DNA barcoding of microgastrine parasitoid wasps (Hymenoptera: Braconidae) using high-throughput methods more than doubles the number of species known for Australia

Scratching the tip of the iceberg: integrative taxonomy reveals 30 new species records of Microgastrinae (Braconidae) parasitoid wasps for Germany, including new Holarctic distributions

Substantial parts of the European and German insect fauna still remain largely unexplored, the so-called "dark taxa". In particular, midges (Diptera) and parasitoid wasps (Hymenoptera) are abundant and species-rich throughout Europe, yet are often neglected in biodiversity research. One such dark taxon is Microgastrinae wasps (Hymenoptera: Braconidae), a group of parasitoids of lepidopteran caterpillars with 252 species reported in Germany so far. As part of the German Barcode of Life Project GBOL III: Dark Taxa, reverse DNA barcoding and integrative taxonomic approaches were used to shed some light on the German Fauna of Microgastrinae wasps. In our workflow, DNA barcoding was used for molecular clustering of our specimens in a first step, morphological examination of the voucher specimens in a second step, and host data compared in a third step. Here, 30 species are reported for the first time in Germany, adding more than 10% to the known German fauna. Information for four species is provided in a new Holarctic context, reporting them for the Nearctic or, respectively, Palaearctic region, and 26 additional country records are added from sequenced material available in the collections accessible to us. Molecular clusters that show signs of discrepancies are discussed. Results show that we are just scratching the tip of the iceberg of the unexplored Microgastrinae diversity in Germany.

Local adaptation to hosts and parasitoids shape Hamiltonella defensa genotypes across aphid species

Facultative symbionts are common in insects and can provide their hosts with significant adaptations. Yet we still have a limited understanding of what shapes their distributions, such as why particular symbiont strains are common in some host species yet absent in others. To address this question, we genotyped the defensive symbiont Hamiltonella defensa in 26 aphid species that commonly carry this microbe. We found that Hamiltonella strains were strongly associated with specific aphid species and that strains found in one host species rarely occurred in others. To explain these associations, we reciprocally transferred the Hamiltonella strains of three aphid species, Acyrthosiphon pisum, Macrosiphoniella artemisiae and Macrosiphum euphorbiae, and assessed the impact of Hamiltonella strain on: the stability of the symbiosis, aphid fecundity and parasitoid resistance. We demonstrate that the Hamiltonella strains found in nature are locally adapted to specific aphid hosts, and their ecology: aphids tend to carry Hamiltonella strains that are efficiently transmitted to their offspring, non-lethal, and that provide strong protection against their dominant parasitoid species. Our results suggest that facultative symbiont distributions are shaped by selection from natural enemies, and the host itself, resulting in locally adapted symbioses that provide significant benefits against prevailing natural enemies.

The gender-specific impact of starvation on mitotypes diversity in adults of Drosophila melanogaster

In animals, starvation can increase the level of reactive oxygen species (ROS) in some tissues. Mitochondrial DNA (mtDNA) is more vulnerable to being attacked by ROS due to the lack of histone protection, leading to oxidative damage. However, whether starvation is associated with the genetic diversity of mtDNA remains unclear. Here, by using adult individuals of Drosophila melanogaster under three different feeding treatments (starvation, with the provision of only water, and normal feeding), based on the high-throughput sequencing results of the PCR amplicons of the partial sequences of the mitochondrial gene cytochrome c oxidase subunit I (mt-cox1), no significant difference in the mean number of mitochondrial haplotypes and the mean genetic distance of haplotypes within individuals were identified between the three treatment groups. Coupled with the low proportion of heterogeneous mt-cox1 sequences within each individual, it suggested that starvation had a limited impact on mitotype genetic diversity and mitochondrial function. Nevertheless, starvation could significantly increase the sequence number of haplotypes containing specific mutations, and for males with higher levels of mitochondrial heteroplasmy than females in the normal feeding group, starvation could further increase their mitochondrial heteroplasmy.

Life barcoded by DNA barcodes

The modern concept of DNA-based barcoding for cataloguing biodiversity was proposed in 2003 by first adopting an approximately 600 bp fragment of the mitochondrial COI gene to compare via nucleotide alignments with known sequences from specimens previously identified by taxonomists. Other standardized regions meeting barcoding criteria then are also evolving as DNA barcodes for fast, reliable and inexpensive assessment of species composition across all forms of life, including animals, plants, fungi, bacteria and other microorganisms. Consequently, global DNA barcoding campaigns have resulted in the formation of many online workbenches and databases, such as BOLD system, as barcode references, and facilitated the development of mini-barcodes and metabarcoding strategies as important extensions of barcode techniques. Here we intend to give an overview of the characteristics and features of these barcode markers and major reference libraries existing for barcoding the planet’s life, as well as to address the limitations and opportunities of DNA barcodes to an increasingly broader community of science and society.

