DOI: 10.5061/dryad.h70rxwdjd
title: Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris

description: This dataset contains genetic and landscape data of 19 Primula veris
 populations in Muhu and Saaremaa islands in Estonia. Genetic samples were
 collected in 2015 and 2016. Landscape data was extracted from maps dated
 2016 and 2017 for current data and 1930s for historical data. Data is
 divided to node- and link-based data. Node-based data contains genetic
 diversity data of the P. veris populations and landscape data in circular
 buffers surrounding the populations. Link-based data contains genetic
 differentiation between population pairs and landscape data in buffers
 surrounding a straight line between population pairs.
description: To generate the genetic
 information, the leaves of <i>Primula veris</i> were collected
 from study populations and DNA was extracted from the leaves. Extracted
 DNA was prepared for library using ddRAD (Peterson, Weber, Kay, Fisher,
 & Hoekstra, 2012) method and sequenced. Genetic data was filtered
 geoinformatically (see 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 (F<sub>IS</sub>) and genetic
 differentiation (F<sub>ST</sub>) were calculated using the
 package `genepop´ (Rousset, 2008) in R version 3.4.2 (R Core Team,
 2017). 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). Current grasslands were assessed
 using the map layers of Estonian Seminatural Community Conservation
 Association and Estonian Environmental System (EELIS). Current woody
 elements (forests and shrubs) were obtained from Estonian Basic Map
 (1:10000; Estonian Land Board). 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). 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. <i>PLoS ONE</i>,
 <i>7</i>(5), e37135.
 https://doi.org/10.1371/journal.pone.0037135 Peakall, R., & Smouse, P.
 E. (2005). genalex 6: Genetic analysis in Excel. Population genetic
 software for teaching and research. <i>Molecular Ecology
 Notes</i>, <i>6</i>(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.
 <i>Bioinformatics</i>, <i>28</i>(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. <i>Molecular Ecology Resources</i>,
 <i>8</i>(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/. Laasimer, L. (1965).
 <i>Eesti NSV taimkate.</i> Tallinn, Valgus.
 Reinula, I., Träger, S., Hernández-Agramonte, Ignacio M., Helm,
 A., Aavik, T. (2021). <br> Landscape genetic analysis suggests
 stronger effects of past than current landscape structure on genetic
 patterns of <em>Primula veris</em>. Diversity and
 Distributions, xx.  Träger, S., Rellstab, C., Reinula,
 I., Zemp, N., Helm, A., Holderegger, R., Aavik, T. (2021).<br>
 Genetic diversity at putatively adaptive but not neutral loci in
 <em>Primula veris</em> responds to recent habitat change in
 semi-natural grasslands bioRxiv 2021.05.12.442254; doi:
 https://doi.org/10.1101/2021.05.12.442254
description: Readme file: Primula_veris_landscape_genetics_Readme.txt