Using UCEs to track the influence of sea-level change on leafy seadragon populations

<p>Data and code used in bioinformatic processing, bathymetry calculations, population genetic analyses and their output files. Ultraconserved Elements (UCEs) were sequenced in 68 individuals of leafy seadragons (<em>Phycodurus eques</em>, Syngnathidae) sampled across their range along the southern Australian coast.</p> <p>The repository contains</p> <p>A) Scripts to process the sequence data and the resulting</p> <ul> <li>BAM read mapping files</li> <li>VCF files with SNPs before and after filtering</li> </ul> <p>&nbsp;</p> <p>B) Scripts, input files, and output files for the analyses to</p> <ul> <li>reconstruct shallow water areas at different sea levels</li> <li>estimate population structure (PCA, DAPC, Structure, SVDquartets), and spatial genetic patterns (IBD plots, EEMS)</li> <li>calculate genetic diversity (individual-level heterozygosity, population-level heterozygosity, Tajima&#39;s D)</li> <li>perform phylogeographic modeling (DIYABC).</li> </ul>