島嶼的空間碎片化以及其過去的陸地變化使之成為研究微演化過程的理想系統。這些時空特性影響物種的拓殖模式與族群大小變化，留下了由漂變所驅動的基因組層級之變異。當島嶼分布於較廣的緯度或海拔梯度時，也會進一步包含較大的環境變異，而促進透過選擇所驅動的基因分化演化出當地適應的族群。這些機制共同促進了島嶼之間的物種或族群多樣性，但同時也限制了它們的地理分佈。在這些島嶼物種中，沿海的物種因將受到來自陸地與海洋的氣候變遷與連帶之災難性威脅而特別脆弱，因此迫切需要保護。此外，島嶼上從族群到物種的漸進分化過程也挑戰了現有的分類系統，凸顯了通過綜合方法重新評估分類的必要性。蘇鐵是物種多樣性高的裸子植物，而於現存的380個物種中有68%面臨滅絕的威脅，因此有迫切保育上的必要。然而，蘇鐵的大型基因組（25-64 pg/2C）對於解構基因組層級的漂變或選擇驅動之分化構成了挑戰。在本論文中，我以東方蘇鐵組為研究對象，包括主要分布於琉球群島沿海及台灣低海拔河岸的台東蘇鐵（Cycas taitungensis C. F. Shen）和琉球蘇鐵（C. revoluta Thunb.），來探討物種形成的地理模式。透過雙限制酶切位點測序（ddRADseq）方法，於全面取樣族群中獲得了基因組層級的變異，進一步整合了形態數據後，再進行分類重新評估。儘管最終將這兩個物種做同物異名處理，但其基因組層級的族群分化顯示台灣內部（包括一個高度分化的隱蔽支系）以及琉球群島的沖繩和奄美之間具有空間上分化的結構。因此，我進一步探討了促進它們各自分化的機制。在台灣方面，鬼基因滲入解釋了同域隱蔽支系的分化，並可能伴隨著與沿海適應和抗病性相關的適應性遺傳變異的轉移。這樣的結果也部分解釋了而於琉球群島方面，由於甲蟲在遠距離基因交流中扮演重要角色，因此我探討了與傳粉性狀有關之毬果揮發性有機化合物。沖繩和奄美之間化學變異與基因組結構的匹配結果揭示了可能的傳粉者促進分化之機制。為進一步了解氣候變遷對各遺傳分群的影響，我先定義了保育單元，並估算了目前的地區適應性及未來在氣候變遷下的遺傳適應不良。接著，揭示了與氣候相關的災難性因子對遺傳適應不良的負面影響。為了理解影響族群分化的地景因素，我進一步探討不同地景模型對遺傳分化的影響。最後，推測了可能的演化拯救途徑。研究結果顯示，位於琉球中部的沖繩和奄美島是最需要保護的區域，其中奄美島將需要通過人為基因交流輔助來應對未來的氣候變遷。

Spatial fragmentation combined with temporal land configuration change in islands provides an ideal system for studying microevolutionary processes. The spatiotemporal characteristics primarily influence species colonization patterns, leaving a drift-driven genome-wide signature. When distributed across a broad latitudinal or altitudinal gradient, islands experience increased environmental variation, fostering the evolution of locally adapted populations through selection-driven genetic divergence. These combined mechanisms promote high species or population diversity among islands, while simultaneously restricting their geographic distribution. Among these island species, the coastal species are particularly vulnerable and need urgent conservation act because they will be threatened by climate change and the associated catastrophe from land and sea. Additionally, the gradual divergence from populations to species across islands challenges the taxonomical views, and highlights the importance of taxonomy treatment through integrated methods. Cycads are a species-rich group of gymnosperms with urgent conservation concerns, as 68% of the 380 extant species are threatened with extinction. However, the large genome size (25-64 pg/2C) makes the genome-wide characterization of drift- or selection-driven signature challenging. In this thesis, I used Cycas sect. Asiorientales, including only Cycas taitungensis C. F. Shen and C. revoluta Thunb., that distributed mainly in coastal side of Ryukyu Archipelago and low elevation riverside of Taiwan to study the geographic mode of speciation processes. The SNP markers from double digest restriction-site associated DNA sequencing (ddRADseq) method was applied to capture the genome-wide variations from the comprehensively sampled populations. Then the morphological data of diagnostic traits were integrated for the taxonomy reappraisal. Although the two species have been synonymized, the genomic divergence was still observed within Taiwan, including a highly divergent cryptic lineage, as well as between Okinawa and Amami in the Ryukyu Archipelago. Consequently, I further examined the mechanisms that facilitated their respective divergence. The ghost introgression was demonstrated to be a crucial driver for the sympatric cryptic lineage divergence in Taiwan, together with possible transfer of adaptive genetic variations regarding coastal adaptation and resistance. This process may partially explain the coastal distribution of the main populations. Along the Ryukyu Archipelago, because of the important role of beetle for longer distance gene flow compared to wind, the pollination traits from cone volatile organic compounds were explored. Match of chemo-variations with genomic structure between Okinawa and Amami implied pollinator-mediated population divergence. Next, to understand the influence of climate change across different genomic structure, the conservation units were defined, and the present local adaptation plus future genetic vulnerability under climate change was estimated. Subsequently, the negative impact of climate-associated catastrophe events on genetic vulnerability was revealed. The landscape variables that were associated with population divergence were further investigated to understand the determinant of spatial dispersal. Finally, possible evolutionary rescue routes were inferred. In concert with genetic vulnerability, the results suggested Okinawa and Amami in central Ryukyu were the sites need the most conservation concerns, of which the assisted gene flow will be required in Amami to cope with future climate change.

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