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

Abstract

DNA barcoding has tremendous potential for advancing species knowledge for many diverse groups of insects, potentially paving way for machine identification and semi-automated monitoring of whole insect faunas. Here, I review the current state of DNA barcoding of the superfamily Sciaroidea (Diptera), a diverse group consisting of eight understudied fly families where the described species in the world makes up some 10% (≈16,000 species) of all Diptera. World data of Sciaroidea were extracted from the Barcode of Life online database BoldSystems (BOLD) and contrasted with results and experiences from a Nordic project to build the reference library. Well over 1.2 million (1,224,877) Sciaroidea specimens have been submitted for barcoding, giving barcode-compliant sequences resulting in 56,648 so-called barcode index numbers (BINs, machine-generated proxies for species). Although the BINs on BOLD already represent 3.5 times the number of described species, merely some 2850 named species (described or interim names, 5% of the BINs) currently have been assigned a BIN. The other 95% remain as dark taxa figuring in many frontier publications as statistics representing proxies for species diversity within a family. In the Nordic region, however, substantial progress has been made towards building a complete reference library, currently making up 55% of all named Sciaroidea BINs on BOLD. Another major source (31%) of named Sciaroidea BINs on BOLD comes from COI sequences mined from GenBank, generated through phylogenetic and integrative studies outside of BOLD. Building a quality reference library for understudied insects such as Sciaroidea requires heavy investment, both pre sequence and post sequence, by trained taxonomists to build and curate voucher collections, to continually improve the quality of the data and describe new species. Only when the BINs are properly calibrated by a rigorously quality-checked reference library can the great potential of both classical taxonomic barcoding, metabarcoding, and eDNA ecology be realized.

A Rarely Seen Taxonomic Revision with Immense Value for 41 Years and Counting: Reflections on the 1981 Monograph of Trichonta Winnertz, 1864 (Diptera: Mycetophilidae) by Raymond Gagné, with an Integrative Revision of the Trichonta Vulcani (Dziedzicki, 1889) Species Complex

“…Insofar Gagné's paper on Trichonta may be seen as an important contribution to a trend in the early 1980s that, although short-lived, was groundbreaking for revisionary work on Mycetophilidae. Interestingly, this trend coincides with the more general observation that there was a peak in the number of taxonomic revisions around 1990, before a dramatic and rapid decrease in revisionary taxonomy similar to levels seen in the 1950s (Kjaerandsen 2022). As taxonomists who have used his monograph of Trichonta extensively for several decades, we are truly grateful for Gagné´s tenacity, farsightedness, and accuracy.…”

Improving theCOIDNA barcoding library for Neotropical phlebotomine sand flies (Diptera, Psychodidae)

“…CC-BY-ND 4.0 International license perpetuity. It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted December 16, 2022. ; https://doi.org/10.1101/2022.12.14.520486 doi: bioRxiv preprint One of the main benefits of integrating molecular data into insect taxonomy is the association of immature life stages of holometabolous taxa with adults and isomorphic females with males identified by morphology [52][53]. The present study focused only on generating COI sequences for adult specimens.…”

“…One of the main benefits of integrating molecular data into insect taxonomy is the association of immature life stages of holometabolous taxa with adults and isomorphic females with males identified by morphology [52][53]. The present study focused only on generating COI sequences for adult specimens.…”

Biodiversity and Distribution of Reticulitermes in the Southeastern USA

“…Biodiversity is a term used to describe the variety of living organisms on Earth that is founded on the nomenclature used to identify an animal life form to a species designation. A number of broad issues constrain delineating species, not the least of which are long-standing, global concerns affecting all biological systems, including the taxonomic impediment [ 1 ], taxonomic wrong-headiness [ 2 ], and lack of consensus on appropriate integrative methods for species identification [ 3 , 4 , 5 , 6 , 7 ] all contingent on adherence to the internationally agreed codes of rules for animals outlined in International Code of Zoological Nomenclature (ICZN) [ 8 ]. Measuring insect biodiversity is a critical component of understanding the impact of anthropogenic changes affecting life on Earth, as exemplified by discussions surrounding the so-called insect apocalypse [ 9 , 10 ].…”