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Data from: Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species

Citation

Walters, Sheree et al. (2020), Data from: Contrasting patterns of local adaptation along climatic gradients between a sympatric parasitic and autotrophic tree species, Dryad, Dataset, https://doi.org/10.5061/dryad.0p2ngf1xn

Abstract

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.

Methods

Genomic data was generated from individual genotyping of 272 Melaleuca rhaphiophylla individuals and 264 Nuytsia floribunda 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).

Usage Notes

SNP Data file for Melaleuca rhaphiophylla

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

SNP Data file for Nuytsia floribunda

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

LFMM file for Melaleuca rhaphiophylla

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

LFMM file for Nuytsia floribunda

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

RDA file for Melaleuca rhaphiophylla

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

RDA file for Nuytsia floribunda

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

File with climate data for EAA analysis of Melaleuca rhaphiophylla

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

File with climate data for EAA analysis of Nuytsia floribunda

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

FST Matrix for Melaleuca rhaphiophylla reference SNPs

Pairwise FST matrix for 17 populations of reference SNPs for GDM analysis.

ReferenceFST_Melaleuca_rhaphiophylla.txt

FST Matrix for Melaleuca rhaphiophylla candidate SNPs

Pairwise FST matrix for 17 populations of candidate SNPs for GDM analysis.

CandidateFST_Melaleuca_rhaphiophylla.txt

FST Matrix for Nuytsia floribunda reference SNPs

Pairwise FST matrix for 17 populations of reference SNPs for GDM analysis.

ReferenceFST_Nuytsia_floribunda.txt

FST Matrix for Nuytsia floribunda candidate SNPs

Pairwise FST matrix for 17 populations of candidate SNPs for GDM analysis.

CandidateFST_Nuytsia_floribunda.txt

Climate and geographical information for GDM analysis of Melaleuca rhaphiophylla

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

Climate and geographical information for GDM analysis of Nuytsia floribunda

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

R code for GDM analysis and mapping spatial patterns of local adaptation

R code for GDM analysis and mapping spatial patterns of local adaptation.

Walters_GDM_code.R

Funding

Australian Research Council, Award: ICI150100041