DROP: Molecular voucher database for identification of Drosophila parasitoids

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, 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 six 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 catalyse 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.

Longer is Not Always Better: Optimizing Barcode Length for Large-Scale Species Discovery and Identification

New techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable, and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared with full-length barcodes. This is here tested based on 20 empirical data sets covering ca. 30,000 specimens (5500 species) and six clade-specific data sets from GenBank covering ca. 98,000 specimens ($>$20,000 species). All specimens in these data sets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtained in silico from full-length barcodes using a sliding window approach (three windows: 100 bp, 200 bp, and 300 bp) and by excising nine mini-barcodes with established primers (length: 94-407 bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular operational taxonomic units (mOTUs) that were obtained using three different species delimitation techniques (Poisson Tree Process, Automatic Barcode Gap Discovery, and Objective Clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length ($>$200 bp). Only very short mini-barcodes (<200 bp) perform poorly, especially when they are located near the 5$^\prime$ end of the Folmer region. The mean congruence between morphospecies and mOTUs was ca. 75% for barcodes $>$200 bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes. [DNA barcoding; metabarcoding; mini-barcodes; species discovery.].

Molecular diversity and species delimitation in the family Gasteruptiidae (Hymenoptera: Evanioidea)

Gasteruptiidae Ashmead is an easily recognised family of wasps with ∼589 described species worldwide. Although well characterised by traditional taxonomy, multiple authors have commented on the extreme morphological uniformity of the group, making species-level identification difficult. This problem is enhanced by the lack of molecular data and molecular phylogenetic research for the group. We used 187 cytochrome c oxidase subunit I (COI) barcodes to explore the efficiency of sequence data to delimitate species in Gasteruptiidae. We undertook a graphical and discussion-based comparison of six methods for species delimitation, with the success of methods judged based on known species boundaries and morphology. Both distance-based (ABGD and jMOTU threshold analysis) and tree-based (GMYC and PTP) methods compared across multiple parameters recovered variable molecular operational taxonomic units (MOTUs), ranging from 55 to 123 MOTUs. Tree-based methods tended to split known morphological species less than distance-based methods, with the single-threshold GMYC method the most concordant with known morphospecies. Our results suggest that the incorporation of molecular species delimitation techniques provides a powerful tool to assist in the interpretation of species and help direct informed decisions with taxonomic uncertainty in the family.

Annotated and illustrated world checklist of Microgastrinae parasitoid wasps (Hymenoptera, Braconidae)

