Current State of DNA Barcoding of Sciaroidea (Diptera)—Highlighting the Need to Build the Reference Library

taxalogue: a toolkit to create comprehensive CO1 reference databases

Background

Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses.

Methods

taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered.

Results

taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities.

eDNA metabarcoding of avocado flowers: 'Hass' it got potential to survey arthropods in food production systems?

In the face of global biodiversity declines, surveys of beneficial and antagonistic arthropod diversity as well as the ecological services that they provide are increasingly important in both natural and agro-ecosystems. Conventional survey methods used to monitor these communities often require extensive taxonomic expertise and are time-intensive, potentially limiting their application in industries such as agriculture, where arthropods often play a critical role in productivity (e.g. pollinators, pests and predators). Environmental DNA (eDNA) metabarcoding of a novel substrate, crop flowers, may offer an accurate and high throughput alternative to aid in the detection of these managed and unmanaged taxa. Here, we compared the arthropod communities detected with eDNA metabarcoding of flowers, from an agricultural species (Persea americana-'Hass' avocado), with two conventional survey techniques: digital video recording (DVR) devices and pan traps. In total, 80 eDNA flower samples, 96 h of DVRs and 48 pan trap samples were collected. Across the three methods, 49 arthropod families were identified, of which 12 were unique to the eDNA dataset. Environmental DNA metabarcoding from flowers revealed potential arthropod pollinators, as well as plant pests and parasites. Alpha diversity levels did not differ across the three survey methods although taxonomic composition varied significantly, with only 12% of arthropod families found to be common across all three methods. eDNA metabarcoding of flowers has the potential to revolutionize the way arthropod communities are monitored in natural and agro-ecosystems, potentially detecting the response of pollinators and pests to climate change, diseases, habitat loss and other disturbances.

Taxonomic status of two European sibling and barcode-sharing species of Brachypogon Kieffer, 1899 (Diptera: Ceratopogonidae)

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Improving the COI DNA barcoding library for Neotropical phlebotomine sand flies (Diptera: Psychodidae)

Sand fly species are traditionally identified using morphological traits, though this method is hampered by the presence of cryptic species. DNA barcoding is a widely used tool in the case of insects of medical importance, where it is necessary to know quickly which species are present in a transmission area. Here, we assess the usefulness of mitochondrial cytochrome c oxidase subunit I (COI) DNA barcoding as a practical tool for species identification, correct assignment of isomorphic females, and to evaluate the detection of cryptic diversity that occurs in the same species. A fragment of the COI gene was used to generate 156 new barcode sequences for sand flies from different countries of the Neotropical region, mainly Colombia, which had been identified morphologically as 43 species. The sequencing of the COI gene allowed the detection of cryptic diversity within species and correctly associated isomorphic females with males identified by morphology. The maximum intraspecific genetic distances ranged from 0 to 8.32% and 0 to 8.92% using uncorrected p distances and the Kimura 2-parameter (K2P) model, respectively. The minimum interspecific distance (nearest neighbor) for each species ranged from 1.5 to 14.14% and 1.51 to 15.7% using p and K2P distances, respectively. Three species had more than 3% maximum intraspecific distance: Psychodopygus panamensis, Micropygomyia cayennensis cayennensis, and Pintomyia evansi. They also were split into at least two molecular operational taxonomic units (MOTUs) each, using different species delimitation algorithms. Regarding interspecific genetic distances, the species of the genera Nyssomyia and Trichophoromyia generated values lower than 3% (except Nyssomyia ylephiletor and Ny. trapidoi). However, the maximum intraspecific distances did not exceed these values, indicating the presence of a barcode gap despite their proximity. Also, nine sand fly species were DNA barcoded for the first time: Evandromyia georgii, Lutzomyia sherlocki, Ny. ylephiletor, Ny. yuilli pajoti, Psathyromyia punctigeniculata, Sciopemyia preclara, Trichopygomyia triramula, Trichophoromyia howardi, and Th. velezbernali. The COI DNA barcode analysis enabled the correct delimitation of several Neotropical sand fly species from South and Central America and raised questions about the presence of cryptic species for some taxa, which should be further assessed.

