A <scp>DNA</scp> barcode library for Germany′s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera)

Morinière, Jérôme; Hendrich, Lars; Balke, Michael; Beermann, Arne J.; König, Tobias; Hess, Monika; Koch, Stefan; Müller, Reinhard; Leese, Florian; Hebert, Paul D. N.; Hausmann, Axel; Schubart, Christoph D.; Haszprunar, Gerhard

doi:10.1111/1755-0998.12683

Cited by 82 publications

(98 citation statements)

References 106 publications

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“…Taxonomic practices can contribute more to the mechanistic understanding of morphological crypsis as well as to the integration of cryptic species into biodiversity research. Aside from technical issues such as development of barcoding libraries (Morinière et al., ), we envision three important issues.…”

Section: Taxonomic Practices In Delimiting Cryptic Speciesmentioning

confidence: 99%

Cryptic species as a window into the paradigm shift of the species concept

2018

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The species concept is the cornerstone of biodiversity science, and any paradigm shift in the delimitation of species affects many research fields. Many biologists now are embracing a new "species" paradigm as separately evolving populations using different delimitation criteria. Individual criteria can emerge during different periods of speciation; some may never evolve. As such, a paradigm shift in the species concept relates to this inherent heterogeneity in the speciation process and species category-which is fundamentally overlooked in biodiversity research. Cryptic species fall within this paradigm shift: they are continuously being reported from diverse animal phyla but are poorly considered in current tests of ecological and evolutionary theory. The aim of this review is to integrate cryptic species in biodiversity science. In the first section, we address that the absence of morphological diversification is an evolutionary phenomenon, a "process" counterpart to the long-studied mechanisms of morphological diversification. In the next section regarding taxonomy, we show that molecular delimitation of cryptic species is heavily biased towards distance-based methods. We also stress the importance of formally naming of cryptic species for better integration into research fields that use species as units of analysis. Finally, we show that incorporating cryptic species leads to novel insights regarding biodiversity patterns and processes, including large-scale biodiversity assessments, geographic variation in species distribution and species coexistence. It is time for incorporating multicriteria species approaches aiming to understand speciation across space and taxa, thus allowing integration into biodiversity conservation while accommodating for species uncertainty.

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Section: Taxonomic Practices In Delimiting Cryptic Speciesmentioning

confidence: 99%

Cryptic species as a window into the paradigm shift of the species concept

2018

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“…Various aquatic macroinvertebrates, such as mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera) are commonly used as bio-indicator organisms for water quality and ecosystem assessments 4–6 . This is down to their rapid reaction to anthropogenic change such as levels of pollution, climate change, fracking, mining, and the construction of hydroelectric stations for example 5,7–9 .…”

Section: Introductionmentioning

confidence: 99%

“…Traditional monitoring of macroinvertebrates via kick-sampling and/or capture-recapture methods, is, however, costly (i.e. time consuming), labour intensive and, above all, known to be limited in effective detection of populations below a certain threshold 5,10 . Further, such methods are ecologically invasive i.e.…”

Section: Introductionmentioning

confidence: 99%

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

Mauvisseau

Davy‐Bowker

Bulling

et al. 2019

Preprint

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21Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, the 22 species was recently rediscovered in one location of the river Dee in Wales after 22 years of absence. As 23 many species belonging to the Perlodidae, this species can be a bio-indicator, utilised for assessing 24 water quality and health status of a given freshwater system. However, conventional monitoring of 25 invertebrates via kick-sampling for example, is an invasive and expensive (time consuming). Further, 26 such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-27 sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we 28 sampled eDNA from twelve locations on the river Dee. I. nubecula was detected using kick-sampling in 29 five of these locations, three locations using both eDNA detection and kick-sampling and one location 30 using eDNA detection alone -resulting in a total of six known and distinct populations of this critically 31 endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and 32 results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In 33 contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that 34 inhibition most likely explains the big discrepancy between the obtained qPCR and ddPCR results. It is 35 therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR 36 may well be the best option for the detection of aquatic organisms which are either rare or likely to shed 37 low levels of eDNA into their environment. 38

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“…There are several Ephemeroptera barcode libraries currently available with a large number of taxa in diverse geographic regions such as North America (Alexander et al 2009;Webb et al 2012), Germany (Morinière et al 2017), Mediterranean region (Cardoni et al 2015), and Canada (Zhou et al 2009(Zhou et al , 2010. Barcode sequences of East Asian Ephemeroptera, which were mainly collected from Japan and Taiwan, were recently published (Wakimura et al 2016).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive DNA barcodes for species identification and discovery of cryptic diversity in mayfly larvae from South Korea: Implications for freshwater ecosystem biomonitoring

Suh

Hwang

Bae

et al. 2019

Entomological Research

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DNA barcoding of aquatic macroinvertebrates holds much promise as a tool for taxonomic research and for providing baseline reference for phylogenetic analysis and aquatic ecosystem biomonitoring. We obtained 112 novel sequences of the barcode region of the mitochondrial DNA cytochrome c oxidase subunit I gene representing 11 families, 25 genera, and 43 species of mayfly (Insecta: Ephemeroptera) from South Korea. No species shared barcode sequences and all can be identified with barcodes with a possible exception of some species. Minimum levels of interspecific genetic distances ranged from 6.7 to 32.9% (mean: 23.7%), whereas average levels of intraspecific divergence was 3.7%. The latter value was inflated by the presence of very high divergences within some taxa. In fact, approximately 33.3% (15/45) of the species included two or more haplotype clusters showing greater than 5.0% sequence divergence and some values were as high as 32.9%. Many of the species with high intraspecific divergences are para‐ or polyphyletic and represent the possibility of species complexes. Our study suggests that type or topotype specimens should be sequenced to identify accurate barcoding clusters with morphological species concepts and also to determine the status of currently synonymized species.

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A DNA barcode library for Germany′s mayflies, stoneflies and caddisflies (Ephemeroptera, Plecoptera and Trichoptera)

Cited by 82 publications

References 106 publications

Cryptic species as a window into the paradigm shift of the species concept

Cryptic species as a window into the paradigm shift of the species concept

Improving detection capabilities of a critically endangered freshwater invertebrate with environmental DNA using digital droplet PCR

Comprehensive DNA barcodes for species identification and discovery of cryptic diversity in mayfly larvae from South Korea: Implications for freshwater ecosystem biomonitoring

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