Data from: Multi-generation analysis of whether local or genetically mixed populations perform best in restoration plantings
Data files
Apr 06, 2026 version files 12.26 MB
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2017data_density.csv
604.18 KB
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AllYrsdata.csv
119.70 KB
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aster_dat3.csv
216.96 KB
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CrossEckert2026_RestorationAnalyses.Rmd
35.52 KB
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latlongs.csv
375 B
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newfitclimdat.csv
15.21 KB
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README.md
12.57 KB
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Resto_Fig1_Maps_Rev2.R
11.92 KB
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tplantlatlongs.csv
157 B
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tplants.csv
11.24 MB
Abstract
Data and analysis files to support the manuscript "Multi-generation analysis of whether local or genetically mixed populations perform best in restoration plantings".
Proper selection of genetic material is critical for restoring populations, with local seed often selected to maximize local adaptation. But, if local populations are small, inbred, or maladapted, then including genotypes from various populations may enhance population growth and long-term adaptation.
In the article, we report a novel test of whether planting locally sourced or genetically mixed populations results in higher fitness over single and multiple generations using Camissoniopsis cheiranthifolia, a species widely used in Pacific coastal dune restoration.
We tested for benefits of planting local vs. nonlocal seed using two reciprocal transplant experiments in unmanipulated dune habitat. In the second experiment, we also compared the fitness of descendants from unmanipulated populations to those from populations where genotypes from genetically differentiated populations were transplanted ~ 10 generations previously. Several datasets are provided here based on these experiments, including data formatted for aster modelling.
Dataset DOI: 10.5061/dryad.tb2rbp0h6
Description of the data and file structure
These data were collected at Pacific coastal dune sites on individuals of the species Camissoniopsis cheiranthifolia. A transplant experiment was conducted in 2005 and the allyrs and dens_dat datasets are results of measuring random individuals at the transplant site and source populations from that experiment after several generations had passed. An additional transplant experiment was executed in 2018, and the tplants and aster_dat3 datasets are results of monitoring the fitness of those transplants throughout their lives. fitclimdat combines fitness data of the transplants from both 2005 and 2018 experiments with relevant climate variables from ClimateNA.
Most analyses are conducted in CrossEckert2026_RestorationAnalyses.Rmd, with the datasets read in at the top of the analysis file.
All measures of length, width, and precipitation are in mm unless otherwise stated.
Figure 1, the map, is generated in its own R file, Resto_Fig1_Maps_Rev2.R. latlongs.csv and tplantlatlongs.csv are used in this R file.
Please see the manuscript for additional methodological details.
Files and variables
File: Resto_Fig1_Maps_Rev2.R
Description: Code to generate figure 1 map
File: latlongs.csv
Description: latitude and longitude of sites, used in map Figure 1
File: tplantlatlongs.csv
Description: latitude and longitude of transplant sites, used in Map Figure 1
File: newfitclimdat.csv
Description: Fitness data from 2005 and 2018 transplants; combined with relevant climate data variables.
Variables
- yr: year of experiment
- site: transplant site
- source: source population
- fit: average lifetime fitness
- se: standard error of fitness
- rel_fit_at_site: relativized fitness
- rel_fit_across_sites: relativized fitness across sites
- site_distrl_km: distance from site to range limit in kilometers
- source_distrl_km: distance from source to range limit in kilometers
- sourcetositedist_km: distance from site to source in kilometers
- lat_site: latitude of transplant site
- lon_site: longitude of transplant site
- lat_source: latitude of source population
- lon_source: longitude of source population
- sitetosource_lat_deg: degrees latitude from site to source
- abs_sitetosource_lat_deg: absolute value of above
- sourcetosite_lat_deg: degrees latitude from source to site
- abs_sourcetosite_lat_deg: absolute value of above
- yr_site: year and site combined
- yr_source: year and source combined
- mDD5_hist: historical mean growing degree days above 5°C
- mDD_0_hist: historical mean chilling degree days below 0°C
- mPPT_sm_hist: historical mean summer precipitation
- mPPT_wt_hist: historical mean winter precipitation
- mDD5_site: mean growing degree days above 5°C at site
- mDD_0_site: mean chilling degree days below 0°C at site
- mPPT_sm_site: mean summer precipitation at site
- mPPT_wt_site: mean winter precipitation at site
- mDD5_source: mean growing degree days above 5°C at source
- mDD_0_source: mean chilling degree days below 0°C at source
- mPPT_sm_source: mean summer precipitation at source
- mPPT_wt_source: mean winter precipitation at source
File: AllYrsdata.csv
Description: Reproduction measurements on random plants at unmanipulated source and mixed-genotype transplant site locations from 2005 experiment; measurements taken 2017-2019 (~ ten generations after transplant).
