Lauren N. Carley et al.

lauren.n.carley@gmail.com

STRUCTURE OF THIS ARCHIVE:

Details on the purpose of each file in these folders, and their subdirectories, is provided below, following the general outline:

• Clarkia-LTREB-transplant-archive/
  • README.txt
  • 1-data/
  • 2-analyses/
  • 2a-seed-prediction/
  • 2b-aster/
  • 2c-dist-calcs/
    • out/
  • 2d-dist-analyses/
  • 2e-permutation-tests/
    • Fdists/
  • 3-figures/
  • supplemental/

NOTE: Throughout the whole directory, variables in datasets are unitless unless otherwise defined, and "NA" values represent missing data unless otherwise defined.

Clarkia-LTREB-transplant-archive-R2/

This directory contains all of the other subdirectories, which take you
through data processing, modeling, and analysis step by step.

It also contains one file:

README.txt

You are currently reading this text file. It explains all of the other files associated with this archive.

Clarkia-LTREB-transplant-archive-R2/1-data/

This folder contains data gathered and analyzed in this manuscript. It contains 7 files, organized by data type. The contents of each file are described below.

a1-clarkia_ltreb_lambdas.csv

This data file (.csv format, sep=",") contains the population growth rates for the 10 focal population in this study, estimated from empirical field census data from 2005-2016.

Columns are as follows:

• Population: Population ID, the abbreviations "BR", "URS", and others are used to identify populations. These abbreviations match the population nicknames shown on the map in Figure 1 of this manuscript, and are further defined in other datafiles (e.g. "b-compiled-climate-data-final.csv" has a column with population ID linked to a full, more descriptive site name). However, the full site name is somewhat arbitrary and the populations are best defined by their locations, which are already identified in this datasheet (and others) by the geographical location (here, northing and easting).
• Northing(km): population North-South position in UTM NAD 27 (km north of the equator)
• Easting(km): population East-West position in UTM NAD 27 (km east of the beginning of UTM zone 11)
• Lam1: the deterministic population growth rate (see Appendix S1 and Eckhart et al. 2011, Am. Nat. for further detail)
• Lambda_S: the stochastic population growth rate(see Appendix S1 and Eckhart et al. 2011, Am. Nat. for further detail)

a2-clarkia_ltreb_elasticities_compiled.csv
This data file (.csv format, sep=",") contains the elasticities of each population's growth rate to each underlying vital rate or life-cycle loop (see Appendix S1 for additional detail).

Columns are as follows:

• population: Population ID, The abbreviations "BR", "URS", and others are used to identify populations; see above for full description of this.
• incl_transplant: designation of whether each population was included in the reciprocal transplant (1) or not (0). Values of 0 and 1 occur in one column, "incl_transplant", and the meanings of these values are defined in the (lengthy and detailed) README file containing metadata for this archive.
• demog_pair: Assignment of each population to its demographic pair, as in Fig. 1 of the main text. Populations not included in the transplant are listed as NA since they have no pair assignment.
• data_year: the final year of field census data used to estimate population dynamics and elasticities.
• e_L1: the elasticity of lambda to loop 1 (Appendix S1; Figure S7)
• e_L2: the elasticity of lambda to loop 2 (Appendix S1; Figure S7)
• e_L3: the elasticity of lambda to loop 3 (Appendix S1; Figure S7)
• e_L4: the elasticity of lambda to loop 4 (Appendix S1; Figure S7)
• s1: the elasticity of lambda to vital rate s1 (Appendix S1; Figure S7)
• s2: the elasticity of lambda to vital rate s2 (Appendix S1; Figure S7)
• s3: the elasticity of lambda to vital rate s3 (Appendix S1; Figure S7)
• s4: the elasticity of lambda to vital rate s4 (Appendix S1; Figure S7)
• s5: the elasticity of lambda to vital rate s5 (Appendix S1; Figure S7)
• s6: the elasticity of lambda to vital rate s6 (Appendix S1; Figure S7)
• g1: the elasticity of lambda to vital rate g1 (Appendix S1; Figure S7)
• g2: the elasticity of lambda to vital rate g2 (Appendix S1; Figure S7)
• g3: the elasticity of lambda to vital rate g3 (Appendix S1; Figure S7)
• sigma: the elasticity of lambda to vital rate sigma (Appendix S1; Figure S7)
• F: the elasticity of lambda to vital rate F (Appendix S1; Figure S7)
• phi: the elasticity of lambda to vital rate phi (Appendix S1; Figure S7)

b-compiled-climate-data-final.csv

This data file (.csv format, sep=",") contains the long-term trends (means and SDs) in temperature and precipitation, as well as solar radiation data.

