45 results on '"Shih-Ying Hwang"'
Search Results
2. The Contribution of Epigenetics to Evolutionary Adaptation in Zingiber kawagoii Hayata (Zingiberaceae) Endemic to Taiwan
- Author
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Yi-Shao Li, Pei-Chun Liao, Chung-Te Chang, and Shih-Ying Hwang
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Ecology ,Plant Science ,environmentally associated epigenetic variation ,isolation-by-distance ,isolation-by-environment ,local adaptation ,redundancy analysis ,Zingiber kawagoii ,Ecology, Evolution, Behavior and Systematics - Abstract
We epigenotyped 211 individuals from 17 Zingiber kawagoii populations using methylation-sensitive amplification polymorphism (MSAP) and investigated the associations of methylated (mMSAP) and unmethylated (uMSAP) loci with 16 environmental variables. Data regarding genetic variation based on amplified fragment length polymorphism (AFLP) were obtained from an earlier study. We found a significant positive correlation between genetic and epigenetic variation. Significantly higher mean mMSAP and uMSAP uHE (unbiased expected heterozygosity: 0.223 and 0.131, respectively, p < 0.001) per locus than that estimated based on AFLP (uHE = 0.104) were found. Genome scans detected 10 mMSAP and 9 uMSAP FST outliers associated with various environmental variables. A significant linear fit for 11 and 12 environmental variables with outlier mMSAP and uMSAP ordination, respectively, generated using full model redundancy analysis (RDA) was found. When conditioned on geography, partial RDA revealed that five and six environmental variables, respectively, were the most important variables influencing outlier mMSAP and uMSAP variation. We found higher genetic (average FST = 0.298) than epigenetic (mMSAP and uMSAP average FST = 0.044 and 0.106, respectively) differentiation and higher genetic isolation-by-distance (IBD) than epigenetic IBD. Strong epigenetic isolation-by-environment (IBE) was found, particularly based on the outlier data, controlling either for geography (mMSAP and uMSAP βE = 0.128 and 0.132, respectively, p = 0.001) or for genetic structure (mMSAP and uMSAP βE = 0.105 and 0.136, respectively, p = 0.001). Our results suggest that epigenetic variants can be substrates for natural selection linked to environmental variables and complement genetic changes in the adaptive evolution of Z. kawagoii populations.
- Published
- 2023
3. Adaptive Divergence without Distinct Species Relationships Indicate Early Stage Ecological Speciation in Species of the
- Author
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Jia-Jia, Cao, Yi-Shao, Li, Chung-Te, Chang, Jeng-Der, Chung, and Shih-Ying, Hwang
- Abstract
The testing association of environmental variables with genetic and epigenetic variation could be crucial to deciphering the effects of environmental factors playing roles as selective drivers in ecological speciation. Although ecological speciation may occur in closely related species, species boundaries may not be established over a short evolutionary timescale. Here, we investigated the genetic and epigenetic variations using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP), respectively, and tested their associations with environmental variables in populations of four closely related species in the
- Published
- 2022
4. Pattern of Adaptive Divergence in Zingiber kawagoii Hayata (Zingiberaceae) along a Narrow Latitudinal Range
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Yi-Shao Li, Pei-Chun Liao, Chung-Te Chang, and Shih-Ying Hwang
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Ecology ,adaptive divergence ,AFLP ,allele frequency ,annual temperature range ,latitudinal gradient ,population mean FST ,Zingiber kawagoii ,Plant Science ,Ecology, Evolution, Behavior and Systematics - Abstract
Ecological and evolutionary processes linking adaptation to environment are related to species’ range shifts. In this study, we employed amplified-fragment-length-polymorphism-based genome scan methods to identify candidate loci among Zingiber kawagoii populations inhabiting varying environments distributed at low to middle elevations (143–1488 m) in a narrow latitudinal range (between 21.90 and 25.30° N). Here, we show evidence of selection driving the divergence of Z. kawagoii. Twenty-six FST outliers were detected, which were significantly correlated with various environmental variables. The allele frequencies of nine FST outliers were either positively or negatively correlated with the population mean FST. Using several independent approaches, we found environmental variables act in a combinatorial fashion, best explaining outlier genetic variation. Nonetheless, we found that adaptive divergence was affected mostly by annual temperature range, and it is significantly positively correlated with latitude and significantly negatively correlated with the population mean FST. This study addresses a latitudinal pattern of changes in annual temperature range (which ranged from 13.8 °C in the Lanyu population to 18.5 °C in the Wulai population) and emphasizes the pattern of latitudinal population divergence closely linked to the allele frequencies of adaptive loci, acting in a narrow latitudinal range. Our results also indicate environmentally dependent local adaptation for both leading- and trailing-edge populations.
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- 2022
5. Adaptive Divergence without Distinct Species Relationships Indicate Early Stage Ecological Speciation in Species of the Rhododendronpseudochrysanthum Complex Endemic to Taiwan
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Jia-Jia Cao, Yi-Shao Li, Chung-Te Chang, Jeng-Der Chung, and Shih-Ying Hwang
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Ecology ,ecological speciation ,environmentally-associated dependent evolution ,genetic and epigenetic variation ,incomplete lineage sorting ,local adaptation ,Plant Science ,Ecology, Evolution, Behavior and Systematics - Abstract
The testing association of environmental variables with genetic and epigenetic variation could be crucial to deciphering the effects of environmental factors playing roles as selective drivers in ecological speciation. Although ecological speciation may occur in closely related species, species boundaries may not be established over a short evolutionary timescale. Here, we investigated the genetic and epigenetic variations using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP), respectively, and tested their associations with environmental variables in populations of four closely related species in the R. pseudochrysanthum complex. No distinctive species relationships were found using genetic clustering analyses, neighbor-joining tree, and neighbor-net tree based on the total AFLP variation, which is suggestive of the incomplete lineage sorting of ancestral variation. Nonetheless, strong isolation-by-environment and adaptive divergence were revealed, despite the significant isolation-by-distance. Annual mean temperature, elevation, normalized difference vegetation index, and annual total potential evapotranspiration were found to be the most important environmental variables explaining outlier genetic and epigenetic variations. Our results suggest that the four closely related species of the R. pseudochrysanthum complex share the polymorphism of their ancestor, but reproductive isolation due to ecological speciation can occur if local environmental divergence persists over time.
- Published
- 2022
6. Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar (Calocedrus formosana)
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Yu-Chung Chiang, Chung Te Chang, Shih Ying Hwang, and Wei Ming Chien
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0301 basic medicine ,AFLP ,lcsh:QH426-470 ,Keteleeria davidiana ,Population ,Biology ,Gene flow ,03 medical and health sciences ,0302 clinical medicine ,elevational range margin populations ,Genetic variation ,Genetics ,education ,Genetics (clinical) ,Local adaptation ,education.field_of_study ,Genetic diversity ,adaptive evolution ,Ecology ,Calocedrus formosana ,biology.organism_classification ,Divergent evolution ,lcsh:Genetics ,030104 developmental biology ,030220 oncology & carcinogenesis ,Molecular Medicine ,environment ,allele frequency - Abstract
Population diversification can be shaped by a combination of environmental factors as well as geographic isolation interacting with gene flow. We surveyed genetic variation of 243 samples from 12 populations of Calocedrus formosana using amplified fragment length polymorphism (AFLP) and scored a total of 437 AFLP fragments using 11 selective amplification primer pairs. The AFLP variation was used to assess the role of gene flow on the pattern of genetic diversity and to test environments in driving population adaptive evolution. This study found the relatively lower level of genetic diversity and the higher level of population differentiation in C. formosana compared with those estimated in previous studies of conifers including Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides occurring in Taiwan. BAYESCAN detected 26 FST outlier loci that were found to be associated strongly with various environmental variables using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression. We found several environmentally dependent adaptive loci with high frequencies in low- or high-elevation populations, suggesting their involvement in local adaptation. Ecological factors, including relative humidity and sunshine hours, that are generally not altitude related could have been the most important selective drivers for population divergent evolution in C. formosana. The present study provides fundamental information in relation to adaptive evolution and can be useful for assisted migration program of C. formosana in the future conservation of this species.
- Published
- 2020
7. Demographic history and adaptive synonymous and nonsynonymous variants of nuclear genes in Rhododendron oldhamii (Ericaceae)
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Jeng Der Chung, Shih Ying Hwang, Chung Te Chang, and Yi Chiang Hsieh
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0106 biological sciences ,0301 basic medicine ,Nonsynonymous substitution ,Rhododendron ,Nuclear gene ,Evolution ,Population ,lcsh:Medicine ,Biology ,Genes, Plant ,01 natural sciences ,Article ,03 medical and health sciences ,Exon ,Genetic drift ,Genetic variation ,Genetics ,lcsh:Science ,education ,education.field_of_study ,Multidisciplinary ,lcsh:R ,Genetic Drift ,Intron ,Genetic Variation ,Phylogeography ,Genetics, Population ,030104 developmental biology ,Evolutionary biology ,lcsh:Q ,GC-content ,010606 plant biology & botany - Abstract
Demographic events are important in shaping the population genetic structure and exon variation can play roles in adaptive divergence. Twelve nuclear genes were used to investigate the species-level phylogeography of Rhododendron oldhamii, test the difference in the average GC content of coding sites and of third codon positions with that of surrounding non-coding regions, and test exon variants associated with environmental variables. Spatial expansion was suggested by R2 index of the aligned intron sequences of all genes of the regional samples and sum of squared deviations statistic of the aligned intron sequences of all genes individually and of all genes of the regional and pooled samples. The level of genetic differentiation was significantly different between regional samples. Significantly lower and higher average GC contents across 94 sequences of the 12 genes at third codon positions of coding sequences than that of surrounding non-coding regions were found. We found seven exon variants associated strongly with environmental variables. Our results demonstrated spatial expansion of R. oldhamii in the late Pleistocene and the optimal third codon position could end in A or T rather than G or C as frequent alleles and could have been important for adaptive divergence in R. oldhamii.
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- 2020
8. Ecological Factors Generally Not Altitude Related Played Main Roles in Driving Potential Adaptive Evolution at Elevational Range Margin Populations of Taiwan Incense Cedar (
- Author
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Wei-Ming, Chien, Chung-Te, Chang, Yu-Chung, Chiang, and Shih-Ying, Hwang
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adaptive evolution ,AFLP ,elevational range margin populations ,Genetics ,Calocedrus formosana ,gene flow ,environment ,allele frequency ,Original Research - Abstract
Population diversification can be shaped by a combination of environmental factors as well as geographic isolation interacting with gene flow. We surveyed genetic variation of 243 samples from 12 populations of Calocedrus formosana using amplified fragment length polymorphism (AFLP) and scored a total of 437 AFLP fragments using 11 selective amplification primer pairs. The AFLP variation was used to assess the role of gene flow on the pattern of genetic diversity and to test environments in driving population adaptive evolution. This study found the relatively lower level of genetic diversity and the higher level of population differentiation in C. formosana compared with those estimated in previous studies of conifers including Cunninghamia konishii, Keteleeria davidiana var. formosana, and Taiwania cryptomerioides occurring in Taiwan. BAYESCAN detected 26 FST outlier loci that were found to be associated strongly with various environmental variables using multiple univariate logistic regression, latent factor mixed model, and Bayesian logistic regression. We found several environmentally dependent adaptive loci with high frequencies in low- or high-elevation populations, suggesting their involvement in local adaptation. Ecological factors, including relative humidity and sunshine hours, that are generally not altitude related could have been the most important selective drivers for population divergent evolution in C. formosana. The present study provides fundamental information in relation to adaptive evolution and can be useful for assisted migration program of C. formosana in the future conservation of this species.
