DOI: 10.5061/dryad.vt4b8gtxz
title: Data from: The evolutionary genomics of adaptation to stress in wild rhizobium bacteria

description: Microbiota comprise the bulk of life's diversity, yet we know little
 about how populations of microbes accumulate adaptive diversity across
 natural landscapes. Adaptation to stressful soil conditions in plants
 provides seminal examples of adaptation in response to natural selection
 via allelic substitution. For microbes symbiotic with plants however,
 horizontal gene transfer allows for adaptation via gene gain and loss,
 which could generate fundamentally different evolutionary dynamics. We use
 comparative genomics and genetics to elucidate the evolutionary mechanisms
 of adaptation to physiologically stressful serpentine soils in rhizobial
 bacteria in western North American grasslands. In vitro experiments
 demonstrate that the presence of a locus of major effect, the nre operon,
 is necessary and sufficient to confer adaptation to nickel, a heavy metal
 enriched to toxic levels in serpentine soil, and a major axis of
 environmental soil chemistry variation. We find discordance between
 inferred evolutionary histories of the core genome and nreAXY genes, which
 often reside in putative genomic islands. This suggests that the
 evolutionary history of this adaptive variant is marked by frequent
 losses, and/or gains via horizontal acquisition across divergent rhizobium
 clades. However, different nre alleles confer distinct levels of nickel
 resistance, suggesting allelic substitution could also play a role in
 rhizobium adaptation to serpentine soil. These results illustrate that the
 interplay between evolution via gene gain and loss and evolution via
 allelic substitution may underlie adaptation in wild soil microbiota. Both
 processes are important to consider for understanding adaptive diversity
 in microbes and improving stress-adapted microbial inocula for human use.
description: Strain isolation and soil analysis. Acmispon wrangelianus and A.
 brachycarpus were gathered during March 2019 from natural reserves in
 California and in May 2019 from areas in Oregon. Within reserves, both
 serpentine and non-serpentine sites were sampled for: 1) plant root
 nodules, and 2) the soil directly below the plant, if available. Details
 on strain isolation and soil analysis procedures are in SI
 Appendix. Phenotyping Ni tolerance. The minimum
 inhibitory concentration (MIC) of Ni was determined for 681
 field-collected strains of Mesorhizobium by growing the strains on
 NiCl<sub>2</sub> enriched media plates that ranged from 0 mM
 to 5 mM increasing by 1 mM for each treatment with three replicates. Ni
 tolerance was also determined by the growth in liquid media containing 0
 or 1 mM NiCl<sub>2</sub> (OD<sub>600</sub>).
 Details of these procedures are in SI Appendix.
description: # Data from: The evolutionary genomics of adaptation to stress in wild
 rhizobium bacteria --- Brief summary of dataset contents: rhizobia
 phenotypes by strain and replicate within strain as well as soil chemical
 and ecological characteristics for the soils rhizobia were collected from
 ## Description of the data and file structure This data supports the
 manuscript Kehlet-Delgado et al (in prep) The evolutionary genomics of
 adaptation to stress in wild rhizobium bacteria Abstract: Microbiota
 comprise the bulk of life's diversity, yet we know little about how
 populations of microbes accumulate adaptive diversity across natural
 landscapes. Adaptation to stressful soil conditions in plants provides
 seminal examples of adaptation in response to natural selection via
 allelic substitution. For microbes symbiotic with plants however,
 horizontal gene transfer allows for adaptation via gene gain and loss
 which could generate fundamentally different evolutionary dynamics. We use
 comparative genomics and genetics to elucidate the evolutionary mechanisms
 of adaptation to physiologically stressful serpentine soils in rhizobial
 bacteria in western North American grasslands. We demonstrate that the
 presence of a locus of major effect, the nre operon, is necessary and
 sufficient to confer adaptation to nickel, a heavy metal enriched to toxic
 levels in serpentine soil, and a major axis of environmental soil
 chemistry variation. We find discordance between inferred evolutionary
 histories of the core genome and nreAXY genes, which often reside in
 putative genomic islands. This suggests that the evolutionary history of
 this adaptive variant is marked by frequent losses, and/or gains via
 horizontal acquisition across divergent rhizobium clades. However,
 different nre alleles associate with distinct levels of nickel resistance,
 suggesting allelic substitution could also play a role in rhizobium
 adaptation to serpentine soil. These results illustrate that the interplay
 between evolution via gene gain and loss and evolution via allelic
 substitution may underlie adaptation in wild soil microbiota. Both
 processes are important to consider for understanding adaptive diversity
 in microbes and improving stress-adapted microbial inocula for human use.