Columns are as follows:

• site: Full site name
• id: Population ID, The abbreviations "BR", "URS", and others are used to identify population IDs; see above for full description of this. In this datasheet, population ID is linked to a longer, more descriptive name in the "site" column.
• intense_demog: indication of whether each population is a part of annual demographic censuses (1) or not (0)
• incl_trans: indication of whether each population was included in the demographic reciprocal transplant (1) or not (0)
• demog_pair: Assignment of each population to its demographic pair, as in Fig. 1 of the main text. Populations not included in the transplant are listed as 'X' since they have no pair assignment.
• easting: population East-West position in UTM NAD 27 (m east of the beginning of UTM zone 11)
• northing: population North-South position in UTM NAD 27 (m north of the equator)
• elevation: elevation in m
• area: estimated area of the circumscribed population, in ha
• dominant.surface.rock.type: the dominant surface rock type in that population
• Tsp.mean: mean spring temperature from 2005-2021 (C)
• Tsu.mean: mean summer temperature from 2005-2021 (C)
• Tw.mean: mean winter temperature from 2005-2021 (C)
• Psp.mean: mean total spring precipitation from 2005-2021 (mm)
• Psu.mean: mean total summer precipitation from 2005-2021 (mm)
• Pw.mean: mean total winter precipitation from 2005-2021 (mm)
• Tsp.sd: standard deviation of spring temperatures from 2005-2021
• Tsu.sd: standard deviation of winter temperatures from 2005-2021
• Tw.sd: standard deviation of winter temperatures from 2005-2021
• Psp.sd: standard deviation of spring precipitation from 2005-2021
• Psu.sd: standard deviation of summer precipitation from 2005-2021
• Pw.sd: standard deviation of winter precipitation from 2005-2021
• label: Population ID, but left blank for non-focal populations (for placing labels on environmental PCA)
• winter_solstice_rad..w.m2.: solar radiation on the winter solstice in watts per m^2
• equinox_rad: solar radiation on the equinox in watts per m^2

c-LTREB_transplant_coordinates.csv
This data file (.csv format; sep=",") contains information about the geographic position of each focal population. Columns are as follows:

• id: Population ID
• demog_pair: Assignment of each population to its demographic pair, as in Fig. 1 of the main text
• Lat: Latitude, in decimal degrees
• Lon: Longitude, in decimal degrees

d1-LTREB_transplant_data_round1_clean.csv

This data file (.csv format, sep=",") contains data from Cohort 1 of the demographic transplant experiment. Columns are as follows:

• row_number: unique number for each row of data in the dataset
• site: growth site during the reciprocal transplant, identified by the local population's ID
• sourceSiteActual: the actual source population planted into the grid cell
• grid: planting grid number (i.e. one randomized complete statistical block)
• rowNo: row where an individual seed was planted within a grid
• colNo: column where an individual seed was planted within a grid
• FebgermNo: number of germinants observed in the grid cell in February
• MarSurv: survival of February germinants to the March census (1=lived; 0=died; NA or blank = there was no germinant in February)
• MarnewGerm: indication of whether a germinant was observed in March that was not observed in February (1 = yes; 0 or blank = no)
• MaySurv: survival of germinants from February or March to the May census
• MaynewGerm: indication of whether a germinant was observed in May that was not observed in February or March (1 = yes; 0 or blank = no)
• flowering: did an individual flower? (1=yes, 0 or blank = no)
• fruiting: did an individual produce fruits? (1=yes, 0 or blank = no)
• no_seeds: total seed set across all fruits produced by an individual plant
• comments: notes
• comments2: notes, continued
• comments3: notes, continued, pt. 2
• exclude: indication of whether a row of data should be excluded from final analyses
• flag: mark for correction or exclusion from analyses, for reasons explained in 'notesLC' column
• notesLC: explanation of why this row was flagged during data cleanup
• concat_surv: concatenated survival across multiple time points in the life cycle, to check for issues with contingency (e.g. 1-0-1 implies a plant died and then was reincarnated)
• didgerm: indication of whether a plant ever germinated at any time point in the season after planting (1=yes, 0=no)
• ever_alive: indication of whether a plant was ever marked as alive during the duration of the 2020 field season

