The philosophical basis and utility of DNA barcoding have been a subject of numerous debates. While most literature embraces it, some studies continue to question its use in dipterans, butterflies and marine gastropods. Here, we explore the utility of DNA barcoding in identifying spider species that vary in taxonomic affiliation, morphological diagnosibility and geographic distribution. Our first test searched for a 'barcoding gap' by comparing intra- and interspecific means, medians and overlap in more than 75,000 computed Kimura 2-parameter (K2P) genetic distances in three families. Our second test compared K2P distances of congeneric species with high vs. low morphological distinctness in 20 genera of 11 families. Our third test explored the effect of enlarging geographical sampling area at a continental scale on genetic variability in DNA barcodes within 20 species of nine families. Our results generally point towards a high utility of DNA barcodes in identifying spider species. However, the size of the barcoding gap strongly depends on taxonomic groups and practices. It is becoming critical to define the barcoding gap statistically more consistently and to document its variation over taxonomic scales. Our results support models of independent patterns of morphological and molecular evolution by showing that DNA barcodes are effective in species identification regardless of their morphological diagnosibility. We also show that DNA barcodes represent an effective tool for identifying spider species over geographic scales, yet their variation contains useful biogeographic information.

DNA barcoding gap: reliable species identification over morphological and geographical scales.

Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an next-generation sequencing (NGS) barcoding pipeline that allows for cost-effective high-throughput generation of short specimen-specific barcodes (313 bp of COI; laboratory cost <$0.50 per specimen) through next-generation sequencing of tagged amplicons. We applied our approach to a large sample of tropical ants, obtaining barcodes for 3,290 of 4,032 specimens (82%). NGS barcodes and their corresponding specimens were then sorted into molecular operational taxonomic units (mOTUs) based on objective clustering and Automated Barcode Gap Discovery (ABGD). High diversity of 88-90 mOTUs (4% clustering) was found and morphologically validated based on preserved vouchers. The mOTUs were overwhelmingly in agreement with morphospecies (match ratio 0.95 at 4% clustering). Because of lack of coverage in existing barcode databases, only 18 could be accurately identified to named species, but our study yielded new barcodes for 48 species, including 28 that are potentially new to science. With its low cost and technical simplicity, the NGS barcoding pipeline can be implemented by a large range of laboratories. It accelerates invertebrate species discovery, facilitates downstream taxonomic work, helps with building comprehensive barcode databases and yields precise abundance information.

Sorting specimen‐rich invertebrate samples with cost‐effective NGS barcodes: Validating a reverse workflow for specimen processing

Ecuador is considered a megadiverse country but information on the distribution and conservation of its ant species is scarce and scattered through the literature. Here we review 150 years of published literature to assemble the first comprehensive species list of continental Ecuadorian ants (excluding the Galapagos Islands). Our main goals are to provide support to online tools ( www.theantsofecuador.com ), and to serve as a reference to the various research initiatives currently being done in the country. We found 2,124 ant records, from 679 ant species, in 180 localities, reported in 149 articles. We used a subset of this database (i.e. 1,111 records left after removal of duplicates and records with no locality info) to review the Ecuadorian regions, provinces, and national parks covered by the list. For a tropical country, both the number of records per ant species (mean=1.8, SD=1.9) and the number of ant species per locality (mean=6.2, SD=29.7) are extremely low. Moreover, the ant records in our list are biased towards three provinces (Orellana, 410 ant records and 378 ant spp.; Sucumbios, 212 and 177; Pichincha, 129 and 92), one region (Oriente, 779 records and 487 ant species) and non-protected areas (777 ant records and 510 ant spp.). Endemic ants are poorly covered by the Ecuadorian system of protected areas. This study highlights the gaps and opportunities in ant research for the country.

