Integrative ecological and molecular analysis indicate high diversity and strict elevational separation of canopy beetles in tropical mountain forests

Tropical mountain forests contribute disproportionately to terrestrial biodiversity but little is known about insect diversity in the canopy and how it is distributed between tree species. We sampled tree-specific arthropod communities from 28 trees by canopy fogging and analysed beetle communities which were first morphotyped and then identified by their DNA barcodes. Our results show that communities from forests at 1100 and 1700 m a.s.l. are almost completely distinct. Diversity was much lower in the upper forest while community structure changed from many rare, less abundant species to communities with a pronounced dominance structure. We also found significantly higher beta-diversity between trees at the lower than higher elevation forest where community similarity was high. Comparisons on tree species found at both elevations reinforced these results. There was little species overlap between sites indicating limited elevational ranges. Furthermore, we exploited the advantage of DNA barcodes to patterns of haplotype diversity in some of the commoner species. Our results support the advantage of fogging and DNA barcodes for community studies and underline the need for comprehensive research aimed at the preservation of these last remaining pristine forests.

Resolving the Taxonomic Status of Potential Biocontrol Agents Belonging to the Neglected Genus Lipolexis Förster (Hymenoptera, Braconidae, Aphidiinae) with Descriptions of Six New Species

Simple Summary

Lipolexis is small but widely distributed genus across Europe and Asia. Nevertheless, its taxonomic distinctiveness was subsequently questioned by some authors who considered it as a synonym of the genus Diaeretus. Although Lipolexis is widely distributed and one species (Lipolexis oregmae Gahan) is an important biological control agent, the last taxonomic study on it was conducted more than 50 years ago. Our study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were sampled worldwide, including specimens from BOLD database. It led to the description of six new species. Each of the new species possesses clear morphological characters that distinguishes it from its congeners. Our findings suggest that two groups can be differentiated within the genus—oregmae and gracilis. Furthermore, we present a key for the identification to all known Lipolexis species of the world.

Abstract

Lipolexis is a small genus in the subfamily Aphidiinae represented by one species in Europe (Lipolexis gracilis Förster) and by four in Asia (Lipolexis wuyiensis Chen, L. oregmae Gahan, L. myzakkaiae Pramanik and Raychaudhuri and L. pseudoscutellaris Pramanik and Raychaudhuri). Although L. oregmae is employed in biological control programs against pest aphids, the last morphological study on the genus was completed over 50 years ago. This study employs an integrative approach (morphology and molecular analysis (COI barcode region)), to examine Lipolexis specimens that were sampled worldwide, including specimens from BOLD database. These results establish that two currently recognized species of Lipolexis (L. gracilis, L. oregmae) are actually a species complex and also reveal phylogenetic relationships within the genus. Six new species are described and a global key for the identification of Lipolexis species is provided.

A new genus and species of Neotropical gregarious braconine parasitoid (Hymenoptera: Braconidae) of a caterpillar (Lepidoptera: Hesperiidae)

A new genus of braconine parasitoid wasp, Acgorium Sharkey Quicke gen. nov., based on a new species from Costa Rica, Acgorium felipechavarriai Sharkey sp. nov., is described and illustrated, based on specimens reared from wild-caught hesperiid caterpillars of Dyscophellus phraxanor (Hewitson). Acgorium felipechavarriai is the first known braconine gregarious ectoparasitoid of a butterfly caterpillar.

Using DNA-barcoded Malaise trap samples to measure impact of a geothermal energy project on the biodiversity of a Costa Rican old-growth rain forest

We report one year (2013-2014) of biomonitoring an insect community in a tropical old-growth rain forest, during construction of an industrial-level geothermal electricity project. This is the first-year reaction by the species-rich insect biodiversity; six subsequent years are being analyzed now. The site is on the margin of a UNESCO Natural World Heritage Site, Área de Conservación Guanacaste (ACG), in northwestern Costa Rica. This biomonitoring is part of Costa Rica's ongoing efforts to sustainably retain its wild biodiversity through biodevelopmental integration with its societies. Essential tools are geothermal engineering needs, entomological knowledge, insect species-rich forest, government-NGO integration, common sense, DNA barcoding for species-level identification, and Malaise traps. This research is tailored for integration with its society at the product level. We combine an academic view with on-site engineering decisions. This biomonitoring requires alpha-level DNA barcoding combined with centuries of morphology-based entomological taxonomy and ecology. Not all desired insect community analyses are performed; they are for data from subsequent years combined with this year. We provide enough analysis to be used by both guilds now. This biomonitoring has shown, for the first year, that the geothermal project impacts only the biodiversity within a zone less than 50 m from the project margin.

