Integrated Taxonomy and DNA Barcoding of Alpine Midges (Diptera: Chironomidae)

Abstract

Rapid and efficient DNA-based tools are recommended for the evaluation of the insect biodiversity of high-altitude streams. In the present study, focused principally on larvae of the genus Diamesa Meigen 1835 (Diptera: Chironomidae), the congruence between morphological/molecular delimitation of species as well as performances in taxonomic assignments were evaluated. A fragment of the mitochondrial cox1 gene was obtained from 112 larvae, pupae and adults (Diamesinae, Orthocladiinae and Tanypodinae) that were collected in different mountain regions of the Alps and Apennines. On the basis of morphological characters 102 specimens were attributed to 16 species, and the remaining ten specimens were identified to the genus level. Molecular species delimitation was performed using: i) distance-based Automatic Barcode Gap Discovery (ABGD), with no a priori assumptions on species identification; and ii) coalescent tree-based approaches as the Generalized Mixed Yule Coalescent model, its Bayesian implementation and Bayesian Poisson Tree Processes. The ABGD analysis, estimating an optimal intra/interspecific nucleotide distance threshold of 0.7%-1.4%, identified 23 putative species; the tree-based approaches, identified between 25–26 entities, provided nearly identical results. All species belonging to zernyi, steinboecki, latitarsis, bertrami, dampfi and incallida groups, as well as outgroup species, are recovered as separate entities, perfectly matching the identified morphospecies. In contrast, within the cinerella group, cases of discrepancy arose: i) the two morphologically separate species D. cinerella and D. tonsa are neither monophyletic nor diagnosable exhibiting low values of between-taxa nucleotide mean divergence (0.94%); ii) few cases of larvae morphological misidentification were observed. Head capsule color is confirmed to be a valid character able to discriminate larvae of D. zernyi, D. tonsa and D. cinerella, but it is here better defined as a color gradient between the setae submenti and genal setae. DNA barcodes performances were high: average accuracy was ~89% and precision of ~99%. On the basis of the present data, we can thus conclude that molecular identification represents a promising tool that could be effectively adopted in evaluating biodiversity of high-altitude streams.

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding‐based biomonitoring

“…Previous studies have reported on barcoding results for Coleoptera (Hendrich et al, 2015;Raupach, Hannig, Moriniere, & Hendrich, 2016;Raupach, Hannig, Morinière, & Hendrich, 2018;Rulik et al, 2017), Ephemeroptera, Plecoptera and Trichoptera , Heteroptera (Havemann et al, 2018;Raupach et al, 2014), Hymenoptera (Schmid-Egger et al, 2019;Schmidt, Schmid-Egger, Morinière, Haszprunar, & Hebert, 2015;Schmidt et al, 2017), Lepidoptera Hausmann, Haszprunar, Segerer, et al, 2011), Neuroptera , Orthoptera (Hawlitschek et al, 2017), Araneae and Opiliones , and Myriapoda (Spelda, Reip, Oliveira Biener, & Melzer, 2011;Wesener et al, 2015). Concerning DNA barcoding studies performed for Diptera, no comprehensive study encompassing this entire highly diverse order has been published, but data have been used to revise smaller units thereof: for example, for Calliphoridae (Jordaens et al, 2013;Nelson, Wallman, & Dowton, 2007;Reibe, Schmitz, & Madea, 2009), Ceratopogonidae (Stur & Borkent, 2014), Chironomidae (Carew, Pettigrove, Cox, & Hoffmann, 2007;Carew, Pettigrove, & Hoffmann, 2005;Cranston et al, 2013;Ekrem, Stur, & Hebert, 2010;Ekrem, Willassen, & Stur, 2007;Montagna, Mereghetti, Lencioni, & Rossaro, 2016;Pfenninger, Nowak, Kley, Steinke, & Streit, 2007;Sinclair & Gresens, 2008;Stur & Ekrem, 2011), Culicidae (Ashfaq et al, 2014;Cywinska, Hunter, & Hebert, 2006;Kumar, Rajavel, Natarajan, & Jambulingam, 2007;Versteirt et al, 2015;, Hybotidae…”

Morphological redescription and DNA barcoding of Monodiamesa kamora Makarchenko et Yavorskaya (Diptera: Chironomidae) from the Amur River basin (Russian Far East)

“…We obtained 658 bp of COI gene. Intraspecific sequence divergence ranged from 0.0 to 0.76% with a mean divergence value of 0.5%, which is within the normal range for chironomids (Montagna et al, 2016). Within the specimens of M. kamora, four haplotypes were encountered, which are divergent by eight synonymous transitional substitutions.…”

“…6) ranged from 11.9 to 12.5% (mean 12.1%). According to Montagna et al (2016) and Ekrem et al (2010) these values are sufficient to maintain the species level. The Bayesian tree contains all available species of subfamily Prodiamesinae shown in Fig.…”

Quantification of complex modular architecture in plants

“…Following recent studies (Castro-Romero et al, 2016;Montagna et al, 2016;Song et al, 2017), outgroup species were included in the species delimitation analyses for two main reasons. First, although related species tend to be unduly lumped by the GMYC model when distantly related species are included (https://francoismichonneau.net/gmyc-tutorial/), this was clearly not the case here, as more species were recognized with the GMYC criterion than in the two other analyses (Fig.…”