- Published
- 2020
9. ORA47 (octadecanoid‐responsive AP2/ERF‐domain transcription factor 47) regulates jasmonic acid and abscisic acid biosynthesis and signaling through binding to a novel cis ‐element
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Tsan-Piao Lin, Hsing Yu Chen, Mei-Chun Cheng, En Jung Hsieh, Shih Ying Hwang, and Chien-Yu Chen
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0106 biological sciences ,0301 basic medicine ,Physiology ,Arabidopsis ,Cyclopentanes ,Plant Science ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Arabidopsis thaliana ,Oxylipins ,RNA, Messenger ,Jasmonate ,Promoter Regions, Genetic ,Abscisic acid ,Transcription factor ,Base Sequence ,Dehydration ,biology ,Arabidopsis Proteins ,Jasmonic acid ,fungi ,food and beverages ,Plants, Genetically Modified ,biology.organism_classification ,ABI1 ,Repressor Proteins ,Phenotype ,030104 developmental biology ,chemistry ,Biochemistry ,Trans-Activators ,Signal transduction ,Chromatin immunoprecipitation ,Abscisic Acid ,Protein Binding ,Signal Transduction ,010606 plant biology & botany - Abstract
ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47) of Arabidopsis thaliana is an AP2/ERF domain transcription factor that regulates jasmonate (JA) biosynthesis and is induced by methyl JA treatment. The regulatory mechanism of ORA47 remains unclear. ORA47 is shown to bind to the cis-element (NC/GT)CGNCCA, which is referred to as the O-box, in the promoter of ABI2. We proposed that ORA47 acts as a connection between ABA INSENSITIVE1 (ABI1) and ABI2 and mediates an ABI1-ORA47-ABI2 positive feedback loop. PORA47:ORA47-GFP transgenic plants were used in a chromatin immunoprecipitation (ChIP) assay to show that ORA47 participates in the biosynthesis and/or signaling pathways of nine phytohormones. Specifically, many abscisic acid (ABA) and JA biosynthesis and signaling genes were direct targets of ORA47 under stress conditions. The JA content of the P35S:ORA47-GR lines was highly induced under wounding and moderately induced under water stress relative to that of the wild-type plants. The wounding treatment moderately increased ABA accumulation in the transgenic lines, whereas the water stress treatment repressed the ABA content. ORA47 is proposed to play a role in the biosynthesis of JA and ABA and in regulating the biosynthesis and/or signaling of a suite of phytohormone genes when plants are subjected to wounding and water stress.
- Published
- 2016
10. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (Keteleeria davidiana var. formosana)
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Chung Te Chang, Yu-Chung Chiang, Jeng Der Chung, Kai Ming Shih, and Shih Ying Hwang
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0301 basic medicine ,adaptive divergence ,Keteleeria davidiana ,Genetic diversity ,education.field_of_study ,biology ,Population ,population genetics ,SNP ,Population genetics ,Plant Science ,lcsh:Plant culture ,biology.organism_classification ,fine-scale differentiation ,Genetic divergence ,03 medical and health sciences ,030104 developmental biology ,Genetic drift ,Evolutionary biology ,Genetic structure ,K. davidiana var. formosana ,lcsh:SB1-1110 ,education ,Isolation by distance - Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.
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- 2018
11. Adaptive Genetic Divergence Despite Significant Isolation-by-Distance in Populations of Taiwan Cow-Tail Fir (
- Author
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Kai-Ming, Shih, Chung-Te, Chang, Jeng-Der, Chung, Yu-Chung, Chiang, and Shih-Ying, Hwang
- Subjects
fine-scale differentiation ,adaptive divergence ,Keteleeria davidiana ,species delimitation ,K. davidiana var. formosana ,population genetics ,SNP ,Plant Science ,Original Research - Abstract
Double digest restriction site-associated DNA sequencing (ddRADseq) is a tool for delivering genome-wide single nucleotide polymorphism (SNP) markers for non-model organisms useful in resolving fine-scale population structure and detecting signatures of selection. This study performs population genetic analysis, based on ddRADseq data, of a coniferous species, Keteleeria davidiana var. formosana, disjunctly distributed in northern and southern Taiwan, for investigation of population adaptive divergence in response to environmental heterogeneity. A total of 13,914 SNPs were detected and used to assess genetic diversity, FST outlier detection, population genetic structure, and individual assignments of five populations (62 individuals) of K. davidiana var. formosana. Principal component analysis (PCA), individual assignments, and the neighbor-joining tree were successful in differentiating individuals between northern and southern populations of K. davidiana var. formosana, but apparent gene flow between the southern DW30 population and northern populations was also revealed. Fifteen of 23 highly differentiated SNPs identified were found to be strongly associated with environmental variables, suggesting isolation-by-environment (IBE). However, multiple matrix regression with randomization analysis revealed strong IBE as well as significant isolation-by-distance. Environmental impacts on divergence were found between populations of the North and South regions and also between the two southern neighboring populations. BLASTN annotation of the sequences flanking outlier SNPs gave significant hits for three of 23 markers that might have biological relevance to mitochondrial homeostasis involved in the survival of locally adapted lineages. Species delimitation between K. davidiana var. formosana and its ancestor, K. davidiana, was also examined (72 individuals). This study has produced highly informative population genomic data for the understanding of population attributes, such as diversity, connectivity, and adaptive divergence associated with large- and small-scale environmental heterogeneity in K. davidiana var. formosana.
- Published
- 2017
12. Demography of the upward-shifting temperate woody species of the Rhododendron pseudochrysanthum complex and ecologically relevant adaptive divergence in its trailing edge populations
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Teng Chiu Lin, Yi Chiang Hsieh, Chung Te Chang, Bo Kai Liang, Shih Ying Hwang, Jeng Der Chung, and Chia Ying Chen
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Genetic diversity ,Species complex ,Rhododendron hyperythrum ,Natural selection ,Ecology ,Population size ,Forestry ,Horticulture ,Biology ,Effective population size ,Adaptive radiation ,Genetic variation ,Genetics ,Molecular Biology - Abstract
Trailing edge populations of upward migrating species induced by postglacial climatic warming can be evolutionarily significant in the face of global warming. We tested for population size changes between lower- and higher-elevation populations located in the same mountainous regions of the upward-shifting temperate woody species of the Rhododendron pseudochrysanthum complex in Taiwan. We also tested whether natural selection evoked adaptive divergence in trailing edge populations of this species complex. We genotyped 26 expressed sequence tag-simple sequence repeat (EST-SSR) loci of 185 individuals from nine populations of the R. pseudochrysanthum complex including Rhododendron rubropunctatum, Rhododendron hyperythrum, Rhododendron morii, and R. pseudochrysanthum. R. rubropunctatum populations in the R. pseudochrysanthum complex possessed the lowest estimates of genetic diversity and effective population size. Higher-elevation R. pseudochrysanthum populations had lower effective population sizes than lower-elevation R. morii populations in Hohuanshan and Tahsueshan, as revealed by estimates using both MIGRATE-N and approximate Bayesian computation (ABC). R. rubropunctatum populations diverged significantly from populations of other members of the R. pseudochrysanthum complex. An outlier potentially under positive selection specific to R. rubropunctatum populations was identified and strongly associated with ecologically relevant environmental variables. Postglacial climatic warming has a significant influence on population isolation in the R. pseudochrysanthum complex. The results indicate adaptive evolution in the trailing edge populations, i.e., R. rubropunctatum populations of the upward shifting R. pseudochrysanthum complex.
- Published
- 2013
13. Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)
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Chia Ying Chen, Yi Chiang Hsieh, Jeng Der Chung, Chung Te Chang, Shih Ying Hwang, and Chun-Neng Wang
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Gene Flow ,Reproductive Isolation ,Rhododendron ,Population ,Adaptation, Biological ,Taiwan ,Environment ,Biology ,Gene flow ,Genetic drift ,Genetics ,education ,Genetics (clinical) ,Local adaptation ,Expressed Sequence Tags ,education.field_of_study ,Genetic diversity ,Habitat fragmentation ,Plant Dispersal ,Ecology ,Genetic Drift ,Genetic Variation ,Bayes Theorem ,Sequence Analysis, DNA ,Biological Evolution ,Phylogeography ,Evolutionary biology ,Multigene Family ,Biological dispersal ,Original Article ,Microsatellite Repeats - Abstract
Elucidation of the evolutionary processes that constrain or facilitate adaptive divergence is a central goal in evolutionary biology, especially in non-model organisms. We tested whether changes in dynamics of gene flow (historical vs contemporary) caused population isolation and examined local adaptation in response to environmental selective forces in fragmented Rhododendron oldhamii populations. Variation in 26 expressed sequence tag-simple sequence repeat loci from 18 populations in Taiwan was investigated by examining patterns of genetic diversity, inbreeding, geographic structure, recent bottlenecks, and historical and contemporary gene flow. Selection associated with environmental variables was also examined. Bayesian clustering analysis revealed four regional population groups of north, central, south and southeast with significant genetic differentiation. Historical bottlenecks beginning 9168–13,092 years ago and ending 1584–3504 years ago were revealed by estimates using approximate Bayesian computation for all four regional samples analyzed. Recent migration within and across geographic regions was limited. However, major dispersal sources were found within geographic regions. Altitudinal clines of allelic frequencies of environmentally associated positively selected outliers were found, indicating adaptive divergence. Our results point to a transition from historical population connectivity toward contemporary population isolation and divergence on a regional scale. Spatial and temporal dispersal differences may have resulted in regional population divergence and local adaptation associated with environmental variables, which may have played roles as selective forces at a regional scale.
