Data and code from: The role of microbial resource mutualists in plant adaptation to abiotic environments
Data files
May 27, 2026 version files 284.36 KB
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Field_Experiment_Data.csv
103.34 KB
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Greenhouse_Experiment_Data.csv
62.03 KB
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isotope.csv
14.52 KB
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README.md
9.48 KB
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Suwa_and_Lau_Field_Experiment_FINAL_21_May_2025.R
41.72 KB
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Suwa_and_Lau_Greenhouse_Experiment_FINAL.R
38.30 KB
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Suwa_and_Lau_Greenhouse_Experiment_Isotope_Analyses_FINAL.R
14.98 KB
Abstract
Despite more than eighty years of study, the selective agents driving local adaptation largely remain unknown, in part because populations exist in complex environments where they experience both abiotic and biotic factors that can exert strong selection. We used a replicated reciprocal transplant experiment combined with a greenhouse inoculation experiment to investigate plant adaptation to soil moisture and the role of nitrogen-fixing rhizobium mutualists in plant local adaptation. We find that the annual legume hog peanut (Amphicarpaea bracteata) is locally adapted to soil moisture conditions and that interactions with nitrogen-fixing rhizobia likely contribute to the observed local adaptation. Specifically, plant populations from wet sites transplanted into wet habitats were more likely than those from dry sites to associate with rhizobium mutualists and formed more nodules and had higher nitrogen fixation rates when inoculated with rhizobium strains isolated from wet compared to dry habitats. As a result, local adaptation to wet environments was most apparent when plants successfully associated with rhizobia in the field. In sum, our results suggest that: 1) soil moisture is a strong cause of local adaptation in this system, and 2) divergence in how plant populations interact with rhizobia likely contributes to plant local adaptation to soil moisture. These findings illustrate how biotic interactions can influence plant adaptation to a strong abiotic gradient and highlight the need to consider microbial mutualists in studies of plant local adaptation.
Dataset DOI: 10.5061/dryad.g4f4qrg27
Description of the data and file structure
This data package includes the plant phenotypic data from a field reciprocal transplant experiment (“Field Experiment Data.csv”), plant phenotypic data from a greenhouse experiment manipulating soil moisture and rhizobium presence and genetic identity (“Greenhouse Experiment Data.csv”), and isotope data from a subset of plants included in the greenhouse experiment (“isotope.csv"). In addition, we include the R scripts for analyses of each dataset (“Suwa and Lau Field Experiment Final 21 May 2025.R”, “Suwa and Lau Greenhouse Experiment FINAL.R”, and “Suwa and Lau Greenhouse Experiment Isotope Analyses.R”). These data were collected from a replicated reciprocal transplant experiment involving 3 Amphicarpaea bracteata populations from dry habitats and 3 from wet habitats and a greenhouse experiment that grew these same populations under wet and dry soil moisture conditions in the absence of rhizobia or the presence of rhizobia isolated from the 6 original plant populations. We measured a number of plant traits in the experiments, including growth and fitness traits (e.g., aboveground biomass, root:shoot ratios, and seed production), leaf traits (precent nitrogen and delta 15N isotopes to estimate biological nitrogen fixation), and nodulation traits (nodule presence and nodule numbers). Any empty cell (1 or 2) represent data not available.
Files and variables
File: Greenhouse_Experiment_Data.csv
Description: Plant growth, fitness, and nodulation data from the greenhouse experiment manipulating soil moisture, rhizobia, and plant population. Any missing values are indicated with "NA."
Variables
- ID: Unique identifier for each plant in the experiment
- bench : Greenhouse bench describing the spatial location of the plant; can be used to control for environmental variation across the greenhouse.
- Moisture: Experimental treatment of soil moisture (well-watered = “high” vs. minimally watered = “low”)
- Plant_pop: Source plant population. 6 populations were included in the analyses. Although a 7th population was included in the experiment (CCB), it was not included in the analysis because rhizobium strains from that population were not included in the study.
- Plant_ID: Full-sib family from which the seed originated.
- Rhizobia: Population from which the rhizobia were isolated. “Control” designates uninoculated plants.
- survival: 1 if the plant survived til harvest; 0 if it did not.
- AG_biomass: Aboveground biomass in grams dry weight (i.e., mass after drying).
- BG_biomass: Belowground biomass in grams dry weight (i.e., mass after drying).
- Total Nod Weight: Mass of all nodules
- nod.num: Number of nodules produced
- contaminated: 1 if an uninoculated (“Control”) plant, produced nodules; 0 if no nodules were produced on an uninoculated plant OR if the plant was inoculated.
- seed.wt: mass of seeds.
- seed.num: Number of seeds produced.
- lateral.shoots1: Amphicarpaea sometimes produces lateral shoots which then can lead to production of additional subterranean seeds. These are the measured lengths of each lateral shoot produced in centimeters (cm). The maximum number of lateral shoots produced was 4 (latera.shoots4).
- lateral.shoots2: Amphicarpaea sometimes produces lateral shoots which then can lead to production of additional subterranean seeds. These are the measured lengths of each lateral shoot produced in centimeters. The maximum number of lateral shoots produced was 4 (latera.shoots4).
- lateral.shoots3: Amphicarpaea sometimes produces lateral shoots which then can lead to production of additional subterranean seeds. These are the measured lengths of each lateral shoot produced in centimeters. The maximum number of lateral shoots produced was 4 (latera.shoots4).
