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:<b>Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population</b>Alina K. Niskanen1,3, Sonja T. Kujala2, Katri Kärkkäinen2, Outi Savolainen1, Tanja Pyhäjärvi3<br>1Ecology and Genetics Research Unit, University of Oulu, 90014 University of Oulu, Finland2Natural Resources Institute Finland (Luke), University of Oulu, 90014 University of Oulu, Finland3Department of Forest Sciences, University of Helsinki, 00014 University of Helsinki, FinlandInquiries about the data:Alina Niskanen, [e-mail]<br>Files included in the dataset:<b>1. &amp; 2. "Genotypes.ped" &amp; Genotypes.map"</b>: 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.<b>3. "MAF_01_pine_426inds_23623_loci.raw"</b> : Plink Genotype file in .raw format including 23 623 SNPs for 426 unrelated Scots pines used in the rare allele analyses.<b>4. "Locations_population.txt"</b> : Location information for 469 Scots pines in Punkaharju research area. The sampling site ("Ranta-Halola" or "Mäkrä") is given.<br>Command files included:<b>5. "Spatial_R_commands_fighsare.R"</b>: Main R commands of the PCA, FST and Mantel analyses.<b>6. "GCTA_commands_figshare.txt"</b>: Main GCTA commands for estimating relatedness and inbreeding.<br>Supplementary data file:<b>7. "Niskanen_etal_2024_Supplements.pdf"</b>: Includes Supplementary figures S1-S6 and tables S1-S2.

本数据集配套学术论文为：**《Does the seed fall far from the tree? Weak fine-scale genetic structure in a continuous Scots pine population》**
作者：Alina K. Niskanen¹,³、Sonja T. Kujala²、Katri Kärkkäinen²、Outi Savolainen¹、Tanja Pyhäjärvi³
¹奥卢大学生态学与遗传学研究室，芬兰奥卢，邮编90014
²芬兰自然资源研究所（Luke），奥卢大学，芬兰奥卢，邮编90014
³赫尔辛基大学森林科学系，芬兰赫尔辛基，邮编00014

数据咨询联系人：Alina Niskanen，电子邮箱：[e-mail]

数据集包含文件如下：
1. 与2. "Genotypes.ped"及"Genotypes.map"：分别为.ped格式的PLINK基因型文件、.map格式的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点坐标文件，收录了469个个体与65498个SNP的过滤后基因型数据，用于主成分分析（Principal Component Analysis, PCA）及成对亲缘关系估算。
3. "MAF_01_pine_426inds_23623_loci.raw"：.raw格式的PLINK基因型文件，包含426株无亲缘关系欧洲赤松（Scots pine）的23623个SNP位点数据，用于稀有等位基因分析。
4. "Locations_population.txt"：Punkaharju研究区域内469株欧洲赤松的采样位置信息，标注了对应采样点（"Ranta-Halola"或"Mäkrä"）。

附带命令文件如下：
5. "Spatial_R_commands_fighsare.R"：用于主成分分析、固定化指数（Fixation Index, FST）检验及Mantel检验的核心R脚本命令。
6. "GCTA_commands_figshare.txt"：用于估算亲缘关系与近交系数的核心GCTA命令。

补充数据文件：
7. "Niskanen_etal_2024_Supplements.pdf"：包含补充图S1~S6及补充表S1~S2。