Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths

Lopez‐Vaamonde, Carlos; Kirichenko, Natalia; Cama, Alain; Doorenweerd, Camiel; Charles, Hubert; Guiguet, Antoine; Gomboc, Stanislav; Huemer, Peter; Landry, Jean-François; Laštůvka, A.; Laštůvka, Zdeněk; Lee, Kyung Min; Lees, David C.; Mutanen, Marko; Nieukerken, E.J. van; Segerer, Andreas H.; Triberti, Paolo; Wieser, Christian; Rougerie, Rodolphe

doi:10.3389/fevo.2021.626752

Cited by 57 publications

(41 citation statements)

References 75 publications

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“…The remaining 5-10% will need even more detailed population-level studies to uncover haplotype networks of complex species relations, as demonstrated for birds [104]. As such, results on DNA barcoding of Sciaroidea from the Nordic region are in line with great success rates reported after a rigorous revision for several other, better-studied taxa, such as gracillariid moths [105,106].…”

Section: There Is Hope For You Yet Taxonomymentioning

confidence: 76%

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

Kjærandsen¹

2022

Insects

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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.

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Section: There Is Hope For You Yet Taxonomymentioning

confidence: 76%

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

Kjærandsen¹

2022

Insects

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“…On the basis of the forewing pattern and genitalia we follow Z. Laštůvka (in Lopez-Vaamonde et al 2021) who regards this as Phyllonorycter ochreojunctella, a species not considered by Varenne & Nel (2015), and we hereby introduce the synonymy.…”

Section: Phyllonorycter Acericorsica Varenne and Nel 2015mentioning

confidence: 99%

“…However, the majority of Hyperlais have not been barcoded so far. Leraut (2012) discussed an eventual conspecitify with H. dulcinalis (Treitschke, 1835) and H. glyceralis (Staudinger, 1859) with subspecific status, but both species lack DNA barcodes.…”

Section: Hyperlais Rosseti Varenne 2009mentioning

confidence: 99%

Identity of some recently described Lepidoptera from France—re-assessed with DNA barcodes and morphology

Huemer

Nieukerken

2021

Zootaxa

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Seventy-three species of Lepidoptera described from France since 2000, particularly by Jacques Nel and Thierry Varenne, are re-assessed from largely unpublished molecular data. We tried to obtain DNA barcode sequences from 62 holotypes, supplemented by paratypes of eight species and on one case by non-type material, whereas one previously synonymized species was not sequenced. Altogether we obtained 78 DNA barcode sequences for 65 nominal taxa while sequencing failed for six holotypes. An integrative analysis from molecular data and morphology supports the validity of the majority of species but also resulted in the re-assessment of several taxa. The following 13 new synonymies are established: Stigmella cyrneorolandi Nel & Varenne, 2013 syn. nov. of Stigmella rolandi van Nieukerken, 1990; Stigmella thibaulti Varenne & Nel, 2019 syn. nov. of Stigmella nivenburgensis (Preissecker, 1942) (Nepticulidae); Nemapogon peslieri Varenne & Nel, 2017 syn. nov. of Nemapogon inexpectata Varenne & Nel, 2017 (Tineidae); Phyllonorycter acericorsica Varenne & Nel, 2015 syn. nov. of Phyllonorycter ochreojunctella (Klimesch, 1942) (Gracillariidae); Ancylis paraobtusana Varenne, Nel, & Peslier, 2020 syn. nov. of Ancylis comptana (Frölich, 1828) (Tortricidae); Celypha paludicolella Varenne & Nel, 2017 syn. nov. of Celypha doubledayana (Barrett, 1872) (Tortricidae); Cydia oxytropidana Nel & Varenne, 2016 syn. nov. of Cydia oxytropidis (Martini, 1912) (Tortricidae); Sorhagenia orocorsa Varenne & Nel, 2016 syn. nov. of Sorhagenia janiszewskae Riedl, 1962 (Cosmopterigidae); Chionodes cerdanica Peslier, Nel & Varenne, 2020 syn. nov. of Chionodes distinctella (Zeller, 1839) (Gelechiidae); Elachista bidentata Varenne & Nel, 2019 syn. nov. of Elachista orstadii Palm, 1943; Elachista karsticola Varenne & Nel, 2018 syn. nov. of Elachista maculosella Chrétien, 1896 (Elachistidae); Scythris chablaisensis Delmas, 2018 syn. nov. of Scythris laminella ([Denis & Schiffermüller], 1775) (Scythrididae); Epermenia pumila (Buvat & Nel, 2000) syn. nov. of Epermenia profugella (Stainton, 1856) (Epermeniidae). Finally, the status of some taxa still remains unclear due to the lack of DNA barcodes of closely related species and the absence of convincing diagnostic characters in morphology.

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“…We expected to find archival leaf mines in herbaria specimens in Eastern Asia well before the beginning of the invasion and in Western Europe only after the invasion event. We also took advantage of the recent advances in DNA barcoding of samples with degraded DNA 22,23 to analyse larvae and pupae found inside archival leaf mines to understand the genetics of invasion and explain the high level of haplotype diversity in the neocolonized area in Europe.…”

Section: Introductionmentioning

confidence: 99%

“…(Malvaceae) in the Palearctic. In the last few decades, this species, which was originally known from East Asia (Japan, Korea, Russian Far East) 14,15,16,17 , invaded Western Palearctic and became a pest of lime trees 18,19,20,21,22 . In a recent analysis of COI mtDNA barcodes of 377 P. issikii's specimens collected across the modern rage in the Palearctic, we revealed unusually high genetic diversity of the species in the recently invaded region (Western Palearctic) compared to the putative native region (Eastern Palearctic, in particular Eastern Asia) questioning the hypotheses about the moth's region of origin and geographic expansion 20 .…”

Section: Introductionmentioning

confidence: 99%

Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria

Kirichenko

Zakharov

Lopez-Vaamonde

2021

Preprint

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Historical herbaria are valuable sources of data in invasion biology. Here we study the invasion history of the lime leafminer, Phyllonorycter issikii, by surveying over 15 thousand herbarium specimens of limes (Tilia spp.) collected in the Palearctic during last 253 years (1764-2016). The majority of herbarium specimens with the pest mines (89%) originated from East Asia (1859-2015), whereas remaining 11% of specimens with the mines came from Europe, European Russia and Western Siberia (1987-2015). These results support the hypothesis of a recent Ph. issikii invasion from Eastern to Western Palearctic. Single molecule real-time sequencing of the COI barcode region of 93 archival larvae and pupae (7-162 years old) dissected from the mines on historical herbaria allowed to distinguish between Ph. issikii and Ph. messaniella, a polyphagous species rarely feeding on Tilia, which mines were found in herbarium from Europe dated by 1915-1942. We discovered 25 haplotypes of Ph. issikii, of which 16 haplotypes were present solely in East Asia, and revealed wide distribution of the species in China. Six haplotypes shared between Eastern and Western Palearctic suggest the contribution of Ph. issikii populations from the Russian Far East, China and Japan to the westward invasion.

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Evaluating DNA Barcoding for Species Identification and Discovery in European Gracillariid Moths

Cited by 57 publications

References 75 publications

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

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

Identity of some recently described Lepidoptera from France—re-assessed with DNA barcodes and morphology

Tracing the invasion of a leaf-mining moth in the Palearctic through DNA barcoding of historical herbaria

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