Chloroplast DNA diversity in Castanopsis hystrix populations in south China J. Li a,b , X.J. Ge a,c , H.L. Cao a , W.H. Ye a, * a South China Botanical Garden, The Chinese Academy of Sciences, Guangzhou 510650, PR China b Graduate School of the Chinese Academy of Sciences, Beijing 100049, PR China c School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, PR China Abstract Nineteen Chinese populations of Castanopsis hystrix were examined to quantify genetic diversity and genetic structure at chloroplast DNA. Microsatellites (SSR) were analyzed by PCR using conserved primers. The average within population gene diversity (H S ), the total gene diversity (H T ), and the differentiation for unordered alleles (G ST ) and for ordered alleles (N ST ) were measured. Fourteen different haplotypes were detected, two of them very common. The level of differentiation among populations (G ST = 23.6%) indicates a highly efficient seed dispersal mechanism. In addition, the difference between G ST and N ST for the species is not significant, suggesting that the phylogeographic structure is weak or absent. The geographical pattern of C. hystrix haplotypes could be attributed to its migration from the numerous and scattered refugia, where the species confined during the last glacial period. These results provide an important insight into patterns of postglacial recolonization of this tree species. Keywords: cpDNA; SSR; Genetic differentiation; Castanopsis hystrix 1. Introduction The modern distribution of plant and animal taxa is determined not only by the current environment, but also by historic events such as the last glacial period (Hengeveld, 1989). Although the land in south China has never been covered by ice sheets, the tremendous temperature and climatic changes might have influenced species’ distributions and evolution. The Holocene postglacial history of many trees is characterized by the northward expansion of southern refugial populations following the retreat of the ice sheets. The last glacial age might have been an important factor in determining the genetic structure and phylogeography of plant species in south China. Fossil pollen deposits can be used to reconstruct long-term vegetation dynamics, such as changes in the distribution and abundance of plant species during the quaternary period. But for the species which produce only small amount of pollen grains, occurrences of their pollen grains in the fossil pollen record may be therefore too infrequent to allow detailed reconstruction of the species’ past range and migration patterns. An alternative approach to the study of postglacial changes in plant distributions developed in recent years is the use of molecular markers (Ferris et al., 1999; Hewitt, 1999). Currently existing plant populations are expected to retain the genetic traces resulting from the migration routes they followed during the past, which could be revealed by studying the spatial distribution pattern of molecular markers. Chloroplast markers have been widely applied to studies of population history in trees (e.g. Walter and Epperson, 2001; Rendell and Ennos, 2003; Cheng et al., 2005). Firstly, because chloroplast genomes are haploid, their effective population size in monoecious outcrossing plants is half of diploid nuclear genomes. As a result, chloroplast-specific markers are considered good indicators of historical bottlenecks, founder effects and genetic drift. The use of chloroplast microsatellites has allowed the examination of these events at a finer level of detail than it was previously possible. Secondly, because chloroplasts evolve slowly and exhibit little variation at the intraspecific level (Clegg et al., 1994), cpDNA markers have been widely used for phylogenetic inference (Olmstead and Palmer, 1994) and to some extent, for within-species genetic studies (Soltis et al., 1992; Ennos et al., 1999). However, microsatellite markers are * Corresponding author. Tel.: +86 20 37252996. E-mail addresses: lijing@scib.ac.cn (J. Li), why@scib.ac.cn (W.H. Ye).