d2-transplants_round2_clean.csv
This data file (.csv format, sep=",") contains data from Cohort 2 of the demographic transplant experiment. Columns are as follows:

• site: growth site during the transplant experiment
• grid: planting grid number (i.e. one randomized complete statistical block)
• row: row where an individual seed was planted within a grid
• col: column where an individual seed was planted within a grid
• Pop: source population planted into the grid cell
• FebGer: number of germinants observed in the grid cell in February
• MarGer: indication of whether a germinant was observed in March that was not observed in February (1 = yes; 0 or blank = no)
• MayGer: indication of whether a germinant was observed in May that was not observed in February or March (1 = yes; 0 or blank = no)
• didgerm: indication of whether a plant ever germinated at any time point in the season after planting (1=yes, 0=no)
• MarSurv: survival of February germinants to the March census (1=lived; 0=died; NA or blank = there was no germinant in February)
• MaySurv: survival of germinants from February or March to the May census (1=yes, 0 or blank = no)
• LateSurv: survival to flowering in June (0=dead, 1=alive)
• didflr: did an individual flower? (1=yes, 0 or blank = no)
• didfrt: did an individual fruit? (1=yes, 0 or blank = no)
• FrtColl: were fruits collected? (1 = yes, 0 or blank = no)
• undamaged_frts: number of fruits without evidence of herbivore damage produced by each surviving plant
• damaged_frts: number of fruits with evidence of herbivore damage produced by each surviving plant
• TotalFrt: the total number of fruits produced per individual (sum of undamaged_frts and damaged_frts)
• undamaged_weight: weight in mg of all undamaged fruits
• damaged_weight: weight in mg of all damaged fruits
• undamaged_seeds: number of seeds in all undamaged fruits
• damaged_seeds: number of seeds in all damaged fruits
• FieldNotes: notes from field censuses
• flag: indication that this row of data should be excluded or corrected
• notesLC: context for flagging this row, if the row is flagged

d2b-transplants_round2_clean_predseeds.csv
This data file (.csv format, sep=',') contains the data for Cohort 2 of the demographic reciprocal transplant experiment, plus predicted seed numbers for all individuals. It is written out by the analysis script 'LTREB-year2-seedprediction-archive.Rmd' in subdirectory 2a.

Columns are the same as in 'd2-transplants_round2_clean.csv', but with the following additions:

• total_seeds: the total number of directly counted seeds for individuals which were counted (sum of undamaged_seeds+damaged_seeds)
• seeds_counted: indicates whether seeds were counted directly for this individual (1=yes, 0=no)
• pred_u: the predicted number of seeds produced by undamaged fruits
• pred_d: the predicted number of seeds produced by damaged fruits
• total_pred: the sum of pred_u and pred_d
• total_weight: the sum of the mass of undamaged and damaged fruits

Clarkia-LTREB-transplant-archive-R2/2-analyses/

This folder contains code for running the analyses presented in this manuscript, as well as output files generated by that code. It is organized into subdirectories based on the type of analysis, each of which is explained below.