 Delgado_Meso_Mastersheet_by_Replicate_2023-11-14.csv Here are metadata
 that describe each column in the datasets: Note: column names with the
 suffix "_mean" are Mesorhizobium strain mean values for that
 phenotype, averaged across all Replicates. NA means no data. Column
 Description Unique.ID unique identifier for Mesorhizobium strain Reserve
 natural reserve where the strain was collected Site site within reserve
 where the strain was collected Subsite.Strain subsite within site where
 the strain was collected; typically A, B, or C, but X = no subsite at this
 site Subsite.Soil subsite within site where soil was collected and used to
 match soil data to this strain; typically the same as Strain.Site but may
 differ PlantSpecies.Strain plant species from which the strain was
 isolated; b = Acmispon brachycarpus; w = A. wrangelianus; p = A.
 parviflorus PlantSpecies.Soil plant species associated with the
 site/subsite where soil was collected and used to match soil data to this
 strain CollectionDate date when strain's plant host was collected
 from the field Waypoint GPS waypoint corresponding to plant sampling
 location for this strain Lat latitude where strain was collected Lon
 longitude where strain was collected Elev elevation (in feet) where strain
 was collected GenoData indicates if strain has nre genotype data PhenoData
 indicates if strain has any phenotypic data Sequenced indicates if strain
 was sequenced Clade clade to which this strain belongs nreA whether or not
 nreA was detected in this strain's genome nreX whether or not nreX
 was detected in this strain's genome nreY whether or not nreY was
 detected in this strain's genome nreA_alleles identity of detected
 nreA alleles in strain's genome; different alleles are separated by
 commas nreX_alleles identity of detected nreX alleles in strain's
 genome; different alleles are separated by commas nreY_alleles identity of
 detected nreY alleles in strain's genome; different alleles are
 separated by commas Replicate replicate for phenotypic measurements;
 typically ranges 1-3 but some strains have more or fewer replicates
 UV.MITassay identifier for individual UV minimum inhibitory time (MIT)
 assay UV.MITwell identifier for individual UV minimum inhibitory time
 (MIT) plate well within an assay UV.MIT UV minimum inhibitory time in
 seconds; column names ending in \_mean show means for strain across
 Replicates Ni.MICassay identifier for individual nickel minimum inhibitory
 concentration (MIC) assay Ni.MICwell identifier for individual nickel
 minimum inhibitory concentration (MIC) plate well within an assay Ni.MIC
 Nickel minimum inhibitory concentration in mM; column names ending in
 \_mean show means for strain across Replicates Co.MICassay identifier for
 individual cobalt minimum inhibitory concentration (MIC) assay Co.MICwell
 identifier for individual cobalt minimum inhibitory concentration (MIC)
 plate well within an assay Co.MIC Cobalt minimum inhibitory concentration
 in mM; column names ending in \_mean show means for strain across
 Replicates Cr.MICassay identifier for individual chromium minimum
 inhibitory concentration (MIC) assay Cr.MICwell identifier for individual
 chromium minimum inhibitory concentration (MIC) plate well within an assay
 Cr.MIC Chromium minimum inhibitory concentration in mM; column names
 ending in \_mean show means for strain across Replicates GrowthAssayPlate
 identifier for individual growth assay plate where strain growth in nickel
 was tested y0.no initial optical density of strain in the absence of
 nickel; output from growthrates package fit_alleasylinear(); column names
 ending in \_mean show means for strain across Replicates y0_lm.no initial
 optical density of the linear model used to predict the strain's
 growth rate in the absence of nickel (no); output from growthrates package
 fit_alleasylinear(); column names ending in \_mean show means for strain
 across Replicates mumax.no maximum growth rate for strain in absence of
 nickel; output from growthrates package fit_alleasylinear(); column names
 ending in \_mean show means for strain across Replicates lag.no lag time
 of strain in absence of nickel; defined as x-axis corodinate of
 intersection between maxium slope regression line from fit_alleasylinear()
 and initial optical density, output from growthrates package
