Phylogeography of Asparagus schoberioides Kunth (Asparagaceae) in Japan

Tatsuya Fukuda, In-Ja Song, Hokuto Nakayama, Takuro Ito, Akira Kanno, Hiroshi Hayakawa, Yukio Minamiya, Jun Yoko Yama

.

DOI: 10.4236/ajps.2011.26093                

Abstract

To describe the phylogeographic structures of Asparagus schoberioides Kunth (Asparagaceae) in Japan, we investigated its nucleotide sequence variations with respect to its geographic distribution pattern. Sequencing of the internal transcribed spacer (ITS) 1 region in 29 samples of A. schoberioides revealed 20 polymorphic nucleotide sites. As a result, the 29 samples of A. schoberioides fell into 15 distinct haplotypes and phylogenetic analyses revealed these haplotypes fell into two major clades, Clade 1 and Clade 2. The haplotypes of Clade 1 were distributed chiefly along the Pacific Ocean side of Japan, while those of Clade 2 occurred mainly along the Japan Sea side. This result suggests that A. schoberioides has migrated via two routes in Japan.

Keywords

Asparagus schoberioides, Internal Transcribed Spacer (ITS), Phylogeny, Phylogeography

Conflicts of Interest

The authors declare no conflicts of interest.

References

[1]	J. C. Avise, J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb and N. C. Saunders, “Intraspecific Phylogeography: The Mitochondrial DNA Bridge between Population Genetics and Systematics,” Annual Review of Ecology, Evolution, and Systematics, Vol. 18, 1987, pp. 489-552.
[2]	J. C. Avise, “Molecular Markers, Natural History, and Evolution,” Chapman & Hall, New York, 1994. doi:10.1007/978-1-4615-2381-9
[3]	J. C. Avise, “Phylogeography: The History and Formation of Species,” Harvard University Press, London, 2000.
[4]	D. E. Soltis and P. S. Soltis, “Choosing an Approach and an Appropriate Gene for Phylogenetic Analysis,” In: D. E. Soltis, P. S. Soltis and J. J. Doyle, Eds., Molecular Systematics of Plant II: DNA Sequencing, Kluwer Academic Publishers, Massachusetts, 1998, pp. 1-42.
[5]	J. J. Doyle and J. I. Davis, “Homology in Molecular Phylogenetics: A Parsimony Perspective,” In: D. E. Soltis, P. S. Soltis and J. J. Doyle, Eds., Molecular Systematics of Plant II: DNA Sequencing, Kluwer Academic Publishers, Massachusetts, 1998, pp. 101-131. doi:10.1007/978-1-4615-5419-6_4
[6]	J. Ohwi, “Asparagus L.,” In: F. G. Meyer and E. H. Walker, Eds., Flora of Japan, Smithonian Institution, Washington, DC, 1965, p. 300.
[7]	X. Chen and K. G. Tamanian, “Asparagus L.,” In: Z. Y. Wu and P. H. Raven, Eds., Flora of China, Vol. 24, (Flagellariaceae through Marantaceae), Missouri Botanical Garden Press, St. Louis, 2000, pp. 139-146.
[8]	T. Fukuda, H. Ashizawa, T. Nakamura, T. Ochiai, A. Kanno, T. Kameya and J. Yokoyama, “Molecular Phylogeny of the Genus Asparagus (Asparagaceae) Inferred from Plastid petB Intron and petD—rpoA Intergenic Spacer Sequences,” Plant Species Biology, Vol. 20, No. 2, 2005, pp. 123-134.
