Data from: Limited intraspecific variation in drought resistance along a pronounced tropical rainfall gradient
Data files
Apr 30, 2024 version files 11.30 MB
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Data_files.zip
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README.md
Abstract
Assessing within-species variation in response to drought is crucial for predicting species responses to climate change and informing restoration and conservation efforts, yet experimental data are lacking for the vast majority of tropical tree species. We assessed intraspecific variation in response to water availability across a strong rainfall gradient for 16 tropical tree species using reciprocal transplant and common garden field experiments, along with measurements of gene flow and key functional traits linked to drought resistance.
README: Data from: Limited intraspecific variation in drought resistance along a pronounced tropical rainfall gradient
These data were collected as part of a study of intraspecific variation in response to water availability across a strong rainfall gradient for 16 native tropical tree species using reciprocal transplant and common garden field experiments, along with measurements of gene flow, genetic diversity, and key functional traits linked to drought resistance. The study was conducted in tropical moist lowland forests spanning a rainfall gradient in central Panama.
There are 8 data files and 6 files with R code used to analyze the data sets. The data files fall into 5 groups: Focal species information, Common Garden experiment, Reciprocal Transplant experiment, Functional trait measurements, and Genetic data
NA is used to denote missing or unmeasured data in all files
Description of the data and file structure
Focal species information - data on the 16 focal species used in the study
"species.information.csv" - includes information on the focal species and indicates in which parts of the study they were included; columns include:
Species name: the full genus and species name with the botanical authority listed beneath
Family: the family to which the species belongs
Code: the six-letter code of the genus and species of each species (used in the files below)
Phenology: indicates the leaf phenology of the species (E=evergreen, DD=dry season deciduous, WD=wet season deciduous)
Distribution: indicates if the species is found on the drier side, wetter side, or is widespread across the rainfall gradient in central Panama
Collection area: X indicates in which sections of the rainfall gradient (dry, intermediate, wet) seeds and leaf tissue were collected for that species
Performance: X indicates if the species was included in the Common Garden (CG) experiment and D, I, and W indicate if the species was transplanted to the dry, intermediate, and wet sites of the Reciprocal Transplant (RT) experiment
Traits: X indicates if that species traits were measured in the shade house (SH) and Common Garden (CG) experiment
Genetic: X indicates if genetic data was collected for that species
Common Garden experiment data - data on individual seedling growth and survival in a common garden experiment on the Buena Vista (BV) peninsula that included a drought treatment (30 plots) and an irrigated treatment (30 plots). Growth and survival data are in separate files:
"BV.survival.data.for.analysis.txt" - includes data on survival in the experiment; variables include:
unique.id: unique identifier for the seedling in the database
plot: seedling plot number
position: position of the seedling within the plot
specie: six-letter code of the genus and species of the seedling
number: tag number of the seedling
lot: number of the mother tree(s) from which the seed of that seedling was collected
origin: location along the gradient where the seed/seedling was collected (dry=drier side of the gradient, int=intermediate/middle of the gradient; wet=wetter side of the gradient)
treatment: treatment applied to the plot (dr=drought treatment in which any rainfall during the dry season was excluded by clear tarps, or ir=irrigated treatment in which seedlings were watered regularly during the dry season to prevent drought stress)
height.mm: height in mm of the seedling in the first census
status.final.census: status of the seedling at the end of the experiment (A=alive, D=dead)
days.alive: number of days for which the seedling was alive in the experiment (based on the time between the first census and the last census in which the seedling was alive)
death.event: whether the seedling survival until the end of the experiment (1=died, 0=survived)
"BV.growth.survival.to.end.formatted.for.analysis" - includes data on growth rates for seedlings that survived until the end of the experiment; variables include:
unique.id: unique identifier for the seedling in the database
treatment: treatment applied to the plot (dr=drought treatment in which any rainfall during the dry season was excluded by clear tarps, or ir=irrigated treatment in which seedlings were watered regularly during the dry season to prevent drought stress)
plot: seedling plot number
position: position of the seedling within the plot
specie: six-letter code of the genus and species of the seedling
number: tag number of the seedling
lot: number of the mother tree(s) from which the seed of that seedling was collected
origin: location along the gradient where the seed/seedling was collected (dry=drier side of the gradient, int=intermediate/middle of the gradient; wet=wetter side of the gradient)
census.t1: census number used as the initial census (all values = C2)
month.t1: month of the initial census
day.t1: day of the initial census
year.t1: year of the initial census
status.t1: status in the initial census (all values=A, alive)
height.mm.t1: height in mm in the initial census
total.num.leaves.t1: total number of leaves in the initial census
