Contributions to Zoology, 86 (3) – 2017José A. Jurado-Rivera; Genaro Álvarez; José A. Caro; Carlos Juan; Joan Pons; Damià Jaume: Molecular systematics of Haploginglymus, a genus of subterranean amphipods endemic to the Iberian Peninsula (Amphipoda: Niphargidae)

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Sequence statistics of the for the studied DNA datasets and their best partitioning and model selection schemes are shown in Tables 2 and 3, respectively. The topologies derived from the analyses performed both separately on each individual marker (Figs S2-S4) and on their concatenation (Figs 2; 3; v. Figs S5 & S6 for a more detailed version of these trees) were consistent in showing the same evolutionary relationship between Haploginglymus and the rest of niphargid taxa. In all cases, all members of Haploginglymus were recovered as a monophyletic lineage nested within a clade that also included Niphargus, Pontoniphargus, Carinurella and Niphargobates. In turn, this paraphyletic clade appeared as sister to the members of the family Pseudo­niphargidae. Although Xia’s test showed low levels of substitution saturation except for third coding positions of the cox1 alignment (ISS=1.01, ISSc=0.689, P two-tailed < 0.00001), the exclusion of the latter from the alignment did not affect the above-mentioned phylogenetic relationships, although nodal support was generally lower (Fig S7), suggesting third positions contributed phylogenetic signal rather than noise. Seemingly, the exclusion of ambiguous positions in the LSU alignment (58% of the alignment positions were removed using Gblocks) did not affect the relationships among the main lineages (Fig S8).


Table 2. DNA datasets sequence statistics (cod. pos. = coding position; seq = sequence; bp = base pairs; stdev. = standard deviation).


Table 3. Results of partition and model selection analyses carried out in PartitionFinder (cod. pos. = coding position).

As regard the main phylogenetic relationships among the nine Haploginglymus samples (Figs 2; 3; node A), two main lineages could be established. One of them (node B) corresponded to the three species from North Iberia, while the other clade (node C) embraced the species from the southern half of the Peninsula. The latter includes three monophyletic lineages corresponding to the Portuguese taxon (node D), the new species from Cazalla de la Sierra described herein (see Appendix section; Node E), and the three species collected at the Subbaetic System (node F), respectively. The genetic divergence among Haploginglymus lineages – measured as uncorrected pairwise cox1 p-distance – is shown in Table 4.


Table 4. Uncorrected pairwise cox1 distances (p-distance) among Haploginglymus taxa.