Browsing by Author "Huang, Bing-Hong"
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Item 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-ChunAbstract 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.Item 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, YelinAbstract 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.Item 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-ChunAbstract 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.Item 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-ChunAbstract 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.Item 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-ChunAbstract 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.Item 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-ChunAbstract 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.Item 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。