Reassessment of Species Diversity of the Subfamily Denticollinae (Coleoptera: Elateridae) through DNA Barcoding

A review of the species groups of the Western Hemisphere Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae) using COI barcoding and gene trees

Species groups of Western Hemispheric Onthophagus Latreille (Coleoptera: Scarabaeidae: Scarabaeinae: Onthophagini) are suggested using COI barcoding and gene trees and supported by congruence with external morphology, behavior, ecology, and biogeographic evidence. New species groups, complexes, and taxonomic statuses are offered, and other preexisting proposals are confirmed. No barcoding gap w as found between the intragroup and intergroup genetic distance blocks, but the average intragroup (8.38%) and intergroup (13.88%) Kimura-two-parameter distances are statistically different. The following seven preexisting species groups were supported by the congruence between the mtDNA barcode analysis and other independent evidence: O. chevrolati, O. clypeatus, O. dicranius, O. gazellinus, O. hircus, O. landolti, and O. mexicanus. Eight new species groups are suggested: O. crinitus, O. curvicornis, O. eulophus, O. hecate, O. hoepfneri, O. marginatus, O. nasutus, and O. velutinus. Possible behavioral/ecological adaptations of morphological characters are also discussed. New biogeographic and evolutionary hypotheses are also advanced. An identification key for species groups is presented.

Molecular and morphological approaches redefine the limits among polymorphic species in the Neotropical longhorn beetle genus, Myzomorphus Sallé (Coleoptera: Cerambycidae: Prioninae)

Myzomorphus Sallé is a charismatic genus of prionine longhorn beetles (Cerambycidae) composed of nine species. Myzomorphus species are found from Costa Rica to southern Brazil, but only two species have wide distributions across this range: M. scutellatus Sallé from Costa Rica to northern Brazil, and M. quadripunctatus (Gray) from Colombia to southern Brazil. These species are highly polymorphic and their limits are difficult to determine due to their strong morphological similarities--males are only distinguishable by subtle size variations and females by color patterns. Here, we used mitochondrial DNA (cox1 and 12S) to reconstruct the first phylogeny of Myzomorphus and, in combination with morphological data, assess the taxonomic limits between M. scutellatus and M. quadripunctatus. Our phylogenetic results confirm the monophyly of Myzomorphus and reveal a close relationship among M. birai, M. quadripunctatus and M. scutellatus. Using pairwise distance estimations, we found that the intraspecific variation of M. quadripunctatus is remarkably high (K2P: 0-11.7%; p-distances: 0-9.7%) and the interspecific distances of M. quadripunctatus in relation to M. birai and M. scutellatus (K2P: 14.8-20.1%; p-distances: 12-15%) are close to the intraspecific distances of M. quadripunctatus. We further analyzed the diagnostic characters of these species and found that their morphological intraspecific variations largely overlap. Altogether, our results demonstrate that the variability of M. birai, M. scutellatus and M. quadripunctatus represent polymorphisms of a single species. We thus argue for the synonymy of M. birai and M. scutellatus under M. quadripunctatus (syn. nov.) and highlight the need for multiple lines of evidence to solve the taxonomic problems in polymorphic species of Cerambycidae.

A multilocus assessment reveals two new synonymies for East Asian Cyclommatus stag beetles (Coleoptera, Lucanidae)

Cyclommatus scutellaris Möllenkamp, 1912, Cyclommatus elsae Kriesche, 1921 and Cyclommatus tamdaoensis Fujita, 2010 are East Asian stag beetle species with long-debated taxonomic relationships due to high intraspecific morphological variability. In this study, we applied multilocus phylogenetic analyses to reassess their relationships. Two mitochondrial genes (16S rDNA, COI) and two nuclear genes (28S rDNA, Wingless) were used to reconstruct the phylogeny through the Bayesian inference (BI) and Maximum Likelihood (ML) methods. Both topologies supported two clades: the clade C. scutellaris was sister to the clade (C. elsae + C. tamdaoensis) with the subclade C. tamdaoensis embedded in the subclade C. elsae. The Kimura 2-parameter (K2P) genetic distance analysis yielded a low mean value (≤0.035) among the three taxa, which was well below the minimum mean value between other Cyclommatus species (≥0.122). We also compared the accuracy and efficiency of two approaches, GMYC and ABGD, in delimitating the three lineages. The result shows that ABGD is a better approach than GMYC. Our molecular data recognizes the three species as different populations of a single species, ranging from Taiwan Island to the continent. Therefore, we propose two new junior synonyms for C. scutellaris: C. tamdaoensis, syn. nov. and C. elsae syn. nov.

