Nucleotide polymorphism and phylogeographic history of an endangered conifer species Pinus bungeana

• Nucleotide polymorphism and phylogeographic history of an endangered conifer species were determined by three nuclear genes.
• P. bungeana showed the low level of nucleotide diversity and different genetic variation patterns at three nuclear loci.
• Qinling-Daba and Lvliang Mountains may be the glacial refuges of P. bungeana.

Pinus bungeana Zucc. ex Endl. (Pinaceae), is an endangered conifer tree species and is endemic to western central China. In this study, we detected the nucleotide polymorphism and phylogeographic history of P. bungeana based on three nuclear genes. We collected 16 natural populations and covered the entire distributional ranges of P. bungeana. We found that this endangered species have extremely low level of nucleotide diversity (πt = 0.00098, πsil = 0.00229) compared with that of other conifers. Meanwhile, hierarchical AMOVA revealed that genetic variations of two nuclear loci (010054_01 and 0_12329_02) mainly occurred among populations (54% and 55%), and another locus (0_14221_01) existed within populations (64%). This finding may be caused by random fixation of nuclear genes. Neutrality tests and mismatch analysis suggested that P. bungeana may have experienced the recent range expansion. In addition, high genetic diversity and unique haplotypes were identified in the west areas of Qinling-Daba and Lvliang Mountains, and these areas may be the glacial refuges of P. bungeana. After the glaciation, the species expanded or migrated outward from these refuges, and the founder effect or bottleneck effect in this process may have resulted in the low level of nucleotide polymorphism of P. bungeana.