Browsing by Author "Liao, Pei-Chun"

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Changes of diet and dominant intestinal microbes in farmland frogs
(2016-03-10) Chang, Chun-Wen; Huang, Bing-Hong; Lin, Si-Min; Huang, Chia-Lung; Liao, Pei-Chun
Abstract Background Agricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems. Results The occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes. Conclusions This study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife.
Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion
(2018-05-24) Guo, Wuxia; Liu, Ying; Ng, Wei L; Liao, Pei-Chun; Huang, Bing-Hong; Li, Weixi; Li, Chunmei; Shi, Xianggang; Huang, Yelin
Abstract Background Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared. Results A total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness. Conclusions We characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha.
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.
Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species
(2016-09-17) Huang, Bing-Hong; Chen, Yi-Wen; Huang, Chia-Lung; Gao, Jian; Liao, Pei-Chun
Abstract Background Adaptive divergence, which usually explains rapid diversification within island species, might involve the positive selection of genes. Anthocyanin biosynthetic pathway (ABP) genes are important for floral diversity, and are related to stress resistance and pollination, which could be responsible for species diversification. Previous studies have shown that upstream genes of ABP are subject to selective constraints and have a slow evolutionary rate, while the constraints on downstream genes are lower. Results In this study, we confirmed these earlier observations of heterogeneous evolutionary rate in upstream gene CHS and the downstream gene UFGT, both of which were expressed in Scutellaria sp. inflorescence buds. We found a higher evolutionary rate and positive selection for UFGT. The codons under positive selection corresponded to the diversified regions, and the presence or absence of an α-helix might produce conformation changes in the Rossmann-like fold structure. The significantly high evolutionary rates for UFGT genes in Taiwanese lineages suggested rapid accumulation of amino acid mutations in island species. The results showed positive selection in closely related species and explained the high diversification of floral patterns in these recently diverged species. In contrast, non-synonymous mutation rate decreases in long-term divergent species could reduce mutational load and prevent the accumulation of deleterious mutations. Conclusions Together with the positive selection of transcription factors for ABP genes described in a previous study, these results confirmed that positive selection takes place at a translational level and suggested that the high divergence of ABP genes is related to the floral diversity in island Scutellaria species.
Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehiraeHay. (Lauraceae) in Taiwan inferred from nuclear genes
(2010-04-30) Liao, Pei-Chun; Kuo, Dai-Chang; Lin, Chia-Chia; Ho, Kuo-Chieh; Lin, Tsan-Piao; Hwang, Shih-Ying
Abstract Background Species in the varied geographic topology of Taiwan underwent obvious demographic changes during glacial periods. Cinnamomum kanehirae has been exploited for timber and to obtain medicinal fungi for the past 100 years. Understanding anthropogenic factors influencing the demography of this species after the last glacial maximum (LGM) is critically important for the conservation of this species. Results Populations of C. kanehirae were classified into four geographic regions: northwestern (NW), west-central (WC), southwestern (SW), and southeastern (SE). In total, 113 individuals from 19 localities were sampled, and variations in the chalcone synthase gene (Chs) intron and leafy (Lfy) intron-2 sequences of nuclear DNA were examined in order to assess phylogeographic patterns, the timescales of demographic and evolutionary events, and recent anthropogenic effects. In total, 210 Chs and 170 Lfy sequences, which respectively constituted 36 and 35 haplotypes, were used for the analyses. Estimates of the migration rate (M) through time revealed a pattern of frequent gene flow during previous and the present interglacials. The isolation-by-distance test showed that there generally was no significant correlation between genetic and geographic distances. The level of among-region genetic differentiation was significant when comparing eastern to western populations. However, no significant among-region genetic differentiation was found in comparisons among the four geographic regions. Moreover, essentially no genetic structuring was found for the three regions west of the CMR. A fit of spatial range expansion was found for pooled and regional samples according to the non-significant values of the sum of squared deviations. Using the Bayesian skyline plot (BSP) method, a recent bottleneck after the LGM expansion was detected in both regional and pooled samples. Conclusions Common haplotype distributions among geographic regions and the relatively shallow genetic structuring displayed are the result of historical gene flows. Southward dispersals in an earlier time frame from the NW region and in a later time frame from the SE region were inferred. The BSP analysis suggested a postglacial expansion event. Recent trends, however, refer to a bottleneck due to human interventions observed for both pooled and regional C. kanehirae samples.
Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)
(2018-09-17) Yang, Chih-Kai; Huang, Bing-Hong; Ho, Shao-Wei; Huang, Meng-Yuan; Wang, Jenn-Che; Gao, Jian; Liao, Pei-Chun
Abstract Background Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood. Results Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period. Conclusions Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.
Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands
(2018-11-08) Yang, Chih-Kai; Chiang, Yu-Chung; Huang, Bing-Hong; Ju, Li-Ping; Liao, Pei-Chun
Abstract Background Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus. Results Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate. Conclusions The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events.
Screening transferable microsatellite markers across genus Phalaenopsis (Orchidaceae)
(2017-11-15) Ko, Ya-Zhu; Shih, Huei-Chuan; Tsai, Chi-Chu; Ho, Hsing-Hua; Liao, Pei-Chun; Chiang, Yu-Chung
Abstract Background Molecular identification based on microsatellite loci is an important technology to improve the commercial breeding of the moth orchid. There are more than 30,000 cultivars have been enrolled at the Royal Horticultural Society (RHS). In this study, genomic microsatellite primer sets were developed from Phalaenopsis aphrodite subsp. formosana to further examine the transferability of across 21 Phalaenopsis species. Methods and results Twenty-eight polymorphic microsatellite markers were obtained using the magnetic bead enrichment method, with high transferability of the 21 species of the genus Phalaenopsis, especially in the subgenus Phalaenopsis. The 28 newly developed polymorphic microsatellite markers with high polymorphism information content values. The best and second fit grouping (K) are inferred as two and four by the ΔK evaluation in the assignment test. This result indicates that these microsatellite markers are discernible to subgenus Phalaenopsis. Conclusions Our results indicate that these new microsatellite