Data from: An established plant invader may still benefit from increasing genetic diversity – Insights from artificial populations in a common garden experiment
Data files
Feb 06, 2025 version files 44.65 MB
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README.md
7.26 KB
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Watermann_etal_CommonGarden.R
37.65 KB
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Watermann_etal_DW.csv
33.43 KB
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Watermann_etal_GD_data.txt
1.30 KB
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Watermann_etal_Mixes_Id.csv
1.41 KB
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Watermann_etal_Monitoring_13.csv
17.73 KB
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Watermann_etal_Monitoring.csv
253.88 KB
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Watermann_etal_nativcoord.csv
1.58 KB
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Watermann_etal_nonativcoord.csv
1.25 KB
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Watermann_etal_pop_indno.csv
576 B
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Watermann_etal_Popstat.R
10.62 KB
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Watermann_etal_SampleMaster.csv
14.39 KB
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Watermann_etal_SeedSize.csv
27.80 KB
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Watermann_etal_SNPs.g50mac3DP40thin.recode.vcf
44.24 MB
Abstract
Genetic diversity and competitive ability, though extensively studied in the context of biological invasions, are still poorly understood in their relative importance, especially when shifting the perspective from individual plant’s phenotype to overall population performance. Most approaches addressing the role of genetic diversity involve the comparison of standing genetic variation in field populations combined with experimental treatments on individual plants. Composing predefined mixtures of populations to manipulate genetic diversity would be an experimental approach to test for direct effects on population performance. We determined pairwise genetic distances among 16 invasive and 22 native populations of Jacobaea vulgaris GAERTN. using single nucleotide polymorphisms (SNP). Based on this information, we created each 15 de-novo populations with different levels of genetic diversity for both origins. These de-novo populations were subjected to three levels of decreasing microsite availability by using a matrix of either 0, 5 or 10 individuals of Festuca rubra. We monitored population performance continuously throughout two growing seasons to study effects of interactions between origin, microsite availability and genetic diversity with (generalized) linear effects models. This allowed us to uncover whether relative importance of those factors varies with life-stage of this biennial species.
We found no ambiguous patterns on the hypothesized beneficial effect of genetic diversity for Jacobaea vulgaris populations. Native populations tended to respond negatively to increasing genetic diversity, especially under more favorable site conditions, but this was not a persistent pattern and only evident through continuous monitoring. Invasive populations could benefit from increasing genetic diversity during early establishment, but not in interaction with restricted microsite availability.
Our results do suggest that genetic variation supports population establishment and performance under certain environmental conditions. Therefore, for recommendations in nature conservation, efforts should still aim at limiting propagule addition in already invaded areas even in well-established invasive species.
https://doi.org/10.5061/dryad.0000000dr
Description of the data and file structure
This set contains all raw data as well as R script relevant to the manuscript: “An established plant invader may still benefit from increasing genetic diversity – Insights from artificial populations in a common garden experiment” by Watermann LY, Durka W and Erfmeier A
Files and variables
File: Watermann_etal_Popstat.R
Description: R script for He values, Fst, IBD
File: Watermann_etal_CommonGarden.R
Description: R script for common garden experiment analysis
File: Watermann_etal_SampleMaster.csv
Description: File with general information for all experimental units
Variables
- ID: unique identifier for an experimental unit in the common garden experiment
- MS_Level: level of microsite availability according to how many seedling of Festuca rubra were planted at the beginning of the experiment.
- SampleID: Unique identifier that details population identity and which of the nine replicates was used.
- PopID: Identifier for the population. If there is a population identifier (e.g. USA_EVE) the sample was a monoculture population if a source population. Nxx or Ixx refer to one of the native or invasive experimental de-novo populaitons.
- Origin: Identifies population origin. Non-native = invasive
File: Watermann_etal_Mixes_Id.csv
Description: File contains information for all de-novo populations in the experiment
Variables
- MixID: ID of the de-novo populations
- Pop4: source population ID
- Pop5: source population ID
- Pop3: source population ID
- Pop2: source population ID
- Pop1: source population ID
- Pop6 - Kontrolle: data field used for control
File: Watermann_etal_DW.csv
Description: Dry weight at final harvest
Variables
- ID: unique identifier for an experimental unit in the common garden experiment
- Type: not relevant. Was used to identify vegetative and reproductive biomass before values were merged for one sample.
