Genetic diversity and geographic differentiation in endangered Ammopiptanthus (Leguminosae) populations in desert regions of northwest China as revealed by ISSR analysis

center dot Background and Aims The desert legume genus Ammopiptanthus comprises two currently endangered species, A. mongolicus and A. nanus. Genetic variability and genetic differentiation between the two species and within each species were examined. center dot Methods Inter-simple sequence repeal. (ISSR) marker data were obtained and analysed with respect to genetic diversity, structure and gene flow. center dot Key Results Despite the morphological similarity between A. mongolicus and A. nanus, the two species are genetically distinct from each other, indicated by 63 % species-specific bands. Low genetic variability was detected for both population level (Shannon indices of diversity H-pop = 0. 106, percentage of polymorphic loci P = 18-55 % for A. mongolicus; H-pop = 0.070, P = 12-24 % for A. nanus) and species level (H-sp= 0. 1832, P= 39-39 % for A. mongolicus; H-sp = 0. 1026, P = 25-89 % for A. nanus). Moderate genetic differentiation was found based on different measures (AMOVA phi(ST) and Hickory theta(B)) in both A. mongolicus (0-3743-0-3744) and A. nanus (0-2162-0-2369). center dot Conclusions The significant genetic difference between the two species might be due to a possible vicariant evolutionary event from a single common ancestor through the fragmentation of their common ancestor's range. Conservation strategies for these two endangered species are proposed.