Features of the formation of click beetle complexes in perennial plantings of the Western Caucasus

The complexes of click beetles in the perennial plantations of the Western Caucasus are formed at the expense of species from the surrounding (adjacent) biotopes. In the forest zone, the complexes are formed by their similarity to meadow biotopes (biocenoses) with inclusions of dominant species from meadow biotopes of the foothill lane. Agriotes tauricus Heyd., and Drasterius bimaculatus (Rossi) are common species in all lanes and zones of the studied region. Species Agriotes gurgistanus (Fald.), Melanotus fusciceps (Gyll.), Athous Circassiensis Reitt., Agriotes sputator (L.) are most often dominant of elateridocoplex.

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.].

Species diversity revealed in Sigmella Hebard, 1929 (Blattodea, ectobiidae) based on morphology and four molecular species delimitation methods

Cockroaches are one of the major decomposers involved in biogeochemical cycles. Cockroaches have an amazing amount of diversity, but most of them remain unknown due to the shortage of the trained taxonomists and the limitations of morphology-based identification. We obtained 49 COI sequences (including 42 novel sequences) and 32 novel 28S sequences for 5 Sigmella morphospecies collected from 11 localities. Three are new to science: Sigmella digitalis sp. nov., Sigmella exserta sp. nov. and Sigmella normalis sp. nov. Based on four species delimitation methods (ABGD, GMYC, BINs and bPTP), a total of 6 molecular operational taxonomic units (MOTUs) were recovered for 5 morphospecies. These were then confirmed by tree building methods using COI and combined data (COI and 28S). We detected more than one MOTU in the morphospecies S. digitalis sp. nov., which can indicate genetic diversity. Detailed morphological evidence for each MOTU is provided to confirm these slight variations and we conclude that natural barriers are likely the main cause of genetic diversity.

High functionality of DNA barcodes and revealed cases of cryptic diversity in Korean curved-horn moths (Lepidoptera: Gelechioidea)

Curved-horn moths or gelechioid moths (Lepidoptera: Gelechioidea) represent one of the most diverse lepidopteran groups. Due to the large number of species, generally small size of adults and subtle morphological differences, their confident identification requires tenacious and long-term dedication on their diversity. Over the past decade, DNA barcoding has repeatedly been used to elucidate boundaries of species in many large and difficult groups. Here, we conducted a test of DNA barcoding with the diverse fauna of Korean Gelechioidea with very little prior information of COI gene region from the area. Altogether 509 specimens representing 154 morphospecies were included in the study. The species assignments of all three tested species delimitation methods (ABGD, bPTP and PTP) were consistent with morphological identifications for 117 species (75.97%). A threshold of 2.5% genetic divergence was observed to differentiate the morphological species efficiently. Careful morphological examination of morphospecies exceeding 2.5% intraspecific variability prove cryptic diversity in three species (Neoblastobasis biceratala, Evippe albidoesella and Promalactis atriplagata). One morphospecies, Promalactis odaiensis, showed high intraspecific divergence while consisted of only a single MOTU. Overall, DNA barcoding was shown to provide a powerful tool to discriminate species of Korean Gelechioidea and reveal cases of cryptic diversity.

Neural Code for Ambient Heat Detection in Elaterid Beetles

Environmental thermal conditions play a major role at all levels of biological organization; however, there is little information on noxious high temperature sensation crucial in behavioral thermoregulation and survival of small ectothermic animals such as insects. So far, a capability to unambiguously encode heat has been demonstrated only for the sensory triad of the spike bursting thermo- and two bimodal hygro-thermoreceptor neurons located in the antennal dome-shaped sensilla (DSS) in a carabid beetle. We used extracellular single sensillum recording in the range of 20-45°C to demonstrate that a similar sensory triad in the elaterid Agriotes obscurus also produces high temperature-induced bursty spike trains. Several parameters of the bursts are temperature dependent, allowing the neurons in a certain order to encode different, but partly overlapping ranges of heat up to lethal levels in a graded manner. ISI in a burst is the most useful parameter out of six. Our findings consider spike bursting as a general, fundamental quality of the classical sensory triad of antennal thermo- and hygro-thermoreceptor neurons widespread in many insect groups, being a flexible and reliable mode of coding unfavorably high temperatures. The possible involvement of spike bursting in behavioral thermoregulation of the beetles is discussed. By contrast, the mean firing rate of the neurons in regular and bursty spike trains combined does not carry useful thermal information at the high end of noxious heat.

Integrated species-phenon trees: visualizing infraspecific diversity within lineages

The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species-phenon tree merges ancestor-descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into "species boxes" and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent-child hierarchy in the integrated tree has been the progressive population of a species-phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others' important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.

Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

Spiders are mega diverse arthropods and play an important role in the ecosystem. Identification of this group is challenging due to their cryptic behavior, sexual dimorphism, and unavailability of taxonomic keys for juveniles. To overcome these obstacles, DNA barcoding plays a pivotal role in spider identification throughout the globe. This study is the first large scale attempt on DNA barcoding of spiders from India with 101 morphospecies of 72 genera under 21 families, including five endemic species and holotypes of three species. A total of 489 barcodes was generated and analyzed, among them 85 novel barcodes of 22 morphospecies were contributed to the global database. The estimated delimitation threshold of the Indian spiders was 2.6% to 3.7% K2P corrected pairwise distance. The multiple species delimitation methods (BIN, ABGD, GMYC and PTP) revealed a total of 107 molecular operational taxonomic units (MOTUs) for 101 morphospecies. We detected more than one MOTU in 11 morphospecies with discrepancies in genetic distances and tree topologies. Cryptic diversity was detected in Pardosa pusiola, Cyclosa spirifera, and Heteropoda venatoria. The intraspecies distances which were as large as our proposed delimitation threshold were observed in Pardosa sumatrana, Thiania bhamoensis, and Cheiracanthium triviale. Further, shallow genetic distances were detected in Cyrtophora cicatrosa, Hersilia savignyi, Argiope versicolor, Phintella vittata, and Oxyopes birmanicus. Two morphologically distinguished species (Plexippus paykulli and Plexippus petersi) showed intra-individual variation within their DNA barcode data. Additionally, we reinstate the original combination for Linyphia sikkimensis based on both morphology and DNA barcoding. These data show that DNA barcoding is a valuable tool for specimen identification and species discovery of Indian spiders.

A DNA barcode library for ground beetles of Germany: the genus Amara Bonelli, 1810 (Insecta, Coleoptera, Carabidae)

The genus Amara Bonelli, 1810 is a very speciose and taxonomically difficult genus of the Carabidae. The identification of many of the species is accomplished with considerable difficulty, in particular for females and immature stages. In this study the effectiveness of DNA barcoding, the most popular method for molecular species identification, was examined to discriminate various species of this genus from Central Europe. DNA barcodes from 690 individuals and 47 species were analysed, including sequences from previous studies and more than 350 newly generated DNA barcodes. Our analysis revealed unique BINs for 38 species (81%). Interspecific K2P distances below 2.2% were found for three species pairs and one species trio, including haplotype sharing between Amara alpina/Amara torrida and Amara communis/Amara convexior/Amara makolskii. This study represents another step in generating an extensive reference library of DNA barcodes for carabids, highly valuable bioindicators for characterizing disturbances in various habitats.

DNA Barcoding studies on Thrips in India: Cryptic species and Species complexes

Thrips are one of the major sucking pest and vector of plant viruses causing huge economic loss in agriculture. The accurate identification of thrips is crucial for effective pest management strategies. However, morphology based identification has limitations and warrants integration of molecular data. We attempted the largest DNA barcoding initiative on 370 sequences of 89 thrips morphospecies including 104 novel sequences from 39 morphospecies, including the type specimens of four species. The results of multiple species delimitation methods (BIN, ABGD, GMYC and bPTP) were consistent for 73 species (82%) with their morphological identifications. A total of 107 molecular operational taxonomic units (MOTUs) was recovered for 89 morphospecies by superimposing multiple methods and applying a three level nomenclature system. We detected more than one MOTU in 14 morphospecies indicating to have cryptic diversity including, two major vector species (Frankliniella schultzei and Thrips palmi). However, four morphospecies (Thrips moundi, Thrips carthami, Haplothrips andersi and Haplothrips gowdeyi) showed low genetic distances between them with overlapping in barcode gap that requires further analysis with multiple molecular markers and more specimens from wide geographical areas for better taxonomic judgment. We also presented the advantage of simultaneous use of multiple delimitation methods for detection and identification of cryptic species.

Cryptic diversity of the subfamily Calaphidinae (Hemiptera: Aphididae) revealed by comprehensive DNA barcoding

Aphids are a species rich group comprising many important pests. However, species identification can be very difficult for aphids due to their morphological ambiguity. DNA barcoding has been widely adopted for rapid and reliable species identification as well as cryptic species detection. In this study, we investigated cryptic diversity in the subfamily Calaphidinae (Hemiptera: Aphididae) based on 899 sequences of cytochrome c oxidase I (COI) for 115 morphospecies (78 species collected in this study and sequences of 73 species downloaded from Genbank). Among these 115 morphospecies, DNA barcoding results of 90 (78.3%) species were identical to results of morphological identification. However, 25 (21.7%) morphospecies showed discrepancies between DNA barcoding and traditional taxonomy. Among these 25 discordances, a total of 15 cryptic species were identified from 12 morphospecies. We also found three morphologically distinct species pairs that sharing DNA barcoding. Based on molecular operational taxonomic unit (MOTU) estimation, we discussed on species delimitation threshold value for these taxa. Our findings confirm that Calaphidinae has high cryptic diversity even though aphids are relatively well-studied.