- Published
- 2013
14. Disentangling the effects of isolation-by-distance and isolation-by-environment on genetic differentiation among Rhododendron lineages in the subgenus Tsutsusi
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Pei Chun Liao, Shih Ying Hwang, Jui Hung Chen, Jeng Der Chung, Chun Lin Huang, Chung Te Chang, and Jenn Che Wang
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0301 basic medicine ,Lineage (evolution) ,Genetic admixture ,Forestry ,Horticulture ,Biology ,biology.organism_classification ,Ecological speciation ,Rhododendron kanehirai ,03 medical and health sciences ,030104 developmental biology ,Evolutionary biology ,Botany ,Genetic variation ,Genetics ,Subgenus ,Molecular Biology ,Rhododendron simsii ,Isolation by distance - Abstract
Ecological speciation has long been noted as a central topic in the field of evolutionary biology, and investigation into the relative importance of ecological and geographical factors is becoming increasingly emphasized. We surveyed genetic variation of 277 samples from 25 populations of nine Rhododendron species within Tsutsusi subgenus in Taiwan using simple sequence repeats of expressed sequence tags. Bayesian clustering revealed four genetic lineages: (1) the Rhododendron simsii, Rhododendron kanehirai, and Rhododendron nakaharae lineage (lineage 1); (2) the Rhododendron longiperulatum, Rhododendron breviperulatum, and Rhododendron noriakianum lineage (lineage 2); (3) the Rhododendron rubropilosum lineage (lineage 3); and (4) the Rhododendron oldhamii lineage (lineage 4). Asymmetric introgressions were found from lineage 3 into lineages 1 and 2 (introgressed lineages). Genetic admixture of non-R. oldhamii species was also revealed by a neighbor-joining tree. Variation partitioning showed that environment explained much larger portions of genetic variation than geography between non-introgressed lineages (i.e., between R. oldhamii and other lineages). However, the Mantel and partial Mantel tests and the multiple matrix regression with randomization found that isolation-by-distance played a more important role than isolation-by-environment (IBE) in contributing to genetic variation in most between lineage comparisons. Nevertheless, strong IBE was found when compared between non-introgressed lineages of R. oldhamii and R. rubropilosum, suggesting post-speciation ecological divergence. Several environmental variables, including annual mean temperature, aspect, isothermality, seasonal precipitation, slope, and soil pH, could be important ecological drivers involved in reproductive isolation between R. oldhamii and non-R. oldhamii species within the Tsutsusi subgenus.
- Published
- 2016
15. Natural variation, functional divergence, and local adaptation of nucleotide binding site sequences in Rhododendron (Ericaceae)
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Chiun Jr Hwang, Shih Ying Hwang, Ya Hsiu Sung, Jeng Der Chung, Pei Chun Liao, Chia Ling Chen, and Yung Ta Chang
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Nonsynonymous substitution ,Genetics ,education.field_of_study ,Population ,food and beverages ,Forestry ,Horticulture ,Biology ,biology.organism_classification ,Genome ,Divergent evolution ,Ericaceae ,embryonic structures ,education ,Clade ,Molecular Biology ,Functional divergence ,Local adaptation - Abstract
To further understand natural variation and local adaptation in the evolution of plant defense, we analyzed polymorphism data of nucleotide-binding site (NBS) sequences of Rhododendron at both the species and population levels. Multiple duplication events were found in NBS sequence evolution in Rhododendron genomes, which resulted in six clades: A–F. Our results of several NBS clade pair comparisons showed significant evolutionary rate changes based on differences in substitution rates between NBS-encoding protein clades (type I functional divergence). Pairwise comparisons of NBS clades further revealed that many amino acids displayed radical biochemical property changes causing a shift in amino acid preferences between NBS-encoding protein clades (type II functional divergence). Such divergent evolution of NBSs is likely a consequence of positive selection related to differentiation of recognition signals in response to different pathogens. Primers specific to clades B and C, which differed in the number of radical amino acid changes causing type II functional divergence and levels of nucleotide diversities, were further used to amplify population clades B and C NBS sequences of Rhododendron formosanum populations. Higher levels of net nucleotide divergences (measured by D a) between R. formosanum populations were found based on NBS sequences of population clade B compared to population clade C, suggesting local adaptation of population clade B NBS sequences. Local adaptation can be further inferred for R. formosanum population clade B NBS sequences because of significant Φ ST based on variation in nonsynonymous substitutions. Furthermore, local adaptation was also suggested by no significant correlation of population pairwise F ST between population clades B and C in R. formosanum.
- Published
- 2012
16. Molecular evolution of a family of resistance gene analogs of nucleotide-binding site sequences in Solanum lycopersicum
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Shih Ying Hwang, Kuan-Hung Lin, Chin Ling Ko, and Pei Chun Liao
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Plant Science ,Biology ,Genes, Plant ,Evolution, Molecular ,Negative selection ,Solanum lycopersicum ,Molecular evolution ,Genetics ,Gene family ,Selection, Genetic ,Allele ,Binding site ,Codon ,Clade ,Gene ,Phylogeny ,Disease Resistance ,Likelihood Functions ,Binding Sites ,Phylogenetic tree ,Nucleotides ,food and beverages ,General Medicine ,Insect Science ,embryonic structures ,Animal Science and Zoology - Abstract
Nucleotide-binding site-leucine-rich repeats (NBS-LRR) gene families are one of the major plant resistance genes. Genomic NBS evolution was studied in many plant species for diverse arrays of NBS gene families. In this study, we focused on one family of NBS sequences in an attempt to understand how closely related NBS sequences evolved in the light of selection in domesticated plant species. A phylogenetic analysis revealed five major clades (A–E) and five subclades (A1–A5) within clade A of cloned NBS sequences. Positive selection was only detected in newly evolved NBS lineages in subclades of clade A. Positively selected codon sites were found among NBS sequences of clade A. A sliding-window analysis revealed that regions with Ka/Ks ratios of >1 were in the inter-motifs when paired clades were compared, but regions with Ka/Ks ratios of >1 were found across NBS sequences when subclades of clade A were compared. Our results based on a family of closely related NBS sequences showed that positive selection was first exerted on specific lineages across all NBS sequences after selective constraints. Subsequently, sequences with mutations in commonly conserved motifs were scrutinized by purifying selection. In the long term, conserved high frequency alleles in commonly conserved motifs and changes in inter-motifs were maintained in the investigated family of NBS sequences. Moreover, codons identified to be under positive selection in the inter-motifs were mainly located in regions involved in functions of ATP binding or hydrolysis.
- Published
- 2011
17. Two genetic divergence centers revealed by chloroplastic DNA variation in populations of Cinnamomum kanehirae Hay
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Dai Chang Kuo, Yu Pin Cheng, Tsan-Piao Lin, Chia Chia Lin, Kuo Chieh Ho, and Shih Ying Hwang
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education.field_of_study ,Genetic diversity ,Range (biology) ,Population ,Population genetics ,Biology ,Nucleotide diversity ,Genetic divergence ,Intergenic region ,Chloroplast DNA ,Evolutionary biology ,Botany ,Genetics ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Cinnamomum kanehirae Hayata (Lauraceae), the most valuable subtropical and temperate broadleaf timber tree in Taiwan, is rapidly disappearing from the wild. Taking advantage of a scion garden established by the Taiwan Forestry Research Institute, we examined patterns of chloroplast DNA (cpDNA) variations in 19 populations including 94 individuals. By sequencing two cpDNA fragments using universal primers (the trnL-trnF and petG-trnP intergenic spacers), we found eight polymorphic sites, six haplotypes, and extremely low nucleotide diversity (π = 0.00016) from 792 bp aligned sequences. The ancestral haplotype is widely distributed. Among the populations studied, three separated populations, at Yungfeng, Fuli, and Tahu have high nucleotide diversity. No phylogeographical structures of haplotypes were revealed because the tests of NST−GST for populations did not differ from zero in any situations; a ‘star-like’ genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test also suggested demographic expansion. The genetic divergence and diversity analyses suggested that two potential refugia existed during the last glaciation with a major one located in southeastern Taiwan and a minor one located in Tahu in north-central Taiwan in the Hsuehshan Range, west of the Central Mountain Range.
- Published
- 2009
18. Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia
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Tsan-Piao Lin, Shih Ying Hwang, and Sophie S.F. Huang
- Subjects
Genetics ,education.field_of_study ,Haplotype ,Population ,Biology ,Gene flow ,Refugium (population biology) ,Chloroplast DNA ,Evolutionary biology ,Genetic variation ,Genetic structure ,education ,Far East ,Ecology, Evolution, Behavior and Systematics - Abstract
This study examined the spatial pattern of chloroplast DNA (cpDNA) variation in Cyclobalanopsis glauca (Thunb. ex Murray) Oerst. (Fagaceae) in 140 trees from Taiwan (25 populations), Japan (three), Ryukyus (two), Hong Kong (one) and Mainland China (one). By sequencing three cpDNA intergenic spacer fragments using universal primers (trnT-trnL, trnV-trnM, including the trnV intron, and petG-trnP), we found a total of 1,980 bp and 15 polymorphic sites. Among them, 12 sites were caused by point mutation, and three resulted from insertion. This gives rise to a total of 13 cpDNA haplotypes. The level of differentiation among the populations studied is relatively high (GST = 0.612). Two ancestral haplotypes (A and B) are distributed widely in East Asia. Interestingly, all the derived cpDNA variations are found only in Taiwan but not in other areas. The Central Mountain Ridge (CMR) of Taiwan creates an unsurpassed barrier to the east-west gene flow of C. glauca. Among the populations on the west of CMR, only three separated populations, Yangmingshan, Wushe and Chinshuiying, have high haplotype diversity, each consisting of sister haplotypes all mutated from the same ancestral haplotype. Thus, they have probably originated from de novo mutation after the last glaciation. This inference agrees with the observation that no spatial autocorrelation existed on the west side. Two unrelated dominant lineages on the east of the CMR (haplotypes D and F) showed significant spatial genetic structure. Estimate of NST - GST was -0.090 and differed significantly from zero. Thus at the local scale, the phylogeographical component of the genetic structure is significant on the east of the CMR. Accompanied by published palynological records of the last glaciation, this study suggests the possibility that these two types were colonized northward from the southeastern part of Taiwan. 'Star-like' genealogy is characterized, with all the haplotypes coalescing rapidly and as a general outcome of population expansion (Page & Holmes 1998). A neutrality test also suggested a demographic expansion recovered from a bottleneck. We therefore inferred that the southeastern part of Taiwan might be a potential refugium for C. glauca.
