*Haploginglymus*, a genus of subterranean amphipods endemic to the Iberian Peninsula (Amphipoda: Niphargidae)

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# Online Supplementary Information

*S1*. List of all taxa included in the analyses with their respective geographical origin, voucher ID and GenBank accession codes. http://www.ctoz.nl/c/ctz/supp/Supplementary_Table_S1.pdf

*S2*. Maximum likelihood phylogenetic tree based on the analysis of the *cox*1 alignment. Node numbers represent statistical bootstrap support (only values ≥ 70 are shown). Tip labels refer to the species names and their respective GenBank accession codes. http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S2.pdf

*S3*. Maximum likelihood phylogenetic tree based on the analysis of the H3 alignment. Node numbers represent statistical bootstrap support (only values ≥ 70 are shown). Tip labels refer to the species names and their respective GenBank accession codes. http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S3.pdf

*S4*. Maximum likelihood phylogenetic tree based on the analysis of the LSU alignment. Node numbers represent statistical bootstrap support (only values ≥ 70 are shown). Tip labels refer to the species names and their respective GenBank accession codes. http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S4.pdf

*S5*. Maximum likelihood phylogenetic tree based on the combined analysis of *cox*1, H3 and LSU. Node numbers represent statistical bootstrap support (only values ≥ 70 are shown). http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S5.pdf

*S6*. Bayesian phylogenetic tree based on the combined analysis of *cox*1, H3 and LSU. Node numbers represent posterior probabilities (only values ≥ 0.70 are shown). http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S6.pdf

*S7*. Maximum likelihood phylogenetic tree based on the combined analysis of *cox*1 (excluding third coding positions), H3 and LSU. Node numbers represent statistical bootstrap support (only values ≥ 70 are shown). http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S7.pdf

*S8*. Maximum likelihood phylogenetic tree based on the analysis of the reduced LSU alignment (ambiguosly aligned positions removed with Gblocks). Node numbers represent statistical bootstrap support (only values ≥ 70 are shown). http://www.ctoz.nl/c/ctz/supp/Supplementary_Figure_S8.pdf