Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths

Maximizing Identification Precision of Hymenoptera and Brachycera (Diptera) With a Non-Destructive DNA Metabarcoding Approach

In recent years, DNA metabarcoding has been used for a more efficient assessment of bulk samples. However, there remains a paucity of studies examining potential disparities in species identification methodologies. Here, we explore the outcomes of diverse clustering and filtering techniques on data from a non-destructive metabarcoding approach, compared to species-level morphological identification of Brachycera (Diptera) and Hymenoptera of two bulk samples collected with Malaise traps. The study evaluated four distinct approaches, namely clustering to Amplicon Sequence Variants (ASVs) or ASVs clustered to Operational Taxonomic Units (OTUs) coupled with subsequent filtering using the LULU algorithm at 84% and 96% minimum match. In total, 114 species of Brachycera (35 families) and 85 species of Hymenoptera (27 families) were identified morphologically. Depending on the selected approach, DNA metabarcoding results strongly varied in terms of detected molecular units blasted to brachyceran and hymenopteran species. For Brachycera, ASVs clustered into OTUs followed by LULU using a 96% minimum match (OTU96) inferred the number of molecular units closest to the number of morphologically identified species. Using Syrphidae as an exemplary family, we found an overlap ranging from 9% to 81% between the morphological identification and the different clustering and filtering approaches, OTU96 being also here the closest one. For Hymenoptera, while OTU96 also yielded the highest number of molecular units, it was still considerably low compared to the number of morphologically identified species. Our results show that metabarcoding methodology needs to be significantly improved to be applied to Hymenoptera. Conversely, for Brachycera, we acknowledge the promise of employing a non-destructive metabarcoding approach, incorporating ASV clustering into OTUs and filtering with LULU, to derive dependable species lists. Such lists hold significant potential for applications in biomonitoring, conservation efforts, and other related fields.

Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity

Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4-30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.

A database and checklist of geometrid moths (Lepidoptera) from Colombia

Background

Molecular DNA sequence data allow unprecedented advances in biodiversity assessments, monitoring schemes and taxonomic works, particularly in poorly-explored areas. They allow, for instance, the sorting of material rapidly into operational taxonomic units (such as BINs - Barcode Index Numbers), sequences can be subject to diverse analyses and, with linked metadata and physical vouchers, they can be examined further by experts. However, a prerequisite for their exploitation is the construction of reference libraries of DNA sequences that represent the existing biodiversity. To achieve these goals for Geometridae (Lepidoptera) moths in Colombia, expeditions were carried out to 26 localities in the northern part of the country in 2015–2019. The aim was to collect specimens and sequence their DNA barcodes and to record a fraction of the species richness and occurrences in one of the most biodiversity-rich countries. These data are the beginning of an identification guide to Colombian geometrid moths, whose identities are currently often provisional only, being morpho species or operational taxonomic units (OTUs). Prior to the current dataset, 99 Geometridae sequences forming 44 BINs from Colombia were publicly available on the Barcode of Life Data System (BOLD), covering 20 species only.

New information

We enrich the Colombian Geometridae database significantly by including DNA barcodes, two nuclear markers, photos of vouchers and georeferenced occurrences of 281 specimens of geometrid moths from different localities. These specimens are classified into 80 genera. Analytical tools on BOLD clustered 157 of the mentioned sequences to existing BINs identified to species level, identified earlier by experts. Another 115 were assigned to BINs that were identified to genus or tribe level only. Eleven specimens did not match any existing BIN on BOLD and are, therefore, new additions to the database. It is likely that many BINs represent undescribed species. Nine short sequences (< 500bp) were not assigned to BINs, but identified to the lowest taxonomic category by expert taxonomists and with comparisons of type material photos. The released new genetic information will help to further progress the systematics of Geometridae. An illustrated catalogue of all new records allows validation of our identifications; it is also the first document of this kind for Colombian Geometridae. All specimens are deposited at the Museo de Zoología of Universidad de Sucre (MZUS), North Colombia. DNA BINs are reported in this study through dx.doi.org/10.5883/DS-GEOCO, the species occurrences are available on SIB Colombia https://sibcolombia.net/ and the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ through https://doi.org/10.15472/ucfmkh.