 fit_alleasylinear(); column names ending in \_mean show means for strain
 across Replicates r2.no coefficient of determination for linear model used
 to estimate strains's max growth rate in absence of nickel, output
 from growthrates package fit_alleasylinear(); column names ending in
 \_mean show means for strain across Replicates AUC.no area under the
 growth curve in absence of nickel, calculated with trapezoid rule; column
 names ending in \_mean show means for strain across Replicates ODf.no
 final optical density in absence of nickel; column names ending in \_mean
 show means for strain across Replicates ODmax.no maximum OD in absence of
 nickel; column names ending in \_mean show means for strain across
 Replicates OD72hr.no optical density of strain in absence of nickel, 72
 hours post-inoculation; column names ending in \_mean show means for
 strain across Replicates y0.ni initial optical density of strain in the
 presence of nickel; output from growthrates package fit_alleasylinear();
 column names ending in \_mean show means for strain across Replicates
 y0_lm.ni initial optical density of the linear model used to predict the
 strain's growth rate in the presence of nickel; output from
 growthrates package fit_alleasylinear(); column names ending in \_mean
 show means for strain across Replicates mumax.ni maximum growth rate for
 strain in presence of nickel; output from growthrates package
 fit_alleasylinear(); column names ending in \_mean show means for strain
 across Replicates lag.ni lag time of strain in presence of nickel; defined
 as x-axis corodinate of intersection between maxium slope regression line
 from fit_alleasylinear() and initial optical density, output from
 growthrates package fit_alleasylinear(); column names ending in \_mean
 show means for strain across Replicates r2.ni coefficient of determination
 for linear model used to estimate strains's max growth rate in
 presence of nickel, output from growthrates package fit_alleasylinear();
 column names ending in \_mean show means for strain across Replicates
 AUC.ni area under the growth curve in presence of nickel, calculated with
 trapezoid rule; column names ending in \_mean show means for strain across
 Replicates ODf.ni final optical density in presence of nickel; column
 names ending in \_mean show means for strain across Replicates ODmax.ni
 maximum OD in presence of nickel; column names ending in \_mean show means
 for strain across Replicates OD72hr.ni optical density of strain in
 presence of nickel, 72 hours post-inoculation; column names ending in
 \_mean show means for strain across Replicates OD72hrRatio (OD72hr.ni -
 OD72hr.no)/OD72hr.no; column names ending in \_mean show means for strain
 across Replicates Ni.ppm soil nickel (ppm) matched to this strain; see
 Merge.Notes for details CA.MG.RATIO soil calcium:magnesium ratio matched
 to this strain; see Merge.Notes for details SerpentineType soil type
 matched to this strain; serpentine if CA.MG.RATIO is less than 1;
 nonserpentine if CA.MG.RATIO is greater than 1 Ni.ppm.A/C/X soil nickel
 from the A, C, or X subsites associated with this strain's Site
 CA.MG.RATIO.A/C/X soil Ca:Mg ratio from the A, C, or X subsites associated
 with this strain's Site Ni.CV coefficient of variation for the soil
 nickel at this strain's site; calculated for strains with multiple
 soil measures per site CaMg.CV coefficient of variation for the soil Ca:Mg
 ratio at this strain's site; calculated for strains with multiple
 soil measures per site SAMPLEID soil sample ID submitted to A&L
 Western for chemical analysis OM organic matter of soil matched to strain
 ENR estimated nitrogen release of soil matched to strain, from A&L
 Western soil analysis CEC cation exchange capacity of soil matched to
 strain, measured in milliequivalents per 100g soil, from A&L Western
 soil analysis NO3_N nitrate nitrogen (ppm) of soil matched to strain, from
 A&L Western soil analysis P1 Weak Bray phosphorus (ppm) of soil
 matched to strain, from A&L Western soil analysis HCO3_P Olsen (sodium
 bicarbonate) phosphorus (ppm) of soil matched to strain, from A&L
 Western soil analysis PH soil pH measured off a saturated paste using
 deionized water, from A&L Western soil analysis BUFFER_PH measure of
 both active and reserve acidity in soil, measured off a Sikora buffer
