Hymenoptera: Braconidae: Aphidiinae) was sequenced, determined and analyzed. The circular genome is 16,372 bp in length with an overall base composition of 38.9% for A, 46.2% for T, 6.7% for C, and 8.2% for G. The mitochondrial genome of A. colemani contained 13 protein-coding genes that initiated by the ATN codon, 22 transfer RNA genes, two ribosomal RNA genes (rRNAs), and a control region (CR). It shared the same gene arrangement patterns that occurred in two tRNA clusters of trnI-trnQ-trnM and trnW-trnC-trnY with Aphidius gifuensis. Phylogenetic analyses using Bayesian inference and Maximum-likelihood methods supported that the two species of Aphidiinae formed a clade and sister to other subfamilies of Braconidae.

Parasitoid wasps (Ichneumonoidea) collected from faba bean fields, Kharga Oasis, New Valley, Egypt, with new records and the description of a new species

A faunistic inventory of ichneumonoid wasps collected from faba bean fields (Vicia faba L.) in Kharga Oasis, New Valley, Egypt is presented. Fourteen species of Braconidae in 11 genera and five subfamilies (Aphidiinae, Braconinae, Euphorinae, Microgastrinae, and Opiinae); and six ichneumonid species in five genera and three subfamilies (Campopleginae, Diplazontinae, and Ichneumoninae) were collected and identified. Among those, three genera Barichneumon Thomson, and Virgichneumon Heinrich (Ichneumoninae, Ichneumonidae), and Centistes Haliday (Euphorinae, Braconidae), and five species: Cotesia icipe Fernndez & Fiaboe, 2017 (Microgastrinae) (Braconidae), Diadegma trochanteratum (Thomson, 1887), and Sinophorus tibialis Sanborne, 1984 (Campopleginae), Barichneumon bilunulatus (Gravenhorst, 1829), and Virgichneumon callicerus (Gravenhorst, 1820) (Ichneumoninae, Ichneumonidae) are new records to the Egyptian fauna. A new species, Trioxys khargaiensis Gadallah & Edmardash (Aphidiinae: Braconidae) is described and illustrated. A faunistic list comprising diagnostic characters and distribution in the Middle East and North Africa is provided. Illustrations of species characters are also provided.

Impact of increasing morphological information by micro-CT scanning on the phylogenetic placement of Darwin wasps (Hymenoptera, Ichneumonidae) in amber

The correct interpretation of fossils and their reliable taxonomic placements are fundamental for understanding the evolutionary history of biodiversity. Amber inclusions often preserve more morphological information than compression fossils, but are often partially hidden or distorted, which can impede taxonomic identification. Here, we studied four new fossil species of Darwin wasps from Baltic and Dominican amber, using micro computed tomography (micro-CT) scans and 3D reconstructions to accurately interpret and increase the availability of morphological information. We then infer their taxonomic placement in a Bayesian phylogenetic analysis by combining morphological and molecular data of extant and fossil Darwin wasps and evaluate the impact and usefulness of the additional information from micro-CT scanning. The results show that although we gained significant morphological information from micro-CT scanning, especially concerning measurements and hidden dorsal and ventral structures, this did not impact subfamily-level placement for any of the four fossils. However, micro-CT scanning improved the precision of fossil placements at the genus level, which might be key in future dating and diversification analyses. Finally, we describe the four new fossil species as Rhyssa gulliveri sp. nov. in Rhyssinae, Triclistus levii sp. nov. in Metopiinae, Firkantus freddykruegeri gen. et. sp. nov. in Pimplinae and Magnocula sarcophaga gen. et sp. nov. in Phygadeuontinae. The first two species are the first known representatives of the subfamilies Rhyssinae and Metopiinae in amber.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13358-023-00294-2.

The genus Eurymeros Bhat (Hymenoptera, Braconidae, Alysiinae) newly recorded from China

Background

Alysiinae Leach is a species-rich subfamily in Braconidae, of which several species play an important role in biological control. The monotypic genus Eurymerostumespiraculum Bhat, 1980 was discovered in Tibet and Yunnan provinces for the first time, representing the first record of the genus Eurymeros Bhat, 1980 (Braconidae, Alysiinae) in China.

New information

The rare genus Eurymeros Bhat, 1980 (Braconidae, Alysiinae) and its only known species, E.tumespiraculum Bhat, 1980, are newly recorded from China. The morphological variation of the Chinese specimens is described and illustrated.

