Chloroplast DNA phylogeography of Cunninghamia konishii (Cupressaceae), an endemic conifer of Taiwan.

In this study, we investigated the genetic structure and phylogeographic pattern of the genus Cunninghamia, a member of the Cupressaceae restricted to mainland China and Taiwan, based on sequences of the trnD-trnT noncoding spacer of the chloroplast DNA. Maternal inheritance of chloroplasts was determined experimentally. No paternal leakage was detected. Both parsimony and neighbor-joining analyses revealed the polyphyly of Cunninghamia konishii, populations of which were nested in clades of C. lanceolata from mainland China. The nucleotide diversity of chloroplast DNA sequences within C. konishii (0.0118) was higher than that between species (0.0104), which agrees with a previous allozyme investigation. Based on mutational differences between sequences, a minimum spanning network consisting of five clades was constructed. Significant genetic differentiation (phiST = 0.130, P < 0.001) was detected between the clades based on AMOVA analyses. We infer several possible refugia in the Yunnan, Zhejiang, and Guangdong provinces of south China, all located in the minimum network as interior nodes. We also infer possible migration routes of Cunninghamia populations. The phylogeographic pattern shown in the reconstructed network suggests that the present-day Cunninghamia populations in Taiwan were derived from six different sources in continental Asia via long-distance seed dispersal. A migrant-pool model explains the heterogeneous composition of the organelle DNA in Taiwan's populations and the low differentiation between populations of Taiwan and China (phiCT = 0.012, P = 0.454). In contrast with the genetic heterogeneity within geographic populations, many local populations have attained coalescence at the trnD-trnT alleles, which has led to significant differentiation at the population level.