 solution that mimics that of Shoemaker-McLean-Pratt, from A&L Western
 soil analysis S sulfate sulfur (ppm), from A&L Western soil analysis H
 soil hydrogen, from A&L Western soil analysis H_PCT percent cation
 saturation for H, computed after converting exchangeable cations in ppm to
 meq per 100g soil, from A&L Western soil analysis K soil potassium
 (ppm), from A&L Western soil analysis K_PCT percent cation saturation
 for K, computed after converting exchangeable cations in ppm to meq per
 100g soil, from A&L Western soil analysis MG soil magnesium (ppm),
 from A&L Western soil analysis MG_PCT percent cation saturation for
 Mg, computed after converting exchangeable cations in ppm to meq per 100g
 soil, from A&L Western soil analysis CA soil calcium (ppm), from
 A&L Western soil analysis CA_PCT percent cation saturation for Ca,
 computed after converting exchangeable cations in ppm to meq per 100g
 soil, from A&L Western soil analysis NA. soil sodium (ppm), from
 A&L Western soil analysis NA_PCT percent cation saturation for Na,
 computed after converting exchangeable cations in ppm to meq per 100g
 soil, from A&L Western soil analysis AreaCounted area in m2 surveyed
 for plant host density where strain was sampled in the field
 TotalPlantCount total number of the strain's host plant counted in
 AreaCounted Notes.Strain notes about strain isolation Notes.Soil notes
 about soil sampling Merge.Notes notes about matching soil data to strain
 Storage.note indicates any problems with strain cryopreservation
 Strain.issues indicates other issues with strain ---
 Delgado_Meso_Mastersheet_by_Strain_2023-11-14.csv Brief summary of dataset
 contents: Genome and isolation data for strains used in this study.
 (Dataset S1) Here are metadata that describe each column in the datasets:
 Unique.ID unique identifier for Mesorhizobium strain Reserve natural
 reserve where the strain was collected Site site within reserve where the
 strain was collected Subsite.Strain subsite within site where the strain
 was collected; typically A, B, or C, but X = no subsite at this site
 Subsite.Soil subsite within site where soil was collected and used to
 match soil data to this strain; typically the same as Strain.Site but may
 differ PlantSpecies.Strain plant species from which the strain was
 isolated; b = Acmispon brachycarpus; w = A. wrangelianus; p = A.
 parviflorus PlantSpecies.Soil plant species associated with the
 site/subsite where soil was collected and used to match soil data to this
 strain CollectionDate date when strain's plant host was collected
 from the field Waypoint GPS waypoint corresponding to plant sampling
 location for this strain Lat latitude where strain was collected Lon
 longitude where strain was collected Elev elevation (in feet) where strain
 was collected GenoData indicates if strain has nre genotype data PhenoData
 indicates if strain has any phenotypic data Sequenced indicates if strain
 was sequenced Clade clade to which this strain belongs nreA whether or not
 nreA was detected in this strain's genome nreX whether or not nreX
 was detected in this strain's genome nreY whether or not nreY was
 detected in this strain's genome nreA_alleles identity of detected
 nreA alleles in strain's genome; different alleles are separated by
 commas nreX_alleles identity of detected nreX alleles in strain's
 genome; different alleles are separated by commas nreY_alleles identity of
 detected nreY alleles in strain's genome; different alleles are
 separated by commas Replicate replicate for phenotypic measurements;
 typically ranges 1-3 but some strains have more or fewer replicates
 UV.MITassay identifier for individual UV minimum inhibitory time (MIT)
 assay UV.MITwell identifier for individual UV minimum inhibitory time
 (MIT) plate well within an assay UV.MIT UV minimum inhibitory time in
 seconds; column names ending in \_mean show means for strain across
 Replicates Ni.MICassay identifier for individual nickel minimum inhibitory
 concentration (MIC) assay Ni.MICwell identifier for individual nickel
 minimum inhibitory concentration (MIC) plate well within an assay Ni.MIC
 Nickel minimum inhibitory concentration in mM; column names ending in
 \_mean show means for strain across Replicates Co.MICassay identifier for
 individual cobalt minimum inhibitory concentration (MIC) assay Co.MICwell
