Gymnogeophagus labiatus and G. lacustris - ddRADseq - Library 1 - Figueiredo et al.

This dataset contains SNP data for 44 Gymnogeophagus lacustris and 16 G. labiatus individuals.

Genomic DNA was obtained using the CTAB method adapted from Doyle, Doyle (1987). DNA quality was quantified with the QubitTM 3 fluorometer, and only samples with concentrations ≥ 30ng/μl. Two RADSeq libraries were constructed following the double digestion protocol of Peterson et al. (2012) with restriction enzymes SphI and *MluCl. Libraries were sequenced on an Illumina HiSeq 2500, targeting single-end 100 bp reads. Sequencing generated approximately 140 million total reads per library that passed initial quality control at the sequencing facility.

Raw reads were demultiplexed and processed in STACKS (Catchen et al., 2013). The final run of the POPULATIONS module was executed excluding loci with exceeding values for missing data (maximum 25% missing data per unlinked locus and 10% per individual). The --write-single-snp flag was used to take only one SNP per loci to avoid retaining loci in obvious linkage disequilibrium (LD).