DNA metabarcoding for biodiversity monitoring in a national park: Screening for invasive and pest species

DNA metabarcoding was utilized for a large-scale, multiyear assessment of biodiversity in Malaise trap collections from the Bavarian Forest National Park (Germany, Bavaria). Principal component analysis of read count-based biodiversities revealed clustering in concordance with whether collection sites were located inside or outside of the National Park. Jaccard distance matrices of the presences of barcode index numbers (BINs) at collection sites in the two survey years (2016 and 2018) were significantly correlated. Overall similar patterns in the presence of total arthropod BINs, as well as BINs belonging to four major arthropod orders across the study area, were observed in both survey years, and are also comparable with results of a previous study based on DNA barcoding of Sanger-sequenced specimens. A custom reference sequence library was assembled from publicly available data to screen for pest or invasive arthropods among the specimens or from the preservative ethanol. A single 98.6% match to the invasive bark beetle Ips duplicatus was detected in an ethanol sample. This species has not previously been detected in the National Park.

Phylogenetic reassignment of basal cyclostome braconid parasitoid wasps (Hymenoptera) with description of a new, enigmatic Afrotropical tribe with a highly anomalous 28S D2 secondary structure

A new tribe of braconid wasps provisionally included in the Rhyssalinae, Laibaleini trib. nov., type genus Laibalea gen. nov. (type species Laibalea enigmatica sp. nov.), from Kenya and the Central African Republic, is described. A molecular dataset, with emphasis on basally derived taxa based on four gene fragments (28S D2–D3 expansion region, COI barcode, elongation factor 1-alpha and 16S ribosomal DNA), was analysed both alone and in combination with a morphological dataset. Molecular phylogenetic placement of the new species into an existing subfamily is complicated by the extreme sequence divergence of the three sequences obtained for Laibalea. In both the combined sequence analysis and the combined DNA plus morphological tree, Laibalea is recovered as a sister group to the Rhyssalinae plus all non-cyclostome lineage braconids excluding Mesostoinae, Maxfischeriinae and Aphidiinae. A consensus of morphological characters and molecular analyses suggests inclusion of Laibalea either in the otherwise principally Holarctic subfamily Rhyssalinae or perhap more basally, in the principally Gondwanan Mesostoinae s.l., although we cannot exclude the possibility that it might represent a separate basal lineage. We place Laibalea in its own tribe, provisionally included in Rhyssalinae. The DNA sequence data are presented for several genera for the first time. Avga, the type genus of Avgini, is shown not to belong to Mesostoinae s.l. or Hormiinae, but its exact relationships remain uncertain. The generic compositions of Rhyssalinae and Mesostoinae s.l. are revised. Anachyra, Apoavga, Neptihormius, Neoavga and Opiopterus are shown to belong to Mesostoinae s.s. A key to the tribes of Rhyssalinae is provided.

BOLD and GenBank revisited - Do identification errors arise in the lab or in the sequence libraries?

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.