[9]	T. Ochiai, T. Sonoda, A. Kanno and T. Kameya, “Interspecific Hybrids between Asparagus schoberioides Kunth and A. officinalis L.,” Acta Horticulturae, Vol. 589, 2002, pp. 225-229.
[10]	T. Ito, T. Ochiai, T. Fukuda, H. Ashizawa, T. Sonoda, T. Kameya and A. Kanno, “Potential of Interspecific Hybrids in Asparagaceae,” Acta Horticulturae, Vol. 776, 2008, pp. 279-284.
[11]	M. L. Arnold, “Natural Hybridization and Evolution,” Oxford University Press, 1997, New York.
[12]	D. Bartsch, M. Lehnen, J. Clegg, M. Pohi-Orf, I. Schuphan and N. C. Ellstrand, “Impact of Gene Flow from Cultivated Beet on Genetic Diversity of Wild Sea Beet Populations,” Molecular Ecology, Vol. 8, No. 10, 1999, pp. 1733-1741. doi:10.1046/j.1365-294x.1999.00769.x
[13]	P. Gepts and R. Papa, “Possible Effects of (trans) Gene Flow from Crops on the Genetic Diversity from Land Races and Wild Relatives,” Environmental Biosafety Research, Vol. 2, No. 2, 2003, pp. 89-103. doi:10.1051/ebr:2003009
[14]	M. A. Chapman and J. M. Burke, “Letting the Gene Out of the Bottle: The Population Genetics of Genetically Modified Crops,” New Phytologist, Vol. 170, No. 3, 2006, pp. 429-443. doi:10.1111/j.1469-8137.2006.01710.x
[15]	E. Bitocchi, L. Nanni, M. Rossi, D. Rau, E. Bellucci, G. G. Vendramin and R. Papa, “Introgression from Modern Hybrid Varieties into Landrace Poplation of Maize (Zea mays ssp. Mays L.) in Central Italy,” Molecular Ecology, Vol. 18, No. 4, 2009, pp. 603-621. doi:10.1111/j.1365-294X.2008.04064.x
[16]	J.-F. Arnaud, S. Fénart, C. Godé, S. Deledicque, P. Touzet and J. Cuguen, “Fine-Scale Geographical Structure of Genetic Diversity in Inland Wild Beet Populations,” Molecular Ecology, Vol. 18, No. 15, 2009, pp. 3201-3215. doi:10.1111/j.1365-294X.2009.04279.x
[17]	Y. Tsumura, H. Taguchi, Y. Suyama and K. Ohba, “Geographical Cline of Chloroplast DNA Variation in Abies mariesii,” Theoretical and Applied Genetics, Vol. 89, No. 7-8, 1994, pp. 922-925. doi:10.1007/BF00224518
[18]	T. Ohi, T. Kajita and J. Murata, “Distinct Geographic Structure as Evidenced by Chloroplast DNA Haplotypes and Ploidy Level in Japanese Aucuba (Aucubaceae),” American Journal of Botany, Vol. 90, No. 11, 2003, pp. 1645-1652. doi:10.3732/ajb.90.11.1645
[19]	N. Tomaru, M. Takahashi, Y. Tsumura, Y. Takahashi and K. Ohba, “Intraspecific Variation and Phylogeographic Patterns of Fagus crenata (Fagaceae) Mitochondrial DNA,” American Journal of Botany, Vol. 85, No. 5, 1998, pp. 629-636. doi:10.2307/2446531
[20]	N. Fujii, N. Tomaru, K. Okuyama, K. Koike, T. Mikami and K. Ueda, “Chloroplast DNA Phylogeography of Fagus crenata (Fagaceae) in Japan,” Plant Systematics and Evolution, Vol. 232, No. 1-2, 2002, pp. 21-33. doi:10.1007/s006060200024
[21]	T. Okura and K. Harada, “Phylogeographical Structure Revealed by Chloroplast DNA Variation in Japanese Beech (Fagus crenata Blime),” Heredity, Vol. 88, No. 4, 2002, pp. 322-329. doi:10.1038/sj.hdy.6800048