A checklist of world species of Microgastrinae parasitoid wasps (Hymenoptera: Braconidae) is provided. A total of 81 genera and 2,999 extant species are recognized as valid, including 36 nominal species that are currently considered as species inquirendae. Two genera are synonymized under Apanteles. Nine lectotypes are designated. A total of 318 new combinations, three new replacement names, three species name amendments, and seven species status revised are proposed. Additionally, three species names are treated as nomina dubia, and 52 species names are considered as unavailable names (including 14 as nomina nuda). A total of three extinct genera and 12 extinct species are also listed. Unlike in many previous treatments of the subfamily, tribal concepts are judged to be inadequate, so genera are listed alphabetically. Brief diagnoses of all Microgastrinae genera, as understood in this paper, are presented. Illustrations of all extant genera (at least one species per genus, usually more) are included to showcase morphological diversity. Primary types of Microgastrinae are deposited in 108 institutions worldwide, although 76% are concentrated in 17 collections. Localities of primary types, in 138 countries, are reported. Recorded species distributions are listed by biogeographical region and by country. Microgastrine wasps are recorded from all continents except Antarctica; specimens can be found in all major terrestrial ecosystems, from 82°N to 55°S, and from sea level up to at least 4,500 m a.s.l. The Oriental (46) and Neotropical (43) regions have the largest number of genera recorded, whereas the Palaearctic region (28) is the least diverse. Currently, the highest species richness is in the Palearctic region (827), due to more historical study there, followed by the Neotropical (768) and Oriental (752) regions, which are expected to be the most species rich. Based on ratios of Lepidoptera and Microgastrinae species from several areas, the actual world diversity of Microgastrinae is expected to be between 30,000–50,000 species; although these ratios were mostly based on data from temperate areas and thus must be treated with caution, the single tropical area included had a similar ratio to the temperate ones. Almost 45,000 specimens of Microgastrinae from 67 different genera (83% of microgastrine genera) have complete or partial DNA barcode sequences deposited in the Barcode of Life Data System; the DNA barcodes represent 3,545 putative species or Barcode Index Numbers (BINs), as estimated from the molecular data. Information on the number of sequences and BINs per genus are detailed in the checklist. Microgastrinae hosts are here considered to be restricted to Eulepidoptera, i.e., most of the Lepidoptera except for the four most basal superfamilies (Micropterigoidea, Eriocranioidea, Hepialoidea and Nepticuloidea), with all previous literature records of other insect orders and those primitive Lepidoptera lineages being considered incorrect. The following nomenclatural acts are proposed: 1) Two genera are synonymyzed under Apanteles: Cecidobracon Kieffer & Jörgensen, 1910, new synonym and Holcapanteles Cameron, 1905, new synonym; 2) Nine lectotype designations are made for Alphomelondisputabile (Ashmead, 1900), Alphomelonnigriceps (Ashmead, 1900), Cotesiasalebrosa (Marshall, 1885), Diolcogasterxanthaspis (Ashmead, 1900), Dolichogenideaononidis (Marshall, 1889), Glyptapantelesacraeae (Wilkinson, 1932), Glyptapantelesguyanensis (Cameron, 1911), Glyptapantelesmilitaris (Walsh, 1861), and Pseudapantelesannulicornis Ashmead, 1900; 3) Three new replacement names are a) Diolcogasteraurangabadensis Fernandez-Triana, replacing Diolcogasterindicus (Rao & Chalikwar, 1970) [nec Diolcogasterindicus (Wilkinson, 1927)], b) Dolichogenideaincystatae Fernandez-Triana, replacing Dolichogenidealobesia Liu & Chen, 2019 [nec Dolichogenidealobesia Fagan-Jeffries & Austin, 2019], and c) Microplitisvitobiasi Fernandez-Triana, replacing Microplitisvariicolor Tobias, 1964 [nec Microplitisvaricolor Viereck, 1917]; 4) Three names amended are Apantelesirenecarrilloae Fernandez-Triana, 2014, Cotesiaayerzai (Brèthes, 1920), and Cotesiariverai (Porter, 1916); 5) Seven species have their status revised: Cotesiaarctica (Thomson, 1895), Cotesiaokamotoi (Watanabe, 