- lateral.shoots4: Amphicarpaea sometimes produces lateral shoots which then can lead to production of additional subterranean seeds. These are the measured lengths of each lateral shoot produced in centimeters. The maximum number of lateral shoots produced was 4 (latera.shoots4).
- total.lateral: This is the summed length (cm) of all lateral shoots produced (sum of columns lateral.shoots1 through lateral.shoots4).
File: isotope.csv
Description: Leaf chemistry and isotope data from the greenhouse experiment manipulating soil moisture, rhizobia, and plant population. Any missing values are indicated with "NA."
Variables
- bench: Greenhouse bench the plant was located on (could be used to account for spatial variation in greenhouse environmental conditions).
- Moisture: Watering treatment imposed on the plant (“high” if well-watered; “low” if dry soil moisture).
- Plant_ID: Plant full-sib family that the plant originated from.
- Rhizobia: Rhizobium population (i.e., the source site that the rhizobia inoculum was calculated from)
- Plant_pop: Plant population (6 plant populations were included in the study; 3 from wet sites and 3 from dry sites).
- Sample_ID: Unique identifier used to keep track of samples sent for analyses
- d13C: The delta C13 isotope value, which can be indicative of water use efficiency.
- C_Amount_ug: Carbon concentration of the leaf tissue in micrograms.
- d15N: The delta N15 isotope value, which is associated with biological nitrogen fixation. Typically, negative values indicate nitrogen fixation; while 0 or positive values indicate limited or no nitrogen fixation.
- N_Amount_ug: Nitrogen concentration of the leaf tissue in micrograms.
- leafmass_mg: Leaf mass in milligrams (needed for calculating percent nitrogen).
File: Field_Experiment_Data.csv
Description: Plant growth, fecundity, and nodulation data from the field reciprocal transplant experiment. Any missing values are indicated with "NA."
Variables
- Tag: Unique identifier for each plant
- Dest: Transplant site. There were 6 transplant sites (identical to the source populations); 3 are wet, and 3 are dry.
- Source: Source population. Three plant populations originated from wet sites and 3 from dry.
- Genotype.Unique: A unique identifier for each full-sib family from which seeds originated.
- Chloro: Chlorophyll concentration measured with a SPAD meter.
- Initial: Initials of person who harvested the plant.
- BG.Seeds: Number of subterranean seeds produced.
- Pods: Number of aboveground fruits produced.
- Nod: 1 if any nodules were observed; 0 if no nodules were observed.
- AG.Seeds: Number aboveground seeds produced.
- Survival: 1 if the plant survived; 0 if the plant did not survive to harvest.
- AG.Biomass: Aboveground biomass in grams; weighed after drying.
- BG.seed.wt: Mass of all belowground seeds.
- No.BG.Seed.weighted: Number of seeds weighed (so that mean seed mass can be estimated, in the event that any seeds were lost before weighing).
- AG.Seeds.wt: Mass of all aboveground seeds collected.
- S.Type: Describes whether the source population originated from a dry or wet site
- D.Type: Classifies the transplant site as dry or wet.
- Block: There were multiple transplant gardens within each transplant destination site; block can be used to account for spatial variation within each transplant site (“Dest”).
File: Suwa_and_Lau_Field_Experiment_FINAL_21_May_2025.R
Description: R Script used to analyze the field reciprocal transplant experiment data. The code uses the data file "Field Experiment Data.csv" and produces figures: 1A, 4, 6A,B and tables: S2, S7 in the associated manuscript. Data were analyzed using R Studio, version 4.2.1 and the packages: DHARMa (0.4.6), dplyr (1.0.9), emmeans (1.8.1-1), glmmTMB (1.1.8). Graphs were produced in R (version 4.2.1) using the ggplot2 package (version 3.5.0).
File: Suwa_and_Lau_Greenhouse_Experiment_Isotope_Analyses_FINAL.R
Description: R Script used to analyze the isotope data from the greenhouse experiment. The code uses the data file "isotope.csv" and produces figure 3 and tables S5, S6. Data were analyzed using R Studio, version 4.2.1 and the packages: DHARMa (0.4.6), dplyr (1.0.9), emmeans (1.8.1-1), glmmTMB (1.1.8). Graphs were produced in R (version 4.2.1) using the ggplot2 package (version 3.5.0).
File: Suwa_and_Lau_Greenhouse_Experiment_FINAL.R
Description: R Script used to analyze the plant biomass, nodulation, and seed production data from the greenhouse experiment. The code uses the data file "Greenhouse Experiment Data.csv" and produces Figures: 1B, 2, 5, 6C,D and tables: S3, S4, S8Data were analyzed using R Studio, version 4.2.1 and the packages: DHARMa (0.4.6), dplyr (1.0.9), emmeans (1.8.1-1), glmmTMB (1.1.8). Graphs were produced in R (version 4.2.1) using the ggplot2 package (version 3.5.0).
Code/software
Data were analyzed using R Studio, version 4.2.1 and the packages: DHARMa (0.4.6), dplyr (1.0.9), emmeans (1.8.1-1), glmmTMB (1.1.8). Graphs were produced in R (version 4.2.1) using the ggplot2 package (version 3.5.0). The datasets used in each R file are listed in the file description for each R file (also noted at the top of each R script):
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- NA