- Published
- 2008
19. Molecular Evolution of thePi-taGene Resistant to Rice Blast in Wild Rice (Oryza rufipogon)
- Author
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Chun Lin Huang, Shih Ying Hwang, Yu Chung Chiang, and Tsan-Piao Lin
- Subjects
Magnaporthe ,DNA, Plant ,Molecular Sequence Data ,Locus (genetics) ,Investigations ,Genes, Plant ,Evolution, Molecular ,Genotype ,Genetics ,Magnaporthe grisea ,Selection, Genetic ,Gene ,Plant Diseases ,Likelihood Functions ,Polymorphism, Genetic ,Oryza sativa ,Base Sequence ,Geography ,Models, Genetic ,biology ,Haplotype ,food and beverages ,Oryza ,biology.organism_classification ,Oryza rufipogon ,Immunity, Innate ,Phenotype - Abstract
Rice blast disease resistance to the fungal pathogen Magnaporthe grisea is triggered by a physical interaction between the protein products of the host R (resistance) gene, Pi-ta, and the pathogen Avr (avirulence) gene, AVR-pita. The genotype variation and resistant/susceptible phenotype at the Pi-ta locus of wild rice (Oryza rufipogon), the ancestor of cultivated rice (O. sativa), was surveyed in 36 locations worldwide to study the molecular evolution and functional adaptation of the Pi-ta gene. The low nucleotide polymorphism of the Pi-ta gene of O. rufipogon was similar to that of O. sativa, but greatly differed from what has been reported for other O. rufipogon genes. The haplotypes can be subdivided into two divergent haplogroups named H1 and H2. H1 is derived from H2, with nearly no variation and at a low frequency. H2 is common and is the ancestral form. The leucine-rich repeat (LRR) domain has a high πnon/πsyn ratio, and the low polymorphism of the Pi-ta gene might have primarily been caused by recurrent selective sweep and constraint by other putative physiological functions. Meanwhile, we provide data to show that the amino acid Ala-918 of H1 in the LRR domain has a close relationship with the resistant phenotype. H1 might have recently arisen during rice domestication and may be associated with the scenario of a blast pathogen–host shift from Italian millet to rice.
- Published
- 2008
20. Calcium chloride enhances the antioxidative system of sweet potato (Ipomoea batatas) under flooding stress
- Author
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Shih Ying Hwang, Y.K. Chiou, Hsiao-Feng Lo, Kuan-Hung Lin, and Long Fang O. Chen
- Subjects
Antioxidant ,biology ,medicine.medical_treatment ,fungi ,Glutathione reductase ,food and beverages ,chemistry.chemical_element ,Glutathione ,Calcium ,biology.organism_classification ,Ipomoea ,Superoxide dismutase ,chemistry.chemical_compound ,Horticulture ,chemistry ,Botany ,biology.protein ,medicine ,Convolvulaceae ,Agronomy and Crop Science ,Peroxidase - Abstract
Three sweet potato varieties, Taoyuan 2, Simon 1 and Sushu 18, were pretreated with four levels of CaCl 2 (0, 60, 120 and 180 kg ha -1 ) weekly for 50 days from planting before being subjected to non-flooding (control) and flooding conditions. The experiment used a randomised complete block design with a split-split plot arrangement of treatments. Young, fully expanded leaves from each plant were clipped for measuring enzyme activities and antioxidant contents. The three genotypes exhibited unique abilities and specificities through the antioxidative systems in response to flooding stress. The level of activity of the antioxidative system in sweet potato leaves was related to CaCl 2 pretreatment during flooding. The ascorbate peroxidase, superoxide dismutase, glutathione reductase, reduced ascorbate, total ascorbate, reduced glutathione and malon-dialdehyde contents of the three sweet potato varieties under flooding stress significantly increased because of pretreatment with 60 and 120 kg ha -1 of CaCl 2 . Moreover, pretreatment with 60 and 120 kg ha -1 CaCl 2 enhanced the flooding tolerance of all three sweet potato varieties and mitigated the effects of flooding stress. However, pretreatment with 180 kg ha -1 CaCl 2 markedly decreased some enzyme activities and antioxidant contents under a flooded condition. Calcium most likely played a role in the antioxidative system in the leaves of these three sweet potato varieties under flooding stress, as an optimum amount strengthened their oxidative systems.
- Published
- 2008
21. Divergent Evolution of the Chloroplast Small Heat Shock Protein Gene in the Genera Rhododendron (Ericaceae) and Machilus (Lauraceae)
- Author
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Yu Pin Cheng, Miao Lun Wu, Min Yi Lin, Tsan-Piao Lin, and Shih Ying Hwang
- Subjects
Chloroplasts ,Rhododendron ,Lineage (evolution) ,Molecular Sequence Data ,Gene Dosage ,Sequence alignment ,Plant Science ,Biology ,Evolution, Molecular ,Lauraceae ,Phylogenetics ,Genetic variation ,Consensus sequence ,Amino Acid Sequence ,Peptide sequence ,Phylogeny ,Genetics ,Genetic Variation ,Original Articles ,biology.organism_classification ,Heat-Shock Proteins, Small ,Protein Structure, Tertiary ,Divergent evolution ,Machilus ,Hydrophobic and Hydrophilic Interactions ,Sequence Alignment - Abstract
† Background and Aims Evolutionary and ecological roles of the chloroplast small heat shock protein (CPsHSP) have been emphasized based on variations in protein contents; however, DNA sequence variations related to the evolutionary and ecological roles of this gene have not been investigated. In the present study, a basal angiosperm, Machilus, together with the eudicot Rhododendron were used to illustrate the evolutionary dynamics of gene divergence in CPsHSPs. † Methods Degenerate primers were used to amplify CPsHSP-related sequences from 16 Rhododendron and eight Machilus species that occur in Taiwan. Manual DNA sequence alignment was carried out according to the deduced amino acid sequence alignment performed by CLUSTAL X. A neighbour-joining tree was generated in MEGA using conceptual translated amino acid sequences from consensus sequences of cloned CPsHSP genes from eight Machilus and 16 Rhododendron species as well as amino acid sequences of CPsHSPs from five monocots and seven other eudicots acquired from GenBank. CPsHSP amino acid sequences of Funaria hygrometrica were used as the outgroups. The aligned DNA and amino acid sequences were used to estimate several parameters of sequence divergence using the MEGA program. Separate Bayesian inference of DNA sequences of Rhododendron and Machilus species was analysed and the resulting gene trees were used for detection of putative positively selected amino acid sites by the Codeml program implemented in the PAML package. Mean hydrophobicity profile analysis was performed with representative amino acid sequences for both Rhododendron and Machilus species by the Bioedit program. The computer program SplitTester was used to examine whether CPsHSPs of Rhododendron lineages and duplicate copies of the Machilus CPsHSPs have evolved functional divergence based on the hydrophobicity distance matrix. † Key Results Only one copy of the CPsHSP was found in Rhododendron. However, a higher evolutionary rate of amino acid substitutions in the Hymenanthes lineage of Rhododendron was inferred. Two positively selected amino acid sites may have resulted in higher hydrophobicity in the region of the a-crystallin domain (ACD) of the CPsHSP. By contrast, the basal angiosperm, Machilus, possessed duplicate copies of the CPsHSP, which also differed in their evolutionary rates of amino acid substitutions. However, no apparent relationship of ecological relevance toward the positively selected amino acid sites was found in Machilus. † Conclusions Divergent evolution was found for both Rhododendron lineages and the paralogues of CPsHSP in Machilus that were directed to the shift in hydrophobicity in the ACD and/or methionine-rich region, which might have played important roles in molecular chaperone activity.
- Published
- 2007
22. Major chemotypes and antioxidative activity of the leaf essential oils of Cinnamomum osmophloeum Kaneh. from a clonal orchard
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Ming-Chih Shih, Kuan-Hung Lin, Kai Ts ung Yang, Shih Ying Hwang, Min Yi Lin, and Shu Yin Yeh
- Subjects
biology ,Chemotype ,DPPH ,Cinnamomum osmophloeum ,General Medicine ,biology.organism_classification ,Cinnamaldehyde ,Analytical Chemistry ,law.invention ,chemistry.chemical_compound ,chemistry ,Linalool ,law ,Botany ,Food science ,Essential oil ,Cinnamon Oil ,Food Science ,Cinnamomum - Abstract
Essential oils of 92 cutting clones from a clonal orchard of Cinnamomum osmophloeum Kaneh. were obtained by hydrodistillation and characterised by gas chromatography–mass spectrometry. Our results showed that the yields of essential oils ranged between 0.09% and 2.65% (vol/fresh wt). The constituents of essential oils varied among samples. The major chemotypes classified in the individual cutting clones were cinnamaldehyde (50 plants, representing 50–95% of the total volatiles), linalool (1 plant, 73.3%), β-cubebene (2 plants, 59.4% and 78.7%), and cinnamyl acetate (1 plant, 61.8%). The antioxidant activities of the four chemotypes were determined using a 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. The antioxidant activities of the essential oil decreased in the order of cinnamyl acetate > cinnamaldehyde > β-cubebene > linalool. Indigenous cinnamon oil extract showed a good free radical-scavenging capacity at all concentrations studied, except at 2 μg/ml. The scavenging activity increased with increasing concentration of the extract. The capability of the four essential oil chemotypes to reduce the stable radical, DPPH, to DPPH-H was assayed by a decrease in the IC50 values of 10.4 (cinnamyl acetate type) to 29.7 (linalool type) μg/ml. These results suggest that the leaf essential oil of C. osmophloeum possesses chemical compounds with antioxidant activity which can be used as natural preservatives in food and/or by the pharmaceutical industry. Trees in this plantation which can be used for further propagation for the production of chemotypes of interest were identified.
- Published
- 2007
23. Genetic relationships and ecological divergence in Salix species and populations in Taiwan
- Author
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Yu-Chung Chiang, Jeng Der Chung, Bing Hong Huang, Chung Te Chang, Chun Lin Huang, Jui Hung Chen, and Shih Ying Hwang
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education.field_of_study ,geography ,Willow ,geography.geographical_feature_category ,Ecology ,ved/biology ,Population ,ved/biology.organism_classification_rank.species ,Forestry ,Horticulture ,Biology ,biology.organism_classification ,Shrub ,Genetic divergence ,Genetic variation ,Genetics ,Species richness ,education ,Molecular Biology ,Local adaptation ,Riparian zone - Abstract
Linking ecology with evolutionary biology is important to understand how environments drive population and species divergence. Phenotypically diverse Salix species, such as lowland riparian willow trees and middle- to high-elevation multistemmed shrubs and alpine dwarf shrubs, provide opportunities for studying genetic divergence driven by ecological factors. We used amplified fragment length polymorphism (AFLP) to quantify the genetic variation of 185 individuals from nine populations of four Salix species in Taiwan. Our phylogenetic analyses distinguished two riparian species and the separation of riparian species from multistemmed and dwarf shrub species. Variance partitioning for the total data found that environment explained a substantially larger proportion of genetic variation than geography. However, no genetic variation was explained by geography alone when only compared within and between species. Spatially structured regional environmental effects explained more variation than pure environments in most comparisons within and between species, suggesting that unmeasured environmental variables and/or past demographic histories played important roles in shaping population and species divergence. Based on forward selection analysis, annual mean temperature, aspect, and fraction of absorbed photosynthetically active radiation were the most influential ecological factors in shaping genetic variation within and between species. Nevertheless, different combinations of environmental variables correlated significantly with genetic variation within and between species. We identified eight AFLP loci that potentially evolved under selection intraspecifically using different outlier detection methods. These loci correlated with more than one environmental variable, suggesting local adaptation along environmental gradients at the population level.