DNA barcode library for European Gelechiidae (Lepidoptera) suggests greatly underestimated species diversity

For the first time, a nearly complete barcode library for European Gelechiidae is provided. DNA barcode sequences (COI gene – cytochrome c oxidase 1) from 751 out of 865 nominal species, belonging to 105 genera, were successfully recovered. A total of 741 species represented by specimens with sequences ≥ 500bp and an additional ten species represented by specimens with shorter sequences were used to produce 53 NJ trees. Intraspecific barcode divergence averaged only 0.54% whereas distance to the Nearest-Neighbour species averaged 5.58%. Of these, 710 species possessed unique DNA barcodes, but 31 species could not be reliably discriminated because of barcode sharing or partial barcode overlap. Species discrimination based on the Barcode Index System (BIN) was successful for 668 out of 723 species which clustered from minimum one to maximum 22 unique BINs. Fifty-five species shared a BIN with up to four species and identification from DNA barcode data is uncertain. Finally, 65 clusters with a unique BIN remained unidentified to species level. These putative taxa, as well as 114 nominal species with more than one BIN, suggest the presence of considerable cryptic diversity, cases which should be examined in future revisionary studies.

Dynamics of a host-parasitoid interaction clarified by modelling and DNA sequencing

It has been hypothesised that the 2-year oscillations in abundance of Xestia moths are mediated by interactions with 1-year Ophion parasitoid wasps. We tested this hypothesis by modelling a 35-year time series of Xestia and Ophion from Northern Finland. Additionally, we used DNA barcoding to ascertain the species diversity of Ophion and targeted amplicon sequencing of their gut contents to confirm their larval hosts. Modelling of the time-series data strongly supported the hypothesised host-parasitoid dynamics and that periodic occurrence of Xestia moths is mediated by Ophion. DNA barcodes revealed that Ophion included five species rather than just one while targeted amplicon sequencing verified that Ophion does parasitise Xestia. At least one Ophion species employs 1-year Syngrapha interrogationis as an alternate host, but it did not detectably affect Xestia-Ophion dynamics. We also demonstrate the previously unrecognised complexity of this system due to cryptic parasitoid diversity.

Phylogeny of the Subtribe Monoctonina (Hymenoptera, Braconidae, Aphidiinae)

Members of the Monoctonina subtribe have long been neglected in applied studies of the subfamily Aphidiinae, due to their low economic importance, as they do not parasitize pests of cultivated plants. Consequently, data about this group are scarce, including its taxonomy and phylogeny. In the present study, we explore inter- and intraspecific genetic variation of Monoctonina species, including genera Monoctonus Haliday 1833, Monoctonia Starý 1962, Falciconus Mackauer 1959 and Harkeria Cameron 1900. We employ two molecular markers, the barcode region of the mitochondrial cytochrome c oxidase subunit I (COI) and the D2 region of the 28S nuclear gene (28S rDNA), to analyze genetic structuring and phylogeny of all available Monoctonina species, and combine them with morphological data for an integrative approach. We report one new species, and three potentially new species which can be formally described when further specimens are available. Analysis of phylogenetic relationships within the subtribe shows a basal position for the genera Falciconus and Monoctonia, and the close relatedness of Harkeria and Monoctonus.

Using multiple lines of evidence to delimit protogynes and deutogynes of four-legged mites: a case study on Epitrimerus sabinae s.l. (Acari : Eriophyidae)

Accurate species delimitation is essential for the study of biodiversity, but morphological approaches often provide a limited ability to connect different life stages, sexes or other phenotypic variants in eriophyoid mites because many species possess two phenotypically distinct forms: protogynes and deutogynes. In this study, we analysed the morphological variation in 26 populations of the eriophyoid mite, Epitrimerus sabinae Xue & Hong, 2005 s.l., from sites across its entire known distribution and revealed three morphotypes (LNS: large, normal palp seta d; MBS: medium, bifurcated palp seta d; SBS: small, bifurcated palp seta d) distinguished by body size and structure of dorsal pedipalp genual seta. Five lines of evidence (morphometrics, DNA-based species delimitation, phylogenetics, haplotype network, mitochondrial genome architecture) indicated that the MBS and SBS groups were very distinct from LNS (E. sabinae s.s.). In fact, the MBS and SBS morphotypes are properly placed in the genus Leipothrix with the MBS lineage representing the protogyne of L. juniperensis, sp. nov., whereas the SBS lineage is its deutogyne. By expanding the approaches used to link protogynes and deutogynes of eriophyoid mites, this study provides a way to accelerate the delineation of species boundaries in this important group of plant pests.

