AFLP and MS-AFLP data for Spartina alterniflora and Borrichia frutescens collected from three habitats (i.e. low, medium, and high salt) within five sites, respectively, on Sapelo Island, GA in May 2011

Using amplified fragment length polymorphism (AFLP) and methylation sensitive (MS)-AFLP we assessed genetic and epigenetic variation in two salt marsh perennials, Spartina alterniflora and Borrichia frutescens, in Sapelo Island, Georgia. We sampled Apex (A), Cabretta (C), Hunt Camp (H), Lighthouse (L), and Marsh Landing (M) for S. alterniflora, and C, H, L, M, and Shell Hammock for B. frutescens due to site specific differences in species among the sites. We tested the hypothesis that populatation structure at the habitat level would be due to epigenetic loci and not genetic. The presence and absence AFLP bands and MS-AFLP methylation respresents a genome-wide snapsnot of variation within individuals. We used hierarchical AMOVAs, permutational MANOVA, Bayesian clustering (genetic only), Mantel and partial Mantel tests, and generalized linear models to assess the spatial structure of genetic and epigenetic variation among our two study organisms across five sites for each organism. (Note: genetic and habitat distance tables were normalized for database compatibility. These data must be formatted as a square dissimilarity matrix for input to the code files.)本研究借助扩增片段长度多态性（amplified fragment length polymorphism, AFLP）与甲基化敏感扩增片段长度多态性（methylation sensitive, MS-AFLP），对美国佐治亚州萨佩洛岛的两种盐沼多年生植物——互花米草（Spartina alterniflora）与灌丛滨菊（Borrichia frutescens）的遗传与表观遗传变异进行评估。针对互花米草，我们于Apex（A）、Cabretta（C）、Hunt Camp（H）、Lighthouse（L）及Marsh Landing（M）五个样点完成采样；鉴于各站点间的物种分布存在位点特异性差异，灌丛滨菊的采样样点为C、H、L、M与Shell Hammock。我们验证了如下假说：生境水平的种群结构由表观遗传位点决定，而非遗传位点。AFLP条带的有无与MS-AFLP甲基化检测结果，可呈现个体内全基因组范围的变异快照。本研究采用分层分子变异方差分析（Analysis of Molecular Variance, AMOVA）、置换多变量方差分析（permutational MANOVA）、贝叶斯聚类（Bayesian clustering，仅针对遗传数据）、Mantel检验（Mantel test）与偏Mantel检验（partial Mantel test），以及广义线性模型（generalized linear models），对两种研究生物各自在5个样点间的遗传与表观遗传变异的空间结构进行评估。（注：为适配数据库兼容性，遗传与生境距离表已完成标准化处理。所有用于输入代码文件的数据需整理为方形相异矩阵格式。）