Variables
- site: location
- order1: data tracking variable
- yr_plant_id: plant identification number
- block: transplant block (at mixed sites)
- observer: person measuring plant
- id: plant ID in field
- pl: plant length
- pw: plant width
- rl: rosette length
- rw: rosette width
- sec_br: number of secondary branches
- tert_br: number of tertiary branches
- quat_br: number of quaternary of higher branches
- bud: number of buds
- ab: number of aborted buds
- of:number of open flowers
- sf: number of spent flowers
- dfr: number of developing fruits
- mfr: number of mature fruits
- af: number of aborted fruits
- scribe: person writing down the data in the field
- enterer: person entering data into computer
- day: day of measurement
- month: month of measurement
- year: year of measurement
- doy: day of year of measurement
- reproOutput: reproductive output total
- logRO: log(10) of reproductive ouput
- st: source (unmanipulated site) or transplant (mixed genotype site)
- state: US state
- latitude: latitude
File: tplants.csv
Description: Plant size and reproduction measurements on transplants planted in 2018 experiment
Variables
- plant_id: plant ID; three-digit code indicating where the individual was planted; sites OPR = W133; OBU = W36; OHF = E0; OSJ = B60; OBS = B220. First number is the block where it was planted, second number is the individual position.
- site: transplant site
- round: round of data collection on transplants
- date: date of measurements
- page: pg number
- plot: transplant block
- obs: observer ID
- plant_pos: plant's position in transplant block
- pl: plant length (mm)
- pw: plant width (mm)
- rl: rosette length (mm)
- rw: rosette width (mm)
- sec: number of secondary branches (coming out from the rosette)
- tert: number of tertiary branches (coming off secondary branches)
- quat: number of quaternary branches
- L5: number of branches less than 5 cm long
- X5_10: number of branches 5-10 cm long
- X10_15: number of branches 10-15 cm long
- G15: number of branches > 15 cm long
- bud: number of buds
- ab: number of aborted buds
- of: number of open flowers
- sf: number of spent flowers
- dfr: number of developing fruit
- mfr: number of mature fruit
- afr: number of aborted fruit
- lvs: number of leaves in the rosette
- herb: number of rosette leaves that are herbivorized
- ch: number of rosette leaves that have been bitten completely off
- scr: scribe initials
- notes: in-field notes about plant
- ent_notes: notes from the data enterer
- enterer: data entry initials
- Columns created after field data collection complete
- buds: number of buds
- db: is the buds divided into small and large buds (Y/N)
- div_buds: small and large buds separated by _
- smbud: number of small buds (<5 mm long)
- lgbud: number of large buds (>5 mm long)
- pa: plant area (l x w; mm^2)
- ra: rosette area (l x w; mm^2)
- reproOutput: number of reproductive structures (buds, flowers, or fruits; not aborted)
- logpa: log10 pa
- logRO: log10 reproOutput
- sum_branches: total number of branches
- logbranches: log10 sum_branches
- day: day of date
- month: month of date
- year: year of date
- doy: day of year
- sqrtRO: square root of reproOutput
- order: dataset ordering
- latitude: latitude of planting site
- order2: more dataset ordering
- occupant: ID of the occupant from the roottrainer
- rt_pos: roottrainer position (for verification)
- tray_cell: position in plug trays in greenhouse from before transfer to roottrainers
- maternal_line: ID of the maternal line (source genotype)
- uniqueMatID: ID of the mother plant from the field (2017 fruit collection)
- source: source population
- L5mc: are there multiple categories of branches in the L5 column?
- X510mc: are there multiple categories of branches in the 5-10 column?
- X1015mc: are there multiple categories of branches in the 10-15 column?
- G15mc: are there multiple categories of branches in the G15 column?
