Arabidopsis halleri 為模式物種阿拉伯芥的近緣種植物，是一自交不親和並且高度異型雜交常年均可見的物種。阿拉伯芥屬植物的演化分歧時間大約為一千三百萬年前A. halleri主要分布的地區是歐亞大陸，其生長的環境為山區、微酸的土壤，近年有數篇分子研究顯示，在人為的金屬汙染環境下A. halleri能夠適應金屬所造成的環境壓力。A. halleri有五個亞種，其生長條件相似，生長在溫帶。
　　本論文以多基因分析A. halleri的四個亞種，藉以了解各個亞種所透露的演化訊息。藉由100基因分析比較物種間的遺傳歧異度，可提供訊息去探討族群的遺傳結構，進一步去推測四個亞種的演化情況。以親緣樹圖的樹型統計分析，有65個基因支持A. halleri族群為單一系群；18個基因支持各亞種可為單一系群。藉由將基因隨機重組分析親緣推測 ssp. ovirensis 可能為祖先型進而演化成 gemmifera、halleri 與 tatrica ，而ssp. ovirensis 與其他物種的分歧時間約為一百八十萬年前；而A. lyrata 與A. halleri的分歧時間約為五百七十萬年前。以STRUCTURE分析在最佳K值=3時將ssp. halleri與 tatrica 分為一群， ssp. ovirensis為一群以及外群為一群，K=5時，能將四個亞種清楚的分成四群以及外群；ssp. ovirensis 與其他物種有高度的分化 (FST= 0.38-0.47)。此外，在所有亞種中發現了一高度分化的基因ALY9為一自交不親和的重要基因。IMa2分析，顯示A. halleri ssp. ovirensis分化程度較高，而ssp. ovirensis 對於halleri 與tatrica有單方向的基因交流現象; ssp. halleri 與tatrica 則有相互的基因交流。而ssp. gemmifera 只對於 tatrcia 有少量的基因交流，與其他亞種皆沒有基因交流的現象，可能在地理上有天山阻隔的關係。

Arabidopsis halleri, a species related to A. thaliana, is a self-incompatible and highly outcrossing perennial species. A. halleri with five subspecies is distributed in Eurasia. In this study, genomic divergence among four subspecies of halleri, ovirensis, gemmifera, and tatrica was examined based on 100 randomly selected genes. In total, 65 genes displayed tree topologies consistent with the putative species tree that supported monophyly of A. halleri; 18 genes supported reciprocal monophyly of subspecies. Systematic simulation via random sampling of alleles suggested ancestry of ssp. ovirensis, from which other halleri subspeciessplit about 1.86 MYA, as calibrated at the split between A. lyrata and A. halleri 5.75 MYA based on nrITS. STRUCTURE analysis indicated that ssp. ovirensis was differentiated from the other subspecies at K=3, and that the four subspecies were well defined at K=5. Genetically ssp. ovirensis was differentiated from other subspecies (Fst = 0.38-0.47). In addition, ALY9, a gene responsible for self-incompatibility, was the most diverged gene among species. IMa2 analysis for estimating the extent of gene flow between populations revealed non-zero gene flow between ssp. halleri and tatrica, and unidirectional gene flow from ssp. ovirensis to halleri and tatrica. However, only very little gene flow was detected from ssp. gemmifera to ssp. halleri, while no gene flow was detected between ssp. gemmifera with other subspecies, likely due to the existence of geographic barriers of Tian Shan.

Balloux, F. and Lugon-Moulin, N. (2002). "The estimation of population differentiation with microsatellite markers." Molecular ecology 11: 155-165.
Bonin, A., Taberlet, P., Miaud, C. and Pompanon, F. (2006). "Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria)." Mol Biol Evol 23(4): 773-783.
Clauss, M.J. and Koch, M.A. (2006). "Poorly known relatives of Arabidopsis thaliana." Trends in plant science 11(9): 449-459.
Evanno, G., Regnaut, S. and Goudet, J. (2005). "Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study." Mol Ecol 14(8): 2611-2620.
Felsenstein, J. (1985). "Confidence-Limits on Phylogenies - an Approach Using the Bootstrap." Evolution 39(4): 783-791.
Franzke, A., Lysak, M.A., Al-Shehbaz, I.A., Koch, M.A. and Mummenhoff, K. (2011). "Cabbage family affairs: the evolutionary history of Brassicaceae." Trends Plant Sci 16(2): 108-116.
