Population genetic structure of Miscanthus sacchariflorus

This repository contains datasets and R scripts that were used in a study of the population structure of Miscanthus sacchariflorus in its native range across East Asia. Notably, genotypes of 764 individuals at 34,605 SNPs, called from reduced-representation DNA sequencing using a non-reference bioinformatics pipeline, are provided. Two similar SNP datasets, used for identifying clonal duplicates and for determining the ancestry of ornamental and hybrid Miscanthus plants identified in previous studies respectively, are also provided. There is also a spreadsheet listing the provenance and ploidy of all individuals along with their plastid (chloroplast) haplotypes. Software output for Structure, Treemix, and DIYABC is also included. See README.txt for more information about individual files. Results of this study are described in a manuscript in revision in Annals of Botany by the same authors, "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid Miscanthus sinensis, and diversity centered around the Yellow Sea."

本仓库收录了一项针对东亚原生分布区内荻（Miscanthus sacchariflorus）种群结构的研究所用的全部数据集与R脚本。尤为关键的是，本数据集提供了通过无参考基因组生物信息学分析流程从简化基因组测序数据中鉴定得到的764个个体的34605个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因型。此外还提供了两套类似的SNP数据集，分别用于鉴定克隆重复个体，以及追溯既往研究中已报道的观赏芒草与杂交芒草植株的祖先起源。另有一份电子表格，汇总了所有个体的种质来源、倍性及其质体（叶绿体）单倍型信息。同时还附带了Structure、Treemix与DIYABC三款群体遗传学分析软件的输出结果文件。各文件的详细说明请参阅README.txt文档。本研究的相关结果已撰写为稿件，提交至《植物学年鉴》（Annals of Botany）待修回，论文标题为：荻（Miscanthus sacchariflorus）种群结构揭示两次主要多倍化事件、四倍体介导的二倍体芒（Miscanthus sinensis）单向基因渐渗及以黄海为中心的多样性分布格局。