Mapping continental Ecuadorian ant species

Understanding patterns of species diversity relies on accurate taxonomy which can only be achieved by long-term natural history research and the use of complementary information to establish species boundaries among cryptic taxa. We used DNA barcoding to characterize the ant diversity of Iguazu National Park (INP), a protected area of the Upper Parana Atlantic Forest ecoregion, located at the southernmost extent of this forest. We assessed ant diversity using both cytochrome c oxidase subunit 1 (COI) sequences and traditional morphological approaches, and compared the results of these two methods. We successfully obtained COI sequences for 312 specimens belonging to 124 species, providing a DNA barcode reference library for nearly 50% of the currently known ant fauna of INP. Our results support a clear barcode gap for all but two species, with a mean intraspecific divergence of 0.72%, and an average congeneric distance of 17.25%. Congruently, the library assembled here was useful for the discrimination of the ants of INP and allowed us to link unidentified males and queens to their worker castes. To detect overlooked diversity, we classified the DNA barcodes into Molecular Operational Taxonomic Units (MOTUs) using three different clustering algorithms, and compared their number and composition to that of reference species identified based on morphology. The MOTU count was always higher than that of reference species regardless of the method, suggesting that the diversity of ants at INP could be between 6% and 10% higher than currently recognized. Lastly, our survey contributed with 78 new barcode clusters to the global DNA barcode reference library, and added 36 new records of ant species for the INP, being 23 of them new citations for Argentina.

https://www.onlinelibrary.wiley.com/doi/pdf/10.1002/ece3.3549

Mind the gap! Integrating taxonomic approaches to assess ant diversity at the southern extreme of the Atlantic Forest.

DNA barcoding has emerged as a routine tool in modern taxonomy. Although straightforward, this approach faces new challenges, when applied to difficult situation such as defining cryptic biodiversity. Ants are prime examples for high degrees of cryptic biodiversity due to complex population differentiation, hybridization and speciation processes. Here, we test the DNA barcoding region, cytochrome c oxidase 1 and two supplementary markers, 28S ribosomal DNA and long-wavelength rhodopsin, commonly used in ant taxonomy, for their potential in a layered, character-based barcoding approach across different taxonomic levels. Furthermore, we assess performance of the character-based barcoding approach to determine cryptic species diversity in ants. We found (i) that the barcode potential of a specific genetic marker varied widely among taxonomic levels in ants; (ii) that application of a layered, character-based barcode for identification of specimens can be a solution to taxonomical challenging groups; (iii) that the character-based barcoding approach allows us to differentiate specimens even within locations based on pure characters. In summary, (layered) character-based barcoding offers a reliable alternative for problematic species identification in ants and can be used as a fast and cost-efficient approach to estimate presence, absence or frequency of cryptic species.

Some ‘ant’swers: Application of a layered barcode approach to problems in ant taxonomy

Solenopsis is a widespread ant genus and the identification of its species is notoriously difficult. Hence, investigation of their distribution along elevational gradients is challenging. Our aims were (1) to test the complementarity of the morphological and DNA barcoding approaches for Solenopsis species identification, and (2) to assess species diversity and distribution along an altitudinal gradient in the Ecuadorian Andes. Ants were collected in five localities between 1000 and 3000 m above sea level. In total, 24 morphospecies were identified along the gradient and 14 of them were barcoded. Seven morphospecies were confirmed by the molecular approach. Three others, occurring sympatrically and possessing clear diagnostic characters, showed low genetic divergence. Representatives of a further four morphospecies were split into nine clusters by COI and nuclear wingless genetic markers, suggesting the existence of cryptic species. Examination of gynes revealed potential diagnostic characters for morphological discrimination. Solenopsis species were found up to an altitudinal record of 3000 m. Most morphospecies (20 of 24) were found at a single elevation. Our results suggest a high species turnover along the gradient, and point to the use of morphological and DNA barcoding approaches as necessary for differentiating among Solenopsis species.

High species turnover of the ant genus Solenopsis (Hymenoptera : Formicidae) along an altitudinal gradient in the Ecuadorian Andes, indicated by a combined DNA sequencing and morphological approach

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High species turnover of the ant genus Solenopsis (Hymenoptera : Formicidae) along an altitudinal gradient in the Ecuadorian Andes, indicated by a combined DNA sequencing and morphological approach