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 F (ST) 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.