potential.leaf.area.cm2.t1: total potential leaf area in cm-squared in the initial census, estimated based on species-specific equations for leaf area as a function of length and width measured for each leaf of the seedlings; potential leaf area does not account for the area of leaves missing due to herbivore damage
damaged.leaf.area.cm2.t1: estimated area in cm-squared of leaf tissue missing due to herbivore damage (for leaves present on the plant, does not account for removal of entire leaves)
actual.leaf.area.cm2.t1: total leaf area in cm-squared after accounting for damage (i.e., potential.leaf.area - damaged.leaf.area)
census.t2: census number used as the final census (all values = C5)
month.t2: month of the final census
day.t2: day of the final census
year.t2: year of the final census
status.t2: status in the final census (A=alive, D=dead)
height.mm.t2: height in mm in the final census
total.num.leaves.t2: total number of leaves in the final census
potential.leaf.area.cm2.t2: potential leaf area in the final census (see explanation above)
damaged.leaf.area.cm2.t2: damaged leaf area in the final census (see explanation above)
actual.leaf.area.cm2.t2: actual leaf area in the final census (see explanation above)
time.days: time in days between the initial and final census of the seedling
rgr.pot: relative growth rate, calculated as (ln(potential.leaf.area.cm2.t2) - ln(potential.leaf.area.cm2.t1))/time in years
rgr.act: relative growth rate, calculated as rgr.pot but using actual.leaf.area instead of potential.leaf.area
ag.pot: absolute growth rate, calculated as (potential.leaf.area.cm2.t2 - potential.leaf.area.cm2.t1)/time in years
ag.act: absolute growth rate, calculated as act.pot but using actual.leaf.area instead of potential.leaf.area
Reciprocal transplant experiment data - data on individual seedling growth and survival at the three reciprocal transplant sites along the rainfall gradient. Growth and survival data are in the same file:
"transplant.growth.survival.to.2018.for.analysis.txt" - includes data on survival and growth of seedlings transplanted to 3 sites along the rainfall gradient, with each site containing 30 seedlings plots; variables include:
unique.id: unique identifier for the seedling in the database
site: transplant site (dry.pnm = dry transplant site, Parque Natural Metropolitnao; int.plr = intermediate rainfall site, Pipeline Road; wet.sherman = wet transplant site, Sherman/San Lorenzo National Park)
plot: seedling plot number (1-30) at each transplant site
position: position of the seedling within the plot
specie: six-letter code of the genus and species of the seedling
number: tag number of the seedling
lot: number of the mother tree(s) from which the seed of that seedling was collected
origin: location along the gradient where the seed/seedling was collected (dry=drier side of the gradient, int=intermediate/middle of the gradient; wet=wetter side of the gradient)
census.t1: census number used as the initial census (all values = C2)
month.t1: month of the initial census
day.t1: day of the initial census
year.t1: year of the initial census
status.t1: status in the initial census (all values=A, alive)
height.mm.t1: height in mm in the initial census
total.num.leaves.t1: total number of leaves in the initial census
potential.leaf.area.cm2.t1: total potential leaf area in cm-squared in the initial census, estimated based on species-specific equations for leaf area as a function of length and width measured for each leaf of the seedlings; potential leaf area does not account for an area of leaves missing due to herbivore damage
damaged.leaf.area.cm2.t1: estimated area in cm-squared of leaf tissue missing due to herbivore damage (for leaves present on the plant, does not account for removal of entire leaves)
actual.leaf.area.cm2.t1: total leaf area in cm-squared after accounting for damage (i.e., potential.leaf.area - damaged.leaf.area)
census.t2: census number used as the final growth census (all values = C5; note that final survival was assessed in the later census, see below)
month.t2: month of the final growth census
day.t2: day of the final growth census
year.t2: year of the final growth census
status.t2: status in the final growth census (A=alive, D=dead)
height.mm.t2: height in mm in the final growth census
total.num.leaves.t2: total number of leaves in the final growth census
potential.leaf.area.cm2.t2: potential leaf area in the final growth census (see explanation above)
damaged.leaf.area.cm2.t2: damaged leaf area in the final growth census (see explanation above)
actual.leaf.area.cm2.t2: actual leaf area in the final growth census (see explanation above)
time.days: time in days between initial and final growth census of the seedling
rgr.pot: relative growth rate, calculated as (ln(potential.leaf.area.cm2.t2) - ln(potential.leaf.area.cm2.t1))/time in years
rgr.act: relative growth rate, calculated as rgr.pot but using actual.leaf.area instead of potential.leaf.area
ag.pot: absolute growth rate, calculated as (potential.leaf.area.cm2.t2 - potential.leaf.area.cm2.t1)/time in years
ag.act: absolute growth rate, calculated as act.pot but using actual.leaf.area instead of potential.leaf.area
census.2018: census number used as the final survival census (C6 if seedling was alive in a prior census (C5); NA if seedling was dead in the prior census)
month.2018: the month of the final survival census
day.2018: the day of the final survival census
year.2018: year of the final survival census
status.2018: status in the final survival census (A=alive, D=dead)
u.plot: unique seedling plot number (combines site and plot number so that each plot has a unique identifier)
survived.2018: whether the seedling survived until the final survival census (0=died, 1=survived)
