Molecular identification of Epitrix potato flea beetles (Coleoptera: Chrysomelidae) in Europe and North America

Developmental Biology and Identification of a Garden Pest, Otiorhynchus (Podoropelmus) smreczynskii Cmoluch, 1968 (Coleoptera, Curculionidae, Entiminae), with Comments on Its Origin and Distribution

The mature larva and pupa of Otiorhynchus smreczynskii are described and illustrated with complete chaetotaxy for the first time. Five larval instars and the factors for larval growth are determined, and the larval development of this species is comprehensively described. In order to confirm species affiliation, selected larvae were subjected to genetic analysis (mtCOI). Host plants and unique feeding signs of some Entiminae species are presented, and all available data on development are documented and interpreted. Additionally, the morphometry of 78 specimens (48 of O. smreczynskii and 30 of O. rotundus) was examined in order to verify the usefulness of morphological features in distinguishing both species. The female genitalia of both species are illustrated, described and compared with each other for the first time. Finally, the updated distribution of O. smreczynskii is given, and a possible origin of O. smreczynskii and O. rotundus is proposed.

Evolution, systematics and historical biogeography of sand flies of the subgenus Paraphlebotomus (Diptera, Psychodidae, Phlebotomus) inferred using restriction-site associated DNA markers

Phlebotomine sand flies are the main natural vectors of Leishmania, which cause visceral and tegumentary tropical diseases worldwide. However, their taxonomy and evolutionary history remain poorly studied. Indeed, as for many human disease vectors, their small size is a challenge for morphological and molecular works. Here, we successfully amplified unbiased copies of whole genome to sequence thousands of restriction-site associated DNA (RAD) markers from single specimens of phlebotomines. RAD markers were used to infer a fully resolved phylogeny of the subgenus Paraphlebotomus (11 species + 5 outgroups, 32 specimens). The subgenus was not recovered as monophyletic and we describe a new subgenus Artemievus subg. nov. Depaquit for Phlebotomus alexandri. We also confirm the validity of Ph. riouxi which is reinstated as valid species. Our analyses suggest that Paraphlebotomus sensu nov. originated ca 12.9-8.5 Ma and was possibly largely distributed from peri-Mediterranean to Irano-Turanian regions. Its biogeographical history can be summarized into three phases: i) a first split between Ph. riouxi + Ph. chabaudi and other species that may have resulted from the rise of the Saharan belt ca 8.5 Ma; ii) a Messinian vicariant event (7.3-5.3 Ma) during which the prolonged drought could have resulted in the divergence of main lineages; iii) a recent radiation event (3-2 Ma) that correspond to cycles of wet and dry periods in the Middle East and the East African subregions during the Pleistocene. Interestingly these cycles are also hypothetical drivers of the diversification of rodents, in the burrows of which Paraphlebotomus larvae develop. By meeting the challenge of sequencing pangenomics markers from single, minute phlebotomines, this work opens new avenues for improving our understanding of the epidemiology of leishmaniases and possibly other human diseases transmitted by arthropod vectors.

Barcoding pest species in a biodiversity hot-spot: the South African polyphagous broad-nosed weevils (Coleoptera, Curculionidae, Entiminae)

Polyphagous broad nosed weevils (Curculionidae: Entiminae) constitute a large and taxonomically challenging subfamily that contains economically significant agricultural pests worldwide. South Africa is a hot-spot for biodiversity and several species of indigenous and endemic genera of Entiminae have shifted on to cultivated plants, with some being phytosanitary pests. The sporadic pest status of many species (where the species has an occasional economic impact on the agricultural industry, but is not encountered often enough that is is readily recognisable by researchers and agricultural extension workers) and the presence of pest complexes and cryptic species represent an identification challenge to non-specialists. Furthermore, no comprehensive identification tools exist to identify immature stages that may be found in crops/soil. In this paper, a curated barcoding database with 70 COI sequences from 41 species (39 Entiminae, 2 Cyclominae) is initiated, to assist with the complexity of identification of species in this group.

