This Primula_veris_landscape_genetics_Readme.txt file was generated on 2021-05-17 by Iris Reinula GENERAL INFORMATION 1. Title of Dataset: Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris 2. Author Information A. Principal Investigator Contact Information Name: Iris Reinula Institution: University of Tartu, Institute of Ecology and Earth Sciences Address: Lai 40, 51005 Tartu, Estonia Email: iris.reinula@ut.ee B. Associate or Co-investigator Contact Information Name: Tsipe Aavik Institution: University of Tartu, Institute of Ecology and Earth Sciences Address: Lai 40, 51005 Tartu, Estonia Email: tsipe.aavik@ut.ee C. Alternate Contact Information Name: Sabrina Träger Institution: Martin-Luther-University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden Address: Große Steinstr. 79/80, 06108 Halle (Saale), Germany Email: sabrina.traeger@botanik.uni-halle.de 3. Date of data collection (single date, range, approximate date): genetic data: 2015-2016 map data originally created: historical maps 1930s, current maps 2015-2017 map data modified for this dataset: 2019-2020 4. Geographic location of data collection: Muhu and Saaremaa islands, Estonia 5. Information about funding sources that supported the collection of the data: Financial support was obtained from the Estonian Research Council (MOBJD427, PUT589 and PRG874), the European Regional Development Fund (Centre of Excellence EcolChange), and the European Commission LIFE+ Nature program (LIFE13NAT/EE/000082). SHARING/ACCESS INFORMATION 1. Licenses/restrictions placed on the data: - 2. Links to publications that cite or use the data: Reinula, I., Träger, S., Hernández-Agramonte, Ignacio M., Helm, A., Aavik, T. (2021). Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris. Diversity and Distributions, xx. 3. Links to other publicly accessible locations of the data: should I add Reinula et al. 2021 later? 4. Links/relationships to ancillary data sets: Sequence data used to generate this data will be made available at the European Nucleotide Archive (ENA) upon acceptance of Träger et al. 2021 (doi: https://doi.org/10.1101/2021.05.12.442254) (ERS5253979 – ERS5254546). 5. Was data derived from another source? yes A. If yes, list source(s): Map data: Laasimer, L. (1965). Eesti NSV taimkate. Tallinn, Valgus Estonian Seminatural Community Conservation Association Estonian Environmental System (EELIS) Estonian Basic Map (1:10000; Estonian Land Board) 6. Recommended citation for this dataset: Reinula, I., Träger, S., Hernández-Agramonte, Ignacio M., Helm, A., Aavik, T. (2021). Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris, Estonia. Dryad, Dataset. DATA & FILE OVERVIEW 1. File List: node_gen_div_landscape_variables.csv - Genetic diversity data for Primula veris populations and landscape data surrounding the populations link_gen_diff_landscape_variables.csv - Genetic differentiation data for Primula veris and landscape data between the populations 2. Relationship between files, if important: 3. Additional related data collected that was not included in the current data package: Träger, S., Rellstab, C., Reinula, I., Zemp, N., Helm, A., Holderegger, R., Aavik, T. (2021). Genetic diversity at putatively adaptive but not neutral loci in Primula veris responds to recent habitat change in semi-natural grasslands bioRxiv 2021.05.12.442254; doi: https://doi.org/10.1101/2021.05.12.442254 4. Are there multiple versions of the dataset? no A. If yes, name of file(s) that was updated: i. Why was the file updated? ii. When was the file updated? METHODOLOGICAL INFORMATION 1. Description of methods used for collection/generation of data: To generate the genetic information, the leaves of Primula veris were collected from study populations and DNA was extracted from the leaves. Extracted DNA was prepared for library using ddRAD method (Peterson, Weber, Kay, Fisher, & Hoekstra, 2012) and sequenced. We obtained historical landscape data (woody elements and grasslands) from digitalised maps of historical vegetation survey, which was carried out in the 1930s, i.e. when the distribution of Estonian alvar grasslands was at its maximum (Laasimer, 1965).Historical grassland data includes all vegetation types from vegetation category 7 (Veget__cat = 7; Dry and/or wooded meadow). Historical woody