金毛杜鵑(Rhododendron oldhamii)為廣泛分布的台灣特有種杜鵑，其生長的棲地氣候條件不同，主要開花季節也有差異。已知DNA甲基化可調節基因表現，使個體面臨環境變化時，表現型產生變異，以適應環境。本研究欲檢測金毛杜鵑DNA甲基化的變異情形，探討在天擇作用之下，DNA甲基化的多型性與族群適應性演化之關係。利用Methylation-sensitive amplified polymorphism (MSAP)分子標誌掃描基因組，檢測18個族群，共205個體，篩選出有甲基化變異的基因座，估算多種族群遺傳參數與分析族群結構，並篩選出受天擇選汰的甲基化基因座。此外，結合氣象因子，檢測受到天擇選汰的基因座是否與環境因子有關連。結果顯示，金毛杜鵑各族群有DNA甲基化多型性，可分成2個分群；某些族群受天擇選汰基因座有連鎖不平衡的現象，形成分歧型天擇；以FST中性檢測方式篩選出13個受正向天擇選汰的甲基化基因座，其中2個與環境因子平均風速有關連。這些結果皆顯示金毛杜鵑各族群受到不同棲地環境因子的天擇壓力，而有正向天擇作用，造成族群有DNA甲基化多型性的分化與適應性演化的現象。

Rhododendron oldhamii is an endemic rhododendron species that widespread but discontinuously distributed in Taiwan. Environmental variables among habitats and population flowering times are different. Because epigenetic processes such as DNA methylation may contribute to environmentally induced phenotypic variation by modifying gene expression, individuals can adapt to the changing environment. Therefore, the main purpose of this study is to understand the variations in DNA methylation patterns and the adaptive evolution of R. oldhamii. We used methylation-sensitive amplified polymorphism (MSAP) molecular markers to scan the whole genome for 205 individuals from 18 populations. Based on MSAP genotyping data, we can explore the population structure and population adaptive evolution under natural selection. Furthermore, with the environmental variables incorporated, we can detect the association between the environmental variables and the MSAP polymorphisms. The results showed that R. oldhamii have DNA methylation polymorphism. The Bayesian cluster analysis revealed that 18 populations could be assigned to two clusters. We find 13 outliers under positive selection, of which two are associated with environmental variables such as mean wind speed. Moreover, populations had different linkage disequilibrium blocks of outlier loci. These results indicated that R. oldhamii populations were mainly affected by different selection pressures of habitats, resulting in differentiation of DNA methylation polymorphism within and among populations. Therefore, the results suggested that different environmental variables of habitats would promote distinct adaptive evolution and population differentiation in R. oldhamii.

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