Chromosome-Scale Genome Assembly of the Solitary Parasitoid Wasp Microplitis manilae Ashmead, 1904 (Braconidae: Microgastrinae)

Parasitoid wasps are invaluable natural enemies extensively used to control coleopteran, dipteran, and lepidopteran pests in agriculture and forestry owing to their killing and reproductive actions on hosts. The important larval endoparasitoid wasp Microplitis manilae, which belongs to the Microgastrinae subfamily, parasitizes the larval stages of Spodoptera spp., such as Spodoptera litura and Spodoptera frugiperda. The absence of a genomic resource for M. manilae has impeded studies on chemosensory- and detoxification-related genes. This study presents a chromosome-level genome assembly of M. manilae with a genome size of 293.18 Mb, which includes 222 contigs (N50 size, 7.58 Mb) and 134 scaffolds (N50 size, 27.33 Mb). A major proportion of the genome (284.76 Mb; 97.13%) was anchored to 11 pseudochromosomes with a single-copy BUSCO score of 98.4%. Furthermore, 14,316 protein-coding genes, 165.14 Mb (57.99%) repetitive elements, and 871 noncoding RNAs were annotated and identified. Additionally, a manual annotation of 399 genes associated with chemosensation and 168 genes involved in detoxification was conducted. This study provides a valuable and high-quality genomic resource to facilitate further functional genomics research on parasitoid wasps.

Dietary Challenges for Parasitoid Wasps (Hymenoptera: Ichneumonoidea); Coping with Toxic Hosts, or Not?

Many insects defend themselves against predation by being distasteful or toxic. The chemicals involved may be sequestered from their diet or synthesized de novo in the insects' body tissues. Parasitoid wasps are a diverse group of insects that play a critical role in regulating their host insect populations such as lepidopteran caterpillars. The successful parasitization of caterpillars by parasitoid wasps is contingent upon their aptitude for locating and selecting suitable hosts, thereby determining their efficacy in parasitism. However, some hosts can be toxic to parasitoid wasps, which can pose challenges to their survival and reproduction. Caterpillars employ a varied array of defensive mechanisms to safeguard themselves against natural predators, particularly parasitoid wasps. These defenses are deployed pre-emptively, concurrently, or subsequently during encounters with such natural enemies. Caterpillars utilize a range of strategies to evade detection or deter and evade attackers. These tactics encompass both measures to prevent being noticed and mechanisms aimed at repelling or eluding potential threats. Post-attack strategies aim to eliminate or incapacitate the eggs or larvae of parasitoids. In this review, we investigate the dietary challenges faced by parasitoid wasps when encountering toxic hosts. We first summarize the known mechanisms through which insect hosts can be toxic to parasitoids and which protect caterpillars from parasitization. We then discuss the dietary adaptations and physiological mechanisms that parasitoid wasps have evolved to overcome these challenges, such as changes in feeding behavior, detoxification enzymes, and immune responses. We present new analyses of all published parasitoid-host records for the Ichneumonoidea that attack Lepidoptera caterpillars and show that classically toxic host groups are indeed hosts to significantly fewer species of parasitoid than most other lepidopteran groups.

Biodiversity of hymenopteran parasitoids

Parasitoid wasps are the most successful group of insect parasitoids, comprising more than half the known diversity of Hymenoptera and probably most of the unknown diversity. This lifestyle has enabled them to be used as pest control agents conferring substantial economic benefits to global agriculture. Major lineages of parasitoid wasps include Ichneumonoidea, Ceraphronoidea, Proctotrupomorpha, and a number of aculeate families. The parasitoid lifestyle arose only once among basal Hymenoptera, in the common ancestor of the Orussidae and Apocrita some 200+ Ma ago. The ancestral parasitoid wasp was probably an idiobiont on wood-living beetle larvae. From this comparatively simple biology, Hymenoptera radiated into an incredible diversity of hosts and parasitoid lifestyles, including hyperparasitoidism, kleptoparasitoidism, egg parasitoidism, and polyembryony, in several instances co-opting viruses to subdue their hosts. Many lineages evolved beyond the parasitoid niche, becoming secondarily herbivorous or predatory nest provisioners and eventually giving rise to most instances of insect societies.