elements data includes vegetation types (Kooslus_1) number 1-17, 34-38. Current grasslands were assessed using the map layers for wet and dry grasslands from Estonian Seminatural Community Conservation Association, the layers for alvars from Estonian Environmental System (EELIS) with Natura codes 6210, 6210*, 6280. The areas included in the layer for shrubs (Nature code 5130) from from Estonian Environmental System (EELIS) that overlapped with the previous layers were excluded. The resulting layer was slightly modified by hand when comparing with orthophotos. Current woody elements (forests and shrubs) were obtained from Estonian Basic Map (1:10000; Estonian Land Board). See Reinula et al. 2021 for more info. References: Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE, 7(5), e37135. https://doi.org/10.1371/journal.pone.0037135 Reinula, I., Träger, S., Hernández-Agramonte, Ignacio M., Helm, A., Aavik, T. (2021). Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris. Diversity and Distributions, xx. Laasimer, L. (1965). Eesti NSV taimkate. Tallinn, Valgus. 2. Methods for processing the data: Genetic data was filtered geoinformatically (Träger et al. 2021) and population-based genetic diversity indices (unbiased expected and observed heterozygosity, uHe and Ho, respectively, and percentage of polymorphic loci, %P) were calculated using GENALEX version 6.503 (Peakall & Smouse, 2005, 2012). Inbreeding coefficients (FIS) and genetic differentiation (FST) were calculated using the package `genepop´ (Rousset, 2008) in R version 3.4.2 (R Core Team, 2017). We calculated the amount or density of landscape elements in circular buffers with different radii (500 m, 1000 m, 2000 m) surrounding the populations. We calculated the proportional amount of landscape elements surrounding the straight line between population pairs in different buffers (200 m, 500 m, 1000 m). Maximum distance between population pairs was 27 km. See Reinula et al. 2021 for more info. References: Peakall, R., & Smouse, P. E. (2005). genalex 6: Genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes, 6(1), 288–295. https://doi.org/10.1111/j.1471-8286.2005.01155.x Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics, 28(19), 2537–2539. https://doi.org/10.1093/bioinformatics/bts460 Rousset, F. (2008). genepop’007: A complete re-implementation of the genepop software for Windows and Linux. Molecular Ecology Resources, 8(1), 103–106. https://doi.org/10.1111/j.1471-8286.2007.01931.x R Core Team. (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/. Reinula, I., Träger, S., Hernández-Agramonte, Ignacio M., Helm, A., Aavik, T. (2021). Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris. Diversity and Distributions, xx. Träger, S., Rellstab, C., Reinula, I., Zemp, N., Helm, A., Holderegger, R., Aavik, T. (2021). Genetic diversity at putatively adaptive but not neutral loci in Primula veris responds to recent habitat change in semi-natural grasslands bioRxiv 2021.05.12.442254; doi: https://doi.org/10.1101/2021.05.12.442254 3. Instrument- or software-specific information needed to interpret the data: - 4. Standards and calibration information, if appropriate: - 5. Environmental/experimental conditions: Experimental conditions don't apply. Environmental conditions: samples for genetic analysis were collected during summer with mostly dry and sunny weather. 6. Describe any quality-assurance procedures performed on the data: Current grasslands map layer used to get landscape data was slightly modified by hand when comparing with orthophotos. 7. People involved with sample collection, processing, analysis and/or submission: Iris Reinula, Sabrina Träger, Ignacio M. Hernández-Agramonte, Aveliina Helm, Marge Thetloff, Liis Kasari-Toussaint, Elisabeth Prangel DATA-SPECIFIC INFORMATION FOR: node_gen_div_landscape_variables.csv 1. Number of variables: 38 2. Number of cases/rows: 19 3. Variable List: Population_ID: identification number of the population Region: the island of Muhu or Saaremaa Site: name of the site Longitude Latitude Samples_before_filtering: number of samples in each population befor bioinformatic filtering Samples_after_filtering: number of samples in each population befor bioinformatic filtering Unbiased_expected_heterozygosity: genetic diversity index (uHe) Observed_heterozygosity: genetic diversity index (Ho) Inbreeding_coefficient: genetic diversity index (Fis) Percentage_of_polymorphic_loci: genetic diversity index (%P) Current_grassland_amount_500m: the amount of current (2017) grassland (ha) in circular buffer with a radius of 500 m around the population Historical_grassland_amount_500m: the amount of historical (1930s) grassland (ha) in circular buffer with a radius of 500 m around the population Current_woody_elements_amount_500m: the amount of current (2016) forests and shrubs (ha) in circular buffer with a radius of 500 m around the population Historical_woody_elements_amount_500m: the amount of historical (1930s) forests and shrubs (ha) in circular buffer with a radius of 500 m around the population Grassland_amount_change_500m: change in the amount of grasslands (ha) in circular buffer with a radius of 500 m around the population Woody_elements_amount_change_500m: change in the amount of forests and shrubs (ha) in circular buffer with a radius of 500 m around the population Water_amount_500m: the amount of water (ha) in circular buffer with a radius of 500 m around the population Current_edge_density_500m: the length of current (2017) grassland habitat edge (m/ha) in a circular buffer with a radius of 500 m around the population Historical_edge_density_500m: the length of historical (1930s) grassland habitat edge (m/ha) in a circular buffer with a radius of 500 m around the population Current_grassland_amount_1000m: the amount of current (2017) grassland (ha) in circular buffer with a radius of 1000 m around the population Historical_grassland_amount_1000m: the amount of historical (1930s) grassland (ha) in circular buffer with a radius of 1000 m around the population Current_woody_elements_amount_1000m: the amount of current (2016) forests and shrubs (ha) in circular buffer with a radius of 1000 m around the population Historical_woody_elements_amount_1000m: the amount of historical (1930s) forests and shrubs (ha) in circular buffer with a radius of 1000 m around the population Grassland_amount_change_1000m: change in the amount of grasslands (ha) in circular buffer with a radius of 1000 m around the population Woody_elements_amount_change_1000m: change in the amount of forests and shrubs (ha) in circular buffer with a radius of 1000 m around the population Water_amount_1000m: the amount of water (ha) in circular buffer with a radius of 1000 m around the population Current_edge_density_1000m: the length of current (2017) grassland habitat edge (m/ha) in a circular buffer with a radius of 1000 m around the population Historical_edge_density_1000m: the length of historical (1930s) grassland habitat edge (m/ha) in a circular buffer with a radius of 2000 m around the population Current_grassland_amount_2000m: the amount of current (2017) grassland (ha) in circular buffer with a radius of 2000 m around the population Historical_grassland_amount_2000m: the amount of historical (1930s) grassland (ha) in circular buffer with a radius of 2000 m around the population Current_woody_elements_amount_2000m: the amount of current (2016) forests and shrubs (ha) in circular buffer with a radius of 2000 m around the population Historical_woody_elements_amount_2000m: the amount of historical (1930s) forests and shrubs (ha) in circular buffer with a radius of 2000 m around the population Grassland_amount_change_2000m: change in the amount of grasslands (ha) in circular buffer with a radius of 2000 m around the population Woody_elements_amount_change_2000m: change in the amount of forests and shrubs (ha) in circular buffer with a radius of 2000 m around the population Water_amount_2000m: the amount of water (ha) in circular buffer with a radius of 2000 m around the population Current_edge_density_2000m: the length of current (2017) grassland habitat edge (m/ha) in a circular buffer with a radius of 2000 m around the population Historical_edge_density_2000m: the length of historical (1930s) grassland habitat edge (m/ha) in a circular buffer with a radius of 2000 m around the population 4. Missing data codes: - 5. Specialized formats or other abbreviations used: - DATA-SPECIFIC INFORMATION FOR: link_gen_diff_landscape_variables.csv 1. Number of variables: 27 2. Number of cases/rows: 71 