Genetic variation in neotropical butterflies is associated with sampling scale, species distributions, and historical forest dynamics

Previous studies of butterfly diversification in the Neotropics have focused on Amazonia and the tropical Andes, while southern regions of the continent have received little attention. To address the gap in knowledge about the Lepidoptera of temperate South America, we analysed over 3000 specimens representing nearly 500 species from Argentina for a segment of the mitochondrial cytochrome c oxidase subunit I (COI) gene. Representing 42% of the country's butterfly fauna, collections targeted species from the Atlantic and Andean forests, and biodiversity hotspots that were previously connected but are now isolated. We assessed COI effectiveness for species discrimination and identification and how its performance was affected by geographic distances and taxon coverage. COI data also allowed to study patterns of genetic variation across Argentina, particularly between populations in the Atlantic and Andean forests. Our results show that COI discriminates species well, but that identification success is reduced on average by ~20% as spatial and taxonomic coverage rises. We also found that levels of genetic variation are associated with species' spatial distribution type, a pattern which might reflect differences in their dispersal and colonization abilities. In particular, intraspecific distance between populations in the Atlantic and Andean forests was significantly higher in species with disjunct distributions than in those with a continuous range. All splits between lineages in these forests dated to the Pleistocene, but divergence dates varied considerably, suggesting that historical connections between the Atlantic and Andean forests have differentially affected their shared butterfly fauna. Our study supports the fact that large-scale assessments of mitochondrial DNA variation are a powerful tool for evolutionary studies.

Use of species delimitation approaches to tackle the cryptic diversity of an assemblage of high Andean butterflies (Lepidoptera: Papilionoidea)

Cryptic biological diversity has generated ambiguity in taxonomic and evolutionary studies. Single-locus methods and other approaches for species delimitation are useful for addressing this challenge, enabling the practical processing of large numbers of samples for identification and inventory purposes. This study analyzed an assemblage of high Andean butterflies using DNA barcoding and compared the identifications based on the current morphological taxonomy with three methods of species delimitation (automatic barcode gap discovery, generalized mixed Yule coalescent model, and Poisson tree processes). Sixteen potential cryptic species were recognized using these three methods, representing a net richness increase of 11.3% in the assemblage. A well-studied taxon of the genus Vanessa, which has a wide geographical distribution, appeared with the potential cryptic species that had a higher genetic differentiation at the local level than at the continental level. The analyses were useful for identifying the potential cryptic species in Pedaliodes and Forsterinaria complexes, which also show differentiation along altitudinal and latitudinal gradients. This genetic assessment of an entire assemblage of high Andean butterflies (Papilionoidea) provides baseline information for future research in a region characterized by high rates of endemism and population isolation.

Assessing insect biodiversity with automatic light traps in Brazil: Pearls and pitfalls of metabarcoding samples in preservative ethanol

Automated species identification based on data produced with metabarcoding offers an alternative for assessing biodiversity of bulk insect samples obtained with traps. We used a standard two-step PCR approach to amplify a 313 bp fragment of the barcoding region of the mitochondrial COI gene. The PCR products were sequenced on an Illumina MiSeq platform, and the OTUs production and taxonomic identifications were performed with a customized pipeline and database. The DNA used in the PCR procedures was extracted directly from the preservative ethanol of bulk insect samples obtained with automatic light traps in 12 sampling areas located in different biomes of Brazil, during wet and dry seasons. Agricultural field and forest edge habitats were collected for all sampling areas. A total of 119 insect OTUs and nine additional OTUs assigned to other arthropod taxa were obtained at a ≥97% sequence similarity level. The alpha and beta diversity analyses comparing biomes, habitats, and seasons were mostly inconclusive, except for a significant difference in beta diversity between biomes. In this study, we were able to metabarcode and HTS adult insects from their preservative medium. Notwithstanding, our results underrepresent the true magnitude of insect diversity expected from samples obtained with automatic light traps in Brazil. Although biological and technical factors might have impacted our results, measures to optimize and standardize eDNA HTS should be in place to improve taxonomic coverage of samples of unknown diversity and stored in suboptimal conditions, which is the case of most eDNA samples.

