川崎氏阿拉伯芥 ( Arabidopsis kamchatica subsp. kawasakiana ) 為多年生 ( perennial ) 的阿拉伯芥，是琴葉阿拉伯芥 ( Arabidopsis lyrata ) 以及葉芽阿拉伯芥 ( Arabidopsis halleri subsp. gemmifera ) 的異源四倍體 ( allotetraploid ) 雜交種，生長於沙質海岸和低緯度的湖邊。 此物種在生理以及生態方面與亞種 ( subspecies ) 玉山阿拉伯芥 ( Arabidopsis kamchatica ) 有明顯分化。 在地理分佈上，玉山阿拉伯芥分佈在北美及歐亞大陸東部高山，而川崎氏阿拉伯芥卻僅分佈於日本西部。 為了進一步釐清這兩個物種的遺傳分化 ( genetic differentiation )，本研究隨機選定分析川崎氏阿拉伯芥的97個基因。 在本研究中，大部分 A.k. kawasakiana的基因保有來自兩個父母種的基因序列，在這些基因中有兩個基因 ( 2.1% )，At5g47690和SHR，Ka/Ks值大於1且重組率 ( recombination rate ) 高，此為平衡選汰 ( balancing selection ) 的現象。 在親緣關係上，比起A. lyrata， A. k. kawasakiana與A. h. gemmifera較近。 有趣的是，有六個基因僅保留A. lyrata的基因序列，八個基因僅保留A. h. gemmifera的基因序列，暗示了在雜交子代中會有不均等的的父母種基因體組成。 在這些基因中，At4g00335，IRX9-L，CA3，以及23.5MT這四個基因的Ka/Ks值大於1，顯示其承受了正向選汰 ( positive selection ) 作用。 另外，ENT, FT, 17.6I, and CYCA1四個基因呈現高度連鎖不平衡 ( linkage disequilibrium )，表示此物種發生了選擇性清除 ( selecive sweeps ) 的現象。 更甚者，僅保留其中一方父母種基因序列的基因，呈現與A. kamchatica顯著的遺傳分化，表示此兩物種具有在適應上的分化。

Arabidopsis kamchatica subsp. kawasakiana is a perennial allotetraploid plant derived from A. lyrata and A. halleri subsp. gemmifera. It grows at habitats along sandy coasts and lakes at low elevations, and is physiologically and ecologically differentiated from another hybrid from the same parental species, A. kamchatica. Geographically, A. kamchatica is distributed in North America and northeastern Asia, while A. k. kawasakiana is restrictedly distributed in western Japan. To clarify the genetic differentiation between the two hybrids, 97 genes were randomly selected. In this study, most of the A.k. kawasakiana genes retained genomic regions of both parental species; two (2.1%) of these genes, At5g47690 and SHR, displayed Ka/Ks>1 and high Rm values, suggesting effects of balancing selection. Phylogenetcially, A. k. kawasakiana was closer to A. h. gemmifera than to A. lyrata. Interestingly, 6 genes were exclusively from A. lyrata and 8 genes were from A. h. gemmifera. These uniparentally inherited genes indicated unequal contributions of parental genomes to the hybrid offspring. Four genes, At4g00335, IRX9-L, CA3, and 23.5MT, were shaped by positive selection, as indicated by Ka/Ks > 1. Besides, four other genes of ENT, FT, 17.6I, and CYCA1
displayed high levels of linkage disequilibrium, indicating footprints of selective sweeps. Futhurmore, genes of A. k. kawasakiana that had alleles exclsuievly from one single parental species displayed significant genetic differentiation from A. kamchatica, suggesting adaptive divergence between the two hybrids.

Adams, K. L. 2007. Evolution of duplicate gene expression in polyploid and hybrid plants. Journal of Heredity 98(2):136-141.
Aken, O. V., B. Zhang, C. Carrie, V. Uggalla, E. Paynter, E. Giraud, and J. Whelan. 2009. Defining the mitochondrial stress response in Arabidopsis thaliana. Molecular Plant 2: 1310-1324.
Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb, and N. C. Saunders. 1987. Intraspecific phylogeography: The mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522.
Al-Shehbaz, I. A. and S. L. O'Kane Jr. 2002. Taxonomy and phylogeny of Arabidopsis ( Brassicaceae ). The Arabidopsis Book 1: e0001.
Allnutt, G. V., H.J. Rogers, D. Francis, and R. J. Herbert. 2007. A LEAFY-like gene in the long-day plant, Silene coeli-rosa is dramatically up-regulated in evoked shoot apical meristems but does not complement the Arabidopsis lfy mutant. Journal of Experimental Botany 58 (8): 2249-2259.
Alonso, J. M., A. N. Stepanova, T. J. Leisse, C. J. Kim, H. Chen, P. Shinn, D. K. Stevenson, J. Zimmerman, P. Barajas, R. Cheuk, C. Gadrina, C. Heller, A. Jeske, E. Koesema, C. C. Meyers, H. Parker, L. Prednis, Y. Ansari, N. Choy, H. Deen, M. Geralt, N. Hazari, E. Hom, M. Karnes, C. Mulholland, R. Ndubaku, I. Schmidt, P. Guzman, L. Aguilar-Henonin, M. Schmid, D. Weigel, D. E. Carter, T. Marchand, E. Risseeuw, D. Brogden, A. Zeko, W. L. Crosby, C. C. Berry, J. R. Ecker. 2003. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657.
Auldridge, M. E., A. Block, J. T. Vogel, C. Dabney-Smith, I. Mila, M. Bouzayen, M. Magallanes-Lundback, D. DellaPenna, D. R. McCarty, and H. J. Klee. 2006. Characterization of three members of the Arabidopsis carotenoid cleavage dioxygenase family demonstrates the divergent roles of this multifunctional enzyme family. The Plant Journal 45: 982-993.
Bartlett, J. M. S. and D. Stirling. 2003. A short history of the polymerase chain reaction. Methods In Molecular Biology 226: 3-6.
Bartling, D., H. Bülter, K. Liebeton, and E. W. Weiler. 1992. An Arabidopsis thaliana cDNA clone encoding a 17.6 kDa class II heat shock protein. Plant Molecular Biology 18: 1007-1008.
Bergeron-Sawitzke, J., B. Gold, A. Olsh, S. Schlotterbeck, K. Lemon, K. Visvanathan, R. Allikmets, and M. Dean. 2009. Multilocus analysis of age-related macular degeneration. European Journal of Human Genetics 17: 1190-1199.
Bernard, C., M. Traub, H. H. Kunz, S. Hach, O. Trentmann, and T. Möhlmann. 2011. Equilibrative nucleoside transporter 1 (ENT1) is critical for pollen germination and vegetative growth in Arabidopsis. Journal of Experimental Botany 62(13): 4627-4637.
Buehler, D., R. Graf, R. Holderegger, and F. Gugerli. 2011. Using the 454 pyrosequencing-based technique in the development of nuclear microsatellite loci in the alpine plant Arabis alpina ( Brassicaceae). American Journal of Botany 98(5): e103-e105.
Bürger, R. 2005. A multilocus analysis of intraspecific competition and stabilizing selection on a quantitative trait. Journal of Mathematical Biology 50: 355-396.
Cao, J., K. Schneeberger, S. Ossowski, T. Günther, S. Bender, J. Fitz, D. Koenig, C. Lanz, O. Stegle, C. Lippert, X. Wang, F. Ott, J. Müller, C. Alonso-Blanco, K. Borgwardt, K. J. Schmid, and D. Weigel. 2011. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nature Genetics 43: 956-963.
Chen, I. P., A. Mannuss, N. Orel, F. Heitzeberg, and H. Puchta. 2008. A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis. Plant Physiology 146: 1786-1796.
Clauss, M. J. and M. A. Koch. 2006. Poorly known relatives of Arabidopsis thaliana. Trends in Plant Science 11(9): 449-459.