- VegBM_adj: Vegetative biomass without dry-mass of SLA leaf (SLA was not evaluated)
- SLA_dw: dry weight of SLA leaf
- Veg_Bm: total vegetative biomass
- RepEBM: reproductive biomass that was harvested early due to concerns of spreading seeds
- RepB_adj: reproductive biomass without the part that was harvested early
- RepBM_total: total reproductive biomass
- TBM: overall biomass
- R_Veg: Ratio of reproductive to total biomass
- R_total: Ratio of reproductive total biomass
- GBM_adj: Dry weight of biomass of Festuca rubra
- Total_Gr: Biomass of Jacobaea vulgaris in relation to biomass of Festuca rubra
File: Watermann_etal_SeedSize.csv
Description: File contains information for the average projected area for each experimental unit seed sample
Variables
- SampleID: Unique identifier that details population identity and which of the nine replicates was used.
- GLOBAL: used by software
- ImageFileName: identifier for the acquired image used for seed analysis
- TotalProjAreaObj: total projected area per sample
- AvPA: Average projected area per seed
- AvSTLine: average straight length per seed
- AvStWi: average straight width per seed
File: Watermann_etal_Monitoring_13.csv
Description: Data from last monitoring (at harvest)
Variables
- ID: unique identifier for an experimental unit in the common garden experiment
- Date: Date of monitoring
- MonNum: Number of Monitoring
- Week: Week when monitoring was conducted.
- Vegetative: Number of individuals in Class VI
- Gen_1: Number of individuals in Class VII
- Gen_2: Number of individuals in Class VIII
- Gen_3: Number of individuals in Class IX
- Gen_4: Number of individuals in Class X
- Height: height of tallest individual of Jacobaea vulgaris
- Comment: -
File: Watermann_etal_GD_data.txt
Description: File containing the unbiased expected heterozygosity (He) for de-novo populations.
Variables
- MixID: Identifier of the de-novo population. Relates to PopID in the SampleMaster file
- meanfst: originally used variable
- He, AF=sum over reads: calculated genetic diversity by summing up read counts across samples
- He meanAF: not relevant
- He, AF=sum.filtered.reads: not relevant
- He meanAF.filtered.reads: not relevant
File: Watermann_etal_nativcoord.csv
Description: Information for native source populations
Variables
- PopID: Unique identifier for source populations. Additional populations included.
- Location: Location name
- Latitude
- Longitude
- Elevation_m: elevation in meters
- federalState: federal state of location
- sampledInd: number of sampled individuals
File: Watermann_etal_pop_indno.csv
Description: Number of maternal individuals for source populations
Variables
- PopID: Unique identifier for source populations. Additional populations included.
- Inds: Number of maternal individuals
File: Watermann_etal_nonativcoord.csv
Description: Information for invasive source populations
Variables
- PopID: Unique identifier for source populations. Additional populations included.
- Location: Location name
- Latitude
- Longitude
- Elevation_m: elevation in meters
- federalState: federal state of location
File: Watermann_etal_Monitoring.csv
Description: data from monitorings during common garden experiment. Be aware that not all monitoring dates were used and half weeks assigned to full weeks.
Variables
- ID: unique identifier for an experimental unit in the common garden experiment
- Date: Date of monitoring
- MonNum: Number of Monitoring
- Week: Week when monitoring was conducted.
- Classx = Number of individuals in class. Juv = Class VI, Bolt = Class VII
- Juv: Class VI
- Bolt: Class VII
- Covfes: Cover of *Festuca rubra. *Only assessed at specific date
- CovJac: Cover of *Jacobaea vulgaris. *Only assessed at specific date
- Comment
- Fes_real: Number of established Festuca rubra seedling
- Fungus: note of fungal infection at certain point. No treatment was necessary as infection resolved
File: Watermann_etal_SNPs.g50mac3DP40thin.recode.vcf
Description: Used SNP data (after filtering)
Code/software
Packages for Watermann_etal_CommonGarden:
R version 4.3.1 (2023-06-16 ucrt) – “Beagle Scouts”
library(rstudioapi) #0.16.0
library(reshape2) #1.4.4
library(lme4) #1.1.34
library(lmerTest) #3.1.3
library(car) #3.1.2
library(DHARMa) #0.4.6
library(glmmTMB) #1.1.7
library(ggplot2) #3.4.3
library(ggpubr) #0.6.0
library(emmeans)#1.8.8
library(data.table)#1.14.8
library(EnvStats)#2.8.1
library(mgcv)#1.9-0
Packages for Watermann_etal_PopStat:
R version 4.3.1 (2023-06-16 ucrt) – “Beagle Scouts”
library(vcfR) #1.14.0
library(poolfstat) #2.2.0
library(pcadapt)#4.3.5
library(raster)#3.6.26
library(geodist)#0.0.8
library(vegan)#2.6.4
library(PopGenReport)#3.1
library(ape)#5.7.1
library(ggpubr) #0.6.0
library(ggplot2) #3.4.3