Past shifts in connectivity in riverine environments (for example, sea-level changes) and the properties of current drainages can act as drivers of genetic structure and demographic processes in riverine population of fishes. However, it is unclear whether the same river properties that structure variation on recent timescales will also leave similar genomic signatures that reflect paleodrainage properties. By characterizing genetic structure in a freshwater fish species (Hollandichthys multifasciatus) from a system of basins along the Atlantic coast of Brazil we test for the effects of paleodrainages caused by sea-level changes during the Pleistocene. Given that the paleodrainage properties differ along the Brazilian coast, we also evaluate whether estimated genetic diversity within paleodrainages can be explained by past riverine properties (i.e., area and number of rivers in a paleodrainage). Our results demonstrate that genetic structure between populations is not just highly concordant with ... : Whitelist_STACKSThis R script creates a whitelist to input into STACKS v. 1.35, by eliminating SNPs from the last bp positions, as well as loci with exceedingly high genetic diversity based on theta.Dataset_sumstats_r75_p10.vcfVCF file used to calculate summary statistics and outputted from STACKS v. 1.35 using the parameters -r 75 and -p 10Dataset_sumstats_t75_p10.vcf.zipDataset_Structure_25missingStructure input file allowing 25% missing data maximum.sampleDownGeno2SFS_MODPython script that downsamples the population sizes and calculates the joint folded Site Frequency Spectrum (for the minor allele frequency) of two populations based on a vcf file. Modified from Papadopoulou and Knowles 2015 (DOI: http://dx.doi.org/10.5061/dryad.23hs1) ...