Data from: Convergence and divergence during the adaptation to similar environments by an Australian groundsel

 

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Title Contigs_RADs
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Description Genomic divergence according to RADs genotyping. In this file we present the results of genomic analyses as evaluated by RADs genotyping. For each genomic contig we provide annotation data, including the best BLAST hit as well as the results of a gene set enrichment analysis (enriched biological process in the Gene Ontology, GO). We also present genetic differentiation data obtained with RADtools and Popoolation and summarize results of GxE associations conducted with the Bayenv software. Finally we show the nodal distances (calculated with Topd) between contig-specific trees and two other trees, one showing the parallel evolution of the ecotypes (PE) and one showing a single origin of them (SO). Note that some contigs were not sampled (NS) in all analyses.
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Title Access_Array
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Description This file contains results from the 454-sequencing of 45 genomic regions amplified with the Access-Array system. We summarise analyses of differentiation and phylogenetics (see methods). Gene-specific phylogenetic trees are provided (on nexus format).
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Title FET_RADs
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Description This file contains the results of Fisher exact tests (FET) of allelic differentiation conducted in all pairwise comparisons with the RADtools software. We present the negative logarithm ( -Log10) of the p-value in a FET. SNPs with Bonferroni-corrected p values lower than 5% were considered outliers for that comparison. We provide information on the identity of the SNP, the RAD-tag where it is located and the genomic contig where this tag was mapped.
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Title Frequency_RADs
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Description We present the allelic frequencies of all SNPs and natural populations. We provide information on the identity of the SNP, the RAD-tag where it is located and the genomic contig where this tag was mapped.
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Title Fst_RADs
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Description In this file we present the level of genomic differentiation (Fst) as evaluated with the RADtools software for all SNPs and pairwise genomic comparisons. We provide information on the identity of the SNP, the RAD-tag where it is located and the genomic contig where this tag was mapped.
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Title Pi_RADs
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Description In this file we present the genetic diversity (pi) as evaluated with the RADtools software for all SNPs and Populations. We provide information on the identity of the SNP, the RAD-tag where it is located and the genomic contig where this tag was mapped.
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Title Results_Popoolation
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Title Topd
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Description In this file we present results from analyses of phylogenetic topologies performed with the Topd software. We analysed gene specific phylogenies derived from RADs data. Each phylogeny was compared against two other trees, one showing the parallel evolution of the ecotypes (PE) and one showing a single origin of them (SO). We present the nodal distances to each of these trees as well as the results of a random analyses carried to determine if the phylogenies are more similar than expected by chance.
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When using this data, please cite the original publication:

Roda F, Liu H, Wilkinson MJ, Walter GM, James ME, Bernal DM, Melo MC, Lowe AJ, Rieseberg LH, Prentis P, Ortiz-Barrientos D (2013) Convergence and divergence during the adaptation to similar environments by an Australian groundsel. Evolution 67(9): 2515-2529. http://dx.doi.org/10.1111/evo.12136

Additionally, please cite the Dryad data package:

Roda F, Liu H, Wilkinson MJ, Walter GM, James ME, Bernal DM, Melo MC, Lowe AJ, Rieseberg LH, Prentis P, Ortiz-Barrientos D (2013) Data from: Convergence and divergence during the adaptation to similar environments by an Australian groundsel. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.g08c7
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