Dataset Open Access

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

Stiller, Josefin; Fonseca, Rute R. da; Alfaro, Michael E.; Faircloth, Brant C.; Wilson, Nerida G.; Rouse, Greg W.

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 (Phycodurus eques, Syngnathidae) sampled across their range along the southern Australian coast.

The repository contains

A) Scripts to process the sequence data and the resulting

  • BAM read mapping files
  • VCF files with SNPs before and after filtering

 

B) Scripts, input files, and output files for the analyses to

  • reconstruct shallow water areas at different sea levels
  • estimate population structure (PCA, DAPC, Structure, SVDquartets), and spatial genetic patterns (IBD plots, EEMS)
  • calculate genetic diversity (individual-level heterozygosity, population-level heterozygosity, Tajima's D)
  • perform phylogeographic modeling (DIYABC).
Files (20.7 GB)
Name Size
A_data_processing.zip
md5:2488238ef85f7e194b6245bce3eb9485
20.4 GB Download
B_analyses.zip
md5:034611983166e70ef2f45c58547b1212
319.4 MB Download
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