DOI: 10.5061/dryad.0000000dr
title: Data from: An established plant invader may still benefit from increasing genetic diversity – Insights from artificial populations in a common garden experiment

description: 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.
description: # Data from: An established plant invader may still benefit from
 increasing genetic diversity – Insights from artificial populations in a
 common garden experiment
 [https://doi.org/10.5061/dryad.0000000dr](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 (*H*e) 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