BIN overlap confirms transcontinental distribution of pest aphids (Hemiptera: Aphididae)

DNA barcoding is highly effective for identifying specimens once a reference sequence library is available for the species assemblage targeted for analysis. Despite the great need for an improved capacity to identify the insect pests of crops, the use of DNA barcoding is constrained by the lack of a well-parameterized reference library. The current study begins to address this limitation by developing a DNA barcode reference library for the pest aphids of Pakistan. It also examines the affinities of these species with conspecific populations from other geographic regions based on both conventional taxonomy and Barcode Index Numbers (BINs). A total of 809 aphids were collected from a range of plant species at sites across Pakistan. Morphological study and DNA barcoding allowed 774 specimens to be identified to one of 42 species while the others were placed to a genus or subfamily. Sequences obtained from these specimens were assigned to 52 BINs whose monophyly were supported by neighbor-joining (NJ) clustering and Bayesian inference. The 42 species were assigned to 41 BINs with 38 showing BIN concordance. These species were represented on BOLD by 7,870 records from 69 countries. Combining these records with those from Pakistan produced 60 BINs with 12 species showing a BIN split and three a BIN merger. Geo-distance correlations showed that intraspecific divergence values for 49% of the species were not affected by the distance between populations. Forty four of the 52 BINs from Pakistan had counterparts in 73 countries across six continents, documenting the broad distributions of pest aphids.

A reference library for Canadian invertebrates with 1.5 million barcodes, voucher specimens, and DNA samples

The reliable taxonomic identification of organisms through DNA sequence data requires a well parameterized library of curated reference sequences. However, it is estimated that just 15% of described animal species are represented in public sequence repositories. To begin to address this deficiency, we provide DNA barcodes for 1,500,003 animal specimens collected from 23 terrestrial and aquatic ecozones at sites across Canada, a nation that comprises 7% of the planet's land surface. In total, 14 phyla, 43 classes, 163 orders, 1123 families, 6186 genera, and 64,264 Barcode Index Numbers (BINs; a proxy for species) are represented. Species-level taxonomy was available for 38% of the specimens, but higher proportions were assigned to a genus (69.5%) and a family (99.9%). Voucher specimens and DNA extracts are archived at the Centre for Biodiversity Genomics where they are available for further research. The corresponding sequence and taxonomic data can be accessed through the Barcode of Life Data System, GenBank, the Global Biodiversity Information Facility, and the Global Genome Biodiversity Network Data Portal.

DNA barcodes reveal 63 overlooked species of Canadian beetles (Insecta, Coleoptera)

This study demonstrates the power of DNA barcoding to detect overlooked and newly arrived taxa. Sixty-three species of Coleoptera representing 25 families are studied based on DNA barcode data and morphological analysis of the barcoded specimens. Three of the species involve synonymies or previous taxonomic confusion in North America, while the first Canadian records are published for 60 species. Forty-two species are adventive in North America, and 40 of these adventive species originate from the Palaearctic region. Three genera are recorded from the Nearctic region for the first time: Coelostoma Brullé, 1835 (Hydrophilidae), Scydmoraphes Reitter, 1891 (Staphylinidae), and Lythraria Bedel, 1897 (Chrysomelidae). Two new synonymies are established: Mycetoporus triangulatus Campbell, 1991 (Staphylinidae) is a junior synonym of Mycetoporus reichei Pandellé, 1869, syn. nov. while Bledius philadelphicus Fall, 1919 (Staphylinidae) is a junior synonym of Bledius gallicus (Gravenhorst, 1806), syn. nov. The previously suggested move of Ctenicera tigrina (Fall, 1901) to the genus Pseudanostirus Dolin, 1964 (Elateridae) is formalized, resulting in Pseudanostirus tigrinus (Fall, 1901), comb. nov.