[22]	N. Fujii, K. Ueda, Y. Watano and T. Shimizu, “Further Analysis of Intraspecific Sequence Variation of Chloroplast DNA in Primula cunefolia Ledeb. (Primulaceae): Implications for Biogeography of the Japanese Alpine flora,” Journal of Plant Research, Vol. 112, 1999, pp. 87-95. doi:10.1007/PL00013866
[23]	M. Kanno, J. Yokoyama, Y. Suyama, M. Ohyama, T. Ito and M. Suzuki, “Geographic Distribution of two Haplotypes of Chloroplast DNA in Four Oak Species (Quercus) in Japan,” Journal of Plant Research, Vol. 117, No. 4, 2004, pp. 311-317. doi:10.1007/s10265-004-0160-8
[24]	T. Ohi, M. Wakabayashi, S. Wu and J. Murata, “Phylogeography of Stachyurus praecox (Stachyuraceae) in the Japanese Archipelago Based on Chloroplast DNA Haplotypes,” Journal of Japanese Botany, Vol. 78, No. 1, 2003, pp. 1-14.
[25]	K. Aoki, T. Suzuki, T.-W. Hsu and N. Murakami, “Phylogeography of the Component Species of Broad-Leaved Evergreen Forests in Japan, Based on Chloroplast DNA Variation,” Journal of Plant Research, Vol. 117, No. 1, 2004, pp. 77-94. doi:10.1007/s10265-003-0132-4
[26]	P. Taberlet, L. Fumagalli, A. G. Wust-Saucy and J. F Coson, “Comparative Phylogeography and Postglacial Colonization Routes in Europe,” Molecular Ecology, Vol. 7, No. 4, 1998, pp. 453-464. doi:10.1046/j.1365-294x.1998.00289.x
[27]	T. Nishizawa and Y. Watano, “Primer Pairs Suitable for PCR-SSCP Analysis of Chloroplast DNA in Angiosperms,” Journal of Phytogeography and Taxonomy, Vol. 48, No. 1, 2000, pp. 67-70.
[28]	C. W. Dick, K. Abdul-Salim and E. Bermingham, “Molecular Systematic Analysis Reveals Cryptic Tertiary Diversification of a Widespread Tropical Rain Forest Tree,” American Naturalist, Vol. 162, No. 6, 2003, pp. 691-703. doi:10.1086/379795
[29]	J. Yokoyama, T. Fukuda, A. Yokoyama and M. Maki, “The intersectional hybrid between Weigela hortensis and W. maximowiczii (Caprifoliaceae),” Botanical Journal of the Linnean Society, Vol. 138, No. 3, 2002, pp. 369-380. doi:10.1046/j.1095-8339.2002.00033.x
[30]	T. Yamashiro, T. Fukuda, J. Yokoyama and M. Maki, “Molecular Phylogeny of Vincetoxicum (ApocynaceaeAsclepiadoideae) Based on the Nucleotide Sequences of cpDNA and nrDNA,” Molecular Phylogenetics and Evolution, Vol. 31, No. 2, 2004, pp. 689-700. doi:10.1016/j.ympev.2003.08.016
[31]	H. Tsukaya, “Gene Flow between Inpatiens radicans and I. javensis (Balsaminaceae) in Gunung Pangrango, Central Java, Indonesia,” American Journal of Botany, Vol. 91, No. 12, 2004, pp. 2119-2123. doi:10.3732/ajb.91.12.2119
[32]	H. Tsukaya, Y. Lolawa, M. Kondo and H. Ohba, “LargeScale General Collection of Wild-Plant DNA in Mustang, Nepal,” Journal of Plant Research, Vol. 118, No. 1, 2005, pp. 57-60. doi:10.1007/s10265-005-0196-4
[33]	J. Yokoyama, T. Fukuda and H. Tsukaya, “Morphological and Molecular Variation of Mitchella undulata Sieblod et Zucc., with Special Reference to Systematic Treatment of the Dwarf Form from Yakushima Island,” Journal of Plant Research, Vol. 116, No. 4, 2003, pp. 309-316. doi:10.1007/s10265-003-0105-7
