The first comprehensive DNA barcode reference library of Chinese Tanytarsus (Diptera: Chironomidae) for environmental DNA metabarcoding

Delimiting species, revealing cryptic diversity, and population divergence in Qinghai-Tibet Plateau weevils through DNA barcoding

The Leptomias group represents one of the most diverse taxonomic group of weevils in the Qinghai-Tibet Plateau and its adjacent areas. Despite the potential of hidden diversity, relatively few comprehensive studies have been conducted on species diversity in this taxonomic group. In this study, we performed DNA barcoding analysis for species of the Leptomias group using a comprehensive DNA barcode dataset that included 476 sequences representing 54 morphospecies. Within the dataset, our laboratory contributed 474 sequences, and 390 sequences were newly generated for this study. The average Kimura 2-parameter distances among morphospecies and genera were 0.76% and 19.15%, respectively. In 94.4% of the species, the minimum interspecific distances exceeded the maximum intraspecific distances, indicating the presence of barcode gaps in most species of Leptomias group. The application of Automatic Barcode Gap Discovery, Assemble Species by Automatic Partitioning, Barcode Index Number, Bayesian Poisson tree processes, jMOTU, and Neighbor-joining tree methods revealed 45, 45, 63, 54, and 55 distinct clusters representing single species, respectively. Additionally, a total of four morphospecies, Leptomias kangmarensis, L. midlineatus, L. siahus, and L. sp.9RL, were found to be assigned to multiple subclade each, indicating the geographical divergences and the presence of cryptic diversity. Our findings of this study demonstrate that Qinghai-Tibet Plateau exhibits a higher species diversity of the Leptomias group, and it is imperative to investigate cryptic species within certain morphospecies using integrative taxonomic approaches in future studies. Moreover, the construction of a DNA barcode reference library presented herein establishes a robust foundational dataset to support forthcoming research on weevil taxonomy, phylogenetics, ecology, and evolution.

DNA barcodes and morphology reveal new species within the Rheotanytarsus guineensis species group from China (Diptera: Chironomidae)

The Rheotanytarsus guineensis species group (Diptera: Chironomidae) is a species diverse and taxonomically difficult group. Using DNA barcodes, we found five new species within the R. guineensis species group and reviewed the species group based on adult males from China. Rheotanytarsus guoae Lin & Yao sp. n., Rheotanytarsus miaoae Lin & Yao sp. n., Rheotanytarsus qiangi Lin & Yao sp. n., Rheotanytarsus yueqingensis Lin & Yao sp. n., and Rheotanytarsus yui Lin & Yao sp. n. are all described and figured. A key to known adult males of the R. guineensis species group worldwide is provided for the first time.

The first DNA barcode library of Chironomidae from the Tibetan Plateau with an evaluation of the status of the public databases

The main aim of this study was to curate a COI barcode library of Chironomidae from the Tibetan Plateau (TP) as an essential supplement to the public database. Another aim is to evaluate the current status of the public database of Chironomidae in aspects of taxonomic coverage, geographic representation, barcode quality, and efficiency for molecular identification, the Tibetan Plateau, China. In this study, 512 individuals of Chironomidae from the TP were identified based on morphological taxonomy and barcode analysis. The metadata of public records of Chironomidae were downloaded from the BOLD, and the quality of the public barcodes was ranked using the BAGS program. The reliability of the public library for molecular identification was evaluated with the newly curated library using the BLAST method. The newly curated library comprised 159 barcode species of 54 genera, of which 58.4% of species were likely new to science. There were great gaps in the taxonomic coverage and geographic representation in the public database, and only 29.18% of barcodes were identified at the species level. The quality of the public database was of concern, with only 20% of species being determined as concordant between BINs and morphological species. The accuracy of molecular identification using the public database was poor, and about 50% of matched barcodes could be correctly identified at the species level at the identity threshold of 97%. Based on these data, some recommendations are included here for improving barcoding studies on Chironomidae. The species richness of Chironomidae from the TP is much higher than ever recorded. Barcodes from more taxonomic groups and geographic regions are urgently needed to fill the great gap in the current public database of Chironomidae. Users should take caution when public databases are adopted as reference libraries for the taxonomic assignment.

