肖楠屬是很典型的北美-東亞間斷分布物種，過去研究發現，肖楠
屬植物因為地理隔離，已產生四個種，其中親緣關係相近的物種，翠
柏(Calocedrus macrolepis)及台灣肖楠(C. formosana)已互為單系群。過去由於受限於分子工具，並不了解肖楠屬植物分歧後的遺傳差異，本
研究透過ddRADseq (double digest Restriction Associated DNA
sequencing) 檢測台灣肖楠與翠柏族群基因組的分歧。原本使用48 株
個體進行分析，但ddRADseq 需要高品質之DNA，而肖楠屬植物次
級代謝物較多，以些個體無法只用，導致最後使用28 株肖楠屬植物，
分別有19 株台灣肖楠，來自4 個台灣的族群，以及9 株翠柏樣本，
來自大陸雲南。ddRADseq 獲得1,108 個單一核苷酸多型性位點
(single nucleotide polymorphism, SNP)。雖然使用的個體數較少，但由於利用ddRADseq的方法，我們獲得的SNPs仍比其他的分子工具多。
根據structure 及DAPC 檢測後，仍可發現發現台灣肖楠族群間有分
歧，但是相較於翠柏仍不明顯，又分歧的趨勢跟地理位置有關連性，
推測台灣肖楠可能受到地理位置因素出現分歧的趨勢。
關鍵字：台灣肖楠、ddRADseq、基因組分歧

Calocedrus genus is a classic north American - east Asia conjunct divergent species. In previous studies, we have found that because of geographical isolation, genus has already diverged into four species.
Among these four species, Calocedrus macrolepis and C. formosana are two species that have already shown monophyletic and have close genetic relationship, however, less is known about the genetic difference after
divergence, limited by the genetic tools. In this study, we use ddRADseq (double digest Restriction Associated DNA sequencing) to discover the divergence between C. macrolepis and C. formosana. We use 48 individual in the beginning, since ddRADseq requires high quality of
DNA, the secondary metabolites in these individual is not allowed, we choose the rest 28 individuals that have better DNA quality, which include 19 individuals of C. formosana from four populations and 9 individuals of C. macrolepis from Yunnan, China. The result using ddRADseq generated 1,108 SNPs. Although the number of individuals
were small, ddRADseq still provided more SNPs then other genetic tools.
According to Structure and DAPC, we found that there are divergence among C. formosana population but it’s less than comparing with C. macrolepis. In addition, the divergence appearance is related to geographic location, suggesting that C. formosana may be divergent because of geographic isolation.
Keyword: C. formosana, ddRADseq , genomic divergence

Amselem J, Cuomo CA, van Kan JAL, et al. 2011. Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genetics 7: e1002230.
Baird NA, Etter PD, Atwood TS, et al. 2008. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3: e3376.
Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian Computation in population genetics. Genetics 162: 2025–2035
Catchen J, Hohenlohe PA, Bassham S, et al. 2013. Stacks: an analysis tool set for population genomics. Molecular Ecology 22: 3124–3140.
Chiang TY, Schaal BA. 2006. Phylogeography of plants in Taiwan and the Ryukyu Archipelago. Taxon 55: 31-41.
Chen CH, Huang JP, Tsai CC, et al. 2009. Phylogeny of Calocedrus (Cupressaceae) an eastern asian and western North American disjunct gynosperm genus inferred from nuclear ribosomal nrITS sequence. Botanical Studies 50: 425-433.
Dehestani A, Kazemi Tabar SK. 2007. A rapid efficient method for DNA isolation from plants with high levels of secondary metabolites. Asian Journal of Plant Science 6: 977-981.
Davey JW, Hohenlohe PA, Etter PD, et al. 2011. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Reviews Genetics12, 499-510.
Feder JL, Egan SP, Nosil P. 2012. The genomics of speciation with gene flow. Trends in Genetics 28: 342–350.
Guo Q. 1999. Guest Editorial: Ecological comparisons between Eastern Asia and North America: Historical and geographical perspectives. Journal of Biogeography 26: 199–206.
Hickerson MJ, Stahl EA, Lessios HA. 2006. Test for simultaneous divergence using Approximate Bayesian Computation. Evolution 60: 2435–2453.
Hohenlohe PA, Bassham S, Etter PD, et al. 2010. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags. PLoS Genetics 6: e1000862.
Kircher M, Heyn P, Kelso J. 2011. Addressing challenges in the production and analysis of illumina sequencing data. BMC Genomics 12: 382.
Langmead B, Trapnell C, Pop M, et al. 2009. Ultrafast and
memory-efficient alignment of short DNA sequences to the
human genome. Genome Biology 10: R25.
Minder AM, Widmer A. 2008. A population genomic analysis of species boundaries: neutral processes, adaptive divergence and introgression between two hybridizing plant species. Molecular Ecology 17: 1552–1563.
Mayr E. 1963. Animal Species and Evolution. Cambridge, MA: Harvard University Press.
Nosil P, Funk DJ, Ortiz-Barrientos D. 2009. Divergent selection and heterogeneous genomic divergence. Molecular Ecology 18: 375–402.
Sabeti PC, Varilly P, Fry B, et al. 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449: 913-918.
Sabeti PC, Reich DE, Higgins JM, et al. 2002. Detecting recent positive selection in the human genome from haplotype structure. Nature 419: 832–837.
Shi G, Zhou Z, Xie Z. 2012. A new Oligocene Calocedrus from South China and its implications for transpacific floristic exchanges. American Journal of Botany 99: 108-120.
Smith SE, Read DJ. 2008. Mycorrhizal Symbiosis. Cambridge, UK:Academic Press.
Städler T, Arunyawat U, Stephan W. 2008. Population genetics of speciation in two closely related wild tomatoes (Solanum section Lycopersicon). Genetics 178: 339-350.
Sunnåker M, Busetto AG, Numminen E, et al. 2013. Approximate Bayesian Computation. PLoS Computational Biology 9: e1002803.
Discriminant analysis of principal components:
a new method for the analysis of genetically structured populations
Thibaut Jombart, Sébastien Devillard, François Balloux
Voight BF, Kudaravalli S, Wen X, et al. 2006. A map of recent positive selection in the human genome. PLoS Biology 4: e72.
Wang DL, Li ZC, Hao G, et al. 2004. Genetic diversity of Calocedrus marcrolepis (Cupressaceae) in southwestern China. Biochemical Systematics and Ecology 32: 797-807.
Xiang QY, Soltis DE, Pamela SS, et al. 2000. Timing the eastern Asian– eastern north American floristic disjunction: molecular clock corroborates paleontological estimates. Molecular Phylogenetics and Evolution 15: 462–472.
Xiang QY, Soltis DE, Soltis PS. 1998. The eastern Asian and eastern and western north American floristic disjunction: congruent phylogenetic patterns in seven diverse genera. Molecular Phylogenetics and Evolution 10: 178-190.
Xu TT, Abbott RJ, Milne RI, et al. 2010. Phylogeography and allopatric divergence of cypress species (Cupressus L.) in the Qinghai–Tibetan Plateau and adjacent regions. BMC Evolutionary Biology 10:194.