Comai, L., A. P. Tyagi, K. Winter, R. Holmes-Davis, S. H. Reynolds, Y. Stevens, and B. Byers. 2000. Phenotypic instability and rapid gene silencing in newly formed Arabidopsis allotetraploids. The Plant Cell 12: 1551-1567.
d’Erfurth, I., L. Cromer, S. Jolivet, C. Girard, C. Horlow, Y. Sun, J. P. C. To, L. E. Berchowitz, G. P. Copenhaver, R. Mercier. 2010. The CYCLIN-A CYCA1;2/TAM is required for the meiosis I to meiosis II transition and cooperates with OSD1 for the prophase to first meiotic division transition. PLoS Genetics 6(6): e1000989.
Desikan, R., S. A.-H.-Mackerness, J. T. Hancock, and S. J. Neill. 2001. Regulation of the Arabidopsis transcriptome by oxidative stress. Plant Physiology 127: 159-172.
Downes, B. P., S. A. Saracco, S. S. Lee, D. N. Crowell, and R. D. Vierstra. 2006. MUBs, a Family of ubiquitin-fold proteins that are plasma membrane-anchored by prenylation. The Journal of Biological Chemistry 281(37): 27145-27157.
Fowler, S. and M. F. Thomashow. 2002. Arabidopsis transcriptome profiling indicates that multiple regulatory pathways are activated during cold acclimation in addition to the CBF cold response pathway. The Plant Cell 14: 1675-1690.
Fukaki, H., J. Wysocka-Diller, T. Kato, H. Fujisawa, P. N. Benfey, and M. Tasaka. 1998. Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. The Plant Journal 14(4): 425-430.
Gamburg, K. Z., N. N. Varakina, T. M. Rusaleva, E. L. Tauson, E. G. Rikhvanov, G. B. Borovskii, and V. K. Voinikov. 2011. Comparison of the Resistances of Arabidopsis (Arabidopsis thaliana) and Thellungiella (Thellungiella salsuginea) suspension cultures to high temperatures. Doklady Biological Sciences 439: 232-235.
Gan, X. C., O. Stegle, J. Behr, J. G. Steffen, P. Drewe, K. L. Hildebrand, R. Lyngsoe, S. J. Schultheiss, E. J. Osborne, V. T. Sreedharan, A. Kahles, R. Bohnert, G. Jean, P. Derwent, P. Kersey, E. J. Belfield, N. P. Harberd, E. Kemen, C. Toomajian, P. X. Kover, R. M. Clark, G. Rätsch, and R. Mott. 2011. Multiple reference genomes and transcriptomes for Arabidopsis thaliana. Nature 477: 419-423.
Gardiner, J., T. J. Donner, and E. Scarpella. 2011. Simultaneous activation of SHR and ATHB8 expression defines switch to preprocambial cell state in Arabidopsis leaf development. Developmental Dynamics 240: 261-270.
Ge, W., Y. Song, C. J. Zhang, Y. F. Zhang, A. L. Burlingame, and Y. Guo. 2011. Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen. Biochimica et Biophysica Acta 1814: 1964-1973.
Guo, S. W. and E. A. Thompson. 1992. Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48(2): 361-372.
Hasegawa, Y., M. Seki, Y. Mochizuki, N. Heida, K. Hirosawa, N. Okamoto, T. Sakurai, M. Satou, K. Akiyama, K. Iida, K. Lee, S. Kanaya, T. Demura, K. Shinozaki, A. Konagaya, and T. Toyoda. 2006. A flexible representation of omic knowledge for thorough analysis of microarray data. Plant Methods 2: 5.
Helariutta, Y., H. Fukaki, J. Wysocka-Diller, K. Nakajima, J. Jung, G. Sena, M. Hauser, and P. N. Benfey. 2000. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101: 555-567.
Hewitt, G. M. 1996. Some genetic consequences of Ice Ages, and their role in divergence and speciation. Biological Journal of the Linnaean Society 58: 247-276.
