Data from: Divergence and isolation of cryptic sympatric taxa within the annual legume Amphicarpaea bracteata

The amphicarpic annual legume Amphicarpaea bracteata is unusual in producing aerial and subterranean cleistogamous flowers that always self-fertilize and, less commonly, aerial chasmogamous flowers that outcross. Although both morphologic and genetic variants are known in this highly selfing species, debate continues over whether this variation is continuous, reflecting the segregation of standing genetic variation, or discontinuous, reflecting distinct taxa that rarely intercross. We characterized SNP variation in 128 individuals in southern Wisconsin to assess within- and among-population variation at 3928 SNPs. We also assessed genotype and leaf morphology in an additional 76 individuals to connect phenotypic variation with genetic variation. Genetic variation maps onto three strongly divergent and highly inbred genetic groups showing little relation to site location. Each group has a distinct phenotype, but the divergence of these groups differs from the varietal divisions previously identified based on morphological characters. Like previous authors, we argue that the taxonomy of this species should be revised. Despite extensive sympatry, estimates of among-group migration rates are low, and hybrid individuals were at low frequency (<2%) in our dataset. Restricted gene flow likely results from high selfing rates and partial reproductive incompatibility as evidenced by the U-shaped distribution of pairwise FST values reflecting “islands” of genomic divergence. These islands may be associated with hybrid incompatibility loci that arose in allopatry. The coexistence of lineages within sites may reflect density-dependent attack by species-specific strains of pathogenic fungi and/or root-nodulating bacteria specializing on distinct genotypes.

两型一年生豆科植物苞子两型豆（Amphicarpaea bracteata）具有独特的繁殖策略：可产生始终进行自交的地上与地下闭花受精花（cleistogamous flower），以及较为少见的、可发生异交的地上开花受精花（chasmogamous flower）。尽管在这种高度自交的物种中已被报道存在形态与遗传变异，但学界仍存在争议：这类变异究竟是连续的（反映现存遗传变异的分离），还是不连续的（代表极少发生杂交的不同类群）。本研究对威斯康星州南部128个个体的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）变异进行了分型，基于3928个SNP位点评估了种群内及种群间的遗传变异；我们还对额外76个个体的基因型与叶片形态进行了检测，以关联表型变异与遗传变异。遗传变异可聚类为三个分化显著且高度近交的遗传类群，且这些类群与采样位点的地理位置几乎无关联。每个类群均具有独特的表型，但这些类群间的分化与此前基于形态特征界定的变种划分并不一致。与此前研究者的观点一致，我们认为该物种的分类学界定亟需修订。尽管三个类群存在广泛的同域分布，但其类群间的基因流迁移率仍较低，且本数据集内杂交个体的占比极低（<2%）。受限的基因流可能源于高自交率与部分生殖隔离，成对种群分化指数（Fixation Index, FST）值呈U型分布，这一现象印证了“基因组分化岛”的存在；这类“基因组分化岛”可能与异域分化过程中产生的杂交不亲和位点相关。同一位点内多个谱系的共存现象，可能源于针对特定基因型的专化性致病真菌菌株或根瘤菌（root-nodulating bacteria）的密度依赖性侵染。