Abstract
With only 32 individuals in the northeastern corner of Yunnan Province, China, Pinus squamata is one of the most endangered conifers in the world. Using two classes of molecular markers, RAPD and ISSR, its very low genetic variation was revealed. Shannon's index of phenotypic diversity (I) was 0.030, the mean effective number of alleles per locus (Ae) was 1.032, the percentage of polymorphic loci (P) was 6.45, and the expected heterozygosity (He) was 0.019 at the species level based on RAPD markers. The results of ISSR were consistent with those detected by RAPD but somewhat higher (I = 0.048, Ae = 1.042, P = 12.3, He = 0.029). The genetic variation of the subpopulation on the southwest-facing slope was much higher than that of the subpopulation on the northeast-facing slope, which may be attributed to the more diverse environment on the southwest-facing slope. The genetic differentiation between the two subpopulations was very low. The between-subpopulation variabilities, ΦST, calculated from RAPD and ISSR data were 0.011 and 0.024. Because of the lack of fossil records and geological historical data, it was difficult to explain the extremely low genetic diversity of the species. We postulate that this ancient pine might have experienced strong bottlenecks during its long evolutionary history, which caused the loss of genetic variation. Genetic drift and inbreeding in post-bottlenecked small populations may be the major forces that contribute to low genetic diversity. Human activities such as logging may have accelerated the loss of genetic diversity in P. squamata.
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References
Bucci, O., Vendramin, G. G., Lelli, L., and Vicario, F. (1997). Assessing the genetic divergence of Pinus leucodermis Ant. endangered populations: Use of molecular markers for conservation purposes. Theor. Appl. Genet. 95:1138–1146.
Carson, H. L. (1990). Increasing genetic variance after a population bottleneck. Trends Ecol. Evol. 5:228–231.
Cruzan, M. B. (1998). Genetic markers in plant evolutionary ecology. Ecology 79:400–412.
Delgado, P., Piero, D., Chaos, A., Perez-Nasser, N., and Alvarez-Buylla, E. R. (1999). High population differentiation and genetic variation in the endangered Mexican pine Pinus rzedowskii (Pinaceae). Am. J. Bot. 86:669–676.
Deng, L. L., Lu, S. J., Fan, G. S., and Li, X. W. (1995). Some community characteristics of Pinus squamata. J. Trop. Subtrop. Bot. 3:76–78.
Doyle, J. J., and Doyle, J. L. (1987). A rapid DNA isolation procedure for small quantities of fresh leaf material. Phytochem. Bull. 19:11–15.
Ellstrand, N. C., and Elam, D. R. (1993). Population genetic consequences of small population size: Implications for plant conservation. Annu. Rev. Ecol. Syst. 24:217–242.
Excoffier, L., Smouse, P. E., and Quattro, J. M. (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction data. Genetics 131:479–491.
Fang, D. Q., Roose, M. L., Krueger, R. R., and Federici, C. T. (1997). Fingerprinting trifoliate orange germ plasm accessions with isozymes, RFLPs and intersimple sequence repeat markers. Theor. Appl. Genet. 95:211–219.
Fischer, M., and Matthies, D. (1998). RAPD variation in relation to population size and plant fitness in the rare Gentianella germanica (Gentianaceae). Am. J. Bot. 85:811–819.
Fritsch, P., and Rieseberg, L. H. (1996). The use of random amplified polymorphic DNA (RAPD) in conservation genetics. In Smith, T. B., and Wayne, R. K. (eds.), Molecular Genetic Approaches in Conservation, Oxford University Press, London, pp. 54–73.
Ge, S., Hong, D. Y., Wang, H. Q., Liu, Z. Y., and Zhang, C. M. (1998). Population genetic structure and conservation of an endangered conifer, Cathaya argyrophylla (Pinaceae). Int. J. Plant Sci. 159:351–357.
Godt, M. J. W., Johnson, B. R., and Hamrick, J. L. (1996). Genetic diversity and population size in four rare southern Appalachian plant species. Conserv. Biol. 10:796–805.