Functional trait measurements - Data on functional traits measured on seedlings, with separate files for seedlings measured in the shade house (i.e., under uniform conditions) and at the end of the common garden experiment (i.e., in the field under drought or irrigated conditions)
"greenhouse.traits.txt" - trait values for individual seedlings measured in the shade house; variables include:
species: six-letter code of the genus and species of the seedling
origin: location along the gradient where the seed/seedling was collected (dry=drier side of the gradient, int=intermediate/middle of the gradient; wet=wetter side of the gradient)
plant: number of the seedlings (unique within species only)
lot: number of the mother tree(s) from which the seed of that seedling was collected
tlp: turgor loss point in MPa
root.density: root density in g/cm^3
root.wc: root water content in % fresh weight
stem.density: stem density in g/cm^3
stem.wc stem water content in % fresh weight
sla: specific leaf area in cm2/g
leaf.wc: leaf water content in % fresh weight
nsc.total: total non-structural carbohydrates as % of stem DW
nsc.suc: sucrose component of non-structural carbohydrates
nsc.starch: starch component of non-structural carbohydrates
nsc.gluc.fruc: glucose and fructose component of non-structural carbohydrates
lar: leaf area ratio in cm2/g
lmr: leaf mass ratio in g/g
smr: stem mass ratio in g/g
rmr: root mass ratio in g/g
root.shoot: root to shoot ratio in g/g
g.max: maximum stomatal conductance in mmol/ (m^2 * s)
lwp.g.10: leaf water potential at stomatal closure (WPcrit) in MPa
"BV.traits.txt" - trait values for individual seedlings measured at the end of the common garden experiment; variables include:
Plot: seedling plot number in the common garden experiment
species: six-letter code of the genus and species of the seedling
treatment: treatment applied to the plot (dr=drought treatment in which any rainfall during the dry season was excluded by clear tarps, or ir=irrigated treatment in which seedlings were watered regularly during the dry season to prevent drought stress)
origin: location along the gradient where the seed/seedling was collected (dry=drier side of the gradient, int=intermediate/middle of the gradient; wet=wetter side of the gradient)
position: position of the seedling within the plot
number: tag number of the seedling
lote: number of the mother tree(s) from which the seed of that seedling was collected
root.wc: root water content in % fresh weight
stem.wc: stem water content in % fresh weight
leaf.wc: leaf water content in % fresh weight
stem.density: stem density in g/cm^3
SLA.cm2.g: specific leaf area in cm2/g
RMR: root mass ratio in g/g
SMR: stem mass ratio in g/g
LMR: leaf mass ratio in g/g
Genetic data - A file with the population genetic summary statistics for each origin of each species, plus a zip file containing files with Single Nucleotide Polymorphism (SNP) data for each of 13 tree species sampled across the rainfall gradient spanning the isthmus of Panama
"PANAMA_SNP.zip" - contains the 13 Variant Call Format (VCF) files with the data on single nucleotide polymorphisms (SNPs) for each species, the beginning of each file name is the six-letter code for that species. Below is a brief description of the VCF file data structure:
Header Lines: Begin with ## and provide metadata about the file, such as the VCF format version, reference genome (NA), and descriptions of the fields used in the body of the file.
Column Header Line: Starts with # and lists the column names. Typical columns include:
#CHROM: Chromosome number (Not applicable in this study)
POS: Position of the SNP on the chromosome. Not applicable in this study)
ID: Identifier of the SNP
REF: Reference base(s) at the position
ALT: Alternate base(s) corresponding to the variation
QUAL: Quality score of the variant call
FILTER: Filter status (e.g., PASS if the variant passed all filters)
INFO: Additional information on the variant
FORMAT: Format of the genotype information
Sample columns: Individual or sample IDs with genotype data formatted as specified in the FORMAT column.
Data Lines: Follow the header and provide the actual genetic variation data. Each line corresponds to a variant (e.g., SNP) and contains fields separated by tabs, corresponding to the column headers.
INFO Field: Contains key-value pairs describing the variant, such as allele frequency, effects, and other annotations.
FORMAT Field: Describes the format of the sample-specific data, such as genotype (GT), depth of coverage (DP), and other relevant metrics.
"population.genetic.summary.data.csv" - includes population genetic statistics for each population/origin of each species and seed dispersal mode; columns include:
Species = 6-letter species code
Origin = Location of the population/original along the rainfall gradient (Dry, Int (Intermediate), Wet)
Num = average allelic richness of individuals in the population
Eff_Num = the effective number of alleles in the population
Ho = the average observed heterozygosity
Ht = the average expected heterozygosity (genetic diversity)
Gis = Nei's inbreeding coefficient (heterozygote deficit)
Dispersal = seed dispersal mode
Code/Software
Text files are included with the R code used for the analysis of the trait and performance data:
- "R code for Common Garden survival.txt"- script for analysis of seedling survival in the common garden experiment in R
- "R code for Common Garden growth.txt"- script for analysis of seedling growth in the common garden experiment in R
- "R code for transplant survival.txt" - script for analysis of seedling survival in the reciprocal transplant experiment in R
- "R code for transplant growth.txt"- script for analysis of seedling growth in the reciprocal transplant experiment in R
- "R code BV common garden trait analysis.txt"- script for analysis of common garden trait data in R
- "R code for greenhouse trait analysis.txt" - script for analysis of greenhouse trait data in R