Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda)

Stokkan, Morten; Jurado‐Rivera, José A.; Oromı́, Pedro; Juan, Carlos; Jaume, Damià; Pons, Joan

doi:10.1016/j.ympev.2018.07.002

Cited by 31 publications

(19 citation statements)

References 62 publications

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“…By contrast, the more classical view of marine regressions-transgressions as an alternation between processes of dispersal and vicariance has received little attention in subterranean biology, most likely due to the presumed low dispersal capacity of subterranean organisms (Bregović, Fišer, & Zagmajster, 2019;Trontelj et al, 2009). Few studies to date have invoked this scenario to explain species distributions (Bauzà-Ribot, Jaume, Fornós, Juan, & Pons, 2011;Cánovas et al, 2016;Guy-Haim, Simon-Blecher, Frumkin, Naaman, & Achituv, 2018;Stokkan et al, 2018), and none of these studies explicitly modelled biogeographical patterns using iterative cycles of regression and transgression.…”

Section: Introductionmentioning

confidence: 99%

How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for dispersal–vicariance interplay mediated by marine regression–transgression cycles

Delić

Stoch

Borko

et al. 2020

Journal of Biogeography

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Aim Freshwater subterranean amphipods with low dispersal abilities are known from both sides of the impermeable barrier, the Adriatic Sea. We tested the hypothesis that historical marine regression–transgression cycles shaped the distribution patterns of subterranean amphipods through repeated cycles of dispersal and vicariance against the hypothesis that subterranean amphipods colonized both sides of the Adriatic Sea independently. Location Western Balkan Peninsula, Adriatic Sea Islands and Apennine Peninsula, Europe. Taxon Genus Niphargus, a clade of freshwater subterranean amphipods (Crustacea: Amphipoda). Methods The taxonomic structure of the studied clade was revised using unilocus species delimitation methods. The timeframe of cladogenetic events was inferred using a multi‐locus time‐calibrated phylogeny and compared to the main regression–transgression events in the Miocene and Pleistocene. The geographical origin of the studied clade, species range expansions and contractions, as well as vicariance events were assessed through modelling of historical biogeography. Results Subterranean amphipods of the genus Niphargus, found on both sides of the Adriatic Sea, form a monophylum. The reconstructions of ancestral ranges suggest that the clade emerged in the Balkan Peninsula, dispersed three times independently to the Apennine Peninsula and once back to the Balkans. Adriatic Islands were colonized multiple times, predominantly from the Balkan Peninsula. The dispersal–vicariance events correspond to historical regression–transgression cycles in Miocene and Pleistocene. Main conclusions Marine regression–transgression cycles apparently shaped the distribution patterns of subterranean amphipods while the alternative hypothesis received no support. The actual distribution of subterranean faunas apparently reflects old biogeographical events.

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Section: Introductionmentioning

confidence: 99%

How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for dispersal–vicariance interplay mediated by marine regression–transgression cycles

Delić

Stoch

Borko

et al. 2020

Journal of Biogeography

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“…A subset of the COI sequences (comprising all new Microniphargus sequences, all high-quality, complete Pseudoniphargus COI sequences inferred from complete mitochondrial genome sequences from Bauzà-Ribot et al 2012and Stokkan et al (2016Stokkan et al ( , 2018 plus two sequences of Niphargus and sequences of the Crangonyctidae Crangonyx subterraneus and Synurella ambulans (as outgroups) was used to build a ML tree using IQ-TREE 2 with the same modalities illustrated for 28S; the best-fit substitution model, selected using ModelFinder (according to the Bayesian Information Criterion was TIM+F+I+G4 (codes follow the IQTREE manual).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

The genusMicroniphargus(Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer to Pseudoniphargidae

Weber

Stoch

Knight

et al. 2020

Preprint

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Microniphargus leruthi Schellenberg, 1934 (Amphipoda: Niphargidae) was first described based on samples collected in Belgium and placed in a monotypic genus within the family Niphargidae. However, some details of its morphology as well as recent phylogenetic studies suggest that Microniphargus may be more closely related to Pseudoniphargus (Amphipoda: Pseudoniphargidae) than to Niphargus. Moreover, M. leruthi ranges over 1,469km from Ireland to Germany, which is striking since only a few niphargids have confirmed ranges in excess of 200km. To find out the phylogenetic position of M. leruthi and check whether it may be a complex of cryptic species, we collected material from Ireland, England and Belgium then sequenced fragments of the mitochondrial cytochrome c oxidase subunit 1 gene as well as of the nuclear 28S ribosomal gene. Phylogenetic analyses of both markers confirm that Microniphargus is closer to Pseudoniphargus than to Niphargus, leading us to reallocate Microniphargus to Pseudoniphargidae. We also identify three congruent mito-nuclear lineages present respectively in Ireland, in both Belgium and England, and in England only (with the latter two found in sympatry at one location), suggesting that M. leruthi is a complex of at least three species with a putative centre of origin in England.

