Effective population size (Ne) is a crucial metric for evaluating the current status of genetic diversity and conservation management. Population of Kandelia obovata, a mangrove species that is patchily distributed along the estuaries off Southeastern China, is genetically structured. Here, we applied skyline analyses to infer the demographic history of K. obovata based on Amplified Fragment Length Polymorphisms (AFLP) data. Congruent trends of population growth rate among populations, but concurrent change in Ne estimates, were inferred in all populations. The recent rapid habitat expansion explains the high census population size but small Ne of populations in Northern Taiwan. Our study also revealed lower Ne of reforested populations than their sources. In silico demographic analyses simulate the small or biased sampling of seedlings for reforestation and revealed over 90% and 99% Ne reduction when only 1/2 and 1/10 samples were collected, respectively. These results emphasize the importance of a comprehensive sampling of seeds for restoration. Overall, this study rendered, not only the current Ne of K. obovata populations, but also indicates the importance of Ne estimation on restoration.
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