Unexpected problem in aphid DNA barcoding by universal primers

DNA barcode (mitochondrial COI) sequences have allowed for species identification of aphids. In this study, we newly found a DNA barcoding problem in a part of the DNA sequences for Sitobion avenae. Five S. avenae individuals showed differences of, on average, 32.60% in the DNA sequences from other conspecific individuals, and a BLAST search revealed that the five sequences are similar to those of aphid parasitoids such as Aphidius, Ephedrus and Praon spp. (Hymenoptera: Braconidae). Based on these results, we concluded that the universal primers used in aphid DNA barcodes can amplify barcode sequences from parasitoid species within host aphids.     

First record of Balcha Walker (Hymenoptera,Eupelmidae) in South Korea with the description of one new species

The genus Balcha Walker (Eupelmidae) is recorded for the first time in South Korea, with one newly described species and one newly recorded species. Both sexes of Balcha opaca Fusu sp. n. are described, and the presumed male of B. dictyota Gibson is described for the first time. The newly described species is peculiar in having a comparatively darker and less shiny mesoscutum. In other species of the genus the mesoscutum has brilliant metallic colours that contrast with dorsal dark bands along areas of much finer sculpture.     

Barcoding old Korean lepidopteran specimens using newly designed specific primer pairs

Currently, DNA barcodes are often required to be analyzed using old museum specimens when they are the only available specimens for rare or endangered species, or even type series. In this study, using eight universal primers and newly designed 315 species-specific primers, we tried to recover full-length barcode sequences from 45 dried specimens of 36 butterfly species collected between 1959 and 1980 in Korea. The eight universal primers failed entirely in the PCR amplification and sequencing of all the specimens. On the other hand, 284 primer pairs consisting of the 315 primers, targeting fragments of 71–417 bp, amplified various lengths of barcode sequences from all specimens. The fragments were successfully combined to generate the barcode sequences ranging from 444 bp to 658 bp. Notably, of the 284 primer pairs, 26 primer pairs designed for Limenitis camilla, Argynnis niobe, and Brenthis daphne successfully amplified the barcode sequences of congeneric species, Limenitis doerriesi, Argynnis nerippe, and Brenthis ino, suggesting that the species-specific primers can be available for analyzing barcode sequences of closely related species. Our study reveals that the newly designed species-specific primers will be effective in acquiring COI sequences from old butterfly specimens.     

Genetic divergence between the South Korean and Mongolian populations of the dung beetle,Gymnopleurus mopsus (Coleoptera: Scarabaeidae) based on mitochondrial cytochrome c oxidase subunit I (COI) gene sequences

The locally extinct dung beetle, Gymnopleurus mopsus Pallas, 1781 (Coleoptera: Scarabaeidae), has not been found in South Korea since the 1970s. This research was conducted to understand the genetic divergence between the South Korean and Mongolian populations of G. mopsus as a part of its reintroduction program in South Korea. The genetic distance and diversity were determined using the mitochondrial cytochrome c oxidase subunit I (COI) gene sequence (658 bp ) corresponding to the DNA barcode region. The mitochondrial COI gene sequences of 64 individuals of G. mopsus collected in South Korea (7 individuals) and Mongolia (57 individuals) showed a relatively high level of genetic diversity (nucleotide diversity, 0.0078 ± 0.0007; Haplotype diversity, 0.965 ± 0.017). The genetic distances between the South Korean and Mongolian populations lay within the intraspecific level and the phylogenetic reconstruction using the neighbor‐joining (NJ) method showed that all individuals belonged to a single clade. This result indicates that the current Mongolian population of G. mopsus is a good candidate source population to restore the locally extinct population of the species in South Korea.     