DNA barcoding for bio-surveillance of emerging pests and species identification in Afrotropical Prioninae (Coleoptera, Cerambycidae)

DNA barcoding has been succesfully used for bio-surveillance of forest and agricultural pests in temperate areas, but has few applications in the tropics and particulary in Africa. Cacoscelesnewmannii (Coleoptera: Cerambycidae) is a Prioninae species that is locally causing extensive damage in commercially-grown sugarcane in the KwaZulu-Natal Province in South Africa. Due to the risk of spread of this species to the rest of southern Africa and to other sugarcane growing regions, clear and easy identification of this pest is critical for monitoring and for phytosanitary services. The genus Cacosceles Newman, 1838 includes four species, most being very similar in morphology. The damaging stage of the species is the larva, which is inherently difficult to distinguish morphologically from other Cerambycidae species. A tool for rapid and reliable identification of this species was needed by plant protection and quarantine agencies to monitor its potential abundance and spread. Here, we provide newly-generated barcodes for C.newmannii that can be used to reliably identify any life stage, even by non-trained taxonomists. In addition, we compiled a curated DNA barcoding reference library for 70 specimens of 20 named species of Afrotropical Prioninae to evaluate DNA barcoding as a valid tool to identify them. We also assessed the level of deeply conspecific mitochondrial lineages. Sequences were assigned to 42 different Barcode Index Numbers (BINs), 28 of which were new to BOLD. Out of the 20 named species barcoded, 11 (52.4%) had their own unique Barcode Index Number (BIN). Eight species (38.1%) showed multiple BINs with no morphological differentiation. Amongst them, C.newmannii showed two highly divergent genetic clusters which co-occur sympatrically, but further investigation is required to test whether they could represent new cryptic species.

Factors affecting the efficiency of molecular species delimitation in a species-rich insect family

In the context of global biodiversity loss, molecular species delimitation approaches can be very useful for accelerating species discovery through DNA taxonomy and inventory through DNA metabarcoding. In this study, the effect of some intrinsic factors on the efficiency of various single-marker species delimitation methods (fixed and variable nucleotide distance thresholds, ABGD, ASAP, GMYC, mPTP) was tested on more than 90 empirical data sets, derived from a set of 7,237 COI sequences attributed to 542 leaf beetles species (Coleoptera: Chrysomelidae). The considered factors were: (i) the number of haplotypes per species (as a proxy for genetic diversity), (ii) the geographic distance among conspecific collection localities (as a proxy of sampling width), (iii) the difficulty related to morphological identification of species, and (iv) the taxonomic rank. Distance-based methods, with on average more than 70% of match with morphological identification, outperformed those relying on phylogenetic trees, with less than 59%. A high number of haplotypes per species was found to have a negative effect on delimitation efficiency, whereas large geographic distances within species had a positive effect. All methods delimitations (except for GMYC) were significantly affected by the presence of species that are difficult to be identified, decreasing their efficiency. Finally, the only method influenced by the taxonomic rank of the data set was GMYC, showing lower efficiency in data sets at the genus than at higher levels. The observed biases we highlighted affecting efficiency could be accounted for when developing input data sets for species delimitation analyses to obtain a more reliable representation of biological diversity.

Pest categorisation of non-EU viruses and viroids of potato

Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of those viruses and viroids (hereafter referred to as viruses) of Solanum tuberosum and other tuber-forming Solanum spp. (hereafter referred to as potato) which are considered to be either non-EU or of undetermined standing based on a previous EFSA opinion. These viruses belong to different families and genera and either have an established identity or produce consistent symptoms. Plants for planting is the main pathway for entry for all categorised viruses as they can all be transmitted by vegetative propagation. Several categorised viruses have a relatively wide host range and/or are vector-transmitted, increasing the potential for entry. The information currently available on geographical distribution, biology, epidemiology, impact and potential entry pathways has been evaluated with regard to the criteria to qualify as potential Union quarantine pest or as Union regulated non-quarantine pest (RNQP). Since this opinion addresses specifically the non-EU potato viruses, in general these viruses do not meet the criteria assessed by EFSA to qualify as potential Union regulated non-quarantine pests. The following viruses meet the criteria to qualify as potential Union quarantine pest: APLV, APMMV, APMoV, ChiLCV, CYSDV, PAMV, PBRSV, PVH, PVP, PVT, PYDV, PYMV, PYV, PYVV, RCVMV, SALCV, SB26/29, ToCV, ToLCNDV, ToMHaV, ToMoTV, ToSRV and ToYVSV. With the exception of the criterion regarding the potential for consequences in the EU territory, for which the Panel is unable to conclude because of lack of information, AVB, CPSbV, PaLCrV, PapMV, PVB, PVU, SB41 and TVBMV meet all the other criteria to qualify as potential Union quarantine pest. PotLV and WPMV do not qualify as potential Union quarantine pest, since they are not reported to have any impact. For most of the categorised viruses, the conclusions of the Panel have inherent uncertainties, due to the lack of quantitative data on their impact and/or absence or limited availability of information on the biology, epidemiology and geographical distribution.