[34]	T. J. White, T. Bruns, S. Lee and J. Taylor, “Amplification and Direct Sequencing of Fungal Ribosomal RNA genes for Phylogenetics,” In: M. Innis, D. Gelfan, J. Sninsky and T. J. White, Eds., PCR Protocols: A Guide to Methods and Application, Academic Press, San Diego, 1990, pp. 315-322.
[35]	J. D. Thompson, T. J. Gibson, F. Plewniak, F. Jeanmougin and D. G. Higgins, “The Clustal_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools,” Nucleic Acids Research, Vol. 25, No. 24, 1997, pp. 4876-4882. doi:10.1093/nar/25.24.4876
[36]	D. L. Swofford, “PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4.0b10.,” Sinauer Associates, Sunderland, 2002.
[37]	W. P. Maddison, “The Discovery and Importance of Multiple Islands of Most-Parsimonious Trees,” Systematic Zoology, Vol. 40, No. 3, 1991, pp. 315-328. doi:10.2307/2992325
[38]	J. Felsenstein, “Confidence Limits on Phylogenies: An Approach Using the Bootstrap,” Evolution, Vol. 39, No. 4, 1985, pp. 783-791. doi:10.2307/2408678
[39]	H. Ikenoue and S. Okitsu, “Comparison of Leaf Area and Leaf Shape of Euptelea polyandra Sieb. Et Zucc. between the Pacific Ocean Side and the Sea of Japan Side,” Journal of Phytogeography and Taxonomy, Vol. 42, No. 2, 1995, pp. 125-131.
[40]	K. Yonekura and H. Ohashi, “Geographical Distribution and Variation in Bistorta tenuicaulis and Its New Variety from Japan, with Special Reference to Gynodioecy of B. tenuicaulis and B. abukumensis (Polygonaceae),” Journal of Japanese Botany, Vol. 73, No. 1, 1998, pp. 1-11.
[41]	T. J. Givnish, K. J. Sytsma, J. F. Smith and W. J. Hann, “Thorn-Like Prickles and Heterophylly in Cyanea: Adaptations to Extinct Avian Browsers on Hawaii?” Proceedings of National Academy of Sciences of the USA, Vol. 91, No. 7, 1994, pp. 2810-2814. doi:10.1073/pnas.91.7.2810
[42]	D. G. Howarth, D. E. Gardner and C. W. Morgan, “Phylogeny of Rubus Subgenus Idaeobatus (Rosaceae) and Its Implications toward Colonization of the Hawaii Islands,” Systematic Botany, Vol. 22, No. 3, 1997, pp. 433-442. doi:10.2307/2419819
[43]	T. Fukuda, J. Yokoyama and H. Ohashi, “Phylogeny and Biogeography of the Genus Lycium (Solanaceae): Inferences from Chloroplast DNA Sequences,” Molecular Phylogenetics and Evolution, Vol. 19, No. 2, 2001, pp. 246-258. doi:10.1006/mpev.2001.0921
[44]	J. R. Worth, G. J. Jordan, J. R. Marthick, G. E. Mckinnon and R. E. Vaillancourt, “Chloroplast Evidence for Geographic Stasis of the Australian Bird-Dispersed Shrub Tasmannia lanceolata (Winteraceae),” Molecular Ecology, Vol. 19, No. 14, 2010, pp. 2949-2963. doi:10.1111/j.1365-294X.2010.04725.x
[45]	M. King, “Species Evolution: The Role of Chromosome Change,” Cambridge University Press, Melbourne, 1993.
[46]	Y. Yatabe, D. Darnaedi and N. Murakami, “Allozyme Analysis of Cryptic Species in the Asplenium nidus Complex from West Java, Indonesia,” Journal of Plant Research, Vol. 115, No. 6, 2002, pp. 483-490. doi:10.1007/s10265-002-0060-8