New data on the distribution of six morphologically cryptic species of Niphargus stygius species complex (Amphipoda: Niphargidae)


  • Janko Šet Jovan Hadži Institute of Biology ZRC SAZU, Zagorica 20, SI-1292 Ig, Slovenia
  • Špela Borko SubBio Lab, Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia



cryptic species, Niphargus stygius, molecular taxonomy, distribution, COI, co-occurrence


Subterranean amphipods, morphologically resembling Niphargus stygius species complex, were molecularly analysed. We isolated genomic DNA and amplified the subunit I of mitochondrial cytochrome oxidase gene (COI) for 94 specimens from 37 localities. We report on six new localities for N. chagankae, one for N. cvajcki, eight for N. gottscheeanensis, two for N. kenki, one for N. malagorae and two for N. zagrebensis. New data extend previously known distribution ranges of N. gottscheeanensis and fill the missing gap between the remote N. kenki occurrences. We report on new co-occurrence data for two species pairs, i) N. chagankae and N. likanus, and ii) N. gottscheeanensis and N. podpecanus.


Adams M, Raadik TA, Burridge CP, Georges A. 2014. Global biodiversity assessment and hyper-cryptic species complexes: More than one species of elephant in the room? Systematic Biology. 63: 518-533. DOI:

Bickford D, Lohman DJ, Sohdi NS, Ng PKL, Meier R, Winker K, Ingram KK, Das I. 2007. Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution. 22: 148-155. DOI:

Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N., Madden TL, Matten WT, McGinnis SD, Merezhuk Y, et al. 2013. BLAST: a more efficient report with usability improvements. Nucleic Acids Research. 41: W29-W33. DOI:

Delić T, Trontelj P, Rendoš M, Fišer C. 2017a. The importance of naming cryptic species and the conservation of endemic subterranean amphipods. Scientific Reports. 7: 339. DOI:

Delić T, Švara V, Coleman CO, Trontelj P, Fišer C. 2017b. The giant cryptic amphipod species of the subterranean genus Niphargus (Crustacea, Amphipoda). Zoologica Scripta. 46(6): 740-752. DOI:

Eme D, Zagmajster M, Delić T, Fišer C, Flot JF, Konecny-Dupré L, Pálsson S, Stoch F, Zakšek V, Douady CJ, Malard F. 2018. Do cryptic species matter in macroecology? Sequencing European groundwater crustaceans yields smaller ranges but does not challenge biodiversity determinants. Ecography. 41(2): 424-436. DOI:

Fišer C. 2019. Niphargus A model system for evolution and ecology. In: White W, Culver D, Pipan T, editors. Encyclopedia of Caves. 3rd ed. Cambridge (GB): Academic Press. p. 746-755. DOI:

Fišer C, Zagmajster M. 2009. cryptic species from cryptic space: the case of Niphargus fongi sp. n. (Amphipoda, Niphargidae). Crustaceana. 82(5): 593-614. DOI:

Folmer O, Black M, Hoeh W, Lutz R, Vrijenhoek R. 1994. DNA primers for amplification of mitochondrial cytochrome c oxidase subunit I from diverse metazoan invertebrates. Molecular Marine Biology and Biotechnology. 3: 294-299.

García-Machado E, Hernández DA, García-Debras P, Chevalier-Monteagudo C, Metcalfe L, Bernatchez L, Casane D. 2011. Molecular phylogeny and phylogeography of the Cuban cave-fishes of the genus Lucifuga: Evidence for cryptic allopatric diversity. Molecular Phylogenetics and Evolution. 61: 470-483. DOI:

Juan C, Guzik MT, Jaume D, Cooper SJB. 2010. Evolution in caves: Darwin’s ‘wrecks of ancient life’ in the molecular era. Molecular Ecology. 19: 3865-3880. DOI:

Katouzian AR, Sari A, Macher JN, Weiss M, Saboori A, Leese F, Weigand AM. 2016. Drastic underestimation of amphipod biodiversity in the endangered Irano-Anatolian and Caucasus biodiversity hotspots. Scientific Reports. 6: 22507. DOI:

Lefébure T, Douady CJ, Gouy M, Trontelj P, Briolay J, Gibert J. 2006. Phylogeography of a subterranean amphipod reveals cryptic diversity and dynamic evolution in extreme environments. Molecular Ecology. 15: 1797-1806. DOI:

Lefébure T, Douady CJ, Malard F, Gibert J. 2007. Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis). Molecular Phylogenetics and Evolution. 42: 676-686. DOI:

Niemiller ML, Near TJ, Fitzpatrick BM. 2012. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution. 66: 846-866. DOI:

Parimuchová A, Žurovcová M, Papáč V, Kováč Ľ. 2020. Subterranean Deuteraphorura Absolon, 1901, (Hexapoda, Collembola) of the Western Carpathians – Troglomorphy at the northern distributional limit in Europe. PLoS ONE 15(1): e0226966. DOI:

Švara V, Delić T. Rađa T. Fišer C. 2015. Molecular phylogeny of Niphargus boskovici (Crustacea: Amphipoda) reveals a new species from epikarst. Zootaxa. 3994(3): 354-376. DOI:

Trontelj P, Douady CJ, Fišer C, Gibert J, Gorički Š, Lefebure T, Sket B, Zakšek V. 2009. A molecular test for cryptic diversity in ground water: how large are the ranges of macrostygobionts? Freshwater Biology. 54: 727-744. DOI:

Väinölä R, Witt JDS, Grabowski M, Bradbury JH, Jazdzewski K, Sket B. 2008. Global diversity of amphipods (Amphipoda; Crustacea) in freshwater. Hydrobiologia. 595: 241-255. DOI:

Witt JDS, Threloff DL, Hebert PDN. 2006. DNA barcoding reveals extraordinary cryptic diversity in an amphipod genus: implications for desert spring conservation. Molecular Ecology. 15: 3073-3082. DOI:






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How to Cite

Šet, J., & Borko, Špela. (2020). New data on the distribution of six morphologically cryptic species of Niphargus stygius species complex (Amphipoda: Niphargidae). Natura Sloveniae, 22(2), 69-77.

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