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.

两结实习性一年生豆科植物苞扁豆（Amphicarpaea bracteata）较为特殊，可产生两类闭锁花（cleistogamous flowers）：地上与地下的闭锁花均为严格自花授粉，同时还会产生少量开放花（chasmogamous flowers）以实现异交。尽管在这一高度自交的物种中已发现形态学与遗传学变异，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位点评估了种群内与种群间的遗传变异；同时还对额外76个个体的基因型与叶片形态开展了分析，以关联表型变异与遗传变异。遗传变异可划分为三个高度分化且近交程度极高的遗传类群，其分布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特征，但这些类群间的分化与此前基于形态学特征划分的变种类群并不一致。与此前的研究者一致，我们认为该物种的分类学划分亟需修订。尽管三个类群存在广泛的同域分布，但类群间的迁移率极低，且本数据集内杂交个体的占比不足2%。受限的基因流可能源于高自交率与部分生殖隔离，这一点可通过两两遗传分化系数（Fixation Index, FST）呈U型分布得到佐证——该分布反映了基因组分化的“孤岛”现象。这些基因组分化孤岛可能与异域分化过程中产生的杂交不亲和位点相关。同一位点内不同谱系的共存现象，可能源于专化于不同基因型的病原真菌或根瘤菌菌株的密度依赖性攻击。