Key innovations and the diversification of Hymenoptera

The order Hymenoptera (wasps, ants, sawflies, and bees) represents one of the most diverse animal lineages, but whether specific key innovations have contributed to its diversification is still unknown. We assembled the largest time-calibrated phylogeny of Hymenoptera to date and investigated the origin and possible correlation of particular morphological and behavioral innovations with diversification in the order: the wasp waist of Apocrita; the stinger of Aculeata; parasitoidism, a specialized form of carnivory; and secondary phytophagy, a reversal to plant-feeding. Here, we show that parasitoidism has been the dominant strategy since the Late Triassic in Hymenoptera, but was not an immediate driver of diversification. Instead, transitions to secondary phytophagy (from parasitoidism) had a major influence on diversification rate in Hymenoptera. Support for the stinger and the wasp waist as key innovations remains equivocal, but these traits may have laid the anatomical and behavioral foundations for adaptations more directly associated with diversification.

Comparative mitogenomes reveal diverse and novel gene rearrangements in the genus Meteorus (Hymenoptera: Braconidae)

Meteorus Haliday, 1835 is a cosmopolitan genus within Braconidae (Hymenoptera). They are koinobiont endoparasitoids of Coleoptera or Lepidoptera larvae. Only one mitogenome of this genus was available. Here, we sequenced and annotated three mitogenomes of Meteorus species, and found that the tRNA gene rearrangements in these mitogenomes were rich and diverse. Compared with the ancestral organization, only seven tRNAs (trnW, trnY, trnL2, trnH, trnT, trnP and trnV) were conserved and trnG had its own unique location in the four mitogenomes. This dramatic tRNA rearrangement was not observed in mitogenomes of other insect groups before. In addition, the tRNA cluster (trnA-trnR-trnN-trnS1-trnE-trnF) between nad3 and nad5 was rearranged into two patterns, i.e., trnE-trnA-trnR-trnN-trnS1 and trnA-trnR-trnS1-trnE-trnF-trnN. The phylogenetic results showed that the Meteorus species formed a clade within the subfamily Euphorinae, and were close to Zele (Hymenoptera, Braconidae, Euphorinae). In the Meteorus, two clades were reconstructed: M. sp. USNM and Meteorus pulchricornis forming one clade while the remaining two species forming another clade. This phylogenetic relationship also matched the tRNA rearrangement patterns. The diverse and phylogenetic signal of tRNA rearrangements within one genus provided insights into tRNA rearrangements of the mitochondrial genome at genus/species levels in insects.

New TNT routines for parallel computing with MPI

Phylogenetic inference, which involves time-consuming calculations, is a field where parallelization can speed up the resolution of many problems. TNT (a widely used program for phylogenetic analysis under parsimony) allows parallelization under the PVM system (Parallel Virtual Machine). However, as the basic aspects of the implementation remain unpublished, few studies have taken advantage of the parallelization routines of TNT. In addition, the PVM system is deprecated by many system administrators. One of the most common standards for high performance computing is now MPI (Message Passing Interface). To facilitate the use of the parallel analyses offered by TNT, this paper describes the basic aspects of the implementation, as well as a port of the parallelization interface of TNT into MPI. The use of the new routines is illustrated by reanalysis of seven significant datasets, either recent phylogenomic datasets with many characters (up to 2,509,064 characters) or datasets with large numbers of taxa (up to 13,921 taxa). Versions of TNT including the MPI functionality are available at: http://www.lillo.org.ar/phylogeny/tnt/.

A braconid wasp (Hymenoptera, Braconidae) from the Lower Cretaceous amber of San Just, eastern Iberian Peninsula

Braconid parasitoid wasps are a widely diversified group today, while their fossil record from the Mesozoic is currently poorly known. Here, we describe Utrillabraconelectropteron Álvarez-Parra & Engel, gen. et sp. nov., from the upper Albian (Lower Cretaceous) amber of San Just in the eastern Iberian Peninsula. The holotype specimen is incomplete, although the forewing and hind wing venation are well preserved. The new taxon is assigned to the subfamily †Protorhyssalinae (Braconidae) and, based on characteristics of the wing venation, seems to be closely related to Protorhyssalusgoldmani Basibuyuk & Quicke, 1999 and Diorhyssalusallani (Brues, 1937), both from Upper Cretaceous ambers of North America. We discuss the taxonomy of the Cretaceous braconids, considering †Seneciobraconinae as a valid subfamily. We also comment on possible relationships within †Protorhyssalinae, although a phylogenetic analysis is necessary. Additionally, a checklist is included of braconids known from Cretaceous ambers.