Horwitz, J. P., J. Chua, R. J. Curby, A. J. Tomson, M. A. Darooge, B. E. Fisher, J. Mauricio, and I. Klundt. 1964. Substrates for cytochemical demonstration of enzyme activity. I. some substituted 3-indolyl-β-D-glycopyranosides. Journal of Medicinal Chemistry 7: 574-575.
Hudson, R. R., M. Kreitman, and M. Aguadé. 1987. A Test of neutral molecular evolution based on nucleotide data. Genetics 116: 153-159.
Hudson, R. R., M. Slatkint, and W. P. Maddison. 1992. Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589.
Izawa, T., Y. Takahashiy, and M. Yano. 2003. Comparative biology comes into bloom: genomic and genetic comparison of flowering pathways in rice and Arabidopsis. Current Opinion in Plant Biology 6:113-120.
Joly, S., P. A. McLenachan, and P. J. Lockhart. 2009. A statistical approach for distinguishing hybridization and incomplete lineage sorting. The American Naturalist 174(2): E54-E70.
Josefsson, C., B. Dilkes, and L. Comai. 2006. Parent-dependent loss of gene silencing during interspecies hybridization. Current Biology 16: 1322-1328.
Klodmann, J., S. Sunderhaus, M. Nimtz, L. Jänsch, and H. P. Braun. 2010. Internal architecture of mitochondrial complex I from Arabidopsis thaliana. The Plant Cell 22: 797-810.
Kolnik, M. and K. Marhold. 2006. Distribution, chromosome numbers and nomenclature conspect of Arabidopsis halleri (Brassicaceae) in the carpathians. Biologia 61: 41-50.
Kreps, J. A., Y. J. Wu, H. S. Chang, T. Zhu, X. Wang, and J. F. Harper. 2002. Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiology 130: 2129-2141.
Kumar, S., M. Nei, J. Dudley, and K. Tamura. 2008. MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9(4): 299-306.
Lee, Y. H., T. Ota, and V. D. Vacquier. 1995. Positive selection is a general phenomenon in the evolution of abalone sperm lysin. Molecular Biology and Evolution 12(2): 231-238.
Librado, P. and J. Rozas. 2009. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451-1452.
Liu, H. C., H. T. Liao, and Y. Y. Charng. 2011. The role of class A1 heat shock factors (HSFA1s) in response to heat and other stresses in Arabidopsis. Plant Cell and Environment 34: 738-751.
Llopart, A., D. Lachaise, and J. A. Coyne. 2005. Multilocus analysis of introgression between two sympatric sister species of Drosophila: Drosophila yakuba and D. santomea. Genetics 171: 197-210.
Lv, W. T., B. Lin, M. Zhang, and X. J. Hua. 2011. Proline accumulation is inhibitory to Arabidopsis seedlings during heat stress. Plant Physiology 156(4): 1921-1933.
Maleck, K., A. Levine, T. Eulgem, A. Morgan, J. Schmid, K. A. Lawton, J. L. Dang, and R. A. Dietrich. 2000. The transcriptome of Arabidopsis thaliana during systemic acquired resistance. Nature Genetics 26: 403-410.
Mardis, E. R. 2008. The impact of next-generation sequencing technology on genetics. Trends in Genetics 24(3): 133-141.
Mesicek, J. 1970. Chromosome counts in Cardaminopsis arenosa agg. (Cruciferae). Preslia 42: 225-248.
Murgia, I., D. Tarantino, C. Soave, and P. Morandini. 2011. Arabidopsis CYP82C4 Expression is Dependent on Fe Availability and Circadian Rhythm, and Correlates with Genes Involved in the Early Fe Deficiency Response. Journal of Plant Physiology 168: 894-902.
Nasrallah, M. E., K. Yogeeswaran, S. Snyder, and J. B. Nasrallah. 2000. Arabidopsis species hybrids in the study of species differences and evolution of amphiploidy in plants. Plant Physiology 124: 1605-1614.