markers are useful for delimiting species within genus Phalaenopsis. As expected, the genetic relationships between species of subgenus Phalaenopsis can be well distinguished based on the assignment test. These molecular markers could apply to assess the paternity of Phalaenopsis as well as investigating hybridization among species of genus Phalaenopsis.
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。
共域及異域分布的田代氏黃芩及布烈氏黃芩族群與其土壤基質對根圈微生物組成的協同效應
(2020) 江祖恩; Chiang, Tzu-En
土壤微生物群落與植物有不同的交互作用，而土壤微生物群落的組成受到了寄主植物因子與環境因子的雙重選汰壓力影響。目前較缺乏的是對常見土壤微生物種類的生態功能理解，以及對單一微生物各分類位階在群落內的組成比例及生態功能探討。本研究我將利用兩種最近其分化的台灣特有種黃芩：布烈氏黃芩及田代氏黃芩之根圈微生物作為研究對象，四個不同地理區包含一個共域之樣點共五個樣點。利用16SrRNA Metagenome來評估根圈微生物群落的組成，並以操作分類單元(operational taxonomic unit, OTU)、綱為單位進行分析。本研究使用變異數分析(Analysis of variance, ANOVA)檢測各樣本間α-多樣性是否有顯著差異、使用冗餘分析(redundancy analysis, RDA)檢測寄主植物、土壤基質、土壤顆粒大小對β-多樣性的影響，並使用Clamtest找出微生物在不同寄主間、與不同環境間的分布情形。結果發現寄主植物可以顯著影響樣本間的α-多樣性、土壤基質影響β-多樣性所占比例最多。除此之外，本研究除了探討不同類群微生物的功能，也找到八種與兩種寄主植物都有密切相關的核心微生物，有助於我們更加了解植物與微生物間的交互作用。
冰期後不同拓殖路線的兩種臺灣特有楓屬植物對海拔適應的遺傳機制
(2022) 蔡明威; Chai, Min-Wei
物種是如何應對快速變化的環境以達到區域性適應一直是演化生物學重要的議題，而不同物種在面對環境變化時是否呈現相同的適應性反應也鮮少被探討。本研究使用兩種在末次冰河期後在海拔上有著不同拓殖路線的臺灣楓屬植物-尖葉楓（Acer caudatifolium）以及紅榨楓（A. rubescens）作為研究材料，探討海拔梯度如何影響此二物種在基因組層級上的適應，並比較兩物種對於海拔的適應機制是否相同。我首先使用轉錄組定序（RNA-seq）量化高低海拔族群的基因表現量，並使用表現差異分析篩選出族群之間具有顯著差異的候選基因。接著我使用PAML估算編碼區的同義置換及非同義置換的比值來判斷各個基因在不同的海拔族群是否受到正向天擇。再來我還使用Multiplexed shotgun genotyping（MSG）獲取大量的單位點變異（SNPs）,利用族群基因體的方式檢測與海拔有關的環境因子是否與兩物種的族群遺傳變異有關聯。此外，我也藉由遺傳-環境關聯性分析來檢測單一SNPs與各個環境因子的關聯性，以觀察兩物種在面對相同類型的環境變化時主要是哪些基因座起關鍵作用。最後我將具有表現差異、受到天擇且跟環境因子有關聯的基因座進行資料庫的比對，以了解這些基因座的功能及其代謝途徑。結果顯示大部分海拔之間具有差異表現以及在PAML檢測中有偵測到正向天擇的基因在兩物種之間都不相同；然而遺傳-環境關聯性分析結果發現大部分與海拔環境因子具有顯著關聯性的基因座在兩物種之間具有高度的重疊，說明此二物種對於海拔環境的選汰壓力有著在不同層級的相似以及相異之處。另外，基因功能註解的結果也顯示大部分的候選基因都與環境變化有關，如節律調節、氣孔開關調節、以及開花時間等。本研究結果有助於詮釋不同海拔植物族群的適應機制，以及植物面對不同環境時適應能力的改變有進一步的了解。
台灣牙醫醫病關係中的醫病溝通之探究
(2023) 何懿洲; He, Yi-Zhou
