臺灣島具有豐富且多變的地形景觀，在山地環境中沿海拔梯度的環境變化大。根據過去的研究顯示海拔分布範圍較廣的山地植物，在高海拔及低海拔的族群面臨的選汰壓力可能不同，而有不同的適應性演化。我們採集了臺灣肖楠12個族群共243個個體，利用擴增片段長度多型性（amplified fragment length polymorphism; AFLP）及甲基化敏感擴增多型性（methylation-sensitive amplification polymorphism; MSAP）兩種工具，量化臺灣肖楠的遺傳與表觀遺傳變異。本研究總共得到437個AFLP基因座及832個MSAP基因座。我們發現臺灣肖楠族群已有顯著的遺傳及表觀遺傳分化。將現生的臺灣肖楠族群區分為三個遺傳分群。臺灣肖楠與其他臺灣針葉樹如：香杉、臺灣油杉及臺灣杉相比有較高的遺傳及表觀遺傳分化程度以及較低的遺傳歧異度。利用DFDIST及BAYESCAN檢測臺灣肖楠族群間遺傳及表觀遺傳數據中可能偏離演化受天擇作用的AFLP及MSAP基因座；結果發現有34個AFLP及77個MSAP的基因座可能受天擇作用。我們亦發現這些偏離中性演化的基因座與環境因子有顯著的關聯性。此外，臺灣肖楠的遺傳及表觀遺傳變異與生態相關的環境因子相較於與生物氣候及地形相關的環境因子有較高的相關比例。我們的結果顯示年均溫、相對溼度、平均風速及平均日照時數（SunH）可能為驅動臺灣肖楠產生適應分歧最主要的環境因子。再者，我們在低海拔及高海拔中發現數個適應性演化基因座有相對較高的基因頻率；而這種情形在表觀遺傳變異中更為明顯。因此我們推論與生態相關的環境因子為臺灣肖楠在地適應性演化的關鍵角色。本研究對於我們在未來應用於因應全球氣候變化下臺灣肖楠的保育策略提供基礎的研究證據。

Taiwan has varied topographical landscapes with numerous climate zones. Moreover, there is a broad range of environmental gradients in a relatively short geographical range of mountain habitats. Mountainous plant species occupying wide elevational ranges are thought to experience dissimilar evolutionary trajectories depending on the selective pressures at low and high elevations. We collected 243 samples from 12 populations of the endangered species Calocedrus formosana along elevational gradients. Using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP), genetic and epigenetic variations were generated and scored a total of 437 AFLP loci and a total of 832 MSAP loci. We found relatively lower levels of genetic and epigenetic diversities and higher level of genetic and epigenetic population differentiations comparing with other Taiwan endemic conifers, such as Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides. BAYESCAN and DFDIST identified 34 AFLP and 77 MSAP FST outlier loci. These outlier loci were found to be strongly associated with environmental variables analyzed using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression approaches. Further, ecological factors explained much larger proportion of outlier genetic and epigenetic variations in comparison with bioclimatic and topological factors. Our results suggest that adaptive divergence arising from environmental variation has been driven mainly by annual mean temperature, relative humidity, mean wind speed, and sunshine hours. We also found several adaptive loci with high frequencies in low- and high- elevation populations, suggesting their association with environmental variables underlying local adaptation. Therefore, ecological factors could have played critical roles in local adaptation of Ca. formosana and could be vital factors for the species conservation in the face of global change.

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