- Published
- 2015
24. Partial Concordance between Nuclear and Organelle DNA in Revealing the Genetic Divergence amongQuercus glauca(Fagaceae) Populations in Taiwan
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F. L. Shih, Tsan-Piao Lin, Yu-Che Cheng, and Shih Ying Hwang
- Subjects
education.field_of_study ,Mitochondrial DNA ,Nuclear gene ,biology ,Population ,Haplotype ,Plant Science ,biology.organism_classification ,Quercus glauca ,Fagaceae ,Genetic divergence ,Phylogeography ,Botany ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Quercus glauca (Thunb. ex Murray) Oerst (Fagaceae) has a wide distributional range in Taiwan. In this study, the evolutionary history and the most genetically divergent sites of Q. glauca were studied using a nuclear gene marker, glyceraldehyde‐3‐phosphate dehydrogenase. Also, the consistency of the results obtained from nuclear gene and cytoplasmic loci was investigated. Using a genealogical approach (TCS software), we determined haplotypes and their relationships to one another. We used the level of divergence for each population from the remaining populations (calculated as mean values of pairwise population differentiation, FST, for each population) to locate the most genetically divergent areas in Taiwan. According to the average FST of each population in comparison with the remaining ones, a peak was found in the northern part of central Taiwan, and another was found in the southeastern region. The peak profiles of the mean FST values for all three DNA data sets (nDNA, cpDNA, and mtDNA) showed simil...
- Published
- 2006
25. Allozyme Variation of Populations of Castanopsis carlesii (Fagaceae) Revealing the Diversity Centres and Areas of the Greatest Divergence in Taiwan
- Author
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Yu Pin Cheng, Shih Ying Hwang, Tsan-Piao Lin, and Wen Liang Chiou
- Subjects
Electrophoresis ,Genetic diversity ,education.field_of_study ,Ecology ,Population ,DNA, Chloroplast ,Taiwan ,Genetic Variation ,Locus (genetics) ,Original Articles ,Plant Science ,Biology ,Fagaceae ,Enzymes ,Plant Leaves ,Genetic divergence ,Gene Frequency ,Evolutionary biology ,Genetic variation ,Species richness ,Allele ,education ,Allele frequency - Abstract
Background and Aims The genetic variation and divergence estimated by allozyme analysis were used to reveal the evolutionary history of Castanopsis carlesii in Taiwan. Two major questions were discussed concerning evolutionary issues: where are the diversity centres, and where are the most genetically divergent sites in Taiwan? Methods Twenty-two populations of C. carlesii were sampled throughout Taiwan. Starch gel electrophoresis was used to assay allozyme variation. Genetic parameters and mean FST values of each population were analysed using the BIOSYS-2 program. Mean FST values of each population against the remaining populations, considered as genetic divergence, were estimated using the FSTAT program. Key Results Average values of genetic parameters describing the within-population variation, the average number of alleles per locus (A = 25), the effective number of alleles per locus (Ae = 138), the allelic richness (Ar = 238), the percentage of polymorphic loci (P = 69%), and the expected heterozygosity (He = 0270) were estimated. High levels of genetic diversity were found for C. carlesii compared with other local plant species. Genetic differentiation between populations was generally low. Conclusions From the data of expected heterozygosity, one major diversity centre was situated in central Taiwan corroborating previous reports for other plant species. According to the mean FST value of each population, the most divergent populations were situated in two places. One includes populations located in north central Taiwan between 2480N and 2420N. The other is located in south-eastern Taiwan between 2240N and 2310N. These two regions are approximately convergent with the most divergent locations determined for several other plant species using chloroplast DNA markers published previously. An important finding obtained from this study is that unordered markers like allozymes can be used to infer past population histories as well as chloroplast DNA markers do.
- Published
- 2006
26. Influences of environmental and spatial factors on genetic and epigenetic variations in Rhododendron oldhamii (Ericaceae)
- Author
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Shih Ying Hwang, Chun Lin Huang, Jeng Der Chung, Jui Hung Chen, Ming Hsuan Tsang, and Chung Te Chang
- Subjects
Habitat fragmentation ,Range (biology) ,Ecology ,Forestry ,Horticulture ,Biology ,Habitat ,Genetic variation ,Genetics ,Biological dispersal ,Amplified fragment length polymorphism ,Molecular Biology ,Selection (genetic algorithm) ,Local adaptation - Abstract
Test of the relationship of genetic and particularly epigenetic variation with geographic isolation and environment is important to reveal potential environmental drivers for selection. Rhododendron oldhamii is widespread but inhabits fragmented subtropical forest landscapes, and populations across its range may exhibit different levels of genetic and epigenetic structuring correlated to their environmental conditions. Here, we investigated the genetic and epigenetic variations and their ecological correlates in R. oldhamii. Genetic and epigenetic variations were surveyed using amplified fragment length polymorphism (AFLP) and methylation-sensitive amplification polymorphism (MSAP), respectively. Using variation partitioning by redundant analysis (RDA), we examined the pure and spatially structured environmental effects and pure spatial factors on genetic and epigenetic variations among individuals collected from 18 localities across R. oldhamii distribution range in Taiwan. We found that environments compared to geographic isolation among sites explained more genetic and epigenetic variations. Patchy distribution of the contemporary R. oldhamii populations was revealed by correlograms with patch size of approximately around 20–30 km based on the total genetic and epigenetic data. Spatial variables derived from the method of principal coordinates of neighbor matrices (PCNM), including PCNM3, PCNM5, PCNM7, and PCNM8 representing biotic processes, such as individual dispersal, were found to be important influencing potentially adaptive genetic and epigenetic variations. Annual mean temperature, annual precipitation, precipitation of the warmest quarter, aspect, slope, and soil moisture were the most important environmental variables influencing potentially adaptive genetic and epigenetic variations and could be particularly important for the evolution of local adaptation in R. oldhamii.
- Published
- 2014
27. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae)
- Author
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Yu Pin Cheng, Tsan-Piao Lin, and Shih Ying Hwang
- Subjects
education.field_of_study ,biology ,Ecology ,Range (biology) ,Population ,biology.organism_classification ,Quercus glauca ,Gene flow ,Nucleotide diversity ,Genetic divergence ,Phylogeography ,Refugium (population biology) ,Evolutionary biology ,Genetics ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
In this study, we examined spatial patterns of chloroplast DNA (cpDNA) variation in a total of 30 populations of Castanopsis carlesii Hayata (Fagaceae), a subtropical and temperate tree species, including 201 individuals sampled throughout Taiwan. By sequencing two cpDNA fragments using universal primers (the trnL intron and the trnV-trnM intergenic spacer), we found a total of 1663 bp and 21 polymorphic sites. These gave rise to a total of 28 cpDNA haplotypes. The level of differentiation among the populations studied was relatively high (GST = 0.723). Two ancestral haplotypes are widely distributed. The Central Mountain Ridge (CMR) of Taiwan represents an insurmountable barrier to the east-west gene flow of C. carlesii. Among the populations studied, three separated populations, at Lienhuachih, Fushan and Lichia, have high nucleotide diversity. Estimates of NST-GST for populations on both sides of the CMR indicate that no phylogeographical structure exists. According to the genealogical tree, number of rare haplotype and population genetic divergence, this study suggests that two potential refugia existed during the last glaciation: the first refugium was located in a region to the north of Hsuehshan Range (HR) and west of the CMR; the second refugium was located in south, especially southeastern Taiwan. In fact, the second refugium happens to be the same as that reported for Quercus glauca. A 'star-like' genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test and mismatch distribution also suggest demographic expansion recovering from a bottleneck.
- Published
- 2005
28. Genetic diversity and biogeography of Cunninghamia konishii (Cupressaceae), an island species in Taiwan: a comparison with Cunninghamia lanceolata, a mainland species in China
- Author
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Y.C. Tan, Jeng Der Chung, Tsan-Piao Lin, Shih Ying Hwang, and Min Yi Lin
- Subjects
Genetic diversity ,education.field_of_study ,Polymorphism, Genetic ,Time Factors ,Geography ,biology ,Population ,Genetic Variation ,Outcrossing ,Sequence Analysis, DNA ,biology.organism_classification ,Analysis of molecular variance ,Gene flow ,Plant Leaves ,Tracheophyta ,Species Specificity ,Genetic variation ,Botany ,Genetics ,Amplified fragment length polymorphism ,Cunninghamia ,education ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
Luanta-fir (Cunninghamia konishii), an endemic to Taiwan, is an outcrossing, long-lived conifer. Populations of C. konishii are generally fragmented due to a once high intensity of timber exploitation. C. konishii and Cunninghamia lanceolata are two sibling taxa constituting derivative-progenitor species relationship. The amount of genetic variations within and between 11 and 10 populations of C. konishii and C. lanceolata, respectively, were assessed using amplified fragment length polymorphism (AFLP) markers in this report. Three AFLP primer pairs generated a total of 357 and 226 markers for C. konishii and C. lanceolata samples, of which 56.1 and 65.3% are polymorphic, respectively. Analysis of molecular variance indicates a 4.78% variation between C. konishii and C. lanceolata. A relatively high value of genetic variation (24.60%) was apportioned between the populations of C. konishii. In contrast, a lower divergence value (12.21%) between populations was found for C. lanceolata. The population with the highest genetic diversity was found in Nantou County, which concurred with the results of many other tree species investigated in Taiwan. The estimates of the number of migrants between populations (Nm), obtained from population pair-wise ΦST, suggest that gene flow in C. konishii is efficient in some adjacent populations but is restricted in the rest. Individual UPGMA tree, generated based on AFLP markers, suggests six evolutionary lineages for C. konishii. All evolutionary lineages of C. konishii were derived from C. lanceolata. In conclusion, the migration patterns of Cunninghamia from mainland China may have been established following multiple sources, migrant-pools, long-distance dispersal events, and via different directions.
