Variation at a chloroplast minisatellite locus reveals the signature of habitat fragmentation and genetic bottlenecks in the rare orchid Anacamptis palustris (Orchidaceae).

Geoclimatic changes during the Oligocene and more recent anthropogenic influences have shaped the current distribution and population structure of Mediterranean plant species. Anacamptis palustris (Orchidaceae) is a typical member of coastal wetlands, which have become increasingly fragmented and isolated. As a consequence, this orchid has become rare in the recent past. Length variation at a chloroplast minisatellite locus was used to estimate genetic variation within and between the largest extant populations of A. palustris. Genetic diversity was positively correlated with population size. Estimation of observed and expected gene diversity and analyses of haplotype number and haplotype frequency distributions provided evidence for population bottlenecks in the history of small populations. Comparison with an earlier study suggests that nuclear allozyme diversity was most likely lost during the Oligocene and could not recover subsequently due to low mutation rates, whereas genetic variation was restored at the highly variable chloroplast minisatellite locus. Population bottlenecks indicated by cpDNA variation occurred most likely as a consequence of more recent anthropogenic changes. The comparison of molecular markers with different levels of polymorphism provided valuable insights into the processes shaping genetic diversity and population structure in this rare orchid.