- mc1: L5 if there were multiple categories
- secL5: number of secondary branches less than 5 cm long
- tertL5: number of tertiary branches less than 5 cm long
- quatL5: number of quaternary branches less than 5 cm long
- mc2: X5-10 if there were multiple categories
- sec5_10: number of secondary branches 5-10 cm long
- tert5_10: number of tertiary branches 5-10 cm long
- quat5_10: number of quaternary branches 5-10 cm long
- mc3: X10_15 if there were multiple categories
- sec10_15: number of secondary branches 10-15 cm long
- tert10_15: number of tertiary branches 10-15 cm long
- quat10_15: number of quaternary branches 10-15 cm long
- mc4: G15 if there were multiple categories
- secG15: number of secondary branches >15 cm long
- tertG15: number of tertiary branches >15 cm long
- quatG15: number of quaternary branches >15 cm long
File: aster_dat3.csv
Description: 2018 Transplant fitness data processed for use in aster models.
Variables
- plant_id: as in tplants.csv.
- site: planting site
- occupant: ID of the occupant from the roottrainer
- block: planting block / plot (same as plot in transplant data above)
- rt_pos: roottrainer position (for verification)
- tray_cell: position in plug trays in greenhouse from before transfer to roottrainers
- maternal_line: ID of the maternal line (source genotype)
- uniqueMatID: ID of the mother plant from the field (2017 fruit collection)
- source: source population
- 1: reproduction in year 1 (binary)
- f2: reproduction in year 2 (binary)
- f3: reproduction in year 3 (binary)
- m1: survival in year 1 (binary)
- m2: survival in year 2 (binary)
- m3: survival in year 3 (binary)
- r1: reproductive output in year 1 (count; number of fruits)
- r2: reproductive output in year 2 (count; number of fruits)
- r3: reproductive output in year 3 (count; number of fruits)
File: 2017data_density.csv
Description: Radial density data collected around random individuals at unmanipulated and mixed-genotype sites in 2017 (not related to 2018 transplant experiment).
Variables
- site: site
- order1: for data quality tracking
- date: date of observation
- yr_plant_id: plant ID with year of observation
- uniqueID: plant ID
- plant_id2: in field plant ID
- block: transplant block if applicable (not at unmanipulated sites)
- obs_id: observer and plant ID
- observer: observer
- id: plant ID number
- uniqueIDtb: check of unique ID
- plant_id: same as plant_id2
- pl: plant length
- pw: plant width
- rl: rosette length
- rw: rosette width
- sec _br: number of secondary branches (coming out from the rosette)
- tert_br: number of tertiary branches (coming off secondary branches)
- quat_br: number of quaternary branches
- secbr_L5: number of secondary branches less than 5 cm long
- tertbr_L5: number of tertiary branches less than 5 cm long
- quatbr_L5: number of quaternary branches less than 5 cm long
- secbr_5_10: number of secondary branches 5-10 cm long
- tertbr_5_10: number of tertiary branches 5-10 cm long
- quatbr_5_10: number of quaternary branches 5-10 cm long
- secbr_10_15: number of secondary branches 10-15 cm long
- tertbr_10_15: number of tertiary branches 10-15 cm long
- quatbr_10_15: number of quaternary branches 10-15 cm long
- secbr_G15: number of secondary branches >15 cm long
- tertbr_G15: number of tertiary branches >15 cm long
- quatbr_G15: number of quaternary branches >15 cm long
- age: an estimate of whether the plant was in year 1 or older
- bud: number of buds
- ab: number of aborted buds
- of: number of open flowers
- sf: number of spent flowers
- dfr: number of developing fruit
- mfr: number of mature fruit
- afr: number of aborted fruit
- veg: number of vegetative C cheir plants within the radial density
- repro: number of reproductive C cheir plants within the radial density
- post: number of post-reproductive C cheir plants within the radial density
- scribe: in-field scribe
- notes: notes from field
- enterer: person entering data into computer
- data_entry_notes: notes from data enterer
- data_checked_by: person checking accuracy of data
- sum_branches: total number of branches
- day: day of observation
- month: month of observation
- year: year of observation
- radDensity: radial density total
- reproOutput: total reproductive output
- logRO: log 10 reproOutput
- logRD: log 10 radDensity
- doy: day of year of observation
- state: US state
- sround: sampling round
- st: source (unmanipulated site) or transplant (mixed genotype site)
- latitude: lat of site
File: CrossEckert2026_RestorationAnalyses.Rmd
Description: R script to analyze data and generate figures
Code/software
R and R Studio
Packages: tidyverse, reshape2, MASS, car, emmeans, aster, lme4, rgbif, sf, ggspatial, rnaturalearth, ggpubr, cowplot