Ooctonus vulgatus (Hymenoptera, Mymaridae), a potential biocontrol agent to reduce populations of Philaenus spumarius (Hemiptera, Aphrophoridae) the main vector of Xylella fastidiosa in Europe

As a vector of Xylella fastidiosa (Wells, 1987) in Europe, the meadow spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Aphrophoridae) is a species of major concern. Therefore, tools and agents to control this ubiquitous insect that develops and feeds on hundreds of plant species are wanted. We conducted a field survey of P. spumarius eggs in Corsica and provide a first report of Ooctonus vulgatus Haliday, 1833 (Hymenoptera, Mymaridae) as a potential biocontrol agent of P. spumarius in Europe. To allow species identification, we summarized the main characters distinguishing O. vulgatus from other European species of Ooctonus and generated COI DNA barcodes. Parasitism rates were variable in the four localities included in the survey but could reach 69% (for an average number of eggs that hatched per locality of 109). Based on the geographic occurrences of O. vulgatus obtained from the literature, we calibrated an ecological niche model to assess its potential distribution in the Holarctic. Obviously, several questions need to be addressed to determine whether O. vulgatus could become an effective biocontrol agent of P. spumarius in Europe. So far, O. vulgatus has been reared only from P. spumarius eggs, but its exact host-range should be evaluated to ensure efficiency and avoid non-target effect. The top-down impact of the parasitoid on vector populations should also be assessed on large data sets. Finally, the feasibility of mass rearing should be tested. We hope this report serves as a starting point to initiate research on this parasitoid wasp to assess whether it could contribute to reduce the spread and impact of X. fastidiosa in Europe.

Planthopper family Issidae (Insecta: Hemiptera: Fulgoromorpha): linking molecular phylogeny with classification

A molecular phylogeny of the planthopper family Issidae (Hemiptera, Fulgoroidea) is provided using both Maximum likelihood and Bayesian inference analyses. The phylogeny is based on 18S, two parts of 28S, COXI and Cytb genes from 50 genera and 79 ingroup species (including 8 species recently excluded from Issidae). As with the only few previous studies, an important taxonomic impediment is observed with the sampling; however for the first time, all analyses depict several fully supported lineages, which challenge the recent proposed "modern classification" of the family. It also highlights a strong coherence between these lineages and their respective geographical distribution. All previously excluded taxa are confirmed as not being part of the Issidae as recently defined which monophyly is confirmed. Accordingly, a new classification of the family is proposed with 3 subfamilies and 7 tribes as follows. Neotropical issid Thioniini in Thioniinae stat. rev. is re-established as an independent lineage sister to all other Issidae. Palaearctic Issidae are weakly supported as a monophyletic lineage, Issinae stat. nov., including 2 tribes: Issini stat. nov. (genera Issus and Latissus) and Hysteropterini stat. rev. (all other Palaearctic genera). Oriental Issidae form a strongly supported monophyletic subfamily group Hemisphaeriinae stat. rev. including 4 tribes: Kodaianellini trib. nov., Sarimini trib. nov., Parahiraciini Cheng & Yang, 1991, and Hemisphaeriini Melichar, 1906, the latter including 2 subtribes: Mongolianina s.trib. nov., and Hemisphaeriina Melichar, 1906. A Neotropical lineage including the genus Picumna is provisionally placed in incertae sedis within the Hemisphaeriinae stat. nov.

Subspecific Differentiation Events of Montane Stag Beetles (Coleoptera, Lucanidae) Endemic to Formosa Island

Taxonomic debates have been carrying on for decades over Formosan stag beetles, which consist of a high proportion of endemic species and subspecies featuring morphological variations associated with local adaptation. With the influence of periodical Pleistocene glaciations and the presence of several mountain ranges, the genetic differentiation and taxonomic recognition, within this medium-size island, of two endemic subspecies for each of four montane stag beetles, i.e. Lucanus ogakii, L. kanoi, Prismognathus davidis, and Neolucanus doro, has been an appealing issue. Based on monophyletic lineages and population structure, possible divergent scenarios have been proposed to clarify the subspecific status for each of the above mentioned stag beetles. Phylogenetic inferences based on COI+16S rDNA+28S rDNA of 240 Formosan lucanids have confirmed most species are monophyletic groups; and the intraspecific (<2%) and interspecific (>2%) genetic distances of the two mitochondrial genes could be applied concordantly for taxonomic identification. On account of Bayesian-based species delimitation, geographic distribution, population structure, and sequence divergences, the subspecific status for L. ogakii, L. kanoi, and Pri. davidis are congruent with their geographic distribution in this island; and the calibration time based on the mitochondrial genes shows the subspecific split events occurred 0.7–1 million years ago. In addition, a more complicated scenario, i.e. genetic differentiation including introgression/hybridization events, might have occurred among L. ogakii, L. kanoi, and L. maculifemoratus. The geological effects of mountain hindrance accompanied by periodical glaciations could have been vital in leading to the geographical subspecific differentiation of these montane stag beetles.