1921), Cotesiaukrainica (Tobias, 1986), Dolichogenideaappellator (Telenga, 1949), Dolichogenideamurinanae (Capek & Zwölfer, 1957), Hypomicrogasteracarnas Nixon, 1965, and Nyererianigricoxis (Wilkinson, 1932); 6) New combinations are given for 318 species: Alloplitiscongensis, Alloplitisdetractus, Apantelesasphondyliae, Apantelesbraziliensis, Apantelessulciscutis, Choerasaper, Choerasapollion, Choerasdaphne, Choerasfomes, Choerasgerontius, Choerashelle, Choerasirates, Choeraslibanius, Choeraslongiterebrus, Choerasloretta, Choerasrecusans, Choerassordidus, Choerasstenoterga, Choerassuperbus, Choerassylleptae, Choerasvacillatrix, Choerasvacillatropsis, Choerasvenilia, Cotesiaasavari, Cotesiabactriana, Cotesiabambeytripla, Cotesiaberberidis, Cotesiabhairavi, Cotesiabiezankoi, Cotesiabifida, Cotesiacaligophagus, Cotesiacheesmanae, Cotesiacompressithorax, Cotesiadelphinensis, Cotesiaeffrena, Cotesiaeuphobetri, Cotesiaelaeodes, Cotesiaendii, Cotesiaeuthaliae, Cotesiaexelastisae, Cotesiahiberniae, Cotesiahyperion, Cotesiahypopygialis, Cotesiahypsipylae, Cotesiajujubae, Cotesialesbiae, Cotesialevigaster, Cotesializeri, Cotesiamalevola, Cotesiamalshri, Cotesiamenezesi, Cotesiamuzaffarensis, Cotesianeptisis, Cotesianycteus, Cotesiaoeceticola, Cotesiaoppidicola, Cotesiaopsiphanis, Cotesiapachkuriae, Cotesiapaludicolae, Cotesiaparbhanii, Cotesiaparvicornis, Cotesiapratapae, Cotesiaprozorovi, Cotesiapterophoriphagus, Cotesiaradiarytensis, Cotesiarangii, Cotesiariverai, Cotesiaruficoxis, Cotesiasenegalensis, Cotesiaseyali, Cotesiasphenarchi, Cotesiasphingivora, Cotesiatransuta, Cotesiaturkestanica, Diolcogasterabengouroui, Diolcogasteragama, Diolcogasterambositrensis, Diolcogasteranandra, Diolcogasterannulata, Diolcogasterbambeyi, Diolcogasterbicolorina, Diolcogastercariniger, Diolcogastercincticornis, Diolcogastercingulata, Diolcogastercoronata, Diolcogastercoxalis, Diolcogasterdipika, Diolcogasterearina, Diolcogasterepectina, Diolcogasterepectinopsis, Diolcogastergrangeri, Diolcogasterheterocera, Diolcogasterhomocera, Diolcogasterindica, Diolcogasterinsularis, Diolcogasterkivuana, Diolcogastermediosulcata, Diolcogastermegaulax, Diolcogasterneglecta, Diolcogasternigromacula, Diolcogasterpalpicolor, Diolcogasterpersimilis, Diolcogasterplecopterae, Diolcogasterplutocongoensis, Diolcogasterpsilocnema, Diolcogasterrufithorax, Diolcogastersemirufa, Diolcogasterseyrigi, Diolcogastersubtorquata, Diolcogastersulcata, Diolcogastertorquatiger, Diolcogastertristiculus, Diolcogasterturneri, Diolcogastervulcana, Diolcogasterwittei, Distatrixanthedon, Distatrixcerales, Distatrixcuspidalis, Distatrixeuproctidis, Distatrixflava, Distatrixgeometrivora, Distatrixmaia, Distatrixtookei, Distatrixtermina, Distatrixsimulissima, Dolichogenideaagamedes, Dolichogenideaaluella, Dolichogenideaargiope, Dolichogenideaatreus, Dolichogenideabakeri, Dolichogenideabasiflava, Dolichogenideabersa, Dolichogenideabiplagae, Dolichogenideabisulcata, Dolichogenideacatonix, Dolichogenideachrysis, Dolichogenideacoffea, Dolichogenideacoretas, Dolichogenideacyane, Dolichogenideadiaphantus, Dolichogenideadiparopsidis, Dolichogenideadryas, Dolichogenideaearterus, Dolichogenideaensiger, Dolichogenideaeros, Dolichogenideaevadne, Dolichogenideafalcator, Dolichogenideagelechiidivoris, Dolichogenideagobica, Dolichogenideahyalinis, Dolichogenideairiarte, Dolichogenidealakhaensis, Dolichogenidealampe, Dolichogenidealaspeyresiella, Dolichogenidealatistigma, Dolichogenidealebene, Dolichogenidealucidinervis, Dolichogenideamalacosomae, Dolichogenideamaro, Dolichogenideamendosae, Dolichogenideamonticola, Dolichogenideanigra, Dolichogenideaolivierellae, Dolichogenideaparallelis, Dolichogenideapelopea, Dolichogenideapelops, Dolichogenideaphaenna, Dolichogenideapisenor, Dolichogenidearoepkei, Dolichogenideascabra, Dolichogenideastatius, Dolichogenideastenotelas, Dolichogenideastriata, Dolichogenideawittei, Exoryzaasotae, Exoryzabelippicola, Exoryzahylas, Exoryzamegagaster, Exoryzaoryzae, Glyptapantelesaggestus, Glyptapantelesagynus, Glyptapantelesaithos, Glyptapantelesamenophis, Glyptapantelesantarctiae, Glyptapantelesanubis, Glyptapantelesarginae, Glyptapantelesargus, Glyptapantelesatylana, Glyptapantelesbadgleyi, Glyptapantelesbataviensis, Glyptapantelesbistonis, Glyptapantelesborocerae, Glyptapantelescacao, Glyptapantelescadei, Glyptapantelescinyras, Glyptapanteleseryphanidis, Glyptapanteleseuproctisiphagus, Glyptapanteleseutelus, Glyptapantelesfabiae, Glyptapantelesfulvigaster, Glyptapantelesfuscinervis, Glyptapantelesgahinga, Glyptapantelesglobatus, Glyptapantelesglyphodes, Glyptapantelesguierae, Glyptapanteleshorus, Glyptapantelesintricatus, Glyptapanteleslamprosemae, Glyptapanteleslefevrei, Glyptapantelesleucotretae, Glyptapanteleslissopleurus, Glyptapantelesmadecassus, Glyptapantelesmarquesi, Glyptapantelesmelanotus, Glyptapantelesmelissus, Glyptapantelesmerope, Glyptapantelesnaromae, Glyptapantelesnepitae, Glyptapantelesnigrescens, Glyptapantelesninus, Glyptapantelesnkuli, Glyptapantelesparasundanus, Glyptapantelespenelope, Glyptapantelespenthocratus, Glyptapantelesphilippinensis, Glyptapantelesphilocampus, Glyptapantelesphoebe, Glyptapantelesphytometraduplus, Glyptapantelespropylae, Glyptapantelespuera, Glyptapantelesseydeli, Glyptapantelessiderion, Glyptapantelessimus, Glyptapantelesspeciosissimus, Glyptapantelesspilosomae, Glyptapantelessubpunctatus, Glyptapantelesthespis, Glyptapantelesthoseae, Glyptapantelesvenustus, Glyptapanteleswilkinsoni, Hypomicrogastersamarshalli, Iconellacajani, Iconelladetrectans, Iconellajason, Iconellalynceus, Iconellapyrene, Iconellatedanius, Illidopsazamgarhensis, Illidopslamprosemae, Illidopstrabea, Keylimepiestriatus, Microplitisadisurae, Microplitismexicanus, Neoclarkinellaariadne, Neoclarkinellacurvinervus, Neoclarkinellasundana, Nyereriaituriensis, Nyererianioro, Nyereriaproagynus, Nyereriataoi, Nyereriavallatae, Parapantelesaethiopicus, Parapantelesalternatus, Parapantelesaso, Parapantelesatellae, Parapantelesbagicha, Parapantelescleo, Parapantelescyclorhaphus, Parapantelesdemades, Parapantelesendymion, Parapantelesepiplemicidus, Parapantelesexpulsus, Parapantelesfallax, Parapantelesfolia, Parapantelesfurax, Parapanteleshemitheae, Parapanteleshyposidrae, Parapantelesindicus, Parapantelesjavensis, Parapantelesjhaverii, Parapantelesmaculipalpis, Parapantelesmaynei, Parapantelesneocajani, Parapantelesneohyblaeae, Parapantelesnydia, Parapantelesprosper, Parapantelesprosymna, Parapantelespunctatissimus, Parapantelesregalis, Parapantelessarpedon, Parapantelessartamus, Parapantelesscultena, Parapantelestransvaalensis, Parapantelesturri, Parapantelesxanthopholis, Pholetesoracutus, Pholetesorbrevivalvatus, Pholetesorextentus, Pholetesoringenuoides, Pholetesorkuwayamai, Promicrogasterapidanus, Promicrogasterbriareus, Promicrogasterconopiae, Promicrogasteremesa, Promicrogastergrandicula, Promicrogasterorsedice, Promicrogasterrepleta, Promicrogastertyphon, Sathonbekilyensis, Sathonflavofacialis, Sathonlaurae, Sathonmikeno, Sathonruandanus, Sathonrufotestaceus, Venanidesastydamia, Venanidesdemeter, Venanidesparmula, and Venanidessymmysta.

Intragenomic internal transcribed spacer 2 variation in a genus of parasitoid wasps (Hymenoptera: Braconidae): implications for accurate species delimitation and phylogenetic analysis

A recent DNA barcoding study of Australian microgastrines (Hymenoptera: Braconidae) sought to use next-generation sequencing of the cytochrome c oxidase subunit 1 (COI) barcoding gene region, the wingless (WG) gene and the internal transcribed spacer 2 (ITS2) to delimit molecular species in a highly diverse group of parasitic wasps. Large intragenomic distances between ITS2 variants, often larger than the average interspecific variation, caused difficulties in using ITS2 for species delimitation in both threshold and tree-based approaches, and the gene was not included in the reported results of the previous DNA barcoding study. We here report on the intragenomic, and the intra- and interspecies, variation in ITS2in the microgastrine genus Diolcogasterto further investigate the value of ITS2as a marker for species delimitation and phylogenetics of the Microgastrinae. Distinctive intragenomic variant patterns were found in different species of Diolcogaster, with some species possessing a single major variant, and others possessing many divergent variants. Characterizing intragenomic variation of ITS2is critical as it is a widely used marker in hymenopteran phylogenetics and species delimitation, and large intragenomic distances such as those found in this study may obscure phylogenetic signal.