改善醫患溝通對於優化治療結果和病患滿意度具有重要意義。過去的研究結果強調了根據病患特徵制定定制溝通策略的必要性。為此，將醫患溝通教育納入台灣的牙科教育體系中成為本研究的目標，以加強以病患為中心的護理並減少衝突。本研究通過訪談和問卷調查以及比較不同國家的課程，對醫患溝通的重要性進行了描述性統計和廣義線性混合效應模型分析，涵蓋了牙醫和病患雙方的觀點。本研究共有超過600名病患參與了問卷調查，並且採訪了4名年齡在20歲以上且具有多年牙科經驗的牙醫師。牙科醫師的訪談結果均強調了醫患溝通的重要性，而病患問卷中呈現其年齡和收入與重視醫患溝通呈正相關，但與牙科助理的溝通呈負相關。這可能是由於病患更關注牙科醫師的專業知識和技能，而較少關注助理的溝通能力。牙醫師們強調了溝通教育的必要性，同時也強調了執行力的重要性。另外，本研究亦發現社會經濟地位較高和年齡較大的病人對牙醫與病患的溝通給予更高的評價，這可能是由於這些個體更加注重自我推銷，此結果進一步凸顯醫患關係的多樣性。根據本研究的調查結果，本研究建議在台灣實施醫患溝通課程，以提升牙科專業人員的溝通能力，從而改善醫療服務質量和病患體驗。基於訪談及問卷的研究結果，並參考美英日等國的牙醫課程，本研究建議在大學學習期間開展牙醫溝通教育，並繼續實踐以應對不斷變化的社會動態。這項研究的結果將有助於提高台灣的牙科教育體系，使其更加關注醫患溝通的重要性。透過專注於溝通技巧和策略的教育課程，牙科專業人員將能夠更好地與病患溝通，確保他們獲得所需的醫療護理並提高滿意度。同時，這也有助於減少衝突和誤解，建立良好的醫患關係，從而提升整體醫療體驗和治療結果。
地理與生態因子在島嶼上黃芩屬物種的族群分化與快速種化上的效應
(2020) 黃秉宏; Huang, Bing-Hong
研究背景：島嶼物種的快速種化可以由隨機的力量、遷徙拓殖、基因交流以及天擇等力量驅動。然而島嶼面積不大，頻繁的物種接觸導致的基因交流理應減少物種或族群分化，現今我們常以生態力量趨動的生態種化解釋之，因為生態因子如環境氣候異質性等使族群間有區域性適應阻擋部分基因組的基因交流，區域性適應影響的基因組週邊區域因連鎖而產生搭便車效應加強了該區段的基因交流阻隔，而漸漸的這些阻隔區域增加以到一定程度並完全種化，這些力量可以共同作用以加快島嶼物種的分化速度。研究具高特有種比例的物種有助了解這些力量在祖先物種拓殖入島嶼後加快分化速度的相對重要性。台灣產的黃芩屬特有種比例比起其他東亞及東南亞的鄰近島嶼或陸塊都高上許多，全部共8種，即有6種為特有種。過去的研究指出台灣產黃芩屬的多樣性來自至少三次的拓殖事件以及島嶼在地的快速種化。而台灣產的黃芩利用分子定年計算出的最早分歧時間不過50萬年內，其中被命名作indica group的印度黃芩、布烈氏黃芩、田代氏黃芩及南台灣黃芩形成單一分支且分歧時間短於20萬年內，被認為可能是其中一次拓殖事件後的在地快速種化。我們想以台灣產黃芩屬成員作材料切入生態種化如何與台灣高特有性之關聯性。方法我們使用了微衛星體基因型檢測作為快速變異的遺傳資料進行分析。並輔以溯祖理論分析法及演化模型選擇找出最適合解釋台灣產黃芩是否一如生態種化之預測分化早期有基因交流。並以環境因子與遺傳分化進行關聯性分析，了解遺傳變異或族群分化是否與環境因子有關。結果我們優先了解這群物種來檢測indica group是否主要來自單次的快速種化，以利後續設計實驗了解台灣產黃芩的快速種化之因。然而，依據溯祖理論IMa3分析，我們發現indica group在分歧時伴隨旺盛的基因交流，然而在使用貝氏歸群分析時卻顯示這些近期分歧且鄰域物佈的物種甚少種間遺傳混雜，顯示物種明顯分化，考量過去旺盛的基因交流及台灣島面積不大，物種易接觸，這麼短的分歧時間實難分化出這麼多特有種，我們藉分歧時有種間基因交流的情形，再依生態種化的概念，推論生態因子可能參與在這些快速種化的黃芩的物種維持與分化。我們挑選兩組共域/鄰域分佈的特有種，分別是田代氏與布烈氏黃芩組，以及向天盞與台北黃芩組來問答這個議題。我們利用以approximate Bayesian computation的方法進行溯祖模型選擇，發現田代氏黃芩與布烈氏黃芩有強烈的祖先性基因交流，然而現今已有明顯的分化及基因交流的阻斷。兩個物種的分化都可以由在地環境異質性及多環境因子組合的棲位分化來解釋。而向天盞及台北黃芩則展現不同的結果，不論是溯祖模擬模型選擇、群聚分析及單套形的樹形/網狀分析都無法清楚的區分特有的台北黃芩及廣布於東亞的向天盞。而可供區別的形態特徵如小堅果外衣紋路及葉型，在觀測後也證實僅是採集植物個體發育時期不同所致，並非可供物種區分的特徵。組合台北黃芩及向天盞的族群後發現族群間有明顯的遺傳結構，這些遺傳結構以廣義線性模型及座標軸分析等方法發現夏秋降雨量在族群的差異與族群遺傳分化有關。結論因此，無論是向天盞/台北黃芩組，或是布烈氏黃芩/田代氏黃芩組都發現明顯的族群尺度分化，這些分化都可以由氣候異質性及區域性適應解釋。換言之，氣候異質性及區域性適應均能促進台灣產黃芩屬成員讓族群分化，更可能加速種化以讓多樣性速率提升。