A Checklist of the Caddisflies (Insecta: Trichoptera) from the Middle and Lower Basins of Jinsha River, Southwestern China; Including One New Species and Nine New Records in China

A checklist of trichopteran species in the middle and lower basins of the Jinsha River (southwestern China) is compiled for the first time. upon collected materials. It recorded ten families, 13 genera, and 23 species were recorded. Among them, the male of a new species Cheumatopsyche latisecta Ge & Sun, sp. nov., which can be diagnosed by its genitalia, is described and illustrated. In addition, nine other species are recorded for the first time from China, six species and three ones are recorded for the first time for Yunnan and Sichuan provinces, respectively. This trichopteran species list can provide guidance for caddisfly identification of the river and the region.

A survey of aquatic macroinvertebrates in a river from the dry corridor of Nicaragua using biological indices and DNA barcoding

Aquatic macroinvertebrates are widely used as indicators for water quality assessment around the world. Modern strategies for environmental assessment implement molecular analysis to delimitate species of aquatic macroinvertebrates. Delimitation methods have been established to determine boundaries between species units using sequencing data from DNA barcodes and serve as first exploratory tools for taxonomic revisions. This is useful in regions such as the neotropics where aquatic macroinvertebrate habitats are threatened by human interference and DNA databases remain understudied. We asked whether the biodiversity of aquatic macroinvertebrates in a stream in Nicaragua, within the Central American Dry Corridor, could be characterized with biological indices and DNA barcoding. In this study, we combined regional biological indices (BMWP-CR, IBF-SV-2010) along with distance-based (ASAP, BIN) and tree-based (GMYC, bPTP) delimitation methods, as well as nucleotide BLAST in public barcode databases. We collected samples from the upper, middle, and low reaches of the Petaquilla river. The three sites presented excellent water quality with the BMWP-CR index, but evidence of high organic pollution was found in the middle reach with the IBF-SV-2010 index. We report a total of 219 COI sequences successfully generated from 18 families and 8 orders. Operational taxonomic units (OTUs) designation ranged from 69 to 73 using the four methods, with a congruency of 92% for barcode assignation. Nucleotide BLAST identified 14 species (27.4% of barcodes) and 33 genera (39.3% of barcodes) from query sequences in GenBank and BOLD system databases. This small number of identified OTUs may be explained by the paucity of molecular data from the Neotropical region. Our study provides valuable information about the characterization of macroinvertebrate families that are important biological indicators for the assessment of water quality in Nicaragua. The application of molecular approaches will allow the study of local diversity and further improve the application of molecular techniques for biomonitoring.

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I (COI) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago’s protection.

Net-Winged Midge Genus Blepharicera Macquart (Diptera: Blephariceridae) in China: The First DNA Barcode Database with Descriptions of Four New Species and Notes on Distribution

Mitochondrial (mt) cytochrome c oxidase 1 (COI) gene is more and more widely used for DNA barcoding, which provides a rapid and timely identification as this technique is not limited by polymorphism, sex, and life stages and fundamentally complements traditional evolutionary taxonomy. The present study generated 33 mt COI sequences of seven Chinese Blepharicera Macquart, 1843 species with an average of 594 bp, which represent the first DNA barcode database for Chinese Blepharicera. Genetic distance analysis reveals that intraspecific distances in the genus are generally less than 1.7%, and interspecific distances range from 5.4% to 20.3%. Phylogenetic analysis shows that each species recovered in our analyses is separated from all neighboring species. Based on molecular and morphological data, four Blepharicera species from China, B. beishanica sp. nov., B. dushanzica sp. nov., B. nigra sp. nov. and B. xinjiangica sp. nov., are described and illustrated as new to science. Identification keys for adults and larvae of Chinese Blepharicera are also presented. Geographical analysis shows that Southwest China is the species’ richest region. Our results will be useful in tackling taxonomic problems, understanding species distribution, and resolving nomenclature conflicts associated with Blepharicera species.