A Single-Laboratory Validated Method for the Generation of DNA Barcodes for the Identification of Fish for Regulatory Compliance

The U.S. Food and Drug Administration is responsible for ensuring that the nation's food supply is safe and accurately labeled. This task is particularly challenging in the case of seafood where a large variety of species are marketed, most of this commodity is imported, and processed product is difficult to identify using traditional morphological methods. Reliable species identification is critical for both foodborne illness investigations and for prevention of deceptive practices, such as those where species are intentionally mislabeled to circumvent import restrictions or for resale as species of higher value. New methods that allow accurate and rapid species identifications are needed, but any new methods to be used for regulatory compliance must be both standardized and adequately validated. "DNA barcoding" is a process by which species discriminations are achieved through the use of short, standardized gene fragments. For animals, a fragment (655 base pairs starting near the 5′ end) of the cytochrome c oxidase subunit 1 mitochondrial gene has been shown to provide reliable species level discrimination in most cases. We provide here a protocol with single-laboratory validation for the generation of DNA barcodes suitable for the identification of seafood products, specifically fish, in a manner that is suitable for FDA regulatory use.

A species-level taxonomic review and host associations of Glyptapanteles (Hymenoptera, Braconidae, Microgastrinae) with an emphasis on 136 new reared species from Costa Rica and Ecuador

The descriptive taxonomic study reported here is focused on Glyptapanteles, a species-rich genus of hymenopteran parasitoid wasps. The species were found within the framework of two independent long-term Neotropical caterpillar rearing projects: northwestern Costa Rica (Área de Conservación Guanacaste, ACG) and eastern Andes, Ecuador (centered on Yanayacu Biological Station, YBS). One hundred thirty-six new species of Glyptapanteles Ashmead are described and all of them are authored by Arias-Penna. None of them was recorded in both countries; thus, 78 are from Costa Rica and the remaining 58 from Ecuador. Before this revision, the number of Neotropical described Glyptapanteles did not reach double digits. Reasonable boundaries among species were generated by integrating three datasets: Cytochrome Oxidase I (COI) gene sequencing data, natural history (host records), and external morphological characters. Each species description is accompanied by images and known geographical distribution. Characteristics such as shape, ornamentation, and location of spun Glyptapanteles cocoons were imaged as well. Host-parasitoid associations and food plants are also here published for the first time. A total of 88 species within 84 genera in 15 Lepidoptera families was encountered as hosts in the field. With respect to food plants, these wild-caught parasitized caterpillars were reared on leaves of 147 species within 118 genera in 60 families. The majority of Glyptapanteles species appeared to be relatively specialized on one family of Lepidoptera or even on some much lower level of taxonomic refinement. Those herbivores in turn are highly food-plant specialized, and once caterpillars were collected, early instars (1-3) yielded more parasitoids than later instars. Glyptapanteles jimmilleri Arias-Penna, sp. nov. is the first egg-larval parasitoid recorded within the genus, though there may be many more since such natural history requires a more focused collection of eggs. The rate of hyperparasitoidism within the genus was approximately 4% and was represented by Mesochorus spp. (Ichneumonidae). A single case of multiparasitoidism was reported, Copidosoma floridanum Ashmead (Encyrtidae) and Glyptapanteles ilarisaaksjarvi Arias-Penna, sp. nov. both parasitoid species emerged from the caterpillar of Noctuidae: Condica cupienta (Cramer). Bodyguard behavior was observed in two Glyptapanteles species: G. howelldalyi Arias-Penna, sp. nov. and G. paulhansoni Arias-Penna, sp. nov. A dichotomous key for all the new species is provided. The numerous species described here, and an equal number already reared but not formally described, signal a far greater Glyptapanteles species richness in the Neotropics than suggested by the few described previously.

Review of the world Monoctonina Mackauer 1961 (Hymenoptera, Braconidae, Aphidiinae): key for their identification and descriptions of five new species

The subtribe Monoctonina has long been overlooked when it comes to morphological studies, probably due to the low economic importance of its members. Mainly distributed in high montane areas and forest ecosystems, species of Monoctonina are not often found in large populations and do not parasitize pests of cultivated plants. Our research uncovered five new species belonging to this subtribe (Monoctonus brachyradius sp. n., M. canadensis sp. n., M. inexpectatus sp. n., M. luteus sp. n., and M. parvipalpus sp. n.). We also redescribe species originally described over a century ago, and discuss the utility of certain morphological characters, as well as status of some species within Monoctonina.

