Molecular phylogeny of the subterranean genus Niphargus (Crustacea: Amphipoda) in the Middle East: a comparison with European Niphargids SOMAYEH ESMAEILI-RINEH 1 , ALIREZA SARI 2 *, TEO DELIC ´ 3 , AJDA MOŠKRIC ˇ 3 and CENE FIŠER 3 1 Department of Biology, Faculty of Science, Razi University of Kermanshah, Kermanshah, Iran 2 Department of Animal Biology, School of Biology and Centre of Excellence in Phylogeny of Living Organisms, University of Tehran, Tehran, Iran 3 Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia Received 7 September 2014; revised 26 April 2015; accepted for publication 20 May 2015 The subterranean genus Niphargus is one of the most species-rich genera among freshwater amphipods in the world, distributed in the Western Palearctic. Thus far, taxonomic and phylogenetic research has focused mainly on the European half of the genus range. In this study, 25 populations of Niphargus from Iran, Lebanon and the Crimean Peninsula were investigated. Bayesian inference based on 28S, H3 and COI gene sequences suggests that populations from the area belong to four different clades. Three species from Crimea and one species from Iran are nested at basal nodes, indicating their rather ancient origin. The rest of the species are younger and belong to two separate clades. One Crimean species is a sister-species to east Romanian species. The second clade includes one species from Lebanon and all but one population from Iran. The origin of this clade corresponds to marine transgression between the Black Sea and Mediterranean approximately 12 Mya. This clade was further investigated taxonomically. Revision of qualitative morphological traits and unilocus species delimitation methods using COI suggest that this clade comprises 12–16 species, of which only three have been described so far. Multilocus coalescence delimitation methods (using fragments of COI, 28S, H3 and ITS) strongly supported 11 of these species. The remaining populations comprise at least two species complexes that require further and more detailed taxo- nomic research. © 2015 The Linnean Society of London, Zoological Journal of the Linnean Society, 2015, 175, 812–826. doi: 10.1111/zoj.12296 ADDITIONAL KEYWORDS: Iran – multilocus species delimitation – new species. INTRODUCTION With over 330 species, Niphargus is the largest genus of freshwater amphipods distributed across the Western Palearctic (Väinölä et al., 2008). All members of the genus live in subterranean waters or waters related to subterranean environments, such as springs (Fišer, 2012). The taxonomy and phylogeny of the genus has been only partially resolved. Extensive cryptic specia- tion has been well documented (Mathieu et al., 1997; Lefébure et al., 2006, 2007; Trontelj et al., 2009). Many species are distinguished on the basis of only a few, easily overlooked morphological characters and mo- lecular data are often needed to determine whether sets of populations deserve species status (Fišer & Zagmajster, 2009). Comprehensive phylogenetic analy- ses have suggested that morphology is strongly influ- enced by convergent selection and therefore the inferences of phylogenetic relationships should also include molecular markers (Fišer, Sket & Trontelj, 2008a). Unfortunately, frequently used genetic markers *Corresponding author E-mail: sari@ut.ac.ir Zoological Journal of the Linnean Society, 2015, 175, 812–826. With 4 figures © 2015 The Linnean Society of London, Zoological Journal of the Linnean Society, 2015, 175, 812–826 812 Downloaded from https://academic.oup.com/zoolinnean/article/175/4/812/2449818 by guest on 03 September 2023