Browsing by Author "Lu, Hsin-Pei"

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    Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species
    (2018-09-21) Huang, Bing-Hong; Lin, Yuan-Chien; Huang, Chih-Wei; Lu, Hsin-Pei; Luo, Min-Xin; Liao, Pei-Chun
    Abstract Background Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses. Results Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in Z. kawagoii than in Z. shuanglongensis explains the more widespread distribution of Z. kawagoii in Taiwan. Conclusions Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.
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    兩種臺灣特有薑屬植物的族群遺傳結構及區域性適應
    (2020) 呂欣蓓; Lu, Hsin-Pei
    研究物種在異質性的地景環境中的地理空間分布及遺傳結構之間的關係是重要的，這有助於了解物種如何適應不同天擇壓力以及牽涉到族群分化、區域性適應、遷徙及拓殖能力，以及族群間基因交流的過程。本研究以廣布及侷限兩種不同分布形式的台灣特有薑屬植物─三奈(Zingiber kawagoii)及雙龍薑 (Z. shuanglongensis)作為研究題材，探討其在高異質性地景中的氣候、地形以及族群遺傳結構之間的關係。推測不同的氣候或地形條件是影響兩物種之地理分布及遺傳結構的可能原因。在此研究中，我利用生態棲位模擬探討三奈及雙龍薑在過去氣候動盪的環境下是如何隨時間在棲位範圍上改變；並透過ddRADseq獲得基因組尺度的單核苷酸多型性(SNPs)，利用離群值檢測篩選出潛在適應性SNPs及中性的SNPs去探討地理距離、環境差異、適應程度等是否影響中性的SNPs及適應性SNPs在族群之間的分化。另外，我也藉由遺傳-環境關聯性分析去分析兩物種各自族群間的區域性適應是受到哪些因子影響，並更進一步進行功能性基因註解。結果顯示即使是親緣關係接近且分布於類似環境的物種，其遺傳結構在高異質性的地景下會受氣候差異及地形的影響，導致族群分化或是區域性適應的產生。三奈及雙龍薑在不同地質年代的棲位模擬中擁有不同的分布形式以及漸進式的擴張及限縮。三奈的分布範圍在末次冰盛期時有往低海拔退縮的趨勢，而後在緯度上有逐漸北移，而雙龍薑的分布範圍則是在海拔上有逐漸往高海拔限縮的趨勢。在兩物種族群中發生族群分化的原因中，三奈為受到氣候上的限制影響，而雙龍薑則受到地形上的限制影響。另外，就兩物種族群間發生區域性適應的原因也不相同。從基因註解的結果可以得知三奈族群間在區域性適應與個體發育過程有關，而雙龍薑族群間則是與植物免疫過程有關。所有結果皆指向高異質性地景會影響物種在空間上的遺傳結構分布。本研究顯示空間異質性及區域性適應導致兩個特有薑屬植物族群遺傳結構呈現不一致的模式，並指出兩個近期分化的物種可能是藉由不同的策略來面對不同的環境壓力。