It is not known how the profoundly complex topography and habitat heterogeneity generated by the uplift of the Qinghai-Tibetan Plateau (QTP) during the late Tertiary affected population genetic structure of endangered Taxus yunnanensis. In addition, the effects of habitat fragmentation due to anthropogenic disturbance on genetic diversity and population differentiation of this species have not been studied. T. yunnanensis is an ancient tree/shrub mainly distributed in southwest China. Recently, the species has suffered a sharp decline due to excessive logging for its famous anticancer metabolite taxol, resulting in smaller and more isolated populations. To understand the phylogeography and genetic consequences of habitat fragmentation of this endangered species, using 11 polymorphic microsatellites, we genotyped 288 individuals from 14 populations from a range-wide sampling in China. Our results suggest that two different population groups that were once isolated have persisted in situ during glacial periods in both areas, and have not merged since. Habitat fragmentation has led to significant genetic bottlenecks, high inbreeding and population divergence in this species. The two different population groups of T. yunnanensis could be attributed to restricted gene flow caused through isolation by geographical barriers and by habitat heterogeneity during uplift of the QTP, or the existence of two separate glacial refugia during the Pleistocene. In situ and ex situ conservation of the two Evolutionarily Significant Units (ESUs), artificial gene flow between populations and a comprehensive understanding of the pollination system in this endangered species are suggested from this study.

Eleven polymorphic microsatellite loci were characterized for the endangered conifer Taxus yunnanensis. Eight loci were isolated through SSR-anchored PCR, one locus was developed by cross-species amplification tests, while the last two loci were obtained from crossspecies microsatellite sequences available in GenBank.Variability of these markers was tested in 48 individuals collected from its main distribution range in Southwest China. The number of alleles per locus ranged from 2 to 9, and the observed and expected heterozygosity varied from 0.000 to 0.625 and from 0.062 to 0.853, respectively. Ten of these eleven loci were significantly deviated from Hardy-Weinberg expectation, except TS07 which showed a distinct heterozygote excess. The availability of these new polymorphic microsatellite markers will provide an ideal marker system for detailed population genetics studies in T. yunnanensis and potentially also for closely related species.

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 (GST = 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.