Revision of Mandarella Duvivier from Taiwan, with a new species, new synonymies and identities of highly variable species (Insecta, Chrysomelidae, Galerucinae, Alticini)

Taiwanese species of Mandarella Duvivier are compared on the basis of morphological and molecular evidence. Only three of eleven morphospecies are considered to be valid. Mandarellauenoi (Kimoto, 1969) is transferred from the genus Luperus Geoffroy. Stenoluperustaiwanus Kimoto, 1991 and Stenoluperuskimotoi Döberl, 2001 are synonymized with Mandarellauenoi. Taiwanese records of Stenoluperustibialis Chen, 1942, Stenoluperusnipponensis Laboissière, 1913, and Stenoluperuspotanini (Weise, 1889) were based on misidentifications and represent Mandarellauenoi. The Taiwanese population previously erroneously identified as Stenoluperuspallipes Gressitt and Kimoto, 1963 is here described as a new species, Mandarellatsouisp. n., Stenoluperusesakii Kimoto, 1969, Stenoluperusmatsumurai Takizawa, 1978, and Mandarellataiwanensis Medvedev, 2012 are synonymized with Mandarellaflaviventris (Chen, 1942).

A molecular framework for the identification of planthopper vectors (Hemiptera: Delphacidae) of central Argentina

Planthoppers are important worldwide crop pests as well as vectors of numerous diseases. Different species transmit Mal de Río Cuarto virus, which causes the most economically important corn disease in central Argentina. Epidemiological studies rely on the accurate identification of the species present in the field. Presently, morphological identification of planthoppers requires taxonomic expertise and there are no taxonomic keys for females and nymphs. Nevertheless, no molecular protocols are available for accurate species identification of most frequent delphacid species from central Argentina. In this context, the aim of this study was to evaluate the utility of the cytochrome oxidase I gene (COI) as a DNA barcode and its digestion with restriction enzymes (Restriction Fragment Length Polymorphism, RFLP) for the identification of the most common species of planthoppers in central Argentina. We amplified and sequenced a 843 bp fragment of the COI gene of taxonomically identified specimens and evaluated its use as a DNA barcode. Restriction enzymes were also selected for digesting the COI fragment via RFLP. The high interspecific variability (20.79%; ± 2.32%) and low intraspecific divergence (0.12%; ± 0.17%) observed in the studied species, demonstrate the effectiveness of the COI gene for species identification of major vector delphacids affecting corn crops in Argentina. Moreover, the digestion of this COI gene fragment with Bfa I and Apo I enzymes allows a fast and cost-effective species identification method when numerous specimens need to be processed. Both molecular techniques developed here, allow the accurate identification of planthopper species at regional scale. These new tools would assist traditional identification of these insects, especially for aiding non-experts in morphological taxonomy.

Identification of Eastern United States Reticulitermes Termite Species via PCR-RFLP, Assessed Using Training and Test Data

Reticulitermes termites play key roles in dead wood decomposition and nutrient cycling in forests. They also damage man-made structures, resulting in considerable economic loss. In the eastern United States, five species (R. flavipes, R. virginicus, R. nelsonae, R. hageni and R. malletei) have overlapping ranges and are difficult to distinguish morphologically. Here we present a molecular tool for species identification. It is based on polymerase chain reaction (PCR) amplification of a section of the mitochondrial cytochrome oxidase subunit II gene, followed by a three-enzyme restriction fragment length polymorphism (RFLP) assay, with banding patterns resolved via agarose gel electrophoresis. The assay was designed using a large set of training data obtained from a public DNA sequence database, then evaluated using an independent test panel of Reticulitermes from the Southern Appalachian Mountains, for which species assignments were determined via phylogenetic comparison to reference sequences. After refining the interpretive framework, the PCR-RFLP assay was shown to provide accurate identification of four co-occurring species (the fifth species, R. hageni, was absent from the test panel, so accuracy cannot yet be extended to training data). The assay is cost- and time-efficient, and will help improve knowledge of Reticulitermes species distributions.