- Published
- 2004
29. Phylogeography of Trochodendron aralioides (Trochodendraceae) in Taiwan and its adjacent areas
- Author
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Tsan-Piao Lin, Jenn Che Wang, Shing Fan Huang, and Shih Ying Hwang
- Subjects
Genetic diversity ,education.field_of_study ,Ecology ,Population ,Population genetics ,Trochodendraceae ,Biology ,biology.organism_classification ,Phylogeography ,Refugium (population biology) ,Trochodendron aralioides ,Evolutionary biology ,Genetic structure ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Aim This paper described current phylogeographical patterns of chloroplastic DNA variation of Trochodendron aralioides, a temperate tree species, and inferred its possible refugium in Taiwan. This information was compared with the known phylogeographical pattern of subtropical tree species. Location A total of 24 populations were sampled including 20 from Taiwan, two each from the Ryukyus and Japan. Methods A haplotype network was constructed by computer program TCS, various parameters of genetic diversity were calculated and neutrality was tested by computer program DnaSP. To examine the similarity of genetic structure among populations, a maximum parsimony tree was reconstructed by computer program PAUP*. The results of isozyme of T. aralioides from a previous publication were incorporated into this study to infer the phylogeographical history. Results Nine haplotypes according to six substitutions, two indels and one inversion of the two cpDNA intergenic spacer fragments (petG-trnP and petA-psbJ) of T. aralioides were recognized. Genetic structure of the population of Japan is totally different from those of Taiwan and the Ryukyus. In Taiwan, the genetic structure was differentiated among populations revealed by Gst = 0.700 and Nst = 0.542, and the population genetics was clearly spatially structured. Two population groups were recognized. The first group was distributed islandwide and extended to the Ryukyus. The second group contained five of the seven known haplotypes, and was restricted to the area between latitude 24°46′ and 24°06′ N. Conclusions In Taiwan, north-central area between latitude 24°46′ and 24°06′ N is potentially a refugium during the last glaciations. This finding is contradicted to subtropical species as Cyclobalanopsis glauca.
- Published
- 2004
30. Historical biogeography and phylogenetic relationships of the genus Chamaecyparis (Cupressaceae) inferred from chloroplast DNA polymorphism
- Author
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Tsan-Piao Lin, Shih Ying Hwang, W. P. Wang, and C. Y. Hwang
- Subjects
Divergent evolution ,Monophyly ,biology ,Phylogenetic tree ,Genus ,Biogeography ,Chamaecyparis ,Botany ,Disjunct distribution ,Plant Science ,Disjunct ,biology.organism_classification ,Ecology, Evolution, Behavior and Systematics - Abstract
The genus Chamaecyparis comprises five species and one variety native to Taiwan, Japan, Canada, and USA, which demonstrates a classical eastern Asian, western North American, and eastern North American disjunct distributional pattern. The phylogenetic relationships of the species of Chamaecyparis were inferred by comparing 1130 bp of the combined data set of chloroplast trnV intron and petG-trnP intergenic spacer. The phylogenetic tree shows that Chamaecyparis nootkatensis (Cupressus nootkatensis or Xanthocyparis nootkatensis) is clearly diverged from other Chamaecyparis species. For Chamaecyparis species, C. thyoides is sister to C. formosensis and C. pisifera and these together form a monophyletic group. C. lawsoniana is sister to C. obtusa and C. taiwanensis; and these form another monophyletic group. Homogeneity in evolutionary rates was found among species in these two monophyletic groups. Results indicate the divergent evolution of C. taiwanensis and C. formosensis and molecular evidence in this investigation supports C. taiwanensis as a variety of C. obtusa. Utility of cpDNA intergenic spacer petG-trnP in Chamaecyparis is also discussed. Several biogeographical implications were inferred: (1) at least two divergence events have produced the eastern Asian, and both western and eastern North American disjunct distribution in Chamaecyparis; (2) intercontinental sister species pairs are found in Chamaecyparis; (3) cpDNA divergence between two intercontinental sister pairs of C. thyoides and C. pisifera, and C. lawsoniana and C. obtusa is 2.8% and 1.1%, which suggest an estimated divergence time of 14 and 5.5 million years ago during middle and late Miocene, respectively; (4) cpDNA divergence of two Asian Chamaecyparis groups between C. obtusa and C. taiwanensis, and between C. pisifera and C. formosensis is 0.25% and 0.57%, which suggest an estimated divergence time of 1.3 and 2.9 million years ago during Pleistocene and late Pliocene, respectively; these estimated divergence times suggest a relatively recent migration of Chamaecyparis to Taiwan from the Japanese Archipelago; (5) that climatic deterioration caused the disappearance of Chamaecyparis in continental Asia is probable.
- Published
- 2003
31. Application of simple sequence repeats in determining the genetic relationships of cultivars used in sweet potato polycross breeding in Taiwan
- Author
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Hsiao F. Lo, Shih Ying Hwang, and Yu T. Tseng
- Subjects
Genetics ,Genetic diversity ,Genetic distance ,Genetic marker ,Genetic variation ,Genotype ,UPGMA ,food and beverages ,Microsatellite ,Locus (genetics) ,Horticulture ,Biology - Abstract
Simple sequence repeats (SSRs) were used to analyze the genetic diversity and genetic relationships among sweet potato [ lpomoea batatas (L.) Lam.] cultivars. These cultivars consisted of Chinese and Japanese materials, landraces as well as cultivars derived either from hybrid or polycross breeding in Taiwan. SSR analysis from eight primer pairs revealed a total of 20 alleles of which 17 were polymorphic (85.0% polymorphism). An average of 2.5 alleles were obtained per SSR primer pair. On average 2.1 alleles per polymorphic SSR locus were amplified. The construction of genetic relationships using unweighted pair group method with arithmetic mean (UPGMA) and principal coordinate analysis (PCA) demonstrated the capability of simple sequence repeats in sweet potato genotype identification and classification of genetic relationships. The UPGMA clustering and PCA revealed that polycross-derived cultivars possessed high levels of genetic diversity and originated from various genetic resources, and suggested the usefulness of polycross breeding strategy in spite of frequent cross-incompatibility. Moreover, high level of genetic variation in polycross breeding lines would assist in obtaining elite sweet potato materials in the future. In addition, most landraces were distantly related to the Chinese and Japanese materials and probably originated from Java and Brahman.
- Published
- 2002
32. [Untitled]
- Author
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Hsiao-Feng Lo, Ruey Houng Chern, Liang Li, Hui Wen Lin, and Shih Ying Hwang
- Subjects
chemistry.chemical_classification ,Reactive oxygen species ,Antioxidant ,biology ,Physiology ,medicine.medical_treatment ,fungi ,food and beverages ,Plant physiology ,Plant Science ,Superoxide dismutase ,Horticulture ,Agronomy ,chemistry ,Catalase ,biology.protein ,medicine ,Cultivar ,Agronomy and Crop Science ,Waterlogging (agriculture) ,Peroxidase - Abstract
We investigated the changes in antioxidative enzyme activities of two sweet potato cultivars under waterlogging and high-light conditions in the growth chamber. The activities of antioxidative enzymes were measured from leaf crude extract of sweet potato during the first five days of the treatments. Activities of superoxide dismutase and catalase were consistently increased in Taoyuan 1 sweet potato over time under waterlogging and high-light conditions. However, decreases in both superoxide dismutase and catalase activities were observed for cultivar Yongtsai under waterlogging and high-light conditions. Waterlogging, together with high-light intensity, impairs superoxide dismutase and catalase activities in the cultivar Yongtsai indicating its greater susceptibility to waterlogging and high-light stress. In contrast, the increase in activities of superoxide dismutase and catalase in Taoyuan 1 indicated its greater ability to detoxify reactive oxygen species during the treatment and ensured its reduced susceptibility to waterlogging and high-light stress. The activities of peroxidase may be inactivated by high-light treatment and, therefore, may not be associated with tolerance of sweet potato plants to waterlogging and high-light stress. Differences in susceptibility to waterlogging and high-light conditions in the leafy vegetable Yongtsai and storage root Taoyuan 1 are discussed.
- Published
- 1999
33. Uniform genetic diversity, low differentiation, and neutral evolution characterize contemporary refuge populations of Taiwan fir (Abies kawakamii, Pinaceae)
- Author
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Shih Ying Hwang, Pei-Fen Lee, Fu Lung Shih, Tsan-Piao Lin, and Yu Pin Cheng
- Subjects
education.field_of_study ,Genetic diversity ,biology ,Ecology ,Abies kawakamii ,Population ,Plant Science ,biology.organism_classification ,Genetic divergence ,Phylogeography ,Intergenic region ,Evolutionary biology ,Pinaceae ,Genetics ,education ,Neutral theory of molecular evolution ,Ecology, Evolution, Behavior and Systematics - Abstract
Based on fossil pollen, the distribution range of Taiwan fir [Abies kawakamii (Hay.) Ito] (Pinaceae) is smaller than it was 50 000 years ago. To characterize the present refuge populations of A. kawakamii, which survive only in subalpine forests in Taiwan, we surveyed nuclear genes and chloroplast intergenic spacers to assess the genetic diversity of Taiwan fir. Populations maintain high genetic diversity and contain similar numbers of haplotypes for the GapC (cytosolic glyceraldehyde 3-phosphate dehydrogenase) fragment. Haplotypes for GapC are generally widespread, and population-specific haplotypes accounted for 2.5% of the total. Differentiation among populations is very low (G(ST) = 0.01). Only three haplotypes were detected for the cpDNA marker, and every population had one or two haplotypes. In a neutrality test, the variation in nucleotides did not deviate from that expected with neutral evolution for either marker. A retreat route to higher elevations was not evident from either the GapC or cpDNA markers. Hsuehshan was the site of the most divergent population in Taiwan. We concluded that uniform genetic diversity, low differentiation, low numbers of population-specific haplotypes, and neutral evolution characterize contemporary refuge populations of Taiwan fir.
- Published
- 2011
34. Historical spatial range expansion and a very recent bottleneck of Cinnamomum kanehiraeHay. (Lauraceae) in Taiwan inferred from nuclear genes
- Author
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Chia Chia Lin, Pei Chun Liao, Dai Chang Kuo, Kuo Chieh Ho, Tsan-Piao Lin, and Shih Ying Hwang
- Subjects
Cell Nucleus ,Gene Flow ,Evolution ,Range (biology) ,Ecology ,Taiwan ,Genetic Variation ,Last Glacial Maximum ,Biology ,Gene flow ,Phylogeography ,Genetics, Population ,Effective population size ,Genetic distance ,Evolutionary biology ,Research article ,Genetic variation ,QH359-425 ,Glacial period ,Ecology, Evolution, Behavior and Systematics ,Cinnamomum - 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.
