The data presented here includes selection of 5 successfully amplified protein-coding markers for inferring phylogenetic relationships of the family of amphipod crustaceans Niphargidae. These markers have been efficiently amplified from niphargid samples for the first time and present the framework for robust phylogenetic assessment of the family Niphargidae. They are useful for phylogenetic purposes among other amphipod genera as well. In detail, the data consists of two parts: 1. Information regarding markers, specific oligonucleotide primer pairs and conditions for PCR reaction that enables successful amplification of specific nucleotide fragments. Two pairs of novel oligonucleotide primers were constructed which enable partial sequence amplification of two housekeeping genes: arginine kinase (ArgKin) and glyceraldehyde phosphate dehydrogenase (GAPDH), respectively. Additionally, 3 existing combinations of oligonucleotide primer pairs for protein-coding loci for glutamyl-prolyl tRNA synthetase (EPRS), opsin (OP) and phosphoenolpyruvate carboxykinase (PEPCK) were proven to be suitable to amplify specific nucleotide fragments from selected amphipod specimens; 2. Information on novel nucleotide sequences from amphipod taxa of the family Niphagidae and related outgroup taxa. Unilocus phylogenetic trees were constructed using Bayesian analysis and show relationships among selected taxa. Altogether 299 new nucleotide sequences from 92 specimens of the family Niphargidae and related outgroup amphipod taxa are deposited in GenBank (NCBI) repository and available for further use in phylogenetic analyses.
Keywords: Arginine kinase; EPRS; Glyceraldehyde phosphate dehydrogenase; Niphargidae; Nuclear protein-coding loci; Nucleotide sequences; Opsin; PCR; Phosphoenolpyruvate carboxykinase; Phylogenetic analyses.