10.5281/zenodo.4268053
https://zenodo.org/records/4268053
oai:zenodo.org:4268053
Stiller, Josefin
Josefin
Stiller
0000-0001-6009-9581
University of Copenhagen
Fonseca, Rute R. da
Rute R. da
Fonseca
Alfaro, Michael E.
Michael E.
Alfaro
Faircloth, Brant C.
Brant C.
Faircloth
Wilson, Nerida G.
Nerida G.
Wilson
Rouse, Greg W.
Greg W.
Rouse
Using UCEs to track the influence of sea-level change on leafy seadragon populations
Zenodo
2020
phylogeography
2020-11-16
eng
10.5281/zenodo.4268052
Creative Commons Attribution 4.0 International
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).