Fu, Y.-X. and Li, W.-H. (1997). "Estimating the age of the common ancestor of a sample of DNA sequences." Molecular biology and evolution 14(2): 195-199.
Futuyma , D. (1998). " Evolutionary Biology, 2nd. Edn, Sinauer, Sunderland, MA.".
Guo, Y.L., Zhao, X., Lanz, C. and Weigel, D. (2011). "Evolution of the S-locus region in Arabidopsis relatives." Plant Physiol 157(2): 937-946.
Hey, J. (2011). "Documentation for IMa2." New Brunswick, NJ: Rutgers Uni.
Hey, J.a.N., R. (2004). "Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis ." Genetics 167: 747-760.
Hillis, D.M. and Bull, J.J. (1993). "An Empirical-Test of Bootstrapping as a Method for Assessing Confidence in Phylogenetic Analysis." Systematic Biology 42(2): 182-192.
Hoffmann, M. (2005). "Evolution of the realized climatic niche in the genus Arabidopsis (Brassicaceae)." Evolution; International Journal of Organic Evolution 59(7): 1425-1436.
Hoffmann, M.H. (2005). "Evolution of the realized climatic niche in the genus Arabidopsis (Brassicaceae)." Evolution 59: 1425–1436.
Huang, C.C., Hung, K.H., Wang, W.K., Ho, C.W., Huang, C.L., Hsu, T.W., Osada, N., Hwang, C.C. and Chiang, T.Y. (2012). "Evolutionary rates of commonly used nuclear and organelle markers of Arabidopsis relatives (Brassicaceae)." Gene 499(1): 194-201.
Hudson , R. (1990). "Gene genealogies and the coalescent process. In Oxford Survey of
Evolutionary biology." Futuyma DJ, Antonovics J eds, Oxford University Press, NewYork.: 1-44.
Jukes, T.H. and Cantor, C.R. (1969). Evolution of protein molecules. Mammalian Protein Metabolism. H. N. Munroled. New York, Academic Press: 31-132.
Kimura (1983). "The Neutral Theory of Molecular Evolution." Cambridge University Press.
Kimura, M. (1980). "A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences." Journal of Molecular Evolution 16: 111-120.
Koch, M.A. and Matschinger, M. (2007). "Evolution and genetic differentiation among relatives of Arabidopsis thaliana." Proc Natl Acad Sci U S A 104(15): 6272-6277.
Larkin, M.A., Blackshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., Thompson, J.D., Gibson, T.J. and Higgins, D.G. (2007). "Clustal W and clustal X version 2.0." Bioinformatics 23(21): 2947-2948.
Larkin, M.A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H.,, Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and and Higgins, D.G. (2007). "Clustal W and clustal X version 2.0. ." Bioinformatics 23(21): 2947-2948.
Lee, Y.-H., Ota, T. and Vacquier, V.D. (1995). "Positive Selection Is a General Phenomenon in the Evolution of Abalone Sperm Lysin." Mol Biol Evol 12(2): 231-238.
Lee, Y.H., Ota, T. and Vacquier, V.D. (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 Rozas, J. (2009). "DnaSP v5: a software for comprehensive analysis of DNA polymorphism data." Bioinformatics 25(11): 1451-1452.
Mark A. Beilsteina, N.S.N., Mark D. Clementsa, Steven R. Manchesterb, and Sarah Mathews (2010). "Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana." PNAS 107(. 43): 18724–18728.
Mayr, E. (1942). "Systematics and the origin of species from the viewpoint of a zoologist." Columbia University Press, New York.
Nei, M. and Tajima, F. (1983). "Maximum-Likelihood Estimation of the Number of Nucleotide Substitutions from Restriction Sites Data." Genetics 105(1): 207-217.
Oleksyk, T.K., Smith, M.W. and O'Brien, S.J. (2010). "Genome-wide scans for footprints of natural selection." Philos Trans R Soc Lond B Biol Sci 365(1537): 185-205.
Osada, N. and Wu, C.-I. (2005). "Inferring the mode of speciation from genomic data: a study of the great apes." Genetics 169: 259-264.
Pauwels, M., Frerot, H., Bonnin, I. and Saumitou-Laprade, P. (2006). "A broad-scale analysis of population differentiation for Zn tolerance in an emerging model species for tolerance study: Arabidopsis halleri (Brassicaceae)." J Evol Biol 19(6): 1838-1850.