Clarkia-LTREB-transplant-archive-R2/2-analyses/2a-seed-prediction/

LTREB-year2-seedprediction-archive.Rmd

This code file (.Rmd format) fits linear models relating fruit mass to seed number for Cohort 2 transplants which had seeds counted. It then extracts the coefficients from the models to use to predict seed count for Cohort 2 transplants that only had fruits weighed.

seed-coefs.csv

This data file (.csv format, sep=",") contains the coefficient estimates linking fruit mass to seed number for each source-site combination in Cohort 2 of the reciprocal transplant. Columns are as follows:

• site: the growth site in the reciprocal transplant experiment
• pop: the source population in the reciprocal transplant experiment
• dam: damage status; separate models were fit for damaged (d) and undamaged (u) fruits in each source-site combination, since damaged and undamaged fruits may contain different amounts of seeds
• int: the estimated intercept of the linear model
• int.se: the standard error of the estimated intercept in the linear model weight: the estimated coefficient relating fruit mass to seed number
• weight.se: the standard error of the estimated weight coefficient
• r2: the R^2 for the linear model
• p: the p-value for the effect of fruit mass on seed number
• n: the sample size informing the linear model

Clarkia-LTREB-transplant-archive-R2/2-analyses/2b-aster/

LTREB-aster-models-archive.Rmd

This code file (.Rmd format) uses aster models to estimate source- and site-specific lifetime fitness in the first year following seed dispersal for both cohorts of the demographic reciprocal transplant experiment.

transplant_yr1_aster.csv

This data file (.csv, sep=",") contains life-history information for all indivdiuals in Cohort 1 of the reciprocal transplant, formatted in a way compatible with aster modeling. Columns are as follows:

• site: growth site in the reciprocal transplant experiment
• pop: source population in the reciprocal transplant experiment
• grid: grid number (i.e. randomized complete block) in the reciprocal transplant experiment
• row: row position of a transplanted individual within a grid
• col: column position of a transplanted individual with a grid
• varb: variable, i.e. life-history transition or fitness component; options include: "didgerm", indicating whether germination ever occurred in a transplant cell at any time (0=no, 1=yes); "marsurv", indicating whether an individual survived to the March census of the transplant year (0=no, 1=yes); "maysurv", indicating whether an individual survived to May of the transplant year (0=no, 1=yes); "didflr", indicating whether an individual produced any flowers (0=no, 1=yes); "didfrt", indicating whether an indivudal produced any fruits (0=no, 1=yes) and "seeds" (indicating the number of seeds produced)
• resp: the response variable for this varb; responses for all varbs are binary (0 or 1; see above) except for the varb "seeds", for which responses are integers
• id: unique numerical identifier of individual plants; each id is repeated once per observed life-history transition per individual
• root: '1'; necessary for aster modeling; aliased for all individuals/varbs
• seeds: identifies whether this row is associated with the varb 'seeds' (0=no, 1=yes)

transplant_yr2_aster.csv
This data file (.csv, sep=",") contains life-history information for all indivdiuals in Cohort 2 of the reciprocal transplant, formatted in a way compatible with aster modeling. Column contents are identical to those in 'transplant_yr1_aster.csv'.

transplant_yr2_aster_b.csv
This data file (.csv, sep=",") contains life-history information for all individuals in Cohort 2 of the reciprocal transplant, formatted in a way compatible with aster modeling. Column contents are identical to those in 'transplant_yr1_aster.csv' and 'transplant_yr2_aster.csv' except this cohort 2 data frame excludes one life-history node which could not be included in the aster model for one site (GCN).

year1-lifetimefitness-means.csv
This data file (.csv, sep=',') contains aster-estimated lifetime fitness for each source-site combination in Cohort 1 of the reciprocal transplant experiment. Columns are as follows:

• varb: variable, i.e. life-history transition or fitness component; defined above in metadata for aster datasets
• pop: source population in the reciprocal transplant experiment
• est: aster-estimated lifetime fitness, i.e. seeds set per seed planted, for this source-site combination
• est.se: the standard error around the estimate 'est'
• site: growth site in the reciprocal transplant experiment
• col: identifier of whether a given source-site combination is matched ('home'), mismatched but demographically paired ('pair'), or mismatched but demographically unpaired ('away')

year1-lifetimefitness.csv
This data file (.csv format, sep=',') contains aster-modeled estimates of each life-history transition (i.e. fitness component) for each individual plant in Cohort 1 of the reciprocal transplant experiment. Note that because this model contains no random effects, the estimates are identical for all individuals within a given source-site combination. Columns are as follows:

• site: growth site in the reciprocal transplant experiment
• pop: source population in the reciprocal transplant experiment
• grid: grid number (i.e. randomized complete block) in the reciprocal transplant experiment
• row: row position of a transplanted individual within a grid
• col: column position of a transplanted individual with a grid
• varb: variable, i.e. life-history transition or fitness component; defined above in metadata for aster datasets
• resp: the response variable for this varb
• id: unique identifier of individual plants; each id is repeated once per observed
• life-history transition per individual
• root: '1'; necessary for aster modeling; aliased for all individuals/varbs
• seeds: identifies whether this row is associated with the varb 'seeds' (0=no, 1=yes)
• fit: the aster-estimated fitted response of this varb; for the varb 'seeds', the units of the fitted values are seeds produced per seed sown given an individual's source population and growth environment; for all other varbs, the units of the fitted values are transition rates (i.e. proportions)
• se: the standard error around the 'fit' estimate

year2-lifetimefitness-means.csv
This data file (.csv, sep=',') contains estimated lifetime fitness for each source-site combination in Cohort 2 of the reciprocal transplant experiment. Column contents are identical to those in 'year2-lifetimefitness-means.csv'.

year2-lifetimefitness.csv
This data file (.csv format, sep=',') contains aster-modeled estimates of each life-history transition (i.e. fitness component) for each individual plant in Cohort 2 of the reciprocal transplant experiment. Note that because this model contains no random effects, the estimates are identical for all individuals within a given source-site combination. Column contents are identical to those in 'year1-lifetimefitness.csv'.

Clarkia-LTREB-transplant-archive-R2/2-analyses/2c-dist-calcs/

LTREB-pairwise-distance-calculations-archive.Rmd

This code file (.Rmd format) uses underlying demographic, environmental, and geographic data to estimate pairwise distances in demographic, environmental, and geographic space. In so doing, it also writes out most of the files in the /out subdirectory, as well as four of the .csv files in this directory describing demographic and environmental PCAs.

final-env-PCA-loading.csv

This data file (.csv, sep=',') contains information on the loading of each underlying environmental variable onto environmental principal components axes. It is formatted as a matrix, with variables as row names and PCs as column names. The correlation coefficients between each variable and PC populate the matrix elements.

final-env-PCA-scores.csv

This data file (.csv, sep=',') contains information on each population's position in environmental space. Columns are as follows:

• id: Population ID
• demog_pair: Assignment of each population to its demographic pair, as in Fig. 1 of the main text
• PC1: position on environmental PC axis 1 (unitless)
• PC2: position on environmental PC axis 2 (unitless)
• PC3: position on environmental PC axis 3 (unitless)
• PC4: position on environmental PC axis 4 (unitless)
• PC5: position on environmental PC axis 5 (unitless)

final-VR-elas-PCA-loading.csv
This data file (.csv, sep=',') contains information on the loading of each underlying vital rate elasticity onto demographic principal components axes. It is formatted as a matrix, with elasticities as row names and PCs as column names. The correlation coefficients between each elasticity and PC populate the matrix elements.

final-VR-elas-PCA-scores.csv
This data file (.csv, sep=',') contains information on each population's position in vital rate elasticity space. Columns are as follows:

• id: Population ID
• demog_pair: Assignment of each population to its demographic pair, as in Fig. 1 of the main text
• PC1: position on vital rate elasticity PC axis 1 (unitless)
• PC2: position on vital rate elasticity PC axis 2 (unitless)
• PC3: position on vital rate elasticity PC axis 3 (unitless)

LTREB-fitness-contrasts-archive.Rmd
This code file (.Rmd format) uses aster-derived fitness data from the reciprocal transplant to estimate pairwise HA and LF fitness contrasts. In so doing, it also writes out some of the files in the /out subdirectory.

Clarkia-LTREB-transplant-archive-R2/2-analyses/2c-dist-calcs/out

This subdirectory contains the output of the code file 'LTREB-pairwise-distance-calculations-archive.Rmd'. Ten of these files are in matrix format, i.e. each population is one row and one column, and matrix elements are the pairwise distance between the population named in that row and column. The pairwise distances in each file is listed below.