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“…The discordance between the bPTP and the morphological methods might be because the bPTP tends to overestimate the number of species when using multiple sequences per population (Zhang et al, 2013). Similarly, the single-threshold GMYC method also yielded a high number of MOTUs, which is not surprising since GMYC usually over-splits species, mainly due to low genetic divergence between lineages and overlap of inter-and intraspecific divergences, or due to lack of reciprocal monophyly between sister clades (Pentinsaari et al, 2016;Stokkan et al, 2018;Talavera, Dincă, & Vila, 2013). In addition, sampling bias, differences in population size and speciation rates might also be the reason for the overestimate with GMYC (Esselstyn, Evans, Sedlock, Khan, & Heaney, 2012;Pentinsaari et al, 2016;Talavera et al, 2013).…”

Section: Species Delimitationmentioning

confidence: 99%

“…Mitochondrial genomes are considered powerful markers for resolving different levels of phylogenetics that include deep divergent lineages (Condamine, Nabholz, Clamens, Dupuis, & Sperling, 2018;Tang et al, 2018) or recently radiated groups (Jacobsen et al, 2012;Stokkan et al, 2018), due to their maternal inheritance, relatively high evolutionary rate and rare recombination (Barr, Neiman, & Taylor, 2005;Boore, 1999;Cameron, 2014;Curole & Kocher, 1999). In addition to the information on nucleotide sequences, the significance of mitochondrial gene rearrangement to support relationships of taxa that are inferred from the phylogenetic context have been proposed since the mid-1980s (Brown, 1985) and have been elucidated by some previous studies (Cameron, 2014;Galaska, Li, Kocot, Mahon, & Halanych, 2018;Rokas & Holland, 2000).…”

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confidence: 99%

Integrative taxonomy uncovers hidden species diversity in the rheophilic genus Potamometra (Hemiptera: Gerridae)

Zheng

Zhu

et al. 2019

Zoologica Scripta

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The genus Potamometra Bianchi, 1896 represents big rheophilic semi‐aquatic bugs that typically inhabit middle‐altitude mountainous streams. Here, we integrated molecular and morphological data for delimiting species boundaries and understanding the evolutionary history of the genus Potamometra. Twenty‐seven complete mitochondrial genomes of Potamometra were sequenced, with samples representing most of the known geographically distributed locations around the Sichuan Basin. The results of different species delimitation methods (ABGD, bPTP, GMYC and BPP) based on the monolocus or multilocus data strongly supported the existence of two cryptic new species (Potamometra anderseni Zheng, Ye & Bu, sp. nov. and Potamometra zhengi Zheng, Ye & Bu, sp. nov.) although more entities were found in the tree‐based delimitation methods. The two new species were successfully validated using morphological characters within a detailed taxonomic framework. Phylogenetic analyses supported the reciprocal monophyly of the seven highly node‐supported clades, which were matched with the five known species and two new taxa. A novel gene arrangement pattern that two trnF (trnF1 and trnF2) genes separated by an intergenic spacer (IGS) were found in all the species except the sister group of Potamometra berezowskii Bianchi, 1896 and Potamometra linnavuorii Chen, Nieser & Bu, 2016. This gene rearrangement event could be explained by the tandem duplication and random loss (TDRL) model. Our study emphasized that the combination of molecular sequence data, morphological characters and mitochondrial structural information could improve the accuracy of species delimitation.

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Species delimitation and mitogenome phylogenetics in the subterranean genus Pseudoniphargus (Crustacea: Amphipoda)

Cited by 31 publications

References 62 publications

How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for dispersal–vicariance interplay mediated by marine regression–transgression cycles

How did subterranean amphipods cross the Adriatic Sea? Phylogenetic evidence for dispersal–vicariance interplay mediated by marine regression–transgression cycles

The genusMicroniphargus(Crustacea, Amphipoda): evidence for three lineages distributed across northwestern Europe and transfer to Pseudoniphargidae

Integrative taxonomy uncovers hidden species diversity in the rheophilic genus Potamometra (Hemiptera: Gerridae)

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