Data for: Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides)

In support of the manuscript by Bagley et al. (2020; see below) on quaking aspen phylogeography and ecological niche modeling (ENM), this accession provides 1) the in-house laboratory protocol used to extract DNA from aspen leaf tissues (modified from Strauss Lab); 2) the Supporting Information files for the corresponding manuscript (Bagley et al. 2020); 3) code used to conduct independent runs of the TASSEL-GBSv2 SNP discovery pipeline (Glaubitz et al. 2014) on our final (combined) genotyping-by-sequencing (GBS) dataset; 4) resulting SNP variant files from TASSEL-GBSv2 and final filtered variant call format (VCF) and genotype data files used during our genomic analyses; 5) R script and metadata used during basic population genomics analyses of the final filtered SNP data (final VCF file); and 6) unfiltered vs filtered species occurrence data files and computer code (R scripts) used during our ENM analyses of our focal taxon, Populus tremuloides.

REFERENCES
Bagley, J. C., Heming, N. M., Gutiérrez, E. E., Devisetty, U. K., Mock, K. E., Eckert, A. J., & Strauss, S. H. (2020). Genotyping-by-sequencing and ecological niche modeling illuminate phylogeography, admixture, and Pleistocene range dynamics in quaking aspen (Populus tremuloides). Ecology and Evolution.

Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q., & Buckler, E. S. (2014). TASSEL-GBS: a high capacity genotyping by sequencing analysis pipeline. PLoS One, 9(2): e90346

本数据集存档用于支撑Bagley等人（2020年；详见下文）关于颤杨谱系地理学与生态位模型（Ecological Niche Modeling, ENM）的研究手稿，包含以下6项内容：
1. 改编自Strauss实验室方案的杨树叶组织DNA提取实验室内部操作流程；
2. 对应研究手稿（Bagley等，2020）的补充信息文件；
3. 针对最终合并的测序分型（Genotyping-by-Sequencing, GBS）数据集，运行TASSEL-GBSv2单核苷酸多态性（Single Nucleotide Polymorphism, SNP）发现流程的独立批次代码（源自Glaubitz等，2014）；
4. TASSEL-GBSv2产出的SNP变异文件，以及基因组分析中使用的最终过滤版变异调用格式（Variant Call Format, VCF）文件与基因型数据文件；
5. 针对最终过滤后的SNP数据（最终VCF文件）开展基础群体基因组分析所用的R脚本与元数据；
6. 针对目标类群颤杨（Populus tremuloides）开展生态位模型分析时所用的未过滤与过滤后的物种出现数据文件，以及配套计算机代码（R脚本）。

参考文献
1. Bagley, J. C., Heming, N. M., Gutiérrez, E. E., Devisetty, U. K., Mock, K. E., Eckert, A. J., & Strauss, S. H. (2020). 测序分型与生态位模型揭示颤杨（Populus tremuloides）的谱系地理学、基因渐渗与更新世种群动态. 《生态学与进化（Ecology and Evolution）》.
2. Glaubitz, J. C., Casstevens, T. M., Lu, F., Harriman, J., Elshire, R. J., Sun, Q., & Buckler, E. S. (2014). TASSEL-GBS：一款高通量测序分型分析流程. 《公共科学图书馆·综合（PLoS One）》, 9(2): e90346