Genetic structure of three orchid species with contrasting breeding systems using RAPD and allozyme markers

<jats:p><jats:italic>Zeuxine gracilis</jats:italic>, <jats:italic>Zeuxine strateumatica</jats:italic>, and <jats:italic>Eulophia sinensis</jats:italic> are wild orchids with different breeding systems and colonizing abilities. <jats:italic>Zeuxine gracilis</jats:italic> is an outcrosser with restricted distribution, whereas <jats:italic>S. strateumatica</jats:italic> is an apomictic colonizer found only in newly available open habitats. <jats:italic>Eulophia sinensis</jats:italic> is an outcrossing colonizer. This study investigates the levels of genetic variation and patterns of population structure in these wild orchids to provide genetic information for the development of suitable conservation strategies. Lack of allozyme variation was characteristic of all three species, especially in populations of the two colonizing orchids, <jats:italic>Z. strateumatica</jats:italic> and <jats:italic>E. sinensis</jats:italic>. More variable markers, randomly amplified polymorphic DNAs (RAPDs), were further employed to characterize population structure of these species. Substantial genetic variation was found at the RAPD loci within populations of <jats:italic>Z. gracilis</jats:italic> (<jats:italic>p</jats:italic> = 21.65 ± 15.88%, <jats:italic>A</jats:italic> = 1.217 ± 0.159, and <jats:italic>H</jats:italic> = 0.076 ± 0.054) and <jats:italic>E. sinensis</jats:italic> (<jats:italic>p</jats:italic> = 17.82 ± 20.97%, <jats:italic>A</jats:italic> = 1.179 ± 0.209, and <jats:italic>H</jats:italic> = 0.070 ± 0.084), but little variation existed within populations of <jats:italic>Z. strateumatica</jats:italic> (<jats:italic>p</jats:italic> = 2.84 ± 2.58%, <jats:italic>A</jats:italic> = 1.029 ± 0.026, and <jats:italic>H</jats:italic> = 0.011 ± 0.011). Regardless of the breeding system, the total gene diversity at the species level was partitioned primarily between populations, as shown by high <jats:italic>G</jats:italic><jats:sub>ST</jats:sub> values, in all three species. An extremely high level of population differentiation (<jats:italic>G</jats:italic><jats:sub>ST</jats:sub> = 0.924) was found in the apomictic colonizer <jats:italic>Z. strateumatica</jats:italic>. The patterns of genetic variation in these wild orchids are apparently related to their differences in breeding system and colonizing ability. Different conservation strategies are needed for the long‐term survival of these species.</jats:p>