Gupta, M., Chyi, Y.-S., Romero-Severson, J., and Owen, J. L. (1994). Amplification of DNA markers from evolutionarily diverse genomes using single primers of simple-sequence repeats. Theor. Appl. Genet. 89:998–1006.
Hamrick, J. L., and Godt, M. J. W. (1989). Allozyme diversity in plant species. In Brown, A. H. D., Clegg, M. T., Kahler, A. L., and Weir, B. S. (eds.), Plant Population Genetics, Breeding and Genetic Resources, Sinauer Associates, Sunderland, MA, pp. 43–63.
Hamrick, J. L., and Godt, M. J. W. (1996). Conservation genetics of endemic plant species. In Avise, J. C., and Hamrick, J. L. (eds.), Conservation Genetics: Case Histories from Nature, Chapman and Hall, New York, pp. 281–304.
Hamrick, J. L., Godt, M. J. W., Murawski, D. A., and Loveless, M. D. (1991). Correlations between species and allozyme diversity: Implications for conservation biology. In Falk, D.A., and Holsinger, K. E. (eds.), Genetics and Conservation of Rare Plants, Oxford University Press, New York, pp. 75–86.
Hamrick, J. L., Godt, M. J. W., and Sherman-Broyles, S. L. (1992). Factors influencing levels of genetic diversity in woody plant species. New Forest 6:95–124
Hedrick, P. W. (2001). Conservation genetics: Where are we now? Trends Ecol. Evol. 16:629–636.
Hedrick, P. W., and Kalinowski, S. T. (2000). Inbreeding depression in conservation biology. Annu. Rev. Ecol. Syst. 31:139–162.
Hu, S. Y. (1980). The metasequoia flora and its phytogeographic significance. J. Arnold Arbor. 61:41–94.
Isabel, N., Beaulieu, J., and Bousquet, J. (1995). Complete congruence between gene diversity estimates derived from genotypic data at enzyme and random amplified polymorphic DNA loci in black spruce. Proc. Natl. Acad. Sci. USA 92:6369–6373.
Isabel, N., Beaulieu, J., Theriault, P., and Bousquet, J. (1999). Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints. Mol. Ecol. 8:477–483.
Lee, C. T., Wickneswari, R., Mahani, M. C., and Zakri, A. H. (2002). Effect of selective logging on the genetic diversity of Scaphium macropodum. Biol. Conserv. 104:107–118.
Lee, S.-W., Ledig, F. T., and Johnson, D. R. (2002). Genetic variation at allozyme and RAPD markers in Pinus longaeva (Pinaceae) of the White mountains, California. Am. J. Bot. 89:566–577.
Li, C. X., Yang, Q., Zhou, J. P., Fan, S. H., and Yang, H. (1999). RAPD analysis of genetic diversity in the natural population of Metasequoia glyptostrocoides, central China. Acta Sci. Nat. Univ. Sunyatseni 38:59–63.
Li, X. P., and Zhu, Z. D. (1993). Studies on constituents of fatty acids from seed oils of Pinus bungeana and its taxonomic position. J. Nanjing Forest Univ. 17:27–34.
Li, X. W. (1992). A new series and a new species of Pinus from Yunnan. Acta Bot. Yunnan. 14:258–260.
Li, X. W. (1995). A floristic study on the seed plants from the region of Yunnan Plateau. Acta Bot. Yunnan. 17:1–14.
Li, X. W., and Li, J. (1997). The Tanaka-Kaiyong Line: An important floristic line for the study of the flora of east Asia. Ann. Missouri Bot. Garden 84:888–892.
Lu, S. J., Wang, J., and Zhu, H. P. (1999). A study on some biological characteristics of Pinus squamata. J. Southwest Forest Coll. 19:86–89.
Mosseler, A., Innes, D. J., and Robert, B. A. (1991). Lack of allozymic variation in disjunct Newfoundland populations of red pine (Pinus resinosa). Can. J. Forest Res. 21:525–528.
