DOI: 10.5061/dryad.0p2ngf1xn
title: Data from: Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species

description: Sympatric tree species are subject to similar climatic drivers, posing a
 question as to whether they display comparable adaptive responses.
 However, no study has explicitly examined local adaptation of co-occurring
 parasitic and autotrophic plant species to the abiotic environment. Here
 we test the hypotheses that a generalist parasitic tree would display a
 weaker signal of selection and genomic variation would associate with
 fewer climatic variables (particularly precipitation) but have similar
 spatial patterns to a sympatric autotrophic tree species. To test these
 hypotheses, we collected samples from 17 sites across the range of two
 tree species, the hemi-parasite Nuytsia floribunda (n=264) and sympatric
 autotroph Melaleuca rhaphiophylla (n=272). We obtained 5,531 high-quality
 genome-wide single nucleotide polymorphisms (SNPs) for M. rhaphiophylla
 and 6,727 SNPs for N. floribunda using DArTseq™ genome scan technology.
 Population differentiation and environmental association approaches were
 used to identify signals of selection. Generalized dissimilarly modelling
 was used to detect climatic and spatial patterns of local adaptation
 across climatic gradients. Overall, 322 SNPs were identified as putatively
 adaptive for the autotroph, while only 57 SNPs were identified for the
 parasitic species. We found genomic variation to associate with different
 sets of bioclimatic variables for each species, with precipitation
 relatively less important for the parasite. Spatial patterns of predicted
 adaptive variability were different and indicate that co-occurring species
 with disparate life history traits may not respond equally to selective
 pressures (i.e. temperature and precipitation). Together, these findings
 provide insight into local adaptation of sympatric parasitic and
 autotrophic tree species to abiotic environments.
description: Genomic data was generated from individual genotyping of 272
 <em>Melaleuca rhaphiophylla</em> individuals and 264
 <em>Nuytsia floribunda</em> individuals sampled at 17
 populations across each species range. Climatic data was downloaded with 1
 km cell resolution from the Worldclim 2.0 database (Fick &
 Hijmans, 2017; Hijmans et al. 2005).
description: <b>SNP Data file for Melaleuca
 rhaphiophylla</b> This data has 5,531 SNPs row
 wise and 272 individuals' column wise. 0 = zero copies of the
 reference allele, 1 = one copy of the reference allele (heterozygote), 2 =
 two copies of the reference allele, 9 = missing data. 
 SNPData_Melaleuca_rhaphiophylla.txt
 <b>SNP Data file for Nuytsia floribunda</b>
 This data has 6,727 SNPs row wise and 264 individuals'
 column wise. 0 = zero copies of the reference allele, 1 = one copy of the
 reference allele (heterozygote), 2 = two copies of the reference allele, 9
 = missing data.
 SNPData_Nuytsia_floribunda.txt <b>LFMM
 file for Melaleuca rhaphiophylla</b> This data
 has 272 individuals row wise and 5,531 SNPs column wise. 0 = zero copies
 of the reference allele, 1 = one copy of the reference allele
 (heterozygote), 2 = two copies of the reference allele.
 LFMM_Melaleuca_rhaphiophylla.lfmm
 <b>LFMM file for Nuytsia floribunda</b>
 This data has 264 individuals row wise and 6,727 SNPs column
 wise. 0 = zero copies of the reference allele, 1 = one copy of the
 reference allele (heterozygote), 2 = two copies of the reference
 allele. LFMM_ Nuytsia_floribunda.lfmm
 <b>RDA file for Melaleuca rhaphiophylla</b>
 This data has 272 individuals row wise and 5,531 SNPs column
 wise. 0 = zero copies of the snp allele, 1 = one copy of the snp allele
 (heterozygote), 2 = two copies of the snp allele. RDA _
 Melaleuca_rhaphiophylla.txt <b>RDA file for
 Nuytsia floribunda</b> This data has 264
 individuals column wise and 6,727 SNPs row wise. 0 = zero copies of the
 snp allele, 1 = one copy of the snp allele (heterozygote), 2 = two copies
 of the snp allele. RDA _
 Nuytsia_floribunda.txt <b>File with climate data
 for EAA analysis of Melaleuca rhaphiophylla</b>
 Climate data for each individual for use in LFMM and RDA
 analysis. Pop = population, ind = individual ID, bio3 = isothermality,
 bio4 = temperature seasonality, bio8 = mean temperature of the wettest
 quarter, bio10 = mean temperature of the warmest quarter, bio15 =
 precipitation seasonality, bio16 = precipitation of the wettest quarter,
 bio17 = precipitation of the driest quarter.
 ClimateDataEAA_Melaleuca_rhaphiophylla.txt
 <b>File with climate data for EAA analysis of Nuytsia
 floribunda</b> Climate data for each individual
 for use in LFMM and RDA analysis. Pop = population, ind = individual ID,
 bio3 = isothermality, bio4 = temperature seasonality, bio8 = mean
 temperature of the wettest quarter, bio10 = mean temperature of the
 warmest quarter, bio15 = precipitation seasonality, bio16 = precipitation
 of the wettest quarter, bio17 = precipitation of the driest
 quarter.
 ClimateDataEAA_Nuytsia_floribunda.txt
 <b>FST Matrix for Melaleuca rhaphiophylla reference
 SNPs</b> Pairwise FST matrix for 17 populations
 of reference SNPs for GDM analysis.
 ReferenceFST_Melaleuca_rhaphiophylla.txt
 <b>FST Matrix for Melaleuca rhaphiophylla candidate
 SNPs</b> Pairwise FST matrix for 17 populations
 of candidate SNPs for GDM analysis.
 CandidateFST_Melaleuca_rhaphiophylla.txt
 <b>FST Matrix for Nuytsia floribunda reference
 SNPs</b> Pairwise FST matrix for 17 populations
 of reference SNPs for GDM analysis.
 ReferenceFST_Nuytsia_floribunda.txt
 <b>FST Matrix for Nuytsia floribunda candidate
 SNPs</b> Pairwise FST matrix for 17 populations
 of candidate SNPs for GDM analysis.
 CandidateFST_Nuytsia_floribunda.txt
 <b>Climate and geographical information for GDM analysis of
 Melaleuca rhaphiophylla</b> Climate and
 geographical information for GDM analysis of Melaleuca rhaphiophylla. Bio3
 = isothermality, bio4 = temperature seasonality, bio8 = mean temperature
 of the wettest quarter, bio10 = mean temperature of the warmest quarter,
 bio15 = precipitation seasonality, bio16 = precipitation of the wettest
 quarter, bio17 = precipitation of the driest quarter.
 ClimateDataGDM_Melaleuca_rhaphiophylla.txt
 <b>Climate and geographical information for GDM analysis of
 Nuytsia floribunda</b> Climate and geographical
 information for GDM analysis of Nuytsia floribunda. Bio3 = isothermality,
 bio4 = temperature seasonality, bio8 = mean temperature of the wettest
 quarter, bio10 = mean temperature of the warmest quarter, bio15 =
 precipitation seasonality, bio16 = precipitation of the wettest quarter,
 bio17 = precipitation of the driest quarter.
 ClimateDataGDM_Nuysia_floribunda.txt
 <b>R code for GDM analysis and mapping spatial patterns of
 local adaptation</b> R code for GDM analysis and
 mapping spatial patterns of local adaptation.
 Walters_GDM_code.R