Pereboev D.D.1, Karabanov D.P.2, Kotov A.A.1* 2025. Metabarcoding for identification of indigenous water fleas (Crustacea: Cladocera) and earlier detecting of the non-indigenous taxa: a gap analysis // Arthropoda Selecta. Vol.34. No.2: 205–215 [in English].
1 A.N. Severtsov Institute of Ecology and Evolution of Russian Academy of Sciences, Leninsky Prospect 33, Moscow 119071 Russia.
2 Papanin Institute for Biology of Inland Waters of Russian Academy of Sciences, Borok, Yaroslavl Area 152742 Russia.
Dmitry Pereboev: dm.pereboev@gmail.com; https://orcid.org/0009-0004-8194-7585
Dmitry Karabanov: dk@ibiw.ru; https://orcid.org/0000-0001-6008
Alexey Kotov: alexey-a-kotov@yandex.ru; https://orcid.org/0000-0002-8863-6438
* Corresponding author
doi: 10.15298/arthsel.34.2.06
ABSTRACT. The next stage in the ecological monitoring of indigenous and non-indigenous species has been opened by the metabarcoding, laying the foundation of the species detection based on the DNA analysis directly in an environmental sample from a water body. Metabarcoding can be very helpful in the comprehensive assessment of biodiversity and the monitoring of harmful species, since it significantly reduces requirements to taxonomic skills and experience, allows fast performing of large-scale analyses, and is sensitive to specimens barely accessible to morphological identification such as juveniles of some species. The aim of this mini-review is to make a critical analysis of the “state of the art” of the cladoceran identification in most recent publications, where metabarcoding techniques were used, paying particular attention to its problems and practical difficulties. We are sure that after some years the eDNA methods will form a basis for the monitoring of indigenous and non-indigenous aquatic taxa, and such methods will be officially recommended by the environmental authorities of different countries. However, now we need to resolve the main problems concerning their use. If the problems of the low quality of the database entries, like misidentifications of taxa or presence of pseudogenes disguised as proper vouchers, etc. will not be resolved, many researchers will be misguided and many automated pipelines will give noisy or outright wrong results. We believe that current efforts of the cladocerologists need to be focused on the filling of the GenBank with sequences of all the loci widely used in the metabarcoding from all the known cladoceran genera and species in different regions of the world. Such efforts could be coordinated with the complete mitogenome (and full genome) sequencing initiatives which allows forming the basis for future eDNA studies, including, but not limited to the metabarcoding.
KEY WORDS: Cladocera, matabarcoding, eDNA.