Species delimitation of neotropical Characins (Stevardiinae): Implications for taxonomy of complex groups

Accurate species delimitation is crucial for studies of phylogeny, phylogeography, ecology, conservation and biogeography. The limits of species and genera in the Characidae family are controversial due to its uncertain phylogenetic relationships, high level of morphological homoplasy and the use of ambiguous morphological characters for descriptions. Here we establish species boundaries for Bryconamericus, Hemibrycon, Knodus and Eretmobrycon (Stevardiinae: Characidae), previously diagnosed with morphology, using three different barcoding approaches (GMYC, PTP, ABGD). Results revealed that species delimitation was successful by the use of a single-gene approach and by following a workflow in the context of integrative taxonomy, making evident problems and mistakes in the cataloging of Characidae species. Hence, it was possible to infer boundaries at genus level for clusters in the trees (GMYC and PTP) and automatic partitions (ABGD) which were consistent with some of recent taxonomic changes proposed in Characidae. We found that discordance cases between methods were linked to limitations of the methods and associated to putative species cluster closely related, some historically problematic in their diagnosis and identification. Furthermore, we suggested taxonomic changes and possibly new species, revealing a high degree of hidden diversity. Finally, we propose a workflow as a fast, accurate and objective way to delimit species from mitochondrial DNA sequences and to help clarify the classification of this group.

Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan

Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.

Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon

Biodiversity research in tropical ecosystems—popularized as the most biodiverse habitats on Earth—often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.

Tiger-Moths in Savannas in Eastern Amazon: First Assessment of Diversity and Seasonal Aspects

Biodiversity knowledge on insects is urgently needed due to the ever growing demand for food and the consequent deforestation process and loss of natural habitats in many understudied tropical regions. In this paper, we describe the outcome of a biodiversity research on tiger moths performed for the first time in a poorly studied Amazonian landscape-the savanna. We sampled tiger moths monthly with UV automatic light traps for 12 consecutive months in two sampling points in an area of savanna in eastern Amazon, and we compared our results to previously available data for eastern Amazon. We found a total of 91 species of which 80 were identified to species level. The most species-rich subtribes were Phaegopterina and Euchromiina with 32 species each. Species richness and abundance did not differ among sampling sites, but in general the species richness was higher during the dry season while abundance was higher during the wet season. This seasonal diversity pattern differs from the most common patterns recorded for savannas in other parts of the world. The species composition also changed in wet and dry seasons and correlated significantly with temperature and relative humidity. Our results suggest that the alpha diversity of the Amazonian savannas in our sampling area is lower than that in nearby rain forests and similar to that in agriculturally disturbed areas surrounded by rain forests. However, the species composition differed considerably from natural and disturbed areas. These results highlight the need of basic biodiversity surveys of insects in Amazonian savannas.

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

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.

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

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 Iguazú National Park (INP), a protected area of the Upper Paraná 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.

Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence

Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

Mapping global biodiversity connections with DNA barcodes: Lepidoptera of Pakistan

Sequences from the DNA barcode region of the mitochondrial COI gene are an effective tool for specimen identification and for the discovery of new species. The Barcode of Life Data Systems (BOLD) (www.boldsystems.org) currently hosts 4.5 million records from animals which have been assigned to more than 490,000 different Barcode Index Numbers (BINs), which serve as a proxy for species. Because a fourth of these BINs derive from Lepidoptera, BOLD has a strong capability to both identify specimens in this order and to support studies of faunal overlap. DNA barcode sequences were obtained from 4503 moths from 329 sites across Pakistan, specimens that represented 981 BINs from 52 families. Among 379 species with a Linnaean name assignment, all were represented by a single BIN excepting five species that showed a BIN split. Less than half (44%) of the 981 BINs had counterparts in other countries; the remaining BINs were unique to Pakistan. Another 218 BINs of Lepidoptera from Pakistan were coupled with the 981 from this study before being compared with all 116,768 BINs for this order. As expected, faunal overlap was highest with India (21%), Sri Lanka (21%), United Arab Emirates (20%) and with other Asian nations (2.1%), but it was very low with other continents including Africa (0.6%), Europe (1.3%), Australia (0.6%), Oceania (1.0%), North America (0.1%), and South America (0.1%). This study indicates the way in which DNA barcoding facilitates measures of faunal overlap even when taxa have not been assigned to a Linnean species.