DNA barcoding of odonates from the Upper Plata basin: Database creation and genetic diversity estimation

Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).

The Quality of Sequence Data Affects Biodiversity and Conservation Perspectives in the Neotropical Damselfly Megaloprepus caerulatus

Ideally, the footprint of the evolutionary history of a species is drawn from integrative studies including quantitative and qualitative taxonomy, biogeography, ecology, and molecular genetics. In today’s research, species delimitations and identification of conservation units is often accompanied by a set of—at minimum—two sequence markers appropriate for the systematic level under investigation. Two such studies re-evaluated the species status in the world’s largest Odonata, the Neotropical damselfly Megaloprepus caerulatus. The species status of the genus Megaloprepus has long been debated. Despite applying a highly similar set of sequence markers, the two studies reached different conclusions concerning species status and population genetic relationships. In this study, we took the unique opportunity to compare the two datasets and analyzed the reasons for those incongruences. The two DNA sequence markers used (16S rDNA and CO1) were re-aligned using a strict conservative approach and the analyses used in both studies were repeated. Going step by step back to the first line of data handling, we show that a high number of unresolved characters in the sequence alignments as well as internal gaps are responsible for the different outcomes in terms of species delimitations and population genetic relationships. Overall, this study shows that high quality raw sequence data are an indispensable requirement, not only in odonate research.

Taxonomic Revision of Eastern Part of Western Palaearctic Cordulegaster Using Molecular Phylogeny and Morphology, with the Description of Two New Species (Odonata: Anisoptera: Cordulegastridae)

Taxonomy of the genus Cordulegaster Leach in Brewster, 1815 in the Eastern part of the Western Palaearctic is poorly resolved. A two-step approach was applied: sequences of mitochondrial and nuclear DNA fragments were used to sort specimens; poorly known or new taxa with their phenotypic variation were described. The existence of two traditional groups (boltonii- and bidentata-group) was confirmed. Cordulegaster coronata Morton, 1916, however, belongs to a different group. Molecular-analysis supported three known and one new species (C. heros Theischinger, 1979, C. picta Selys, 1854, C. vanbrinkae Lohmann, 1993, and C. kalkmani sp. nov.) in the boltonii-group. In the bidentata-group, all specimens from West-Turkey belonged to C. insignis Schneider, 1845, all specimens further east to a complex of four closely related species, which we name charpentieri-complex (C. amasina Morton, 1916, stat. rev., C. mzymtae Bartenev, 1929 C. charpentieri (Kolenati, 1846), stat. rev. and C. cilicia sp. nov.). The following taxa: C. insignis nobilis Morton, 1916, syn. nov., C. nachitschevanica Skvortsov and Snegovaya, 2015, syn. nov. C. plagionyx Skvortsov and Snegovaya, 2015, syn. nov. and the Caucasian subspecies C. insignis lagodechica Bartenev, 1930, syn. nov., were synonymized with C. charpentieri. Finally, we provide a key for all Western Palaearctic Cordulegaster.

Coverage and quality of DNA barcode references for Central and Northern European Odonata

Background

Dragonflies and damselflies (Odonata) are important components in biomonitoring due to their amphibiotic lifecycle and specific habitat requirements. They are charismatic and popular insects, but can be challenging to identify despite large size and often distinct coloration, especially the immature stages. DNA-based assessment tools rely on validated DNA barcode reference libraries evaluated in a supraregional context to minimize taxonomic incongruence and identification mismatches.

Methods

This study reports on findings from the analysis of the most comprehensive DNA barcode dataset for Central European Odonata to date, with 103 out of 145 recorded European species included and publicly deposited in the Barcode of Life Data System (BOLD). The complete dataset includes 697 specimens (548 adults, 108 larvae) from 274 localities in 16 countries with a geographic emphasis on Central Europe. We used BOLD to generate sequence divergence metrics and to examine the taxonomic composition of the DNA barcode clusters within the dataset and in comparison with all data on BOLD.

Results

Over 88% of the species included can be readily identified using their DNA barcodes and the reference dataset provided. Considering the complete European dataset, unambiguous identification is hampered in 12 species due to weak mitochondrial differentiation and partial haplotype sharing. However, considering the known species distributions only two groups of five species possibly co-occur, leading to an unambiguous identification of more than 95% of the analysed Odonata via DNA barcoding in real applications. The cases of small interspecific genetic distances and the observed deep intraspecific variation in Cordulia aenea (Linnaeus, 1758) are discussed in detail and the corresponding taxa in the public reference database are highlighted. They should be considered in future applications of DNA barcoding and metabarcoding and represent interesting evolutionary biological questions, which call for in depth analyses of the involved taxa throughout their distribution ranges.

The use of Odonata species for environmental assessment: a meta-analysis for the Neotropical region

The order Odonata has been regularly used as an indicator of the ecosystem's condition. The objective of this review was to analyze the importance of Odonata for environmental assessments (assessment types, statistical approach, life stages, and sampling method, or particular metric), summarizing the current state, the trends, and identifying related research issues in the Neotropical region. Therefore, we selected 62 articles from 2007 to 2018 based on published research to monitor Odonata assessments in the Neotropical region. We compiled a database and ran statistical analyses for the observed frequencies. We found that ecosystem health was the most frequent assessment type and quality the most used objective. In the case of statistical tests and metrics, multivariate analyses and species richness were most used in these papers. However, because there is a great diversity of habitats in this region, there is no unique monitoring protocol to assess the quality of ecosystem health and it is needed to create a proposal for a standard evaluation protocol. Consequently, guidelines for monitoring are presented, and we suggest three stages to establish a specific protocol for each site, which records the set of species most sensitive to the exchange rate evaluated, as well as the use of rarefaction methods, the index of diversity based on the area under the curve, and multivariate analysis, among other recommendations.