 identifier for individual cobalt minimum inhibitory concentration (MIC)
 plate well within an assay Co.MIC Cobalt minimum inhibitory concentration
 in mM; column names ending in \_mean show means for strain across
 Replicates Cr.MICassay identifier for individual chromium minimum
 inhibitory concentration (MIC) assay Cr.MICwell identifier for individual
 chromium minimum inhibitory concentration (MIC) plate well within an assay
 Cr.MIC Chromium minimum inhibitory concentration in mM; column names
 ending in \_mean show means for strain across Replicates GrowthAssayPlate
 identifier for individual growth assay plate where strain growth in nickel
 was tested y0.no initial optical density of strain in the absence of
 nickel; output from growthrates package fit_alleasylinear(); column names
 ending in \_mean show means for strain across Replicates y0_lm.no initial
 optical density of the linear model used to predict the strain's
 growth rate in the absence of nickel (no); output from growthrates package
 fit_alleasylinear(); column names ending in \_mean show means for strain
 across Replicates mumax.no maximum growth rate for strain in absence of
 nickel; output from growthrates package fit_alleasylinear(); column names
 ending in \_mean show means for strain across Replicates lag.no lag time
 of strain in absence of nickel; defined as x-axis corodinate of
 intersection between maxium slope regression line from fit_alleasylinear()
 and initial optical density, output from growthrates package
 fit_alleasylinear(); column names ending in \_mean show means for strain
 across Replicates r2.no coefficient of determination for linear model used
 to estimate strains's max growth rate in absence of nickel, output
 from growthrates package fit_alleasylinear(); column names ending in
 \_mean show means for strain across Replicates AUC.no area under the
 growth curve in absence of nickel, calculated with trapezoid rule; column
 names ending in \_mean show means for strain across Replicates ODf.no
 final optical density in absence of nickel; column names ending in \_mean
 show means for strain across Replicates ODmax.no maximum OD in absence of
 nickel; column names ending in \_mean show means for strain across
 Replicates OD72hr.no optical density of strain in absence of nickel, 72
 hours post-inoculation; column names ending in \_mean show means for
 strain across Replicates y0.ni initial optical density of strain in the
 presence of nickel; output from growthrates package fit_alleasylinear();
 column names ending in \_mean show means for strain across Replicates
 y0_lm.ni initial optical density of the linear model used to predict the
 strain's growth rate in the presence of nickel; output from
 growthrates package fit_alleasylinear(); column names ending in \_mean
 show means for strain across Replicates mumax.ni maximum growth rate for
 strain in presence of nickel; output from growthrates package
 fit_alleasylinear(); column names ending in \_mean show means for strain
 across Replicates lag.ni lag time of strain in presence of nickel; defined
 as x-axis corodinate of intersection between maxium slope regression line
 from fit_alleasylinear() and initial optical density, output from
 growthrates package fit_alleasylinear(); column names ending in \_mean
 show means for strain across Replicates r2.ni coefficient of determination
 for linear model used to estimate strains's max growth rate in
 presence of nickel, output from growthrates package fit_alleasylinear();
 column names ending in \_mean show means for strain across Replicates
 AUC.ni area under the growth curve in presence of nickel, calculated with
 trapezoid rule; column names ending in \_mean show means for strain across
 Replicates ODf.ni final optical density in presence of nickel; column
 names ending in \_mean show means for strain across Replicates ODmax.ni
 maximum OD in presence of nickel; column names ending in \_mean show means
 for strain across Replicates OD72hr.ni optical density of strain in
 presence of nickel, 72 hours post-inoculation; column names ending in
 \_mean show means for strain across Replicates OD72hrRatio (OD72hr.ni -
 OD72hr.no)/OD72hr.no; column names ending in \_mean show means for strain
 across Replicates Ni.ppm soil nickel (ppm) matched to this strain; see
 Merge.Notes for details CA.MG.RATIO soil calcium:magnesium ratio matched
