DOI: 10.5061/dryad.g08c7
title: Data from: Convergence and divergence during the adaptation to similar environments by an Australian groundsel

description: Adaptation to replicate environments is often achieved through similar
 phenotypic solutions. Whether selection also produces convergent genomic
 changes in these situations remains largely unknown. The variable
 groundsel, Senecio lautus, is an excellent system to investigate the
 genetic underpinnings of convergent evolution, since morphologically
 similar forms of these plants have adapted to the same environments along
 the coast of Australia. We compared range-wide patterns of genomic
 divergence in natural populations of this plant and searched for regions
 putatively affected by natural selection. Our results indicate that
 environmental adaptation followed complex genetic trajectories, affecting
 multiple loci, implying both the parallel recruitment of the same alleles
 and the divergence of completely different genomic regions across
 geography. An analysis of the biological functions of candidate genes
 suggests that adaptation to coastal environments may have occurred through
 the recruitment of different genes participating in similar processes. The
 relatively low genetic convergence that characterizes the parallel
 evolution of S. lautus forms suggests that evolution is more constrained
 at higher levels of biological organization.
description: Contigs_RADsGenomic 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.Access_ArrayThis 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).FET_RADsThis 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.Frequency_RADsWe 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.Fst_RADsIn 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.Pi_RADsIn 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.Results_PopoolationTopdIn 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.