Data from: Intra-population genomics in a model mutualist: population structure and candidate symbiosis genes under selection in Medicago truncatula

Bottom-up evolutionary approaches, including geographically-explicit population genomic analyses, have the power to reveal the mechanistic basis of adaptation. Here we conduct a population genomic analysis in the model legume, Medicago truncatula, in order to characterize population genetic structure and identify symbiosis-related genes showing evidence of spatially-variable selection. Using RAD-seq, we generated over 26,000 SNPs from 191 accessions from within three regions of the native range in Europe. Results from STRUCTURE analysis identify 5 distinct genetic clusters with divisions that separate east and west regions in the Mediterranean basin. Much of the genetic variation is maintained within sampling sites, and there is evidence for isolation by distance. Extensive linkage disequilibrium was identified, particularly within populations. We conducted genetic outlier analysis with FST-based genome scans and a bayesian modeling approach (PCAdapt). There were 70 core outlier loci shared between these distinct methods with one clear candidate symbiosis related gene, DMI1. This work sets that stage for functional experiments to determine the important phenotypes that selection has acted upon and complementary efforts in rhizobium populations.自下而上的演化研究方法（包括地理显性种群基因组分析）能够揭示适应性演化的机制基础。本研究以模式豆科植物蒺藜苜蓿（Medicago truncatula）为对象开展种群基因组分析，旨在解析种群遗传结构，并筛选出呈现空间可变选择信号的共生相关基因。本研究通过RAD-seq技术，从欧洲本土分布区三个区域的191份种质资源中鉴定得到超过26000个单核苷酸多态性（Single Nucleotide Polymorphisms, SNPs）位点。STRUCTURE软件分析结果显示存在5个独立的遗传聚类群，其聚类分界与地中海盆地东西区域的划分相吻合。多数遗传变异保留于采样种群内部，同时存在显著的距离隔离效应。研究检测到广泛的连锁不平衡现象，尤其在种群内部更为显著。本研究采用基于FST的基因组扫描法与贝叶斯建模方法（PCAdapt）开展遗传异常位点分析。两种分析方法共筛选得到70个核心异常位点，其中包含1个明确的共生相关候选基因DMI1。本研究为后续解析选择作用所靶向的关键表型的功能实验，以及根瘤菌种群的相关互补研究奠定了基础。