翠柏與台灣肖楠之分歧演化
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2017
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Abstract
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
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
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Keywords
台灣肖楠, ddRADseq, 基因組分歧, C. formosana, ddRADseq, genomic divergence