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研究生: 林宗翰
Lin, Tzong-Han
論文名稱: 異域種化與過去種間基因交流形塑臺灣攀蜥的演化歷史
Allopatric speciation and ancient gene flow shape the evolutionary history of dragon lizards (Genus: Diploderma) in Taiwan
指導教授: 林思民
Lin, Si-Min
口試委員: 廖培鈞
Liao, Pei-Chun
黃仁磐
Huang, Jen-Pan
林思民
Lin, Si-Min
口試日期: 2024/01/09
學位類別: 碩士
Master
系所名稱: 生命科學系
Department of Life Science
論文出版年: 2024
畢業學年度: 112
語文別: 英文
論文頁數: 111
中文關鍵詞: 雙重酶切DNA定序龍蜥基因流種化物種界定
英文關鍵詞: ddRAD-seq, Diploderma, gene flow, speciation, species delimitation
研究方法: 調查研究主題分析
DOI URL: http://doi.org/10.6345/NTNU202400254
論文種類: 學術論文
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  • 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.

    摘要 I Abstract II Content III Introduction 1 Material and methods 4 Study species and region 4 Sample collection and Molecular data preparation 5 ddRADseq data preparation 6 SNP data assembly 6 Phylogenetic analysis 7 Species delimitation by sequence data 9 Divergence time estimation 11 Population structure analysis 12 Morphological and ornamentation measurement analysis 14 Niche comparative analysis 16 Isolation mechanism analysis 17 Gene flow detection 18 Divergence with gene flow and species delimitation by BPP analysis 20 Demographic history reconstruction 22 Paleo-distribution modeling 23 Results 24 Sequence and ddRAD-seq data compilation 24 Geographic effect and intraspecific mitonuclear discordances in phylogenetic trees 25 Incongruent species delimitation from mitochondrial and nuclear genes 27 Deep divergence time uncovered by fossil-calibrated tree 28 Distinct population structure and shared co-ancestry between D. polygonatum and D. brevipes in contact zone 28 IBD and IBRclim as underlying mechanism for within island differentiation for D. p. xanthostomum, but not in D. brevipes 30 Pholidosis and morphometric traits in identified clusters 31 Diverse ornamentation among identified clusters with traces of potential hybrid 32 Niche analysis provided opposite pattern in divergent clusters 32 Interspecific gene flow between sympatric populations for sister taxa 33 Speciation with pre- and post- divergence gene flow favored by BPP 35 Evidence of demographic contraction after interspecific divergence 36 Overlapped paleo-distribution in pairs of clusters with gene flow 37 Discussion 37 Mito-nuclear discordance 38 Obscure results of species delimitation 39 Taxonomic revisions and recommendation 40 Ancient gene flow as potential source of ornamentation polymorphism in D. brevipes 41 Niches, demography, and dispersal ability 43 Conclusion 44 Reference 46 Tables 69

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