Nucleotide polymorphism and phylogeographic history of an endangered conifer species Pinus bungeana |
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| Institution: | 1. Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan;2. Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan;3. Ibaraki Prefectural Forestry Research Institute, Toh, Naka, Ibaraki, 311-0122, Japan;4. Forestry and Forest Products Research Institute, Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan;5. Division of Terrestrial Ecosystem, Institute of Mountain Science, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan;1. Forest Research and Management Organization, Tsukuba, Ibaraki, 305-8687, Japan;2. Miyagi Prefectural Forestry Technology Institute, Ohira, Miyagi, 981-3602, Japan;3. Nara Forest Research Institute, Takatori, Nara, 635-0133, Japan;4. Shiga Forest Research Center, Yasu, Shiga, 520-2321, Japan;1. Neuroscience Institute, National Research Council of Italy, Section of Cagliari, I-09042 Monserrato, CA, Italy;2. Cagliari Pharmacological Research s.r.l., I-09127 Cagliari, CA, Italy;3. Indena S.p.A., I-20139 Milan, MI, Italy;4. Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, I-53100, Siena, SI, Italy |
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| Abstract: | 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. |
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| Keywords: | Nucleotide polymorphism Population genetic structure Phylogeography |
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