3. Variable List: Population_ID_1: identification number of the first population in a pair Population_ID_2: identification number of the first population in a pair Region_1: region (Muhu/saaremaa) of the first population Region_2: region (Muhu/saaremaa) of the first population Pairwise_genetic_distance_Fst: pairwise genetic differentiation index Geographic_distance_m: geographic distance in a straigt line between two populations (m) Current_grassland_proportion_200m: proportional amount of current (2017) grassland within the buffer zone of 200 m surrounding the straight corridor between two populations. Historical_grassland_proportion_200m: proportional amount of historical (1930s) grassland within the buffer zone of 200 m surrounding the straight corridor between two populations. Current_woody_elements_proportion_200m: proportional amount of current (2016) forests and shrubs within the buffer zone of 200 m surrounding the straight corridor between two populations. Historical_woody_elements_proportion_200m: proportional amount of historical (1930s) forests and shrubs within the buffer zone of 200 m surrounding the straight corridor between two populations. Water_proportion_200m: proportional amount of current (2017) water amount within the buffer zone of 200 m surrounding the straight corridor between two populations. Grassland_proportion_change_200m: change in the proportional amount of grassland within the buffer zone of 200 m surrounding the straight corridor between two populations. Woody_elements_proportion_change_200m: change in the proportional amount of forests and shrubs within the buffer zone of 200 m surrounding the straight corridor between two populations. Current_grassland_proportion_500m: proportional amount of current (2017) grassland within the buffer zone of 500 m surrounding the straight corridor between two populations. Historical_grassland_proportion_500m: proportional amount of historical (1930s) grassland within the buffer zone of 500 m surrounding the straight corridor between two populations. Current_woody_elements_proportion_500m: proportional amount of current (2016) forests and shrubs within the buffer zone of 500 m surrounding the straight corridor between two populations. Historical_woody_elements_proportion_500m: proportional amount of historical (1930s) forests and shrubs within the buffer zone of 500 m surrounding the straight corridor between two populations. Water_proportion_500m: proportional amount of current (2017) water amount within the buffer zone of 500 m surrounding the straight corridor between two populations. Grassland_proportion_change_500m: change in the proportional amount of grassland within the buffer zone of 500 m surrounding the straight corridor between two populations. Woody_elements_proportion_change_500m: change in the proportional amount of forests and shrubs within the buffer zone of 500 m surrounding the straight corridor between two populations. Current_grassland_proportion_1000m: proportional amount of current (2017) grassland within the buffer zone of 1000 m surrounding the straight corridor between two populations. Historical_grassland_proportion_1000m: proportional amount of historical (1930s) grassland within the buffer zone of 1000 m surrounding the straight corridor between two populations. Current_woody_elements_proportion_1000m: proportional amount of current (2016) forests and shrubs within the buffer zone of 1000 m surrounding the straight corridor between two populations. Historical_woody_elements_proportion_1000m: proportional amount of historical (1930s) forests and shrubs within the buffer zone of 1000 m surrounding the straight corridor between two populations. Water_proportion_1000m: proportional amount of current (2017) water amount within the buffer zone of 1000 m surrounding the straight corridor between two populations. Grassland_proportion_change_1000m: change in the proportional amount of grassland within the buffer zone of 1000 m surrounding the straight corridor between two populations. Woody_elements_proportion_change_1000m: change in the proportional amount of forests and shrubs within the buffer zone of 1000 m surrounding the straight corridor between two populations. 4. Missing data codes: - 5. Specialized formats or other abbreviations used: -