Low chloroplast DNA variation and population differentiation of Chamaecyparis formosensis and Chamaecyparis taiwanensis

Polymorphisms in the chloroplast genome of C. formosensis and C. taiwanensis were investigated by a PCR-based RFLP and nucleotide sequences. No fragment length nor nucleotide sequence differences were detected for 2 chloroplast intergenic spacers between Chilanshan and Alishan populations in both Chamaecyparis species. Low genetic variation has probably resulted from the refugial nature of these populations since the last glaciation rather than from recurrent pollen dispersal between Chilanshan and Alishan populations of these 2 Chamaecyparis species. Two Hinf I restriction site differences were found in the trnV-trnM intergenic spacer between C. formosensis and C. taiwanensis. Fragment length difference as well as point mutations in the petG-trnP intergenic spacer between C. formosensis and C. taiwanensis were also found. Further comparison with other Chamaecyparis species, especially C. obtusa, is required in order to understand the phylogenetic relationship between C. formosensis and C. taiwanensis.