Syngonanthus androgynus,a Striking New Species from South America,its Phylogenetic Placement and Implications for Evolution of Bisexuality in Eriocaulaceae

In the present study, we describe and illustrate a remarkable new species of Syngonanthus from South America (Bolivia, Brazil and Peru). This new species is quickly distinguished from all species in the genus by trimerous and bisexual flowers, a unique set of characteristics in Syngonanthus. Complementary to this study, sequences of 33 species were downloaded from GenBank and four species had sequences newly generated for this study. Molecular phylogenetic analyses based on nuclear ribosomal ITS and the plastid regions psbA-trnH and trnL-F were performed to determine its systematic position. The results have shown S. androgynus closely related to a well-supported clade that has been treated as Syngonanthus sect. Carphocephalus. Floral traits associated with this new plant also were surveyed. Character reconstruction suggests that the bisexual flowers originated independently more than once in the genus. However, trimerous flowers appear to be an ancestral condition of the whole genus.     

Multiple species delimitation approaches with COI barcodes poorly fit each other and morphospecies – An integrative taxonomy case of Sri Lankan Sericini chafers (Coleoptera: Scarabaeidae)

DNA taxonomy including barcoding and metabarcoding is widely used to explore the diversity in biodiversity hotspots. In most of these hotspot areas, chafers are represented by a multitude of species, which are well defined by the complex shape of male genitalia. Here, we explore how well COI barcode data reflect morphological species entities and thus their usability for accelerated species inventorization. We conducted dedicated field surveys in Sri Lanka to collect the species‐rich and highly endemic Sericini chafers (Coleoptera: Scarabaeidae). Congruence among results of a series of protocols for de novo species delimitation and with morphology‐based species identifications was investigated. Different delimitation methods, such as the Poisson tree processes (PTP) model, Statistical Parsimony Analysis (TCS), Automatic Barcode Gap Discovery (ABGD), Assemble Species by Automatic Partitioning (ASAP), and Barcode Index Number (BIN) assignments, resulted in different numbers of molecular operational taxonomic units (MOTUs). All methods showed both over‐splitting and lumping of morphologically identified species. Only 18 of the observed 45 morphospecies perfectly matched MOTUs from all methods. The congruence of delimitation between MOTUs and morphospecies expressed by the match ratio was low, ranging from 0.57 to 0.67. TCS and multirate PTP (mPTP) showed the highest match ratio, while (BIN) assignment resulted in the lowest match ratio and most splitting events. mPTP lumped more species than any other method. Principal coordinate analysis (PCoA) on a match ratio‐based distance matrix revealed incongruent outcomes of multiple DNA delimitation methods, although applied to the same data. Our results confirm that COI barcode data alone are unlikely to correctly delimit all species, in particular, when using only a single delimitation approach. We encourage the integration of various approaches and data, particularly morphology, to validate species boundaries.     

Application of DNA barcoding in biodiversity studies of shallow-water octocorals: molecular proxies agree with morphological estimates of species richness in Palau

The application of DNA barcoding to anthozoan cnidarians has been hindered by their slow rates of mitochondrial gene evolution and the failure to identify alternative molecular markers that distinguish species reliably. Among octocorals, however, multilocus barcodes can distinguish up to 70 % of morphospecies, thereby facilitating the identification of species that are ecologically important but still very poorly known taxonomically. We tested the ability of these imperfect DNA barcodes to estimate species richness in a biodiversity survey of the shallow-water octocoral fauna of Palau using multilocus (COI, mtMutS, 28S rDNA) sequences obtained from 305 specimens representing 38 genera of octocorals. Numbers and identities of species were estimated independently (1) by a taxonomic expert using morphological criteria and (2) by assigning sequences to molecular operational taxonomic units (MOTUs) using predefined genetic distance thresholds. Estimated numbers of MOTUs ranged from 73 to 128 depending on the barcode and distance threshold applied, bracketing the estimated number of 118 morphospecies. Concordance between morphospecies identifications and MOTUs ranged from 71 to 75 % and differed little among barcodes. For the speciose and ecologically dominant genus Sinularia, however, we were able to identify 95 % of specimens correctly simply by comparing mtMutS sequences and in situ photographs of colonies to an existing vouchered database. Because we lack a clear understanding of species boundaries in most of these taxa, numbers of morphospecies and MOTUs are both estimates of the true species diversity, and we cannot currently determine which is more accurate. Our results suggest, however, that the two methods provide comparable estimates of species richness for shallow-water Indo-Pacific octocorals. Use of molecular barcodes in biodiversity surveys will facilitate comparisons of species richness and composition among localities and over time, data that do not currently exist for any octocoral community.     