    LTREB-demdistA-loop-elas-matrix.csv

• demographic distance A (distance in life-history loop elasticity space; unitless)

    LTREB-demdistB-VR-elas-PCA-matrix.csv

• demographic distance B (distance in vital rate elasticity space; unitless)

    LTREB-demdistC-VR-elas-aboveground-matrix.csv

• demographic distance C (distance in aboveground vital rate elasticity space; unitless)

    LTREB-envdist-matrix.csv

• distance in environmental space calculated using the Manhattan method (unitless)

    LTREB-envdist-matrix-euc.csv

• distance in environmental space calculated using the Euclidean method (unitless)

    LTREB-geodist-km-matrix.csv

• geographic distance (km)

In addition, there are two files containing pairwise distances formatted as dataframes instead of matrices.

    LTREB-wdist-long.csv

• varb: variable or fitness component (here, all lifetime fitness)
• pop: population 1 contrasted in the pairwise difference
• est: aster-estimated absolute lifetime fitness of a source-site combination in the reciprocal transplant experiment (i.e. seeds produced per seed sown)
• est.se: standard error around 'est'
• site: for estimated lifetime fitness, the site in which each source population was grown. for pairwise differences, the second population contrasted with 'pop'
• col: identifier of whether a given source-site combination is matched ('home'), mismatched but demographically paired ('pair'), or mismatched but demographically unpaired ('away')
• wrel.site: absolute fitness (seeds produced per seed sown) relativized within growth sites, for HA contrasts
• wrel.pop: absolute fitness (seeds produced per seed sown) relativized within source populations, for LF contrasts
• HA_wrel_site: home-away contrast using site-relativized fitness (i.e., the difference between a population's relative fitness in the home environment and the same population's relative fitness in an away environment; see eq. 2 in the main text)
• HA_wabs: home-away contrast using absolute fitness (i.e., the difference between a population's absolute fitness in the home environment and the population's absolute fitness in an away environment)
• mean_HA_wrel_site: population-mean HA contrast using relative fitness (see eq. 3 in the main text)
• mean_HA_wabs: population-mean HA contrast using absolute fitness
• LF_wrel_pop: local-foreign contrast using population-relativized fitness (i.e., the difference between the local population's relative fitness and a foreign population's relative fitness within a site; see eq. S2 in the supporting information)
• LF_wabs: local-foreign contrast using absolute fitness (i.e., the difference between the local population's absolute fitness and a foreign population's absolute fitness within a site)
• mean_LF_wrel_pop: population-mean LF contrast using relative fitness (see eq. S3 in the supporting information)
• mean_LF_wabs: population-mean LF contrast using absolute fitness
• yr: indicates Cohort 1 (yr1) vs Cohort 2 (yr2)

  LTREB-wdist-wide.csv

This file contains the same information as 'LTREB-wdist-long.csv', but spread into 'wide' format such that estimates from separate cohorts are represented in their own columns. Column meanings are as in 'LTREB-wdist-long.csv' but are appended with '_yr1' to indicate Cohort 1 estimates or '_yr2' to indicate Cohort 2 estimates.

Clarkia-LTREB-transplant-archive-R2/2-analyses/2d-dist-analyses/

LTREB-distance-analyses-archive.Rmd

This code file (.Rmd format) uses data generated by code in the previous subdirectories to conduct all of the formal analyses presented in the manuscript. This includes comparisons of pairwise fitness contrasts depending on source-site pair status (Fig. 3), multiple regressions contrasting demographic, environmental, and geographic effects on performance (Fig. 4), and analyses of population-mean local adaptation (Fig. 5).

LTREB-alldist-raw-final.csv

This data file (.csv, sep=',') contains aster-derived fitness estimates from the reciprocal transplant, pairwise distance/difference values, and population-mean local adaptation estimates. Columns are as follows:

