Mitochondrial phylogenomics and mitogenome organization in the parasitoid wasp family Braconidae (Hymenoptera: Ichneumonoidea)

Genera Colastes Haliday, Colastinus Belokobylskij, and Xenarcha Foerster (Hymenoptera, Braconidae, Exothecinae) from the Korean Peninsula with a discussion on the Exothecinae genus and subgenus composition

The Exothecinae genera Colastes Haliday, 1833, Colastinus Belokobylskij, 1984, and Xenarcha Foerster, 1863 of the Korean peninsula are reviewed. The names Pseudophanomeris Belokobylskij, 1984 and Shawiana van Achterberg, 1983 are synonymised with the genus Xenarcha Foerster and treated as subgenera. The two new species of Colastes and one new species and subspecies of Xenarcha are described and illustrated. Exothecuseffectus Papp, 1972 is included in Xenarcha Foerster, comb. nov. The composition and distribution of the world-known Exothecinae genera are discussed and an illustrated key to its genera and subgenera is presented. A key to the Korean species of the genera Colastes, Xenarcha, and Colastinus is also provided.

Systematics of the braconid wasp subfamily Rhysipolinae (Hymenoptera, Braconidae) based on UCE data, with the description of a new Neotropical genus

Rhysipolinae is a small cosmopolitan cyclostome subfamily of braconid wasps, currently comprising 10 genera and more than 80 species. The two species of the subfamily whose biology has been confirmed are koinobiont ectoparasitoids of lepidopteran larvae, deviating from the two common parasitoid strategies in Braconidae (koinobiont-endoparasitoid, idiobiont-ectoparasitoid). Defining the limits of Rhysipolinae has been challenging due to the lack of exclusive morphological features and difficulties in resolving its phylogenetic relationships based on both morphological and Sanger DNA sequence data. However, recent phylogenomic studies using nuclear ultraconserved elements (UCEs) and mitochondrial genome sequences have begun to clarify its relationships, although various generic boundaries remain unclear. Here a phylogenomic analysis based on UCE data was performed including 32 species of nine rhysipoline genera to assess the monophyly of the subfamily as well as its generic limits. Our phylogenetic analysis confirmed the monophyly of Rhysipolinae, but no unique external morphological features were found for its diagnosis. Most genera were recovered as monophyletic except Rhysipolis Förster, 1863, whose clade included Cerophanes Tobias, 1971 and Troporhysipolis Quicke, Belokobylskij & Butcher, 2016. Based on our molecular and morphological evidence, we synonymise Cerophanes syn. nov. with Rhysipolis and describe the new genus and species Rogapolisnomai García-Acosta, Shimbori, Castañeda-Osorio & Zaldívar-Riverón gen. et sp. nov., which is mainly characterised by a median longitudinal carina on the second metasomal tergum, a feature previously predominantly occurring in Rogadinae. Moreover, Pseudavga Tobias, 1964 syn. nov. is proposed as a subgenus of Pachystigmus Hellén, 1927. A taxonomic diagnosis for Rhysipolinae and a key to its currently valid genera are also provided.

Three new species and phylogenetic affinity of the neotropical genus Sericobracon Shaw (Braconidae: Doryctinae)

Sericobracon Shaw is a small doryctine genus which was erected based on two species from Trinidad and the U.S. Virgin Islands (St. Croix) in the Caribbean Sea (S. arimaensis Shaw and S. evansi Shaw). Its type species, S. arimaensis, was reported as endoparasitoid of an Embioptera species, which is a unique biology for known Braconidae. Here we describe three new species of Sericobracon from Costa Rica: S. paulmarshi Zaldívar-Riverón & Shaw, S. puravida Zaldívar-Riverón & Shaw, and S. zunigai Zaldívar-Riverón & Shaw. The former species is characterized with DNA barcoding, providing the first such molecular data for any species in this genus. We also investigated the phylogenetic affinity of the genus within the subfamily Doryctinae based on nuclear UCE data. Sericobracon was recovered within the main Neotropical doryctine clade closely related to Bolivar Zaldívar-Riverón & Rodríguez-Jiménez and Parallorhogas Marsh. We discuss the higher taxonomic classification of Sericobracon and the latter two genera within the Doryctinae based on these relationships recovered and their shared morphological features. A key to species and digital photographs of the five described species of Sericobracon are provided.