Molecular identification of selected bees from the Indian Himalaya: A preliminary effort

DNA barcoding has largely been tested for a wide range of taxa and evidenced as a reliable and rapid molecular tool for species-level identification. The present study lends to generate 156 DNA barcodes, of which 141 belonged to 30 morphologically identified bees from the Indian Himalayan Regions (IHRs). The generated barcode data along with 84 sequences of global database distinctly discriminated all the studied species with sufficient genetic distances and cohesive monophyletic clustering in Bayesian analysis (BA) phylogeny. The species delimitation methods, Automatic Barcode Gap Discovery (ABGD), Bayesian Poisson-Tree-Processes (bPTP), and General Mixed Yule-coalescent (GMYC) yielded 68, 70, and 71 molecular operational taxonomic units (MOTUs) respectively. The present DNA barcode-based examination detected the possible cryptic diversity in two Apis species (A. cerana and A. dorsata), Bombus hypnorum, Lepidotrigona arcifera, and Ceratina sutepensis. The present study also evidenced the species complexes within Bombus albopleuralis and Bombus trifasciatus in the IHRs. The species delimitation methods also detected an additional seven putative species from the IHRs, which were identified up to the genus level. In conclusion, this preliminary effort helps to develop a reliable barcode database of bees from the Indian IHRs to facilitate the future systematics study. These molecular data can be utilized to evaluate the population structures and assist to formulate the effective plans for bee conservation.     

Check list of lace bugs (Hemiptera: Tingidae) of Korea

Tingidae (Hemiptera) of Korea are revised based on literature review as well as recently collected material and museum collections. A genus is recorded for the first time from South Korea for Acalpyta marginata. One species, Stephanitis typica, is removed from Korea. As a result, a total of 39 species in 17 genera, two subfamilies are recognized. An updated checklist including known distributions and host plant information in Korea is provided.     

Morphological,genetic and symptomatic identification of an invasive jujube pest in Korea,Dasineura jujubifolia Jiao & Bu (Diptera: Cecidomyiidae)

Correct identification of invasive species is an important step for further management of this species. New type of leafcurling gall midge feeding on jujube, Ziziphus jujube Miller (Rhamnaceae), was discovered in Korea in 2011. At that time, this species was not identified as specific level, so it was recorded as Dasineura sp. Since then, the jujube gall midge has become a serious alien insect pest in Korea. In this study, this jujube gall midge was surveyed by collecting damaged leaf samples from different major jujube-producing regions in Korea. Morphological, genetic and symptomatic identification of this invasive jujube pest identified as Dasineura jujubifolia Jiao & Bu. Here we provided its taxonomic status, geographical distribution, morphological characteristics of all stages and infestation symptoms. In addition to classical morphological characters, mitochondrial COI barcoding sequences were generated for several specimens. The possible pathway of invasion and subsequent socioeconomic consequences were discussed.     

First record of occurrence of Xenos moutoni (Strepsiptera; Stylopidae), an important parasite of hornets (Hymenoptera: Vespidae: Vespa), in Korea

This is the first record of Xenos moutoni, a specialized parasite of hornets (Vespa spp.), in Korea. Among six Vespa species collected with bait traps in Andong, central South Korea, approximately 10% of female Vespa analis (gynes plus workers) were parasitized, whereas the other five species (V. crabro, V. mandarinia, V. simillima, V. ducalis, and V. dybowskii) were not. Almost all parasitized hornets had a single female parasite in the gaster.     

