Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower

Roda F, Walter GM, Nipper R, Ortiz-Barrientos D

Date Published: April 19, 2017

DOI: http://dx.doi.org/10.5061/dryad.83f17

 

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Title Genotype calls and genetic divergence from bulk segregant analysis of survivorship.
Downloaded 18 times
Description We show results of the analysis of Bulk Segregant Analysis (BSA) of survivorship in reciprocal transplants between sand dune and rocky headland environments at Lennox Head (NSW, Australia) as performed with the Popoolation2 software. RADseq genotypes were mapped the a genome draft. For each SNP (defined by the position along the genomic contig where it was mapped) and genomic comparison between two pools of survivors from contrasting environments we show the identity and read counts for the major allele (maa) in the two populations (i.e. pop1 is the pool of sand dune survivors and pop2 is the pool of headland survivors). We also show the value of Fst, as calculated by Popoolation2, as well as the p-value of a fisher exact test of allelic differentiation (FET). Finally, in the last column we show if the SNPs had outlier Fst values (i.e. upper 5% tail of the distribution) and presented significantly different allelic frequencies in the FET (Bonferroni corrected p-value lower than 5%). Survivors from each environment where included in three different pools which were sequenced individually. Therefore we had three different comparisons between pools of survivors (i.e. F8-A-S-Dune_vs_F8-A-S-Headland, F8-B-S-Dune_vs_F8-B-S-Headland, and F8-C-S-Dune_vs_F8-C-S-Headland).
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Download Fst_BSA.txt (10.61 Mb)
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Title Genotype calls and genetic divergence between parapatric populations.
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Description We show results of the analysis of differentiation between parapatric pairs of parapatric populations as performed with the Popoolation2 software. RADseq genotypes were mapped the a genome draft. For each SNP (defined by the position along the genomic contig where it was mapped) and genomic comparison between two parapatric populations we show the identity and read counts for the major allele (maa) in the two populations (ie.. pop1 is the dune population and pop2 is the headland population). We also show the value of Fst, as calculated by Popoolation2, as well as the p-value of a fisher exact test of allelic differentiation (FET). Finally, in the last column we show if the SNPs had outlier Fst values (i.e. upper 5% tail of the distribution) and presented significantly different allelic frequencies in the FET (Bonferroni corrected p-value lower than 5%).
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Download Fst_Parapatric.txt (64.20 Mb)
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When using this data, please cite the original publication:

Roda F, Walter GM, Nipper R, Ortiz-Barrientos D (2017) Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. Molecular Ecology 26(14): 3687-3699. http://dx.doi.org/10.1111/mec.14150

Additionally, please cite the Dryad data package:

Roda F, Walter GM, Nipper R, Ortiz-Barrientos D (2017) Data from: Genomic clustering of adaptive loci during parallel evolution of an Australian wildflower. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.83f17
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