自達爾文時期以來，物種形成一直是生態演化學者熱衷探索的議題。地理阻隔造成的異域種化是早期被用來解釋分化機制的假說之一，而有限的播遷能力亦被認為會限制物種的活動距離，並強化遺傳上的分化。然而，最近的研究結果表明這僅涉及種化過程的一部分，而雜交物種起源或二次接觸的基因滲入也同樣影響物種分化的過程。在本研究中，我的目標是檢測臺灣產龍蜥屬(Diploderma)的種化過程中是否受到地理阻隔與基因交流事件的影響。這個類群包括五個播遷能力不佳且具有高度形態多樣性的物種，其中多個物種被視為具有潛在的雜交事件或隱蔽種。我們首先透過親緣分析顯示了種內與種間的高度分化，並發現分化情形和族群分布有關，顯示地理距離和地形的潛在影響。使用粒線體和核基因序列進行的物種界定分析則顯示了不一致的結果。為了更進一步了解龍蜥的遺傳結構，我們使用雙重酶切DNA 定序技術(ddRAD)進行了多個族群結構分析，一致地得到了七個分群。我們發現在部份共域物種存在過去的遺傳滲入事件，包括短肢龍蜥(D. brevipes)的北部族群和多稜龍蜥(D. polygonatum)的西部族群，以及短肢龍蜥的中部到南部族群和牧氏龍蜥(D. makii)。我們也檢測了雜交地區族群的形態和生態棲位，發現共有的形態特徵和介於之間的生態棲位。藉由多物種溯祖與遺傳滲入模型(MSCi)估算了這些遺傳滲入事件的時間和方向，發現同時具有分化前和分化後基因流事件的模型具有最高的機率。總結來說，我們發現這些高度分化的物種有三次主要的古老基因流事件。這些事件發生在物種分化的初期，並造成形態和氣候棲位上的混雜，而直到生殖隔離的強化，才中斷了種間雜交事件。這項研究的發現提供了散佈能力有限的物種仍具有種化期間基因交流的例子，也有助於我們了解這些特有物種的種化歷史，並提供未來研究的方向和保育相關的資訊。

Allopatric speciation is one of the earliest proposed hypotheses to interpret the underlying mechanism of differentiation. Concordantly, limited dispersal and niche conservatism constrain distribution ranges and thus facilitate genetic differentiation. However, recent findings have challenged this aspect, emphasizing that the detection of gene flow events during species divergence could provide more detailed information. In this study, we aimed to infer the presence of gene flow in dragon lizards (Agamidae: Diploderma) from Taiwan. This group of lizards comprises five species with limited migration ability and high ornamentation polymorphism, that are suspected with potential hybridization events or cryptic diversity. Our phylogenetic analysis showed deep divergence within and among species that was consistent with geographic distribution, indicating the potential effect of distance and topography. Results from species delimitation using mitochondrial and nuclear sequences were inclusive, masked by the effect of population structure. Seven clusters were identified using ddRAD-seq data in population structure analysis, where gene flow existed within two pairs of clusters that exhibit narrowly distributional overlapping. There were three major ancient gene flow events demonstrated by comparing the multispecies coalescent model with introgression (MSCi). These admixture events occurred during the initial stages of speciation and left traces in morphology, while the enforcement of the reproductive barrier later developed with the effect of genetic drift and niche evolution. Our findings provide an example of speciation with gene flow, and further highlight the potential impacts of niche conservatism and divergence on the completion of allopatric speciation.

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