Polyphyly of theNiphargus stygiusspecies group (Crustacea, Amphipoda, Niphargidae) in the Southern Limestone Alps

Abstract

The Niphargus stygius species complex is a groundwater group of large-sized, sexually dimorphic species inhabiting mainly caves and, less frequently, wells and springs. According to the taxonomists of the last century, this species complex was supposed to be present in the whole Southern Limestone Alps of Italy as well as in peninsular Italy and Slovenia. Considering the large presumed distribution area, we tested the contrasting hypotheses of monophyly versus paraphyly of this subterranean species complex, taking in account the presence of putative cryptic species. For this reason, we sampled the type localities of all the described species in the complex present in the Italian Southern Limestone Alps and neighbouring areas, and used nuclear (28S, ITS region) and mtDNA (COI) sequences to assess their phylogenetic relationships and species richness. Phylogenetic analysis confirmed that the Niphargus stygius complex in the Southern Limestone Alps is not monophyletic but comprises an eastern clade (the N. kenki clade, present in NW Italy, northern Slovenia, and southern Austria) and two western clades (the N. brixianus and N. montellianus clades), _These two clades are not closely related to the eastern one but rather form a monophyletic group together with a widely distributed Apennine clade (N. speziae clade). None of these clades is closely related to typical N. stygius. Three different molecular species delimitation methods applied to COI and ITS recognized different number of putative species, richer for the COI marker, suggesting that each clade is a species complex in itself. Bayesian time-calibrated phylogeny revealed that most clades began to split up during Miocene and Pliocene, ruling out the effect of Pleistocene glaciations in explaining their evolutionary history and justifying the presence of several putative cryptic species.

Pronounced changes of subterranean biodiversity patterns along a Late Pleistocene glaciation gradient

“…This might be a residue of sampling effort. Nevertheless, previous studies found multiple stygobiont species, including groundwater amphipods of the genus Niphargus , to be distributed at LGM glacier margins along the Alps (Foulquier et al 2008, Mammola et al 2019b, Weber et al 2021, Stoch et al 2022). Such findings support the hypothesis that some species distribution ranges might have been limited to unglaciated areas during Pleistocene glacier expansions.…”

“…We investigated community composition changes of subterranean amphipod species along a Late Pleistocene glaciation gradient and revealed how contemporary biodiversity patterns are shaped by the presence/absence of ice during the LGM. In contrast to above‐ground species (Parisod 2008, Jardim de Queiroz et al 2022), contemporary subterranean amphipod communities are not only shaped by refugial persistence in unglaciated regions and subsequent recolonizations (Foulquier et al 2008, Stoch et al 2022), but also have strong patterns of persistence in groundwater habitats covered by ice over extensive periods. These regions are characterized by distinct yet species‐poor communities that have a lower spatial turnover than communities in unglaciated areas.…”

“…Most species are ancient, and their origin is linked to presumably one of the largest surviving pre‐Pleistocene adaptive radiations in Europe (McInerney et al 2014, Borko et al 2021, Jardim de Queiroz et al 2022). For individual species, it is hypothesized that some survived glaciation only in larger ice‐free regions outside of the LGM glacier margins (Foulquier et al 2008, Weber et al 2021, Stoch et al 2022), whereas others might have persisted in smaller isolated, ice‐free refugia within glaciated areas (Lefébure et al 2007, Stoch et al 2020), or even under the ice sheets (Fišer et al 2017, Dumnicka et al 2020).…”

Evolutionary origin of morphologically cryptic species imprints co-occurrence and sympatry patterns

“…Alternatively, it could indicate ecological gradients, possibly enforced by Pleistocene glaciations, prompted speciation through so called “speciation pumps”(Hu et al, 2021), and species rich regions emerge at the junction of species from different elevations. Intensified speciation at mountain slopes is well-known for freshwater amphipods in general (Copilaş-Ciocianu & Petrusek, 2015; Liu et al, 2023; Mamos, Wattier, Majda, Sket, & Grabowski, 2014) and Niphargus in particular (Delić et al, 2021; Lefébure et al, 2007; Stoch, Salussolia, & Flot, 2022). Interestingly, the map showing the biodiversity pattern of MOTUs is similar to the map showing biodiversity pattern of clades (Fig.…”

Integrative taxonomy of the groundwater amphipod Niphargus bihorensis Schellenberg, 1940 reveals a species-rich clade

“…The total length of the concatenated dataset was 2,070 bp. Considering the presence of heterozygous bases in the third codon position of H3 and the saturation (for transversions as well as for transitions) of the third codon positions of coi demonstrated for Niphargidae by Stoch et al (2023), only the first and second H3 and coi codon positions were retained for phylogenetic analyses. The best partitioning scheme and optimal substitution models for the codon positions were searched using PartitionFinder 2.1.1 (Lanfear et al, 2017) and are listed in supplementary table S2.…”