Mosseler, A., Egger, K. N., and Hughes, G. A. (1992). Low levels of genetic diversity in red pine confirmed by random amplified polymorphic DNA markers. Can. J. Forest Res. 22:1332–1337.
Nagaoka, T., and Ogihara, Y. (1997). Applicability of intersimple sequence repeat polymorphisms in wheat for use as DNA markers in comparison to RFLP and RAPD markers. Theor. Appl. Genet. 94:597–602.
Price, R. A., Liston, A., and Strauss, S. H. (1998). Phylogeny and systematics of Pinus. In Richardson, D. M. (ed.), Ecology and Biogeography of Pinus, Cambridge University Press, Cambridge, UK, pp. 49–68.
Qian, W., Ge, S., and Hong, D. Y. (2001). Genetic variation within and among populations of a wild rice Oryza granulata from China detected by RAPD and ISSR. Theor. Appl. Genet. 102:440–449.
Ratnaparkhe, M. B., Tekeoglu, M., and Muehlbauer, F. J. (1998). Intersimple sequence repeat (ISSR) polymorphisms are useful for finding markers associated with disease resistance gene clusters. Theor. Appl. Genet. 97:515–519.
Schmidt, K., and Jensen, K. (2000). Genetic structure and AFLP of remnant populations in the rare plant Pedicularis palustris (Scrophulariaceae) and its relation to population size and reproductive components. Am. J. Bot. 87:678–689.
Wang, C. M., Li, X. W., Mu, Q. Y., and Xiao, S. Q. (1998). Study on the wood anatomy and systematic location of Pinus squamata. J. Sichuan Agric. Univ. 16:165–169.
Wang, X. Q., Zhou, Y. P., Zhang, D. M., and Hong, D. Y. (1996). Genetic diversity analysis by RAPD in Cathaya argyrophylla Chun et Kuang. Sci China (Ser. C) 26:436–441.
Westemeier, R. L., Brown, J. D., and Simpson, S. A. (1998). Tracking the long-term decline and recovery of an isolated population. Science 282:1695–1698.
Williams, J. G. K., Kubelik, A. R., Livak, K. J., Rafalski, J. A., and Tingey, S. V. (1990). DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucleic Acids Res. 18:6531–6535.
Xia, M., Zhou, X. F., and Zhao, S. D. (2001). RAPD analysis on genetic diversity of natural populations of Pinus koraiensis. Acta Ecol. Sin. 21:730–737.
Yeh, F. C., Yang, R. C., Boyle, T. B. J., Ye, Z. H., and Mao, J. X. (1997). POPGENE, the User-Friendly Shareware for Population Genetic Analysis, Molecular Biology and Biotechnology Center, University of Alberta, Canada.
Ying, J. S., Zhang, Y. R., and Boufford, D. F. (1994). The Endemic Genera of Chinese Seed Plants, Science Press, Beijing.
Yu, H., Ge, S., Huang, R. F., and Jiang, H. Q. (2000). A preliminary study on genetic variation and relationships of Pinus yunnanensis and its closely related species. Acta Bot. Sin. 42:107–110.
Zhang, Z. Y., Yang, J. B., and Li, D. Z. (2003). Phylogenetic relationships of the extremely endangered species, Pinus squamata (Pinaceae) inferred from four sequences of the chloroplast genome and ITS of the nuclear genome. Acta Bot. Sin. 45:530–535.
Zietkiewicz, E., Rafalski, A., and Labuda, D. (1994). Genome fingerprinting by simple sequence repeat (SSR)-anchored polymerase chain reaction amplification. Genomics 20:176–183.
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Zhang, ZY., Chen, YY. & Li, DZ. Detection of Low Genetic Variation in a Critically Endangered Chinese Pine, Pinus squamata, Using RAPD and ISSR Markers. Biochem Genet 43, 239–249 (2005). https://doi.org/10.1007/s10528-005-5215-6
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DOI: https://doi.org/10.1007/s10528-005-5215-6