Scots pine genotypes from Finland, code and supplementary data for the paper: "Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population", Niskanen et al. 2024, Peer Community Journal

Supplementary data for the manuscript:

Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population

Alina K. Niskanen1,3, Sonja T. Kujala2, Katri Kärkkäinen2, Outi Savolainen1, Tanja Pyhäjärvi3

1Ecology and Genetics Research Unit, University of Oulu, 90014 University of Oulu, Finland

2Natural Resources Institute Finland (Luke), University of Oulu, 90014 University of Oulu, Finland

3Department of Forest Sciences, University of Helsinki, 00014 University of Helsinki, Finland

Inquiries about the data:

Alina Niskanen, alina.niskanen@gmail.com

Files included in the dataset:

1. & 2. "Genotypes.ped" & Genotypes.map": PLINK genotype file in .ped format and SNP position file in .map format including filtered genotype data for 469 individuals and 65 498 SNPs used for principal component analysis (PCA) and estimating pairwise relatedness.

3. "MAF_01_pine_426inds_23623_loci.raw" : Plink Genotype file in .raw format including 23 623 SNPs for 426 unrelated Scots pines used in the rare allele analyses.

4. "Locations_population.txt" : Location information for 469 Scots pines in Punkaharju research area. The sampling site ("Ranta-Halola" or "Mäkrä") is given.

Command files included:

5. "Spatial_R_commands_fighsare.R": Main R commands of the PCA, FST and Mantel analyses.

6. "GCTA_commands_figshare.txt": Main GCTA commands for estimating relatedness and inbreeding.

Supplementary data file:

7. "Niskanen_etal_2024_Supplements.pdf": Includes Supplementary figures S1-S6 and tables S1-S2.