• varb: variable, i.e. life-history transition or fitness component; here, all 'lifetime_fitness'
• pop: source population in the reciprocal transplant experiment
• site: growth site in the reciprocal transplant experiment
• col: identifier of whether a given source-site combination is matched ('home'), mismatched but demographically paired ('pair'), or mismatched but demographically unpaired ('away')
• est_yr1: aster-estimated lifetime fitness (i.e., seeds produced per seed sown) in a given source-site combination in Cohort 1 of the reciprocal transplant experiment
• est.se_yr1: the standard error of the estimate 'est_yr1'
• wrel.site_yr1: absolute fitness (seeds produced per seed sown) in cohort 1, relativized within sites for calculating HA contrasts (see eq. 1 in the main text)
• wrel.pop_yr1: absolute fitness (seeds produced per seed sown) in cohort 1, relativized within populations for calculating LF contrasts (see eq. S1 in the supporting information)
• HA_wrel_site_yr1: home-away fitness contrasts between the source population grown at home minus the source population grown at the away site specified in 'site', calculated using site-relativized fitness in Cohort 1
• HA_wabs_yr1: home-away fitness contrasts between the source population grown at home minus the source population grown at the away site specified in 'site', calculated using absolute fitness in Cohort 1
• LF_wrel_pop_yr1: local-foreign fitness contrasts between the local population within the site specified in 'site' and a foreign population grown in that site, calculated using population-relativized fitness in Cohort 1
• LF_wabs_yr1: local-foreign fitness contrasts between the local population within the site specified in 'site' and a foreign population grown in that site, calculated using absolute fitness in Cohort 1
• est_yr2: aster-estimated absolute lifetime fitness (seeds produced per seed sown) in a given source-site combination in Cohort 2 of the reciprocal transplant experiment
• est.se_yr2: the standard error of the estimate 'est_yr1'
• wrel.site_yr2: as defined for wrel.site_yr1, but for Cohort 2
• wrel.pop_yr2: as defined for wrel.pop_yr1, but for Cohort 2
• HA_wrel_site_yr2: as defined for HA_wrel_site_yr1, but for Cohort 2
• HA_wabs_yr2: as defined for HA_wabs_yr1, but for Cohort 2
• LF_wrel_pop_yr2: as defined for LF_wrel_pop_yr1, but for Cohort 2
• LF_wabs_yr2: as defined for LF_wabs_yr1, but for Cohort 2
• mean_HA_wrel_site_yr1: population-mean HA local adaptation in Cohort 1, calculated using site-relativized fitness (see eq. 3 of the main text)
• mean_HA_wabs_yr1: population-mean HA local adaptation in Cohort 1, calculated using absolute fitness
• mean_LF_wrel_pop_yr1: population-mean LF local adaptation in Cohort 1, calculated using population-relativized fitness (see eq. S3 of the supporting information)
• mean_LF_wabs_yr1: population-mean LF local adaptation in Cohort 1, calculated using absolute fitness
• mean_HA_wrel_site_yr2: as defined for mean_HA_wrel_site_yr1, but for Cohort 2
• mean_HA_wabs_yr2: as defined for mean_HA_wabs_yr1, but for Cohort 2
• mean_LF_wrel_pop_yr2: as defined for mean_LF_wrel_pop_yr1, but for Cohort 2
• mean_LF_wabs_yr2: as defined for mean_LF_wabs_yr1, but for Cohort 2
• geodist: the geographic distance between the population in 'pop' and the population in 'site' (km)
• envdist.noSoil: the environmental distance between the population in 'pop' and the population in 'site', using the Manhattan method (unitless)
• demdistA: the demographic distance, using metric A, between the population in 'pop' and the population in 'site' (unitless)
• demdistB: the demographic distance, using metric B, between the population in 'pop' and the population in 'site' (unitless)
• demdistC: the demographic distance, using metric C, between the population in 'pop' and the population in 'site' (unitless)
• envdist.noSoil.euc: the environmental distance between the population in 'pop' and the population in 'site', using the Euclidean method (unitless)

LTREB-alldist-stdz-final.csv
This data file (.csv, sep=',') contains the same information as that in the file 'LTREB-alldist-raw-final.csv', except that the values in each pairwise distance column have been standardized to facilitate analyses using multiple regression. Columns meanings are the same as the non-standardized data file.