First record of the western black widow spider Latrodectus hesperus Chamberlin & Ivie, 1935 (Araneae: Theridiidae) in South Korea

Two individuals of Latrodectus hesperus Chamberlin & Ivie were newly found in munitions storage at military facilities in Daegu, South Korea. A female was first discovered on August 31, 2018, and followed by another female along with three egg sacs on September 20, 2018. These spiders were identified based on morphological characters and DNA barcode sequence analysis. Additional surveys were made around the initial detection site to examine the range and spread of this species, but no additional individuals were found.     

Taxonomic review of genus Diaparsis Förster (Hymenoptera: Ichneumonidae: Tersilochinae) from South Korea

Eleven species of the genus Diaparsis, including two unidentified species, are recorded from South Korea. One new species, D. koreana Khalaim, et al., sp. nov., is described, and six species, D. carinifer (Thomson), D. convexa Khalaim, D. egregia Khalaim, D. hyperae Kusigemati, D. jucunda (Holmgren) and D. neoplicator Khalaim, are recorded from this country for the first time. Diaparsis hyperae and D. pulchra are the most abundant species of the genus in the Korean fauna. A key to eleven species of Diaparsis occurring in South Korea is provided.     

Genetic diversity of genus Vespa including an invaded species of V. velutina (Hymenoptera: Vespidae) in Korea inferred from DNA barcoding data

With about 5000 known species, the Vespidae is a large family belongs to order Hymenoptera. The genus Vespa with 22 species is one of the four genera of the subfamily Vespinae. In Korea, 10 species and subspecies are recognized. Because of their social behavior, their treat to human health and their impact in apiculture, the reliable and sometimes automated identification of these insects to species level are important. To test the efficacy of DNA barcoding method for identification of species of the genus Vespa in Korea, 30 samples of eight Korean species of genus Vespa were collected and mitochondrial DNAs of 658 bp fragment cytochrome oxidase subunit 1 (CO1) region were sequenced. A Bayesian Inference based on COI gene of the Korean Vespa species was constructed. The phylogenetic tree shoed that identification of all specimens is possible based on COI gene and we found strong relation between the sequences of the collected species from different localities in South Korea which clustered together with 100% support with sequences of the same species in GenBank. The results demonstrate that DNA barcoding is a useful technique for rapid and accurate species recognition in Korean Vespa species. The DNA barcode part of COI for V. binghami is provided for the first time that can help for identification of this species through DNA barcoding. Also, the genetic diversity among Korean Vespa velutina was zero suggests that the invasion might have occurred in a single event with small number of founders.     

ITS2 barcode for identifying the officinal rhubarb source plants from its adulterants

Officinal rhubarb, the dried root and rhizome of Rheum officinale Baill., Rh. palmatum L., and Rh. tanguticum (Maxim. ex Regel) Maxim. ex Balf. of Polygonaceae family, is one of the most well-known and important traditional Chinese medicines. The growing herbal market has led to the introduction of adulterants, and difficulties in morphological based discrimination has also resulted in concerns over consumer safety. ITS2 as a potential barcode was employed to discriminate officinal rhubarb sampled from the entire distribution range and its adulterants. The minimum K2P interspecific distance between officinal rhubarb source plants and the adulterants were higher than the maximum K2P intraspecific distance within the officinal rhubarb source plants. When the phylogenetic trees were constructed by neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods, all Rheum species were grouped into one clade, while Polygonum and Rumex species were clustered in another clade. In the Rheum clade, all the officinal rhubarb source plants constituted a distinct subclade, while other Rheum species formed other subclades. Our results suggested that the ITS2 region is a more suitable and accurate DNA barcode for distinguishing officinal rhubarb source plants from their adulterants.     

First record of the genus Codrus Panzer (Hymenoptera: Proctotrupidae) from South Korea with description of a new species

The genus Codrus Panzer, 1803 is recorded for the first time from South Korea. A new species and three newly recorded species are described: C. tripotini Lee and Park sp. nov., C. ciliatus Townes, 1981, C. nebriae (Watanabe, 1954) and C. niger Panzer, 1803. Additionally, C. ciliatus Townes is newly added to Chinese fauna. A key to the South Korean Codrus, diagnostic characteristics and photographs are provided.