New species of the genus Molanna Curtis, 1834 (Trichoptera, Molannidae) in China inferred from morphology and DNA barcodes

The male adult of Molannatruncata Ge, Peng & Sun sp. nov. is described and illustrated based on material collected in Si-chuan, China. It could be diagnosed by the subtriangular superior appendages when viewed dorsally, and by the mesal appendages each having a slender thorn and inferior appendages with a tiny inner process. Based on morphology of genitalia, we provide a dichotomous key to adult males of Molanna from the Oriental region. The DNA barcodes (partial mtCOI sequences) of M.truncata sp. nov. are generated and compared with existing sequences of Molanna species from Oriental and Palearctic regions. The mean intraspecific divergence of Molanna was 1.58% with a maximum of 8.50% in M.moesta. The Automatic Barcode Gap Discovery (ABGD) analysis of Molanna inferred 9 OTUs and thresholds of interspecific divergence of 10%. Divergence of M.truncata sp. nov. haplotypes from all other Molanna haplotypes ranged from 10.1% to 18%. We discuss distribution and potential groups of species within the Oriental Molanna species based on morphology.

A New Species in Notobitiella Hsiao in China Confirmed by Morphological and Molecular Data (Hemiptera: Heteroptera: Coreidae)

Simple Summary

Plenty of new species are published every year, but what if a new species could be erected as a new genus by the morphological characteristics of genitalia or a new species of an existing genus by the other morphological characteristics? Recently, we collected a new species of Coreidae facing this problem. The characteristics of genitalia between the new and existing species in Notobitiella (monotypic genus) were too different to compare with the difference among interspecies in tribe Cloresmini. It was reasonable to erect a new genus for this new species. However, considering the similarity between other characteristics, we decided to refer to the results of molecular data. Results showed that the genetic distance within the interspecific interval of the genus and the sister group relationship also supported that the new species should be included in the genus Notobitiella. Finally, a new species was confirmed, named Notobitiella bispinasp. nov. Our research highlighted how molecular data can be used to assist in species delimitation when encountering similar problems.

Abstract

To date, only one species of genus Notobitiella, N. elegans Hsiao, was found in Yunnan, China. Recently, we confirmed a new species, Notobitiella bispinasp. nov., by morphological and molecular data based on new specimens collected from Yunnan, China. The new species is morphologically similar to N. elegans except for the male genitalia and the sternum of the seventh abdominal segment of the female. The extraordinary difference of the genitalia between these two species inspired us to erect a new genus for this new species. However, considering their sister group relationship to other genera in tribe Cloresmini and the 12.56~12.64% genetic distance (meeting the interspecific genetic distance within genus of tribe Cloresmini) by a complete COI gene, this species was more reasonable as a new species of the genus Notobitiella, and the diagnosis of the genus was revised. The photos of the body and critical morphological characteristics for both male and female were provided for accurate identification.

DNA barcoding of Naididae (Annelida, Oligochaeta), based on cytochrome C oxidase gene and ITS2 region in China

Exploring the effectiveness of DNA barcoding in species identification is a prerequisite for biodiversity conservation and environmental monitoring. Aquatic oligochaetes could serve as excellent indicators in aquatic monitoring programmes. However, few studies have examined the effectiveness of DNA barcoding in these specific organisms. The mitochondrial cytochrome C oxidase (COI) gene of 83 specimens belonging to 40 species of 18 genera were sequenced in this study. The results showed that there was a barcode gap between species of Naididae and the intraspecific genetic distances of each species were smaller than interspecific genetic distances. The classification results of ABGD (Automatic Barcode Gap Discovery) were consistent with those of morphological identification, except for Tubifextubifex and Lumbriculusvariegatus. All species were successfully distinguished in the phylogenetic tree, based on the ITS2 region, which was coincident with the morphological result. Our results provided evidence that DNA barcoding can be used as an effective and convenient tool for species identification of the family Naididae and even for other aquatic oligochaetes.