Data from: Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties

Thomaz AT, Malabarba LR, Knowles LL

Date Published: July 3, 2017

DOI: https://doi.org/10.5061/dryad.7hr7f

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Title Whitelist_STACKS
Downloaded 2 times
Description This 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.
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Title Dataset_sumstats_r75_p10.vcf
Downloaded 3 times
Description VCF file used to calculate summary statistics and outputted from STACKS v. 1.35 using the parameters -r 75 and -p 10
Download Dataset_sumstats_t75_p10.vcf.zip (9.905 Mb)
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Title Dataset_Structure_25missing
Downloaded 1 time
Description Structure input file allowing 25% missing data maximum.
Download Dataset_Structure_25missing.stru (3.078 Mb)
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Title sampleDownGeno2SFS_MOD
Downloaded 2 times
Description Python 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)
Download sampleDownGeno2SFS_MOD.py (5.206 Kb)
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When using this data, please cite the original publication:

Thomaz AT, Malabarba LR, Knowles LL (2017) Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties. Heredity 119(4): 287-294. https://doi.org/10.1038/hdy.2017.46

Additionally, please cite the Dryad data package:

Thomaz AT, Malabarba LR, Knowles LL (2017) Data from: Genomic signatures of paleodrainages in a freshwater fish along the southeastern coast of Brazil: genetic structure reflects past riverine properties. Dryad Digital Repository. https://doi.org/10.5061/dryad.7hr7f
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