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Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris

Citation

Reinula, Iris et al. (2021), Data from: Landscape genetic analysis suggests stronger effects of past than current landscape structure on genetic patterns of Primula veris, Dryad, Dataset, https://doi.org/10.5061/dryad.h70rxwdjd

Abstract

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.

Methods

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 (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 (FIS) and genetic differentiation (FST) 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. PLoS ONE, 7(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. 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/.

Laasimer, L. (1965). Eesti NSV taimkate. Tallinn, Valgus.

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

Usage Notes

Readme file: Primula_veris_landscape_genetics_Readme.txt

Funding

Eesti Teadusagentuur, Award: MOBJD427

Eesti Teadusagentuur, Award: PUT589

Eesti Teadusagentuur, Award: PRG874

European Regional Development Fund, Award: Centre of Excellence EcolChange

European Commission LIFE+ Nature program, Award: LIFE13NAT/EE/000082

European Commission LIFE+ Nature program, Award: LIFE13NAT/EE/000082