Molecular identification and allopatric divergence of the white pine species in China based on the cytoplasmic DNA variation

• Range-wide samples were collected for the molecular identification of white pine species.
• Four chloroplast DNA and two mitochondrial DNA regions were determined for sampled species.
• Geographic isolation and speciation stages have affected the molecular identification of pine species.

Molecular identification of plant species may be highly related to the geographic isolation and speciation stages among species. In this study, we examined these possibilities in a group of white pines in China. We sampled 449 individuals from 60 natural populations of seven species from sect. Quinquefoliae subsect. Strobus. We sequenced four chloroplast DNA regions (around 3100 bp in length) and two mitochondrial DNAs (around 1000 bp in length). We identified 21 chlorotypes and 10 mitotypes. Both chlorotypes and mitotypes recovered from four species with long disjunction and restricted distributions in northern or northwestern China, Pinus sibirica, Pinus koraiensis, Pinus wallichiana and Pinus pumila are species-specific, suggesting that these cytoplasmic DNAs can distinguish them from the close relatives. Allopatric isolations should have contributed greatly to their genetic divergences. However, both chlorotypes and mitotypes recovered for Pinus dabeshanensis and Pinus fenzeliana distributed in southeastern and southern China are shared or closely related to those found in the widely distributed Pinus armandii. These two species may have diverged or derived from P. armandii recently. All of our findings together suggest that the discrimination power of the molecular identifications based on the cytoplasmic DNA barcodes may show variable discriminability depending on geographic isolation and speciation stages among the sampled species.