Whether the persistence of natural plant populations is limited by genetic diversity, gene flow, or other ecological and evolutionary factors is an important question in plant population genetics. An assessment of the distribution of genetic variation within and among populations is thus useful for understanding broad-scale gene flow patterns in plants with diverse pollination syndromes. We studied Pogonia ophioglossoides (L.) Ker Gawl., which is self-compatible but a primarily outcrossing species in the Tribe Pogonieae in the family Orchidaceae. Using three self-developed, highly polymorphic nuclear microsatellite (simple sequence repeat, or SSR) markers and two chloroplast microsatellites, we assessed genetic variation in eight populations representing its natural distribution. Relatively high within-population genetic variation (mean An = 9.08, Ho = 0.44, and He = 0.71) was detected in P. ophioglossoides. Eleven different alleles and 13 unique haplotypes were detected for two cpDNA microsatellites. Genetic differentiation based on the hierarchical AMOVA showed that 21% (ФPT = 0.21, P = 0.000) and 63% (ФPT = 0.63, P = 0.000) of the nuclear and cpDNA microsatellite allelic diversity, respectively, was distributed among populations. Pairwise FST values ranged from 0.041 to 0.224 and each was statistically significant at P ≤ 0.05. The isolation by distance estimate did not show an association between genetic differentiation and geographic distance indicating that populations were diverging independently. We documented fine-scale spatial genetic structure (FSGS) up to 40 m distance in Texas. Overall, gene flow across the sampled populations of P. ophioglossoides appears restricted, and the short-distance SGS suggests localized seed dispersal in this locally common North American terrestrial orchid.
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