Molecular phylogeny of the subterranean genusNiphargus(Crustacea: Amphipoda) in the Middle East: a comparison with European Niphargids

Abstract

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 taxonomic research.

Niphargus dancaui sp. nov. (Amphipoda, Niphargidae) – a new species thriving in sulfidic groundwaters in southeastern Romania

“…tridentinus Stoch, 1998 (sequenced using the same protocol as in Flot et al 2010; GenBank accession numbers KT878856 and KT878857) and pre-aligned in MAFFT using the FFT-NS-i mode to identify unsuitable sequences (originating from a different 28S region than our target region). After filtering out these sequences, the remaining dataset of 422 sequences from Lefébure et al (2006Lefébure et al ( , 2007, Fišer et al (2008), Trontelj et al (2009), Flot (2010, Flot et al (2010Flot et al ( , 2014, Hartke et al (2011), Trontelj et al (2012, Hekmatara et al (2013), Fišer et al (2013), McInerney et al (2014), Altermatt et al (2014), Ntakis et al (2015) and Esmaeili-Rineh et al (2015) were screened for perfect duplicates using FaBox (Villesen 2007), resulting in a dataset a 260 unique sequences, to which two outgroup sequences from the genera Synurella Wrzesniowski, 1877 and Gammarus Fabricius, 1775 were added as in Flot et al (2014). The sequences were aligned in MAFFT version 7 (Katoh & Standley 2013) using the E-INS-i option and analyzed in FastTree 2 (Price et al 2010) using the GTR model (Lanave et al 1984;Tavaré 1986) with 1000 bootstrap replicates (Felsenstein 1985).…”

The description of a new species of Niphargus from Iran based on morphological and molecular data

“…n. is a member of the main Iranian clade (Esmaeili-Rineh et al 2015a) and shares common ancestry with N. khwarizmi, N. khayyami, N. kermanshahi and N. bisitunicus.…”

“…A consensus tree with posterior probabilities was generated and visualized using the FigTree v1.4.0 software. Data on analyzed species are available in the Electronic Supplement of Esmaeili-Rineh et al (2015a). Diagnosis.…”

“…In order to figure out the phylogenetic position of the new discovered species, we analyzed the acquired sequences (GenBank accession numbers are KY629001 and KY629002) within the data set of Esmaeili-Rineh et al (2015a) and Esmaeili-Rineh et al (2016). Three species including Synurella ambulans (F. Müller, 1846), Obesogam- marus crassus (Sars G.O., 1894), and Gammarus fossarum Koch, 1836, were used as outgroup (KF719240, KF719242 and KF71924).…”

A new genus for Cirolana troglexuma Botosaneanu & Iliffe, 1997, an anchialine cave dwelling cirolanid isopod (Crustacea, Isopoda, Cirolanidae) from the Bahamas

“…A large number of new species has been revealed for cave crustaceans, e.g. amphipods (Trontelj et al 2007, Esmaeili-Rineh et al 2015, decapods (Trontelj et al 2007), bathynellaceans (Guzik et al 2008) and isopods (Finston et al 2009). Many of those new species are regional endemics rather than geographically widely distributed lineages (e.g.…”