環境會顯著地影響樹木的族群歷史 (demographic history) 與遺傳特徵。研究影響族群分佈、遺傳多樣性、局部適應 (local adaptation)、與棲位分化的因子在生物學當中是至關重要的議題。尤其對於在生態系統當中具有重要角色的森林樹木來說，釐清局部適應與氣候變遷衝擊的關聯對於保育及森林管理有關鍵性的功能。在本論文中，我使用錐果櫟 (Quercus longinux) 作為研究物種，以簡化基因組測序 (RAD-Seq) 建構的單核苷酸多態性 (SNPs) 及葉片特徵來探討在異質性棲地間的族群遺傳、棲位分化、和形態變異等議題。依據族群歷史分析的結果，錐果櫟的族群大小變化和基因交流與更新世 (Pleistocene) 的氣候波動有關。由於末次盛冰期 (LGM) 之後氣候變得更加暖活和濕潤，錐果櫟族群在間冰期經歷了族群擴張和更頻繁的基因交流。錐果櫟族群被發現有向北的不對稱基因交流，可能是開花季節時盛行的西南風或冰河歷史使台灣南部族群有較大的族群數量所造成。使用現在的環境因素，地勢 (topology) 造成的阻礙被認為是藉由阻礙種子或花粉的基因交流而引發遺傳分化最重要的因子。高海拔山區被認為是錐果櫟進行基因交流的重要障礙。然而，從適應的角度來看，土壤和氣候相關因子是影響環境相關天擇 (environment-associated selection) 最重要的因子。季節性季風帶來的降水變化和緯度及海拔造成的溫差可能造成局部適應。我也偵測到環境相關天擇的信號和非生物壓力反應（包括乾旱和霜凍）相關功能的基因有關。除遺傳結構外，葉片形態性狀的變異還受土壤和氣候相關因素的影響，而水分可及性的因子是影響葉片個別性狀最重要的環境因素。最後，從未來脆弱性 (future vulnerability) 的預測來看，面對氣候變化，台灣北部的錐果櫟族群可能因大量增的冬季降水而產生適應不良。冬季降水的增加可能會改變物候並且進一步降低基因交流的效率和遺傳多樣性，這些都會對錐果櫟在未來的存續和適應產生有害影響。輔助性基因交流 (assisted gene flow) 將是可能的保育措施之一，但應在具備足夠背景知識的情況下進行，以避免對錐果櫟族群的適應造成意外後果。

The demographic history and genetic architecture of tree species are noticeably affected by environments. Studying the factors influencing the current distribution, genetic diversity, local adaptation, and niche differentiation are important issues in biology. For forest tree species with important roles in ecosystems, entangling the relationship between local adaptation and vulnerability to future climate change is particularly essential for conservation and forest management. In this thesis, I used Quercus longinux to investigate the issues of population genetics, niche differentiation, and morphological variation across heterogenous habitats with RAD-seq derived SNPs and leaf morphological traits. Results from demographic history demonstrated that population fluctuation and gene flow of Q. longinux were related to Pleistocene climate oscillations. Populations experienced expansion and enhanced gene flow in the interglacial periods with warmer and moister climates after Last glacial maximum (LGM). A northward asymmetric gene flow was also uncovered, which may result from the southwest wind in flowering seasons or larger population abundance in southern Taiwan contributing to glacial-interglacial history. Using current environmental factors, topological resistance was identified as the most profound factor that initiated genetic differentiation through hampering seed or pollen-mediated gene flow. Mountainous regions with high elevation were revealed as significant barriers to gene flow in Q. longinux. Nevertheless, from the perspective of the adaptive process, soil and climate-related factors were the most important variables affecting environment-driven selection. Precipitation variation brought by seasonal monsoons and temperature differences resulting from latitude and elevation may trigger local adaptation. Signals of environment-associated selection were found to be linked to genes with the function of response to abiotic stress including drought and frosty. Aside from genetic architecture, variation of leaf morphological traits was also affected by soil, climate-related factors and water-availability-relevant variables were the most critical environmental factors shaping single leaf traits. Finally, from the prediction of future vulnerability, populations in northern Taiwan may have the highest risk of maladaptation with respect to extremely increased winter precipitation in the face of climate change. Increased winter precipitation may alter the phenology and further reduced the efficiency of gene flow across populations and reduce genetic diversity, which all have deleterious impacts on the persistence and adaptation of Q. longinux populations to future conditions. Assisted gene flow will be one of the potential conservational practices, but it should be conducted with sufficient background knowledge to avoid unexpected consequences on populational fitness.

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