DOI: 10.5061/dryad.g00b7
title: Data from: Exploring the phylogeography of a hexaploid freshwater fish by RAD sequencing

description: The KwaZulu-Natal yellowfish (Labeobarbus natalensis) is an abundant
 cyprinid, endemic to KwaZulu-Natal Province, South Africa. In this study
 we developed a Single Nucleotide Polymorphism (SNP) dataset from
 double-digest Restriction-site Associated DNA (ddRAD) sequencing of
 samples across the distribution. We addressed several hidden challenges,
 primarily focussing on proper filtering of RAD data and selecting optimal
 parameters for data processing in polyploid lineages. We used the
 resulting high-quality SNP dataset to investigate the population genetic
 structure of L. natalensis. A small number of mitochondrial markers
 present in these data had disproportionate influence on the recovered
 genetic structure. The presence of singleton SNPs also confounded genetic
 structure. We found a well-supported division into northern and southern
 lineages, with further subdivision into five populations, one of which
 reflects north-south admixture. Approximate Bayesian Computation scenario
 testing supported a scenario where an ancestral population diverged into
 northern and southern lineages, which then diverged to yield the current
 five populations. All river systems showed similar levels of genetic
 diversity, which appears unrelated to drainage system size. Nucleotide
 diversity was highest in the smallest river system, the Mbokodweni, which,
 together with adjacent small coastal systems, should be considered as a
 key catchment for conservation.
description: raw_RAD_data_unreplicated_samplesThis archive contains the raw RAD sequence data (after initial filtering by the sequencing company) for the 21 un-replicated samples of Labeobarbus natalensis used in this study given as paired-end FastQ read files. Sequence data was generated by an Illumina HiSeq 2000. Read 1 files (_1) are associated with the enzyme NlaIII, whereas Read 2 files (_2) are the paired reads associated with MluCI. FastQ files are in the standard format, with all barcodes and adapters trimmed (apart from any pollution due to overlap - refer to paper). Sample names match the names in the publication Supporting Information Table S1. For more information consult the ReadMe and publication.raw_RAD_data_replicated_samplesThis archive contains the raw RAD sequencing data files in paired-end FastQ format for the two replicated Labeobarbus natalensis samples used in the study, BLU004 (BLA004) and KNU017 (KNB017). Sequence data was generated by an Illumina HiSeq 2000. This data has not undergone initial filtering by the sequencing company. FastQ files are in the standard format, with all barcodes and adapters trimmed (apart from any pollution due to overlap). The two samples are presented differently - for more information please refer to the ReadMe and the publication.final_dataset_and_input_filesThis archive contains several output files from Stacks for the final dataset of 723 SNPs across 23 samples of Labeobarbus natalensis. We also include input files for each of the downstream analysis programs used in this study for the final dataset. The formats given include .arp, .genepop, .gtx, .structure, .vcf and .geste. For a more detailed breakdown of each file, please refer to the ReadMe.regular_expressions_removing_adapter_pollutionThis file contains information on the regular expressions we used to remove adapter pollution from our sequence data.