Molecular phylogeny and species delimitation of the genus Dicerapanorpa (Mecoptera: Panorpidae)

Given that species is the fundamental unit in systematic biology, rigorous species delimitation is crucial for taxonomic studies, yet routine species delimitation remains an ongoing challenge in the taxonomic practice of insects. The two-horned scorpionfly Dicerapanorpa is a small genus in Panorpidae (Mecoptera) endemic to the Qinling-Bashan and Hengduan mountains, a biodiversity hotspot. However, species of Dicerapanorpa are difficult to delineate owing to marked intraspecific variation and interspecific similarity. Here, we investigate the diversity and species boundaries of Dicerapanorpa using an integrative approach based on DNA barcoding, morphological, geometric morphometric and molecular phylogenetic analyses. This integrative analyses confirmed the 13 described species of Dicerapanorpa and revealed three new species: Dicerapanorpa lativalva sp. nov., Dicerapanorpa hualongshana sp. nov. and Dicerapanorpa minshana sp. nov. Most molecular operational taxonomic units are in congruence with morphological clusters. Possible reasons for several discordances in Dicerapanorpa are tentatively discussed.

DNA barcode library of megadiverse Austrian Noctuoidea (Lepidoptera) - a nearly perfect match of Linnean taxonomy

The aim of the study was to establish a nationwide barcode library for the most diverse group of Austrian Lepidoptera, the Noctuoidea, with 5 families (Erebidae, Euteliidae, Noctuidae, Nolidae, Notodontidae) and around 690 species. Altogether, 3431 DNA barcode sequences from COI gene (cytochrome c oxidase 1) belonging to 671 species were gathered, with 3223 sequences >500 bp. The intraspecific divergence with a mean of only 0.17% is low in most species whereas interspecific distances to the Nearest Neighbour are significantly higher with an average of 4.95%. Diagnostic DNA barcodes were obtained for 658 species. Only 13 species (1.9% of the Austrian Noctuoidea) cannot be reliably identified from their DNA barcode (Setina aurita/Setina irrorella, Conisania leineri/Conisania poelli, Photedes captiuncula/Photedes minima, Euxoa obelisca/Euxoa vitta/Euxoa tritici, Mesapamaea secalella/Mesapamea secalis, Amphipoea fucosa/Amphipoea lucens). A similarly high identification performance was achieved by the Barcode Index (BIN) system. 671 species of Austrian Noctuoidea, representing 3202 records with BINs, are assigned to a total of 678 BINs. The vast majority of 649 species is placed into a single BIN, with only 13 species recognised as BIN-sharing (including the barcode sharing species above). Twenty-one species were assigned to more than one BIN and have to be checked for cryptic diversity in the future.

Metabarcoding a diverse arthropod mock community

Although DNA metabarcoding is an attractive approach for monitoring biodiversity, it is often difficult to detect all the species present in a bulk sample. In particular, sequence recovery for a given species depends on its biomass and mitome copy number as well as the primer set employed for PCR. To examine these variables, we constructed a mock community of terrestrial arthropods comprised of 374 species. We used this community to examine how species recovery was impacted when amplicon pools were constructed in four ways. The first two protocols involved the construction of bulk DNA extracts from different body segments (Bulk Abdomen, Bulk Leg). The other protocols involved the production of DNA extracts from single legs which were then merged prior to PCR (Composite Leg) or PCR‐amplified separately (Single Leg) and then pooled. The amplicons generated by these four treatments were then sequenced on three platforms (Illumina MiSeq, Ion Torrent PGM and Ion Torrent S5). The choice of sequencing platform did not substantially influence species recovery, although the Miseq delivered the highest sequence quality. As expected, species recovery was most efficient from the Single Leg treatment because amplicon abundance varied little among taxa. Among the three treatments where PCR occurred after pooling, the Bulk Abdomen treatment produced a more uniform read abundance than the Bulk Leg or Composite Leg treatment. Primer choice also influenced species recovery and evenness. Our results reveal how variation in protocols can have substantial impacts on perceived diversity unless sequencing coverage is sufficient to reach an asymptote.