Nordborg, M., J. O. Borevitz, J. Bergelson, C. C. Berry, J. Chory, J. Hagenblad, M. Kreitman, J. N. Maloof, T. Noyes, P. J. Oefner, E. A. Stahl, and D. Weigel. 2002. The extent of linkage disequilibrium in Arabidopsis thaliana. Nature Genetics 30: 190-193.
O'Kane, S. L. and I. A. Al-Shehbaz. 1997. A synopsis of Arabidopsis (Brassicaceae). Novon 7(3): 323-327.
Peng, L. W., H. Yamamoto, T. Shikanai. 2011. Structure and biogenesis of the chloroplast NAD(P)H dehydrogenase complex. Biochimica et Biophysica Acta 1807: 945-953.
Pritchard, J. K., M. Stephens, and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
Rozas, J., J. C. Sánchez-DelBarrio, X. Messeguer, and R. Rozas. 2003. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics Applications Note 19(18): 2496-2497.
Ryu, M. Y., S. K. Cho, and W. T. Kim. 2010. The Arabidopsis C3H2C3-Type RING E3 Ubiquitin Ligase AtAIRP1 Is a Positive Regulator of an Abscisic Acid-Dependent Response to Drought Stress. Plant Physiology 154: 1983-1997.
Saitou, N. and M. Nei. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4(4):406-425.
Sanger, F., S. Nicklen, A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences 74: 5463-5467.
Sato, Y. K. Yazawa, S. Yoshida, M. Tamaoki, N. Nakajima, H. Iwai, T. Ishii, S. Satoh. 2011. Expression and functions of myo-inositol monophosphatase family genes in seed development of Arabidopsis. Journal of Plant Research 124: 385-394.
Schmickl, R. and M. A. Koch. 2010. Arabidopsis hybrid speciation processes. Proceedings of the National Academy of Sciences 108(34): 14192-14197.
Sharbel,T. F., B. Haubold, and T. Mitchell-olds. 2000. Genetic isolation by distance in Arabidopsis thaliana: Biogeography and postglacial colonization of Europe. Molecular Ecology 9: 2109-2118.
Shendure, J. and J. Hanlee. 2008. Next-generation DNA sequencing. Nature Biotechnology 26(10): 1135-1145.
Shimizu, K. K., S. Fujii, K. Marhold, K. Watanabe, and H, Kudoh. 2005. Arabidopsis kamchatica (Fisch. ex DC.) K. Shimizu & Kudoh and A. kamchatica subsp. kawasakiana (Makino) K. Shimizu & Kudoh, new combinations. Acta Phytotaxonomica et Geobotanica 56(2): 163-172.
Shimizu-Inatsugi, R., J. Lihova, H. Iwanaga, H. Kudoh, K. Marhold, O. Savolainen, K. Wvatanabe, V. V. Yakubov, and K. Shimizu. 2009. The allopolyploid Arabidopsis kamchatica originated from multiple individuals of Arabidopsis lyrata and Arabidopsis halleri. Molecular Ecology 18: 4024-4048.
Slotte, T., H. Huang, M. Lascoux, and A. Ceplitis. 2008. Polyploid speciation did not confer instant reproductive isolation in Capsella (Brassicaceae). Molecular Biology and Evolution 25(7): 1472-1481.
Smadja, C. and R. K. Butlin. 2009. On the scent of speciation: the chemosensory system and its role in premating isolation. Heredity 102: 77-97.
Soeno, K., H. Goda, T. Ishii, T. Ogura, T. Tachikawa, E. Sasaki, S. Yoshida, S. Fujioka, T. Asami, and Y. Shimada. 2010. Auxin biosynthesis inhibitors, identified by a Genomics-Based Approach, Provide Insights into Auxin BiosynthesisPlant Cell Physiology 51(4): 524-536.
Spence, D. H. N. 1959. Studies on the vegetation of shetland: II. reasons for the restriction of the exclusive pioneers to serpentine debris. Journal of Ecology 47(3): 641-649.