Pauwels, M., Roosens, N., Frerot, H. and Saumitou-Laprade, P. (2008). "When population genetics serves genomics: putting adaptation back in a spatial and historical context." Curr Opin Plant Biol 11(2): 129-134.
Pauwels, M., Vekemans, X., Gode, C., Frerot, H., Castric, V. and Saumitou-Laprade, P. (2012). "Nuclear and chloroplast DNA phylogeography reveals vicariance among European populations of the model species for the study of metal tolerance, Arabidopsis halleri (Brassicaceae)." New Phytol 193(4): 916-928.
Pauwels, M., Willems, G., Roosens, N., Frerot, H. and Saumitou-Laprade, P. (2008). "Merging methods in molecular and ecological genetics to study the adaptation of plants to anthropogenic metal-polluted sites: implications for phytoremediation." Mol Ecol 17(1): 108-119.
Prezeworski, M., Coop, G. and Wall, J.D. (2005). "The signature of positive selection on standing genetic variation." Evolution 59(11): 2312-2323.
Pritchard, J.K., Stephens, M. and Donnelly, P. (2000). "Inference of Population Structure Using Multilocus Genotype Data." Genetics 155(2): 945-959.
Saitou, N. and Nei, M. (1987). "The Neighbor-Joining Method - a New Method for Reconstructing Phylogenetic Trees." Molecular Biology and Evolution 4(4): 406-425.
Schmickl, R., Jorgensen, M.H., Brysting, A.K. and Koch, M.A. (2010). "The evolutionary history of the Arabidopsis lyrata complex: a hybrid in the amphi-Beringian area closes a large distribution gap and builds up a genetic barrier." BMC Evol Biol 10: 98.
Shanmugam, V., Lo, J.C., Wu, C.L., Wang, S.L., Lai, C.C., Connolly, E.L., Huang, J.L. and Yeh, K.C. (2011). "Differential expression and regulation of iron‐regulated metal transporters in Arabidopsis halleri and Arabidopsis thaliana–the role in zinc tolerance." New Phytologist 190(1): 125-137.
Shimizu, K.K. and Purugganan, M.D. (2005). "Evolutionary and ecological genomics of Arabidopsis." Plant Physiol 138(2): 578-584.
Sun, S., Ting, C.-T. and Wu, C.-I. (2004). "The normal function of a speciation gene, Odysseus, and its hybrid sterility effect." Science 305: 81-83.
Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. (2011). "MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods." Mol Biol Evol 28(10): 2731-2739.
Thompson, S.W.G.a.E.A. (1992). "Performing the Exact Test of Hardy-Weinberg Proportion for Multiple Alleles." Biometrics 48(2): 361-372.
Tsuchimatsu, T., equal, P.K., Yew, C.-L., Bachelier, J.B. and mail, K.K.S. (2012). "Recent Loss of Self-Incompatibility by Degradation of the Male Component in Allotetraploid Arabidopsis kamchatica." PLoS Genetics 8.
Van Rossum, F., Bonnin, I., Fenart, S., Pauwels, M., Petit, D. and Saumitou-Laprade, P. (2004). "Spatial genetic structure within a metallicolous population of Arabidopsis halleri, a clonal, self-incompatible and heavy-metal-tolerant species." Mol Ecol 13(10): 2959-2967.
Vasemagi, A. and Primmer, C.R. (2005). "Challenges for identifying functionally important genetic variation: the promise of combining complementary research strategies." Mol Ecol 14(12): 3623-3642.
Wang, W.K., Ho, C.W., Hung, K.H., Wang, K.H., Huang, C.C., Araki, H., Hwang, C.C., Hsu, T.W., Osada, N. and Chiang, T.Y. (2010). "Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome-wide admixture." New Phytol 188(2): 488-500.
Wang, W.K., Ho, C.W., Hung, K.H., Wang, K.H., Huang, C.C., Araki, H., Hwang, C.C., Hsu, T.W., Osada, N. and Chiang, T.Y. (2010). "Multilocus analysis of genetic divergence between outcrossing Arabidopsis species: evidence of genome‐wide admixture." New Phytologist 188(2): 488-500.
Wu , C. (2001). "The genic view of the process of speciation." Journal of Evolutionary
Biology 14: 851-865.