DOI: 10.5061/dryad.k3j9kd56n
title: Data from: Association of putatively adaptive genetic variation with climatic variables differs between a parasite and its host

description: Parasitism is a pervasive phenomenon in nature with the relationship
 between species driving evolution in both the parasite and host. Due to
 their host-dependent lifestyle, parasites may adapt to the abiotic
 environment in ways that differ from their hosts or from free living
 relatives; yet rarely has this been assessed. Here, we test two competing
 hypotheses related to whether putatively adaptive genetic variation in a
 specialist mistletoe associates with the same, or different, climatic
 variables as its host species. We sampled 11 populations of the specialist
 mistletoe Amyema gibberula var. tatei (n=154) and 10 populations of its
 associated host Hakea recurva subsp. recurva (n=160).
 Reduced-representation sequencing was used to obtain genome-wide markers
 and putatively adaptive variation detected using genome scan methods.
 Climate associations were identified using generalised dissimilarity
 modelling and these were mapped geographically to visualise the spatial
 patterns of genetic composition. Our results supported the hypothesis of
 parasites and host species responding differently to climatic variables.
 Temperature was relatively more important in predicting allelic turnover
 in the specialist mistletoe while precipitation was more important for the
 host. This suggests that parasitic plants and host species may respond
 differently to selective pressures, potentially as a result of differing
 nutrient acquisition strategies. Specifically, mistletoes acquire water
 from hosts (rather than the abiotic environment), which may provide a
 buffer to precipitation as a selective pressure. This work deepens and
 complements the physiological and other ecological studies of adaptation,
 and provides a window into the evolutionary processes that underlie
 previously observed phenomena. Applying these methods to a comparative
 study in a host-parasite system has also highlighted factors that affect
 the study of selection pressure on non-model organisms, such as differing
 adaptation rates and lack of reference genomes.
description: Genomic data was generated from individual genotyping
 of 154 <em>Amyema gibberula var. tatei</em> individuals
 sampled at 11 populations and 160 <em>Hakea recurva subsp.
 recurva</em> individuals sampled at 10 populations across the
 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 Amyema gibberula var.
 tatei</b> This data has 2,055 SNPs row wise and
 154 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_Amyema_gibberula_var_tatei.txt
   <b>SNP Data file for Hakea recurva
 subsp. recurva</b> This data has 15,422 SNPs row
 wise and 160 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_Hakea_recurva_subsp_recurva.txt
   <b>LFMM file for Amyema gibberula var.
 tatei</b> This data has 154 individuals row wise
 and 2,055 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_Amyema_gibberula_var_tatei.lfmm
   <b>LFMM file for Hakea recurva subsp.
 recurva</b> This data has 160 individuals row
 wise and 15,422 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_Hakea_recurva_subsp_recurva.lfmm
   <b>BayPass file for Amyema gibberula
 var. tatei</b> This data has allele frequency
 data for 2,055 SNPs row wise and 11 populations’ column wise. For each
 population there are two columns, one for the frequency of the reference
 allele and the other for the frequency of the snp allele.
 BayPass_Amyema_gibberula_var_tatei.baypass
   <b>BayPass file for Hakea recurva
 subsp. recurva</b> This data has allele frequency
 data for 15,422 SNPs row wise and 10 populations’ column wise. For each
 population there are two columns, one for the frequency of the reference
 allele and the other for the frequency of the snp allele.
 BayPass_Hakea_recurva_subsp_recurva.baypass
   <b>File with climate data for LFMM
 analysis of Amyema gibberula var. tatei</b>
 Climate data for each individual for use in LFMM analysis. Pop =
 population, ind = individual ID, bio3 = isothermality, bio4 = temperature
 seasonality, bio8 = mean temperature of the wettest quarter, bio9 = mean
 temperature of the driest quarter, bio12 = annual precipitation, bio15 =
 precipitation seasonality, bio18 = precipitation of the warmest
 quarter.
 ClimateDataLFMM_Amyema_gibberula_var_tatei.txt
   <b>File with climate data for LFMM
 analysis of Hakea recurva subsp. recurva</b>
 Climate data for each individual for use in LFMM analysis. Pop =
 population, ind = individual ID, bio3 = isothermality, bio4 = temperature
 seasonality, bio8 = mean temperature of the wettest quarter, bio9 = mean
 temperature of the driest quarter, bio12 = annual precipitation, bio15 =
 precipitation seasonality, bio18 = precipitation of the warmest
 quarter.
 ClimateDataLFMM_Hakea_recurva_subsp_recurva.txt
   <b>Climate and geographical
 information for BayPass and GDM analysis of Amyema gibberula var.
 tatei</b> Climate and geographical information
 for BayPass (climate data only) and GDM analysis of Amyema gibberula var.
 tatei. Bio3 = isothermality, bio4 = temperature seasonality, bio8 = mean
 temperature of the wettest quarter, bio9 = mean temperature of the driest
 quarter, bio12 = annual precipitation, bio15 = precipitation seasonality,
 bio18 = precipitation of the warmest quarter.
 ClimateDataBayPassGDM_Amyema_gibberula_var_tatei.txt
   <b>Climate and geographical
 information for BayPass and GDM analysis of Hakea recurva subsp.
 recurva</b> Climate and geographical information
 for BayPass (climate data only) and GDM analysis of Hakea recurva subsp.
 recurva. Bio3 = isothermality, bio4 = temperature seasonality, bio8 = mean
 temperature of the wettest quarter, bio9 = mean temperature of the driest
 quarter, bio12 = annual precipitation, bio15 = precipitation seasonality,
 bio18 = precipitation of the warmest quarter.
 ClimateDataBayPassGDM_Hakea_recurva_subsp_recurva.txt
   <b>FST Matrix for Amyema gibberula
 var. tatei reference SNPs</b> Pairwise FST matrix
 for 11 populations of reference SNPs for GDM analysis.
 ReferenceFST_Amyema_gibberula_var_tatei.txt
   <b>FST Matrix for Amyema gibberula
 var. tatei candidate SNPs</b> Pairwise FST matrix
 for 11 populations of candidate SNPs for GDM analysis.
 CandidateFST_Amyema_gibberula_var_tatei.txt
   <b>FST Matrix for Hakea recurva subsp.
 recurva reference SNPs</b> Pairwise FST matrix
 for 10 populations of reference SNPs for GDM analysis.
 ReferenceFST_Hakea_recurva_subsp_recurva.txt
   <b>FST Matrix for Hakea recurva subsp.
 recurva candidate SNPs</b> Pairwise FST matrix
 for 10 populations of candidate SNPs for GDM analysis.
 CandidateFST_Hakea_recurva_subsp_recurva.txt