Microsatellite markers indicate genetic differences between cultivated and natural populations of endangered Taxus yunnanensis

Taxus yunnanensis (Taxaceae) is an endangered plant known for its effective natural anti‐cancer metabolite, taxol. To assess the effectiveness of T. yunnanensis ex situ conservation in China, the genetic diversity and genetic structure of nine cultivated and 14 natural populations were compared using 11 polymorphic microsatellite markers. The purpose of this comparison was to determine whether the cultivated populations were genetic representatives of natural types. Among the 14 natural populations studied, three were from Tibet and 11 were from the Hengduan Mountains. There were fewer genetic variations among cultivated populations than among natural populations, but this difference was not significant. However, 23 unique alleles were detected in cultivated populations and 14 were detected in natural populations. Striking differences in genetic structure (G_ST = 0.365) was observed between them. STRUCTURE, AMOVA and cluster analyses also consistently showed a clear genetic separation between the 14 natural and seven cultivated populations. Only five natural populations from the south‐central Hengduan Mountains were genetically represented in two cultivated collections. The reason for the occurrence of distinct genetic differences between cultivated and natural populations and the loss of natural population‐specific alleles in the cultivated populations can be attributed to uneven selection during establishment. These results suggest that the genetic structure of T. yunnanensis may not have been conserved effectively. Based on our study, practical conservation strategies for ex situ preservation of T. yunnanensis have been developed. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 177 , 450–461.