When details matter: Integrative revision of Holarctic Coelophthinia Edwards (Diptera, Mycetophilidae), including mapping of its mitogenome, leads to the description of four new pseudocryptic species

Background

The small genus Coelophthinia Edwards, 1941 of the subfamily Gnoristinae (Diptera, Mycetophilidae) is so far known to harbour four species from the Palaearctic, Nearctic and Neotropical Regions. Extensive DNA barcoding of fungus gnats of the family Mycetophilidae through the International Barcode of Life project (iBOL) have initiated integrative studies resulting in taxonomic upgrades and a better understanding of many species and their delimitation. The opportunity was also taken to describe the mitogenome of a member of Coelophthinia for the first time.

New information

The integrative studies give evidence for splitting the European species C.thoracica Edwards, 1941 into three different species. Four new species are described from the USA, Japan and the Nordic Region in Europe, Coelophthiniacirra Kerr sp. n., Coelophthiniaitoae Kurina sp. n., Coelophthinialata Kjaerandsen sp. n. and Coelophthinialoraasi Kjaerandsen sp. n., raising the number of Holarctic species from two to six. The mitogenome of Coelophthinialoraasi sp. n. is described and analysed.

Biodiversity and Distribution of Reticulitermes in the Southeastern USA

Simple Summary

Describing global biodiversity involves identifying species and describing their distributions. The subterranean termite genus Reticulitermes represents an important group of wood-destroying organisms; however, little is known about their species-specific distribution across the three northern hemisphere continents where they are endemic. We combined several taxonomic methods to identify the species of over 4000 specimens in the first statewide survey of subterranean termites from Georgia, USA. The area surveyed, 153,900 km², represents eco-regions typical of most of the southeast and eastern seaboard of the United States. There were three species, R. flavipes, R. virginicus, and R. nelsonae, found throughout Georgia. R. malletei was predominantly collected in the northern Piedmont soil province, while R. hageni, the least encountered species, was not collected from South Georgia. Our findings support the need for a taxonomic revision of the genus Reticulitermes, agreement on an appropriate integrated taxonomic approach for species determination, and should stimulate future research on diverse topics such as biodiversity, monitoring for these structural pests, and identifying their role in forest ecosystems.

Abstract

Reticulitermes subterranean termites are widely distributed ecosystem engineers and structural pests, yet describing their species distribution worldwide or regionally has been hindered by taxonomic uncertainties. Morphological plasticity confounds the use of taxonomic keys, while recent species descriptions and molecular techniques lacking taxonomic support have caused a muddle in interpreting the literature on Reticulitermes species distributions. We employed an integrative taxonomic approach combining behavioral, morphological, and molecular techniques to identify 4371 Reticulitermes samples to species. Five Reticulitermes species were collected from wood-on-ground at 1570 sites covering 153,900 km² in the state of Georgia, USA. Three species were collected throughout Georgia, with R. flavipes identified from every one of the 159 counties. R. nelsonae was the second most frequently collected species, found in 128 counties, with R. virginicus third with 122. Two species had distributions confined to the northern part of the state. R. malletei was collected from 73 counties, while the least collected species, R. hageni, was found in 16. Results show that the most recently described species (R. nelsonae, 2012) is widely distributed and the second-most frequently encountered termite, representing 23% of all samples. The invasive species R. flavipes represented half of all the samples collected, while R. hageni, the least at less than 1%. A search of GenBank identified a number of accessions mismatched to a species designation resulting in the literature under-reporting the biodiversity of the genus. We, therefore, outline a path to standardize methods for species identification using an integrated taxonomic approach with appropriate barcodes for consistent identification across research teams worldwide. The data also illuminate new opportunities to examine questions related to the ecology, evolution, dispersal, and resource partitioning behaviors of these sympatric species across distinct geographical regions.