DNA barcoding for identification of anuran species in the central region of South America

The use of COI barcodes for specimen identification and species discovery has been a useful molecular approach for the study of Anura. Here, we establish a comprehensive amphibian barcode reference database in a central area of South America, in particular for specimens collected in Mato Grosso do Sul state (Brazil), and to evaluate the applicability of the COI gene for species-level identification. Both distance- and tree-based methods were applied for assessing species boundaries and the accuracy of specimen identification was evaluated. A total of 204 mitochondrial COI barcode sequences were evaluated from 22 genera and 59 species (19 newly barcoded species). Our results indicate that morphological and molecular identifications converge for most species, however, some species may present cryptic species due to high intraspecific variation, and there is a high efficiency of specimen identification. Thus, we show that COI sequencing can be used to identify anuran species present in this region.

Italian odonates in the Pandora's box: A comprehensive DNA barcoding inventory shows taxonomic warnings at the Holarctic scale

The Odonata are considered among the most endangered freshwater faunal taxa. Their DNA-based monitoring relies on validated reference data sets that are often lacking or do not cover important biogeographical centres of diversification. This study presents the results of a DNA barcoding campaign on Odonata, based on the standard 658-bp 5' end region of the mitochondrial COI gene, involving the collection of 812 specimens (409 of which barcoded) from peninsular Italy and its main islands (328 localities), belonging to all the 88 species (31 Zygoptera and 57 Anisoptera) known from the country. Additional BOLD and GenBank data from Holarctic samples expanded the data set to 1,294 DNA barcodes. A multi-approach species delimitation analysis involving two distance (OT and ABGD) and four tree-based (PTP, MPTP, GMYC and bGMYC) methods was used to explore these data. Of the 88 investigated morphospecies, 75 (85%) unequivocally corresponded to distinct molecular operational units, whereas the remaining ones were classified as 'warnings' (i.e. showing a mismatch between morphospecies assignment and DNA-based species delimitation). These results are in contrast with other DNA barcoding studies on Odonata showing up to 95% of identification success. The species causing warnings were grouped into three categories depending on if they showed low, high or mixed genetic divergence patterns. The analysis of haplotype networks revealed unexpected intraspecific complexity at the Italian, Palearctic and Holarctic scale, possibly indicating the occurrence of cryptic species. Overall, this study provides new insights into the taxonomy of odonates and a valuable basis for future DNA and eDNA-based monitoring studies.

First records raise questions: DNA barcoding of Odonata in the middle of the Mediterranean

We present the results of the first-ever DNA barcoding study of odonates from the Maltese Islands. In total, 10 morphologically identified species were collected during a two-week long expedition in 2018. Eighty cytochrome c oxidase subunit I (COI) barcodes were obtained from the collected specimens. Intra- and interspecific distances ranged from 0.00% to 2.24% and 0.48% to 17.62%, respectively. Successful species identification based on ascribing a single morphological species to a single Barcode Index Number (BIN) was achieved for eight species (80%). In the case of two species, Ischnura genei and Anax parthenope, BINs were shared with other closely related species. The taxonomic status of I. genei is questionable and the phylogenetic relationship between A. imperator/parthenope is not clear. Further studies involving a series of adult specimens collected in a wide spatial range and nuclear markers are necessary to resolve these cases. Therefore, this dataset serves as an initial DNA barcode reference library for Maltese odonates, within a larger project: Aquatic Macroinvertebrates DNA Barcode Library of Malta.

A further study on Franciscobasis Machado & Bedê, 2016 (Odonata: Coenagrionidae), a newly described genus from Minas Gerais, Brazil

The genus Franciscobasis Machado & Bedê, 2016 is endemic to the Serra da Canastra National Park in Minas Gerais state, Brazil. Two species of Franciscobasis were described simultaneously with the genus description: F. franciscoi and F. sonia, the latter described only from females. Through morphological and molecular analysis, we investigated if F. sonia may represent the young female of F. franciscoi. Resulting data did not present adequate differences between females to characterize them as different species. Therefore, we suggest that F. sonia is a junior synonym of F. franciscoi, and the female of F. franciscoi goes through a complex ontogenetic color change.

DNA Barcodes for Forensically Important Fly Species in Brazil

Here, we analyze 248 DNA barcode sequences of 35 fly species of forensic importance in Brazil. DNA barcoding can be effectively used for specimen identification of these species, allowing the unambiguous identification of 31 species, an overall success rate of 88%. Our results show a high rate of success for molecular identification using DNA barcoding sequences and open new perspectives for immature species identification, a subject on which limited forensic investigations exist in Tropical regions. We also address the implications of building a robust forensic DNA barcode database. A geographic bias is recognized for the COI dataset available for forensically important fly species in Brazil, with concentration of sequences from specimens collected mainly in sites located in the Cerrado, Mata Atlântica, and Pampa biomes.