尖葉楓與台灣紅榨槭種間的基因漸滲與氣候之關聯
(2019) 熊桓翊; Hsiung, Huan-Yi
物種間的雜交能增加物種對於新環境的適應潛能。在此研究中我利用基因組尺度的遺傳資料檢驗兩個高度分化的楓屬物種間的雜交與天擇，並驗證跨越不同環境下的適應。我從全台灣跨越高低海拔的採集這兩個遺傳上有分化的尖葉楓(Acer caudatifolium)與台灣紅榨槭(A. rubescens)，共271個個體，利用multiple shotgun sequencing所獲得的3281個單一核甘酸多型性檢驗物種間的基因漸滲。族群結構分析與演化模型都指出尖葉楓與台灣紅榨槭間有次級接觸和基因漸滲。基因組-環境相關性分析則顯示這兩個物種在環境上分化。在3281個SNP中有16個SNP是在種間高度分化、與環境因子相關且有基因漸滲的。然而根據CCA的結果卻顯示遺傳混雜的個體並沒有分布在不同於親本的環境。從這些結果指出在高度分化的兩個物種也能有基因漸滲的可能，但大多被物種間的屏障所限制。然而尖葉楓與台灣紅榨槭間的基因漸滲沒有辦法證明與異質環境的適應之間的相關性。
氣候及地理因子與不同海拔楓屬植物族群空間遺傳組成之關係
(2018) 曾怡婷; Tseng, Yi-Ting
物種的分布及遺傳結構可能反應環境差異，氣候變化可能造成族群分歧，而地理距離亦可能影響其遺傳結構。為探討區域環境差異及地理因子與其遺傳結構的關聯性，本研究利用台灣楓屬植物尖葉楓 (Acer caudatifolium)及紅榨楓 (A. rubescens)其廣泛分布以及海拔分布差異的特性，使用17組微衛星標記計算遺傳變異程度，並將遺傳結構與每一個體的經緯度、海拔及氣候變因進行相關性分析。根據Analysis of molecular variance (AMOVA)結果可知尖葉楓及紅榨楓具明顯遺傳分化，也支持STRUCTURE的歸群。由Redundancy analysis (RDA)結果可知尖葉楓和紅榨楓的個體遺傳變異與氣候及地理因子呈現相關，顯示氣候及空間效應可能支配兩物種的遺傳分布。此外地理因子與低海拔尖葉楓個體遺傳分布的相關性更為顯著，表示山脈的隔離效應對低海拔物種的基因交流的阻隔更為明顯。因此本研究推論氣候和地理因子對不同海拔分布物種的遺傳變異產生不同影響壓力，也反應近緣樹種因環境差異而維持其基礎生態棲位及遺傳分化。
環繞客戶的企業成長路徑
(2020) 廖佩君; Liao, Pei-Chun
本文主要探討企業資源與成耐的建構過程，及其與後續成長策略的關係。論文以台灣半導體設備服務業者X公司的成長策略為例，進行分析。X公司的策略規劃邏輯是由內向外，運用企業本身的經營條件，以對抗外在環境的變化，並傾向以內部自行發展搭配合作發展的方式建構資源及能力，目前公司的核心競爭力，更是在為了滿足客戶的需求過程當中逐漸建立。因此發現，個案公司的成長路徑是環繞客戶需求而成。雖然過程中也有失敗的經驗，但個案公司仍持續不斷的修正及調整，試圖找出最佳成長策略，將企業價值極大化。
石櫟屬物種生理生態性狀親緣訊息與蠟生合成基因正向天擇
(2016) 何紹瑋; Ho, Shao-Wei
有些植物表皮細胞中的蠟生合成基因生合成蠟後，經通道蛋白運輸至細胞外堆疊，形成物理性屏障的結晶狀(epicuticular wax crystal)構造，常被認為與化學性防禦特徵(如：酚酸)之間有權衡關係。此外，葉表蠟有無的適應也可能反映在蠟生合成基因及受蠟影響的生態特徵上，如光合作用效率。本研究以石櫟屬物種作為材料，利用遺傳及生理生態分析探討葉表蠟結晶的有/無特徵是否為適應的結果。首先使用6個參考基因重建石櫟屬的親緣關係，發現距今約1400萬年前至800萬年前，至少出現3次獨立由無蠟到產生蠟結晶的特徵轉換的演化事件。在蠟骨架生合成(CER1、CER3)、調節性(CER7)、及運輸蛋白(CER5)等基因中，僅發現CER1在由無蠟到產生蠟結晶的特徵轉換時有正向天擇訊號；生理生態檢測中，蠟結晶均與酚酸及光合作用指數無顯著相關。但Y(II)及δ15N等光合作用指數在CER1基因樹呈現顯著的親緣訊息，顯示光合作用效率在種間的差異反應在蠟骨架合成的演化上。本研究推論，石櫟屬物種在中新世中期至上新世初期發生特徵轉換，當時劇烈的氣候變化也反映了蠟結晶生合成基因的正向天擇及光合作用效率上。
臺灣殼斗科植物分類研究
(2019) 楊智凱; Yang, Chih-Kai
無中文摘要
錐果櫟的遺傳-環境-表現型相關性研究
(2023) 孫沛煒; Sun, Pei-Wei
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。