Genetic structure of Alpinia japonica populations in naturally fragmented habitats

Fragmentation is the process that a large continuous habitat is destructed into a couple of small, spatially isolated habitats. Theoretical and empirical studies have shown that habitat fragmentation is one of the most important threats leading to biodiversity loss. Isolated populations are prone to loss of genetic diversity and to local extinction, through genetic drift, inbreeding and decrease in rescue effect led by reduced gene flow. However, till now most studies concerning the genetic consequences of habitat fragmentation involve fragmentation systems caused by human disturbance. Long-term climatic changes or topography may also lead to habitat fragmentation and result in distinct isolation among populations. Such naturally fragmentation systems have experienced long-term fragmentation, avoiding short history in anthropogenic fragmentation systems. However, genetic structure populations of natural fragmentation has not been well checked. Alpinia japonica (Thunb.) Miq. (Zingiberaceae) is a perennial clonal species of tropical and subtropical areas. It is hermaphroditic, but it has two floral phenotypes and has a mechanism to decrease probability of pollination of the same floral phenotype. This species grows in wet and close forest habitats. In the subtropical area of eastern China, for example in eastern Zhejiang Province, the habitats are naturally patchy and restricted. We studied the genetic structure of naturally fragmented populations in Tiantong Forest Parks using RAPD markers. Seven primers revealed 69 bands, among them 68 were polymorphic. High genetic diversity was found within populations. The percentage of polymorphic loci, expected heterozygosity and Shannon information index were 78.81%-85.51%, 0.3170-0.3430, 0.4560-0.4914, respectively. Relatively high genetic diversity in A. japonica is coincided with its life history characteristics, i.e., outcrossing, long-lived perennial. Within population genetic variation is slightly higher than those of species of Zingiberaceae and means of outcrossers or long-lived perennial, indicating that genetic diversity has not apparently affected by fragmentation. This situation is due to the strong clonality, which prolongs the parental generation and reduces the turnover of generation. However, there is a signal of the consequences of long-term fragmentation on genetic differentiation. Although fine scale in the present study, moderate and significant differentiation has been found among populations (Φ ST= 0.297, p<0.01). The differentiation is much higher than those with similar spatial scale. Furthermore, no isolation-by-distance pattern was found using Mantel test, indicating that genetic drift had overcome the impact of gene flow (0.592).