New fossil species from two genera of the subfamily Hormiinae (Hymenoptera: Braconidae) from Eocene Baltic amber

New species of the genus Prochremylus Brues, 1933, P. museumoceanus Belokobylskij, sp. nov., from the tribe Chremylini and of the genus Aulosaphes Muesebeck, 1935, Aulosaphes fumipennis Belokobylskij, sp. nov., from the tribe Lysitermini of the subfamily Hormiinae are described and illustrated from the late Eocene Baltic amber. The genus Aulosaphes Muesebeck is recorded as a fossil in Baltic amber for the first time. The new subgenus of the genus Aulosaphes, Antiquasaphes Belokobylskij, subgen. nov., is described and key to subgenera is provided. A detailed redescription of the fossil genus Prochremylus Brues is provided. The position of the hormiine taxa previously described as fossils is discussed.

Insect Mitochondrial Genomics: A Decade of Progress

The past decade has seen the availability of insect genomic data explode, with mitochondrial (mt) genome data seeing the greatest growth. The widespread adoption of next-generation sequencing has solved many earlier methodological limitations, allowing the routine sequencing of whole mt genomes, including from degraded or museum specimens and in parallel to nuclear genomic projects. The diversity of available taxa now allows finer-scale comparisons between mt and nuclear phylogenomic analyses; high levels of congruence have been found for most orders, with some significant exceptions (e.g., Odonata, Mantodea, Diptera). The evolution of mt gene rearrangements and their association with haplodiploidy have been tested with expanded taxonomic sampling, and earlier proposed trends have been largely supported. Multiple model systems have been developed based on findings unique to insects, including mt genome fragmentation (lice and relatives) and control region duplication (thrips), allowing testing of hypothesized evolutionary drivers of these aberrant genomic phenomena. Finally, emerging research topics consider the contributions of mt genomes to insect speciation and habitat adaption, with very broad potential impacts. Integration between insect mt genomic research and other fields within entomology continues to be our field's greatest opportunity and challenge.

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.

Drawing mitochondrial genomes with circularMT

SUMMARY

Mitochondrial DNA sequences are used extensively in phylogeographic and phylogenetic studies for a wide range of organisms. With the advent of low-cost, high throughput 'next generation' DNA sequencing, and user-friendly bioinformatics pipelines for generating and annotating whole mitochondrial genome assemblies, the analysis of whole mitochondrial genomes has become an important component of phylogenomic studies for taxa with high species diversity but limited coverage for other genomic resources. An important step in characterizing de novo mitochondrial genome assemblies is to evaluate and describe structural rearrangements relative to reference taxa. Accessible tools are needed to help visualize gene and noncoding feature complement, their order and strand orientation. However, there are few dedicated applications that generate high quality genome diagrams. Here we present circularMT and circularMT-console that allow users to create highly customizable, publication quality images, of linear and circular mitochondrial genome maps, either individually, or integrated into an analysis pipeline.

AVAILABILITY AND IMPLEMENTATION

Both applications are implemented in C#, with binaries, source code and user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319).

SUPPLEMENTARY INFORMATION

This paper has no supplementary data.

First reliable fossil record of the subfamily Rhysipolinae (Hymenoptera: Braconidae): a new subgenus and species of the genus Rhysipolis Foerster, 1863 from Baltic amber

A new fossil subgenus and species of the genus Rhysipolis Foerster, 1863 from the subfamily Rhysipolinae, Rhysipolis (Granulopolis) simutniki Belokobylskij, subgen. et sp. nov., are described and illustrated from late Eocene Baltic amber. The genus Trichelyon Ortega-Blanco & Engel, 2012 is synonymised with Clinocentrus Haliday, 1833 (syn. nov.) and a new combination, Clinocentrus tadkeshwarense (Ortega-Blanco & Engel, 2012), comb. nov., is suggested. The status of the previously described species in the subfamily Rhysipolinae are discussed.

Characterization of the Mitogenome of the Genus Dendrocerus Ratzeburg (Hymenoptera: Megaspilidae) with the Specific Designed Primers

In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of Dendrocerus (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of Dendrocerus and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of D. bellus and D. anisodontus were 15,445 bp and 15,373 bp, respectively, with the trnG of D. bellus missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (D. bellus) and 82.4% (D. anisodontus). Using Ceraphron sp. (Ceraphronidae) as reference, the Ka/Ks values of NAD4L and NAD6 in D. anisodontus were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with Ceraphon sp. gene order, nine operations were identified in D. anisodontus, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the COX1 genes in Megaspilidae and a 60% rate of success was achieved in the genus Dendrocerus.

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.

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.

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.