 to this strain; see Merge.Notes for details SerpentineType soil type
 matched to this strain; serpentine if CA.MG.RATIO is less than 1;
 nonserpentine if CA.MG.RATIO is greater than 1 Ni.ppm.A/C/X soil nickel
 from the A, C, or X subsites associated with this strain's Site
 CA.MG.RATIO.A/C/X soil Ca:Mg ratio from the A, C, or X subsites associated
 with this strain's Site Ni.CV coefficient of variation for the soil
 nickel at this strain's site; calculated for strains with multiple
 soil measures per site CaMg.CV coefficient of variation for the soil Ca:Mg
 ratio at this strain's site; calculated for strains with multiple
 soil measures per site SAMPLEID soil sample ID submitted to A&L
 Western for chemical analysis OM organic matter of soil matched to strain
 ENR estimated nitrogen release of soil matched to strain, from A&L
 Western soil analysis CEC cation exchange capacity of soil matched to
 strain, measured in milliequivalents per 100g soil, from A&L Western
 soil analysis NO3_N nitrate nitrogen (ppm) of soil matched to strain, from
 A&L Western soil analysis P1 Weak Bray phosphorus (ppm) of soil
 matched to strain, from A&L Western soil analysis HCO3_P Olsen (sodium
 bicarbonate) phosphorus (ppm) of soil matched to strain, from A&L
 Western soil analysis PH soil pH measured off a saturated paste using
 deionized water, from A&L Western soil analysis BUFFER_PH measure of
 both active and reserve acidity in soil, measured off a Sikora buffer
 solution that mimics that of Shoemaker-McLean-Pratt, from A&L Western
 soil analysis S sulfate sulfur (ppm), from A&L Western soil analysis H
 soil hydrogen, from A&L Western soil analysis H_PCT percent cation
 saturation for H, computed after converting exchangeable cations in ppm to
 meq per 100g soil, from A&L Western soil analysis K soil potassium
 (ppm), from A&L Western soil analysis K_PCT percent cation saturation
 for K, computed after converting exchangeable cations in ppm to meq per
 100g soil, from A&L Western soil analysis MG soil magnesium (ppm),
 from A&L Western soil analysis MG_PCT percent cation saturation for
 Mg, computed after converting exchangeable cations in ppm to meq per 100g
 soil, from A&L Western soil analysis CA soil calcium (ppm), from
 A&L Western soil analysis CA_PCT percent cation saturation for Ca,
 computed after converting exchangeable cations in ppm to meq per 100g
 soil, from A&L Western soil analysis NA. soil sodium (ppm), from
 A&L Western soil analysis NA_PCT percent cation saturation for Na,
 computed after converting exchangeable cations in ppm to meq per 100g
 soil, from A&L Western soil analysis AreaCounted area in m2 surveyed
 for plant host density where strain was sampled in the field
 TotalPlantCount total number of the strain's host plant counted in
 AreaCounted Notes.Strain notes about strain isolation Notes.Soil notes
 about soil sampling Merge.Notes notes about matching soil data to strain
 Storage.note indicates any problems with strain cryopreservation
 Strain.issues indicates other issues with strain --- GWAS_results.csv
 Brief summary of dataset contents: Pyseer FAST-lmm GWAS results for
 presence/absence of genes. Here are metadata that describe each column in
 the datasets: Columnn Description variant_gene_cluster gene cluster id
 (ortholog) gene annotation function predicted through prokka or ncbi CDD
 search af_cl1 proportion of clade 1 isolates the variant is present in
 af_cl2 proportion of clade 2 isolates the variant is present in
 filter-pvalue.mic_cl1_genes association of the variant with the phenotype,
 unadjusted for population structure. (for clade 1 MIC Ni)
 lrt-pvalue.mic_cl1_genes the p-value from the mixed model association, as
 given by FaST-LMM. (for clade 1 MIC Ni) beta.mic_cl1_genes the effect
 size/slope of the variant. For a binary phenotype, exponentiate to obtain
 the odds-ratio. (for clade 1 MIC Ni) beta-std-err.mic_cl1_genes the
 standard error of the fit on beta. (for clade 1 MIC Ni)
 variant_h2.mic_cl1_genes the variance in phenotype explained by the
 variant. The ℎ2 for this variant alone. (for clade 1 MIC Ni) fdr-adj
 lrt-pvalue.mic_cl1_genes lrt-pvalue adjusted with p.adj "fdr"
 function in R (for clade 1 MIC Ni) filter-pvalue.od_cl1_genes association
 of the variant with the phenotype, unadjusted for population structure.