LTREB-pop-mean-data-final.csv
This data file (.csv, sep=',') contains population-mean data on HA and LF contrasts. Columns are as follows:

• varb: variable, i.e. life-history transition or fitness component; here, all 'lifetime_fitness'
• pop: source population in the reciprocal transplant experiment
• site: growth site in the reciprocal transplant experiment
• col: identifier of whether a given source-site combination is matched ('home'), mismatched but demographically paired ('pair'), or mismatched but demographically unpaired ('away'); here, all rows are "home" because only population-mean values are retained
• mean_HA_wrel_site_yr1: population-mean HA local adaptation in Cohort 1, calculated using site-relativized fitness (see eq. 3 in the main text)
• mean_LF_wrel_pop_yr1: population-mean LF local adaptation in Cohort 1, calculated using population-relativized fitness (see sq. S3 in the supporting information)
• mean_HA_wrel_site_yr2: population-mean HA local adaptation in Cohort 2, calculated using site-relativized fitness (see eq. 3 in the main text)
• mean_LF_wrel_pop_yr2: population-mean LF local adaptation in Cohort 2, calculated using population-relativized fitness (see eq. S3 in the supporting information)
• Lam1: the deterministic population growth rate (see Appendix S1 and Eckhart et al. 2011, Am. Nat. for further detail)
• Lambda_S: the stochastic population growth rate(see Appendix S1 and Eckhart et al. 2011, Am. Nat. for further detail)
• demog_pair: assignment of each population to its demographic pair, as in Fig. 1 of the main text
• weight: relative weight given to each population in weighted regressions; populations in Set I have a weight of 5, while populations in Set II have a weight of 1, which is equivalent to the number of "away" sites each population was tested in to generate population-mean local adaptation estimates.

Clarkia-LTREB-transplant-archive-R2/2-analyses/2e-permutation-tests/

LTREB-permutation-tests-archive.R

This code file (.R format) performs effects tests for all models presented in the manuscript that utilize source-site contrasts, to account for partial non-independence of these contrasts (e.g., for HA, all away sites contrasted against the same home site).

empirical-vs-permuted-summary-final.csv

This data file (.csv, sep=',') contains the output of the permutation tests executed in the code file described above. Each unique combination of yr, type, contrast, and test define a separate statistical model presented in the manuscript. Columns are as follows:

• yr: distinguishes whether the effect test is from Cohort 1 (1) or Cohort 2 (2)
• type: distinguishes whether the response variable in each model is source-site
• contrasts (pairwise fitness contrasts) vs. population-mean local adaptation
• contrast: distinguishes whether the response variable in a given model is home-away local adaptation (ha) or local-foreign (lf)
• test: distinguishes what type independent variables are included in each model; categorical = source-site pair status; multivariateB = continuous metrics of pairwise distance with demographic distance metric B included; multivariate-dem-quadlam = variables describing demographic variation across populations using stochastic lambda
• effect: indicates the independent variable in each model for which effect tests are presented in subsequent columns; pair status = source-site demographic pair status; geodist = continuous pairwise geographic distance; envdist = continuous pairwise environmental distance; demdistB = continuous pairwise demogrpahic distance using metric B; lamstoc-linear = linear effect of stochastic lambda; lamstoc-quadratic = effect of stochastic lambda squared
• F: the F-statistic describing the effect of each independent variable (effect) on the depedent variable (yr+type+contrast) in the 'true' model (actual data)
• p: the p-value describing the effect of each independent variable (effect) on the depedent variable (yr+type+contrast) in the 'true' model (actual data)
• threshold.f: the value of F for a given effect test that defines the beginning of the upper 95% tail of its permuted distribution in 5,000 randomizations
• permuted.p: the p-value inferred from the permutation tests; i.e., the percentile in the permuted F distribution in which the 'true' F statistic falls

Clarkia-LTREB-transplant-archive-R2/2-analyses/2e-permutation-tests/Fdists

Visualizations of outcomes from each individual permuted effect test run in 'LTREB-permutation-tests-archive.R' are stored here.

Clarkia-LTREB-transplant-archive-R2/3-figures/

This subdirectory exists to receive the figures generated by running code housed elsewhere in this repository. Figures from the main text will be written here, and figures appearing in the Supporting Information will be housed in the subdirectory /supplemental. Permuted F distributions for each effects test executed to answer the three main research questions are written to the subdirectory /supplemental/perm-tests.

Because all figures can be reproduced using the data and code files in this archive, these subdirectories are deliberately left blank.