- Published
- 2010
35. Pre-treating paclobutrazol enhanced chilling tolerance of sweetpotato
- Author
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Fu Hsiang Pai, Hsiao-Feng Lo, Kuan-Hung Lin, and Shih Ying Hwang
- Subjects
Physiology ,Low molecular weight antioxidants ,Plant Science ,Grain filling ,Biology ,Paclobutrazol ,Zeatin riboside ,Fight-or-flight response ,chemistry.chemical_compound ,parasitic diseases ,Botany ,Abscisic acid ,Completely randomized design ,Panicle ,Source sink ,fungi ,food and beverages ,Plant physiology ,Factorial experiment ,Glutathione ,APX ,Horticulture ,Agronomy ,chemistry ,Gibberellin ,Sink (computing) ,Agronomy and Crop Science ,Hormone - Abstract
The difference among florets within a panicle in grain filling and four hormone contents was compared by using two rice varieties differing in panicle type, i.e. compact-panicle variety Xiushui 994 and loose-panicle variety Xiushui 11. Meanwhile the effect of changing source (leaf cutting) and sink (floret removal) on grain filling and four hormone (indole-3-acetic acid, gibberellin, zeatin riboside and abscisic acid)level dynamics in developing grains was also examined. The results showed that Xiushui 994 had greater variation in grain filling rate (GFR), grain weight, filled grain percent (FGP) and four hormone contents during grain filling than Xiushui 11. Moreover, the former variety also showed the greater difference in the time of having the highest hormone contents between superior and inferior florets. The change in source and sink size had great effect on grain filling process and dynamics of four hormone contents, and the extent of the effect varied with variety and floret type. For Xiushui 994, floret-removal treatment had little effect on grain weight and FGP of the superior florets, but caused a marked decrease in GFR and four hormone contents, and a delay in the time when the highest GFR and hormone contents occurred. In the source-reducing treatment, GFR, grain weight and FGP for both superior and interior florets were all decreased. For Xiushui 11, both treatments had little effect on grain development in terms of grain filling properties and hormone content change in the two types of florets. The results indicated that the grain filling of compact-panicle variety is more source-limited than that of loose-panicle one, and relative level of hormone in both superior and inferior florets determined development of inferior florets.
- Published
- 2006
36. Source populations of Quercus glauca in the last glacial age in Taiwan revealed by nuclear microsatellite markers
- Author
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Tsan-Piao Lin, Yuan Jr Lee, Kuo Chieh Ho, and Shih Ying Hwang
- Subjects
Cell Nucleus ,Genetic Markers ,education.field_of_study ,Base Sequence ,Ecology ,Population ,Taiwan ,Zoology ,Biology ,biology.organism_classification ,Quercus glauca ,Quercus ,Refugium (population biology) ,Chloroplast DNA ,Genetics ,Microsatellite ,Colonization ,Glacial period ,education ,Molecular Biology ,Genetics (clinical) ,Biotechnology ,Isolation by distance ,DNA Primers ,Microsatellite Repeats - Abstract
In this work, we attempted to study genetic differentiation between populations of Quercus glauca in Taiwan using nuclear microsatellite markers to infer the potential refugium in the last glaciation stage. Four microsatellite loci for 20 individuals each in 10 populations of Taiwan were analyzed. We found that Q. glauca has relatively high within-population diversity (H(E) = 0.741) and low population differentiation (F(ST) = 0.042) but shows isolation by distance. The most divergent populations, according to the average F(ST) for individual populations in comparison with every other population, were found in populations Cy, Sa, and Hy in southern Taiwan and Pa in north-central Taiwan. Moreover, populations Cy, Sa, and Pa were recognized as being the source populations for gene recolonization after the last glaciation stage. In addition, the three sites of Wu, Ym, and Cy exhibited the highest gene diversities that coincided with populations with the highest chloroplast DNA variations. This may have resulted from an admixture of colonization routes. In conclusion, observations of the most divergent populations and source populations suggest that southern and probably north-central Taiwan may have potentially been refugia for Q. glauca in the last glaciation. This agrees with the possible refugium in southern Taiwan revealed by a previous study using chloroplast DNA markers.
- Published
- 2006
37. Phylogeographic study reveals the origin and evolutionary history of a Rhododendron species complex in Taiwan
- Author
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Yu Pin Cheng, Tsan-Piao Lin, Jeng Der Chung, Yu Ling Chen, and Shih Ying Hwang
- Subjects
Species complex ,Population fragmentation ,Rhododendron ,Population ,Molecular Sequence Data ,Taiwan ,Biology ,Analysis of molecular variance ,Gene flow ,Evolution, Molecular ,Botany ,Genetics ,education ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Rhododendron hyperythrum ,education.field_of_study ,Geography ,DNA, Chloroplast ,Genetic Variation ,Sequence Analysis, DNA ,Genetic divergence ,Chloroplast DNA ,Haplotypes ,Evolutionary biology - Abstract
This study infers a single origin and a once-widespread distribution of the Rhododendron pseudochrysanthum species complex in Taiwan based on chloroplast DNA (cpDNA) variation. In total, 124 individuals from five endemic Rhododendron species were used for amplifications of two chloroplast intergenic spacers: trnL-trnF and atpB-rbcL. The haplotype and nucleotide diversities were much lower for the R. pseudochrysanthum complex, comprised of the species R. pseudochrysanthum, R. morii, Rhododendron rubropunctatum, and Rhododendron hyperythrum, than for Rhododendron formosanum. Two measures of pairwise population differentiation, N(ST) and F(ST), consistently revealed mostly non-significant levels of genetic divergence between populations of the R. pseudochrysanthum complex. No genetic difference was found among the four species of the R. pseudochrysanthum complex by analysis of molecular variance (AMOVA), which is concordant with the parsimonious topology of cpDNA haplotypes for the complex. Nested clade analysis (NCA) of the cpDNA haplotypes indicated that restricted gene flow with isolation-by-distance characterized the recolonization pattern of the R. pseudochrysanthum complex. In contrast, the NCA analysis indicated a contiguous range expansion for cpDNA haplotypes of R. formosanum. This research suggests a once-widespread distribution of the R. pseudochrysanthum complex probably via north-to-south colonization of mid-elevations during low-temperature periods of the Pleistocene. Population fragmentation followed the warmer climate which began in the Holocene and resulted in the present-day range contraction into high elevations.
- Published
- 2005
38. Potential refugia in Taiwan revealed by the phylogeographical study of Castanopsis carlesii Hayata (Fagaceae)
- Author
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Yu-Pin, Cheng, Shih-Ying, Hwang, and Tsan-Piao, Lin
- Subjects
Base Sequence ,Geography ,Molecular Sequence Data ,Population Dynamics ,DNA, Chloroplast ,Taiwan ,Genetic Variation ,Sequence Analysis, DNA ,Environment ,Fagaceae ,Genetics, Population ,Haplotypes ,Cluster Analysis ,Sequence Alignment ,Phylogeny ,DNA Primers - Abstract
In this study, we examined spatial patterns of chloroplast DNA (cpDNA) variation in a total of 30 populations of Castanopsis carlesii Hayata (Fagaceae), a subtropical and temperate tree species, including 201 individuals sampled throughout Taiwan. By sequencing two cpDNA fragments using universal primers (the trnL intron and the trnV-trnM intergenic spacer), we found a total of 1663 bp and 21 polymorphic sites. These gave rise to a total of 28 cpDNA haplotypes. The level of differentiation among the populations studied was relatively high (GST = 0.723). Two ancestral haplotypes are widely distributed. The Central Mountain Ridge (CMR) of Taiwan represents an insurmountable barrier to the east-west gene flow of C. carlesii. Among the populations studied, three separated populations, at Lienhuachih, Fushan and Lichia, have high nucleotide diversity. Estimates of NST-GST for populations on both sides of the CMR indicate that no phylogeographical structure exists. According to the genealogical tree, number of rare haplotype and population genetic divergence, this study suggests that two potential refugia existed during the last glaciation: the first refugium was located in a region to the north of Hsuehshan Range (HR) and west of the CMR; the second refugium was located in south, especially southeastern Taiwan. In fact, the second refugium happens to be the same as that reported for Quercus glauca. A 'star-like' genealogy is characteristic when all haplotypes rapidly coalesce and is a general outcome of population expansion. The neutrality test and mismatch distribution also suggest demographic expansion recovering from a bottleneck.
- Published
- 2005
39. Postglacial population growth of Cunninghamia konishii (Cupressaceae) inferred from phylogeographical and mismatch analysis of chloroplast DNA variation
- Author
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Chung Ling Lin, Tsan-Piao Lin, Chiu Shun Ma, Shih Ying Hwang, Jenq Chuan Yang, and Jeng Der Chung
- Subjects
Demographic history ,Climate ,Population ,Population Dynamics ,Taiwan ,Nucleotide diversity ,Intergenic region ,Genetic variation ,Botany ,Genetics ,Cunninghamia ,education ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,education.field_of_study ,biology ,Geography ,Haplotype ,DNA, Chloroplast ,Cupressaceae ,Genetic Variation ,Sequence Analysis, DNA ,biology.organism_classification ,Chloroplast DNA ,Haplotypes ,Evolutionary biology - Abstract
Phylogeographical and mismatch analysis of chloroplast DNA (cpDNA) variation were used to infer the temporal dynamics of distributional and demographic history of Taiwan fir (Cunninghamia konishii). We examined 64 and 52 trees from 17 populations of C. konishii and 14 provenances of C. lanceolata, respectively, by sequencing three intergenic spacers and one intron using cpDNA universal primers. Of the aligned 1888 base pairs (bp) sequence, 30 varied among 28 haplotypes, which consisted of three transitions, 14 transversions and 13 indels. One ancestral haplotype was found in 86 individuals across the surveyed range of both species, C. konishii and C. lanceolata, which was distributed in all populations and provenances. The 28 haplotypes also included 15 C. konishii specific and 12 C. lanceolata-specific haplotypes. Ancestral haplotype was found fixed in five populations of C. konishii and five provenances of C. lanceolata. Other haplotypes occurred mainly as singletons. The levels of population differentiation studied are relatively low in both Cunninghamia species. The nucleotide diversity (theta) of chloroplast DNA sequences within C. konishii was slightly higher than that of C. lanceolata. Excess in singletons as well as star-like phylogeny of haplotypes suggested no clearcut migration patterns of C. konishii after glacial maximum. One probable demographic history of C. konishii is the postglacial population growth of C. konishii after a glacial bottleneck event. This inference is supported by the combined results of fossil pollen record, low nucleotide diversity, significant Tajima's d-value, phylogeographical analysis and unimodal mismatch distribution. Similarities and discrepancies between our results and those of Lu et al. (2001) are discussed.
- Published
- 2003
40. Evidence for the existence of some dissociation in an otherwise strong linkage disequilibrium between mitochondrial and chloroplastic genomes in Cyclobalanopsis glauca
- Author
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Shih Ying Hwang, S. S.F. Huang, Tsan-Piao Lin, and W. J. Chuang
- Subjects
Genetics ,Mitochondrial DNA ,Mutation rate ,education.field_of_study ,Linkage disequilibrium ,Polymorphism, Genetic ,Geography ,Population ,Intron ,DNA, Chloroplast ,Taiwan ,Sequence Analysis, DNA ,Biology ,Fagaceae ,Genome ,DNA, Mitochondrial ,Linkage Disequilibrium ,Evolution, Molecular ,Genetics, Population ,Genetic marker ,education ,Gene ,Ecology, Evolution, Behavior and Systematics ,Phylogeny - Abstract
Variations in mitochondrial DNA in Cyclobalanopsis glauca (Thunb. ex Murray) Oerst. were studied in 140 trees from 32 populations collected from within the tree's natural range. By sequencing two mitochondrial DNA intron fragments (nad4/3-nad4/4r and nad7/2-nad7/3r), we revealed a total of 1788 bp and five polymorphic sites which allowed us to distinguish six mitotypes. The mitochondrial DNA markers provided replicated data to support population phylogeographical scenarios suggested previously using chloroplastic DNA markers. The gene genealogical tree of mitochondrial DNA was partially congruent with the chloroplastic DNA tree owing to the slower mutation rate and different mutational direction. Significant linkage disequilibrium existed between the two organellar genomes. Further paring analyses between fragments synthesized using different primers, accompanied by exclusion of polymorphic sites, showed that the random association could be attributed specifically to one of the polymorphic sites of the petG-trnP fragment of the chloroplastic genome, and the three polymorphic sites of the nad4/3-nad4/4r fragment of the mitochondrial genome. The former was inferred to derive from paternal leakage, and the latter from recurrent mutation. These polymorphic sites were also responsible for uncoupling of the combined gene tree of mitotype and chlorotype. In conclusion, specific fragments found in this study contribute to the incomplete congruence of the two organellar lineages that otherwise associate well phylogeographically.