 (for clade 1 growth in Ni) lrt-pvalue.od_cl1_genes the p-value from the
 mixed model association, as given by FaST-LMM. (for clade 1 growth in Ni)
 beta.od_cl1_genes the effect size/slope of the variant. For a binary
 phenotype, exponentiate to obtain the odds-ratio. (for clade 1 growth in
 Ni) beta-std-err.od_cl1_genes the standard error of the fit on beta. (for
 clade 1 growth in Ni) variant_h2.od_cl1_genes the variance in phenotype
 explained by the variant. The ℎ2 for this variant alone. (for clade 1
 growth in Ni) fdr-adj lrt-pvalue.od_cl1_genes lrt-pvalue adjusted with
 p.adj "fdr" function in R (for clade 1 growth in Ni)
 filter-pvalue.mic_cl2_genes association of the variant with the phenotype,
 unadjusted for population structure. (for clade 2 MIC Ni)
 lrt-pvalue.mic_cl2_genes the p-value from the mixed model association, as
 given by FaST-LMM. (for clade 2 MIC Ni) beta.mic_cl2_genes the effect
 size/slope of the variant. For a binary phenotype, exponentiate to obtain
 the odds-ratio. (for clade 2 MIC Ni) beta-std-err.mic_cl2_genes the
 standard error of the fit on beta. (for clade 2 MIC Ni)
 variant_h2.mic_cl2_genes the variance in phenotype explained by the
 variant. The ℎ2 for this variant alone. (for clade 2 MIC Ni) fdr-adj
 lrt-pvalue.mic_cl2_genes lrt-pvalue adjusted with p.adj "fdr"
 function in R (for clade 2 MIC Ni) filter-pvalue.od_cl2_genes association
 of the variant with the phenotype, unadjusted for population structure.
 (for clade 2 growth in Ni) lrt-pvalue.od_cl2_genes the p-value from the
 mixed model association, as given by FaST-LMM. (for clade 2 growth in Ni)
 beta.od_cl2_genes the effect size/slope of the variant. For a binary
 phenotype, exponentiate to obtain the odds-ratio. (for clade 2 growth in
 Ni) beta-std-err.od_cl2_genes the standard error of the fit on beta. (for
 clade 2 growth in Ni) variant_h2.od_cl2_genes the variance in phenotype
 explained by the variant. The ℎ2 for this variant alone. (for clade 2
 growth in Ni) fdr-adj lrt-pvalue.od_cl2_genes lrt-pvalue adjusted with
 p.adj "fdr" function in R (for clade 2 growth in Ni) ---
 C089B_wt_del_tradeoffs_data_KJ2.csv Brief summary of dataset contents:
 Optical density readings for testing nreXY deletion mutant Here are
 metadata that describe each column in the datasets: Columnn Description
 Strain strain shortname, WT (KJ094) is wild-type C089B and Del (KJ156) is
 C089B with nreXY deleted Ni.mM amount of NiCl2 (mM) OD optical density
 (600nm) Rep replicate number Plate plate assayed, A or B Time.hr time of
 OD reading in hours Strain.ID strain shortname_Ni.mM nreXY present or
 absent for nreXY --- 20_Ni_island_regions_growth_data_KJ2.csv Brief
 summary of dataset contents: Growth data for Ni island regions cloned into
 A. fabrum Here are metadata that describe each column in the datasets:
 Columnn Description Unique.ID Unique ID of the strains used in the growth
 assay (see supplemental table S13) Growth Growth measured as the optical
 density at 600 nm after 24 hours. Rep technical replicate of each strain
 in the growth assay Ni.mm level of nickel used in the growth assay media
 Ni.region region of the Mesorhizobium nickel island (shown in figure 2A)
 cloned into A. fabrum ---
 nreAXY_allele_tolerance_growth_assay_KJ_10.25.2023.2.csv Brief summary of
 dataset contents: Growth data in Ni for cloned strains containing
 different nreAXY alleles Here are metadata that describe each column in
 the datasets: Columnn Description Strain strains used in the growth assay
 (see supplemental table S13) Strain.desc strain name the nreAXY allele
 types, in parentheses is the high tolerance (HT) or low tolerance (LT)
 with the clade of the strain listed after a dash. Ni.mm level of nickel
 used in the growth assay media Rep technical replicate of each strain in
 the growth assay Growth Growth measured as the optical density at 600 nm
 after 24 hours