Sung, K., V. Plagnol, T. T. Hu, C. Toomajian, R. M. Clark, S. Ossowski, J. R. Ecker, D. Weigel, and M. Nordborg. 2007. Recombination and linkage disequilibrium in Arabidopsis thaliana. Nature Genetics 39: 1151-1155.
Takeda, M., N. Sugimori, T. Torizawa, T. Terauchi, A. M. Ono, H. Yagi, Y. Yamaguchi, K. Kato, T. Ikeya, J. Jee, P. Güntert, D. J. Aceti, J. L. Markley, and M. Kainosho. 2008. Structure of the putative 32 kDa myrosinase-binding protein from Arabidopsis (At3g16450.1) determined by SAIL-NMR. Federation of European Biochemical Societies Journal 275: 5873-5884.
The Arabidopsis Genome Initiative. 2000. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815.
The Gene Ontology Consortium. 2000. Gene Ontology: Tool for the unification of biology. Nature Genetics 25: 25-29.
Wang, W. K., C. W. Ho, K. H. Hung, K. H. Wang, C. C. Huang, H. Araki, C. C. Hwang, Tsai-Wen Hsu, N. Osada, and T. Y. Chiang. 2010. Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture. New Phytologist: 1469-8137.
Williams, S. M., M. D. Ritchie, J. A. Phillips, E. Dawson, M. Prince, E. Dzhura, A. Willis, A. Semenya, M. Summar, B. C. White, J. H. Addy, J. Kpodonu, L. J. Wong, R. A. Felder, P. A. Jose, J. H. Moore. 2004. Multilocus analysis of hypertension: A hierarchical approach. Human Heredity 57: 28-38.
Wormit, A., M. Traub, M. Flörchinger, H. E. Neuhaus, and T. Möhlmann. 2004. Characterization of three novel members of the Arabidopsis thaliana equilibrative nucleoside transporter (ENT) family. Biochemistry Journal 383: 19-26.
Wright, S. 1965. The interpretation of population structure by F-statistics with special regard to systems of mating. Evolution 19(3): 395-420.
Wu, A. M., E. Hörnblad, A. Voxeur, L. Gerber, C. Rihouey, P. Lerouge, and A. Marchant. 2010. Analysis of the Arabidopsis IRX9/IRX9-L and IRX14/IRX14-L Pairs of glycosyltransferase genes reveals critical contributions to biosynthesis of the hemicellulose glucuronoxylan. Plant Physiology 153: 542-554.
Zhang, J. H., X. H. Guo, X. S. Li, F. Xiang, B. Zhou, D. S. Yu, D. Y. Tang, and X. M. Liu. 2012. The genetic and physiological analysis of late-flowering phenotype of T-DNA insertion mutants of AtCAL1 and AtCAL2 in Arabidopsis. Molecular Biology Reports 39: 1527-1535.
Zhang, P., K. Dreher, A. Karthikeyan, A. Chi, A. Pujar, R. Caspi, P. Karp, V. Kirkup, M. Latendresse, C. Lee, L. A. Mueller, R. Muller, and S. Y. Rhee. 2010. Creation of a genome-wide metabolic pathway database for Populus trichocarpa using a new approach for reconstruction and curation of metabolic pathways for plants. Plant Physiology 153: 1479-1491.
Zhu, Q., X. M. Zheng, J. C. Luo, B. S. Gaut, and S. Ge. 2007. Multilocus analysis of nucleotide variation of Oryza sativa and its wild relatives: Severe bottleneck during domestication of rice. Molecular Biology and Evolution 24(3): 875-888.
National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/
The Arabidopsis Information Resource http://www.arabidopsis.org/
VassarStats: Website for Statistical Computation http://www.vassarstats.net/
王唯匡。 2008。 以多基因分析探討阿拉伯芥近緣物種的遺傳變異。 國立成功大學生命科學研究所博士論文。 臺南。