- Published
- 2003
41. Spatial pattern of chloroplast DNA variation of Cyclobalanopsis glauca in Taiwan and East Asia
- Author
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Sophie S F, Huang, Shih-Ying, Hwang, and Tsan-Piao, Lin
- Subjects
Genetics, Population ,Haplotypes ,Asia, Eastern ,Molecular Sequence Data ,DNA, Chloroplast ,Taiwan ,Genetic Variation ,Sequence Analysis, DNA ,Fagaceae - Abstract
This study examined the spatial pattern of chloroplast DNA (cpDNA) variation in Cyclobalanopsis glauca (Thunb. ex Murray) Oerst. (Fagaceae) in 140 trees from Taiwan (25 populations), Japan (three), Ryukyus (two), Hong Kong (one) and Mainland China (one). By sequencing three cpDNA intergenic spacer fragments using universal primers (trnT-trnL, trnV-trnM, including the trnV intron, and petG-trnP), we found a total of 1,980 bp and 15 polymorphic sites. Among them, 12 sites were caused by point mutation, and three resulted from insertion. This gives rise to a total of 13 cpDNA haplotypes. The level of differentiation among the populations studied is relatively high (GST = 0.612). Two ancestral haplotypes (A and B) are distributed widely in East Asia. Interestingly, all the derived cpDNA variations are found only in Taiwan but not in other areas. The Central Mountain Ridge (CMR) of Taiwan creates an unsurpassed barrier to the east-west gene flow of C. glauca. Among the populations on the west of CMR, only three separated populations, Yangmingshan, Wushe and Chinshuiying, have high haplotype diversity, each consisting of sister haplotypes all mutated from the same ancestral haplotype. Thus, they have probably originated from de novo mutation after the last glaciation. This inference agrees with the observation that no spatial autocorrelation existed on the west side. Two unrelated dominant lineages on the east of the CMR (haplotypes D and F) showed significant spatial genetic structure. Estimate of NST - GST was -0.090 and differed significantly from zero. Thus at the local scale, the phylogeographical component of the genetic structure is significant on the east of the CMR. Accompanied by published palynological records of the last glaciation, this study suggests the possibility that these two types were colonized northward from the southeastern part of Taiwan. 'Star-like' genealogy is characterized, with all the haplotypes coalescing rapidly and as a general outcome of population expansion (PageHolmes 1998). A neutrality test also suggested a demographic expansion recovered from a bottleneck. We therefore inferred that the southeastern part of Taiwan might be a potential refugium for C. glauca.
- Published
- 2002
42. Contrasting demographic patterns of Ceriops tagal (Rhizophoraceae) populations in the South China Sea
- Author
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Pei Chun Liao, Shih Ying Hwang, Shong Huang, Yu-Chung Chiang, and Jenn Che Wang
- Subjects
education.field_of_study ,Ecology ,Demographic history ,Population ,Plant Science ,Biology ,biology.organism_classification ,Phylogeography ,Propagule ,Ceriops tagal ,Botany ,Biological dispersal ,Ceriops ,Mangrove ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Demographic history and dispersal ability are significant factors in determining the genetic composition of a population. In this study, we examined the phylogeographic patterns of Ceriops tagal from the Hainan Island and the Gulf of Thailand in the South China Sea, where there are abundant mangrove species. Nucleotide variations in two chloroplast DNA spacers were compared with trace Ceriops propagule dispersal routes and demographic history. An analysis of Templeton, Crandall and Sing’s (TCS) parsimonious networks and population demographics suggests that the Ceriops population gradually expanded from the northern parts of the South China Sea to the south-western populations in the Gulf of Thailand. Such phylogeographic inferences reflect a postglacial southward shift in the mangrove genetic diversity centre and a connection between the demographic dynamics and the coastal range expansion caused by the sea-level rise in the Pleistocene. Therefore, the phylogeographic pattern and historical demography of mangrove species were affected by glaciations during the Pleistocene such as temperate biota.
- Published
- 2011
43. Abscisic Acid induces anaerobiosis tolerance in corn
- Author
-
Shih Ying Hwang and Tara T. Vantoai
- Subjects
chemistry.chemical_classification ,biology ,Physiology ,fungi ,food and beverages ,Plant Science ,Cycloheximide ,biology.organism_classification ,Anoxic waters ,Enzyme assay ,chemistry.chemical_compound ,Horticulture ,Enzyme ,chemistry ,Seedling ,Botany ,Genetics ,biology.protein ,Environmental and Stress Physiology ,Poaceae ,Abscisic acid ,Alcohol dehydrogenase - Abstract
Flooding is a frequently occurring environmental stress that can severely affect plant growth. This study shows that treatment of corn (Zea mays L.) seedlings with abscisic acid (ABA) increases their tolerance to anoxia 10-fold over untreated seedlings and twofold over seedlings treated with water. Corn seedlings stressed anoxically for 1 day showed only 8% survival when planted in vermiculite. Pretreatment of root tips with 100 micromolar ABA or water for 24 hours before the 1 day anoxic stress increased the anoxic survivability of seedlings to 87% and 47%, respectively. Cycloheximide (5 milligrams per liter), added together with ABA, reduced the seedling survival rate, indicating that the induction of anoxic tolerance in corn by ABA was partly a result of the synthesis of new proteins. ABA treatment induced a threefold increase in alcohol dehydrogenase enzyme activity in corn roots. However, after 24 h of anoxia, alcohol dehydrogenase enzyme activity between the ABA-pretreated and non-pretreated corn roots was not significantly different. The results indicated that ABA played an important role in inducing anoxic tolerance in corn and that the induced tolerance was probably mediated by an increase in alcohol dehydrogenase enzyme activity before the anoxic stress.
- Published
- 1991
44. Molecular population genetics and gene expression analysis of duplicated CBF genes of Arabidopsis thaliana
- Author
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Chun Lin Huang, Yu-Chung Chiang, Chun-Neng Wang, Yen-Heng Lin, Shih Ying Hwang, Po Yen Hsu, and Tsan-Piao Lin
- Subjects
Transcriptional Activation ,Transcription, Genetic ,Molecular Sequence Data ,Population ,Arabidopsis ,Plant Science ,Gene Knockout Techniques ,Gene Expression Regulation, Plant ,Genes, Duplicate ,lcsh:Botany ,Gene expression ,Gene duplication ,Arabidopsis thaliana ,Amino Acid Sequence ,Selection, Genetic ,Promoter Regions, Genetic ,education ,Gene ,Phylogeny ,Genetics ,Regulation of gene expression ,education.field_of_study ,Polymorphism, Genetic ,biology ,Arabidopsis Proteins ,Promoter ,Sequence Analysis, DNA ,biology.organism_classification ,Protein Structure, Tertiary ,lcsh:QK1-989 ,Genetics, Population ,Gene Knockdown Techniques ,Trans-Activators ,Genome, Plant ,Research Article ,Transcription Factors - Abstract
Background CBF/DREB duplicate genes are widely distributed in higher plants and encode transcriptional factors, or CBFs, which bind a DNA regulatory element and impart responsiveness to low temperatures and dehydration. Results We explored patterns of genetic variations of CBF1, -2, and -3 from 34 accessions of Arabidopsis thaliana. Molecular population genetic analyses of these genes indicated that CBF2 has much reduced nucleotide diversity in the transcriptional unit and promoter, suggesting that CBF2 has been subjected to a recent adaptive sweep, which agrees with reports of a regulatory protein of CBF2. Investigating the ratios of Ka/Ks between all paired CBF paralogus genes, high conservation of the AP2 domain was observed, and the major divergence of proteins was the result of relaxation in two regions within the transcriptional activation domain which was under positive selection after CBF duplication. With respect to the level of CBF gene expression, several mutated nucleotides in the promoters of CBF3 and -1 of specific ecotypes might be responsible for its consistently low expression. Conclusion We concluded from our data that important evolutionary changes in CBF1, -2, and -3 may have primarily occurred at the level of gene regulation as well as in protein function.
- Published
- 2008
45. The selective allelopathic interaction of a pasture-forest intercropping in Taiwan
- Author
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Fu Hsing Hsu, Nien June Chung, Chang-Hung Chou, Yeong Chyn Wang, Shih Ying Hwang, and Ching-I Peng
- Subjects
biology ,Stolon ,Pennisetum clandestinum ,Soil Science ,Intercropping ,Plant Science ,biology.organism_classification ,Weed control ,Agronomy ,Botany ,Litter ,Phytotoxicity ,Cunninghamia ,Allelopathy - Abstract
An allelopathic interaction of a pasture-forest intercropping system was evaluated by experiments conducted in field and by laboratory assays. A study site was situated in the farm of Hoshe Forestry Experiment Station at Nantou County, Taiwan. After deforestation of Chinese fir (Cunninghamia lanceolata), a split plot design of 4 treatments, namely litter removed, litter removed and kikuyu grass (Pennisetum clandestinum) planted, litter left, and litter left and grass planted, was composed. Field meaurements showed that the fir litter left on the ground did not significantly inhibit the growth of weeds, kikuyu grass, and fir seedlings in the first four months following deforestation, while kikuyu grass significantly suppressed the growth of weeds longer than four months but did not reduce growth of fir seedlings. The aqueous extracts of fresh fir leaves, fir litter, and kikuyu leaves were bioassayed by using lettuce and rice seeds and stolon cuttings ofBrachiaria mutica. Bioassays showed that fresh fir leaves produced significant phytotoxicity while fir litter and kikuyu grass gave limited toxicity. Nine phytotoxic phenolics and many unidentified flavonoids were found in the leaf and litter of Chinese fir and kikuyu leaves. A good correlation between the degree of phytotoxicity and phytotoxins was obtained, indicating an allelopathy was involved. This finding suggests that allelopathy may contribute benefits in the intercropping system to reduce the need for herbicides and to lessen the labor cost for weed control.
- Published
- 1987
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