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Yu-chung Chiang - One of the best experts on this subject based on the ideXlab platform.
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phylogeny of the gymnosperm genus Cycas l cycadaceae as inferred from plastid and nuclear loci based on a large scale sampling evolutionary relationships and taxonomical implications
Molecular Phylogenetics and Evolution, 2018Co-Authors: Jian Liu, Yu-chung Chiang, Anders J Lindstrom, Shouzhou Zhang, Nathalie S Nagalingum, Xun GongAbstract:Abstract The gymnosperm genus Cycas is the sole member of Cycadaceae, and is the largest genus of extant cycads. There are about 115 accepted Cycas species mainly distributed in the paleotropics. Based on morphology, the genus has been divided into six sections and eight subsections, but this taxonomy has not yet been tested in a molecular phylogenetic framework. Although the monophyly of Cycas is broadly accepted, the intrageneric relationships inferred from previous molecular phylogenetic analyses are unclear due to insufficient sampling or uninformative DNA sequence data. In this study, we reconstructed a phylogeny of Cycas using four chloroplast intergenic spacers and seven low-copy nuclear genes and sampling 90% of extant Cycas species. The maximum likelihood and Bayesian inference phylogenies suggest: (1) matrices of either concatenated cpDNA markers or of concatenated nDNA lack sufficient informative sites to resolve the phylogeny alone, however, the phylogeny from the combined cpDNA-nDNA dataset suggests the genus can be roughly divided into 13 clades and six sections that are in agreement with the current classification of the genus; (2) although with partial support, a clade combining sections Panzhihuaenses + Asiorientales is resolved as the earliest diverging branch; (3) section Stangerioides is not monophyletic because the species resolve as a grade; (4) section Indosinenses is not monophyletic as it includes Cycas macrocarpa and C. pranburiensis from section Cycas; (5) section Cycas is the most derived group and its subgroups correspond with geography.
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Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach
MDPI AG, 2013Co-Authors: Shong Huang, Pei-chun Liao, Shih-jie Lai, Yu-ting Wan, Chun-wen Chang, Bing-hong Huang, Yu-chung ChiangAbstract:The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct
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Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach
2013Co-Authors: Yu-chung Chiang, Shong Huang, Shih-jie Lai, Yu-ting Wan, Chun-wen Chang, Bing-hong Huang, Pei-chun LiaoAbstract:Abstract: The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. ConsistentInt. J. Mol. Sci. 2013, 14 822
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microsatellite primers in the native perennial cycad Cycas taitungensis cycadaceae
American Journal of Botany, 2011Co-Authors: Chiachi Kuo, Xun Gong, Yishan Chao, Yupin Cheng, Yu-chung ChiangAbstract:Premise of the study: Microsatellite primers were developed for the native perennial cycad Cycas taitungensis to evaluate the genetic variation of this endangered insular species.
Shu Miaw Chaw - One of the best experts on this subject based on the ideXlab platform.
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chloroplast genome cpdna of Cycas taitungensis and 56 cp protein coding genes of gnetum parvifolium insights into cpdna evolution and phylogeny of extant seed plants
Molecular Biology and Evolution, 2007Co-Authors: Yanan Wang, Chungshien Wu, Shu Miaw ChawAbstract:: Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this long-standing debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with 2 typical large inverted repeats (IRs) of 25,074 bp each. We inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies, generated by the use of 3 independent methods, provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms. Within the modern gymnosperms are 2 highly supported sister clades: Cycas-Ginkgo and Gnetum-Pinus. This result agrees with both the "gnetifer" and "gnepines" hypotheses. The sister relationships in Cycas-Ginkgo and Gnetum-Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas-Ginkgo and Gnetum were consistently the shortest and the longest, respectively, in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the 3rd codon positions and the transversional sites of the first 2 codon positions. A PsitufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads, and Ginkgo. We demonstrate that the PsitufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 MYA, and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.
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chloroplast genome cpdna of Cycas taitungensis and 56 cp protein coding genes of gnetum parvifolium insights into cpdna evolution and phylogeny of extant seed plants
Molecular Biology and Evolution, 2007Co-Authors: Yanan Wang, Shumei Liu, Shu Miaw ChawAbstract:Phylogenetic relationships among the 5 groups of extant seed plants are presently unsettled. To reexamine this long-standing debate, we determine the complete chloroplast genome (cpDNA) of Cycas taitungensis and 56 protein-coding genes encoded in the cpDNA of Gnetum parvifolium. The cpDNA of Cycas is a circular molecule of 163,403 bp with 2 typical large inverted repeats (IRs) of 25,074 bp each. We inferred phylogenetic relationships among major seed plant lineages using concatenated 56 protein-coding genes in 37 land plants. Phylogenies, generated by the use of 3 independent methods, provide concordant and robust support for the monophylies of extant seed plants, gymnosperms, and angiosperms. Within the modern gymnosperms are 2 highly supported sister clades: Cycas-Ginkgo and Gnetum-Pinus. This result agrees with both the "gnetifer" and "gnepines" hypotheses. The sister relationships in Cycas-Ginkgo and Gnetum-Pinus clades are further reinforced by cpDNA structural evidence. Branch lengths of Cycas-Ginkgo and Gnetum were consistently the shortest and the longest, respectively, in all separate analyses. However, the Gnetum relative rate test revealed this tendency only for the 3rd codon positions and the transversional sites of the first 2 codon positions. A PsitufA located between psbE and petL genes is here first detected in Anthoceros (a hornwort), cycads, and Ginkgo. We demonstrate that the PsitufA is a footprint descended from the chloroplast tufA of green algae. The duplication of ycf2 genes and their shift into IRs should have taken place at least in the common ancestor of seed plants more than 300 MYA, and the tRNAPro-GGG gene was lost from the angiosperm lineage at least 150 MYA. Additionally, from cpDNA structural comparison, we propose an alternative model for the loss of large IR regions in black pine. More cpDNA data from non-Pinaceae conifers are necessary to justify whether the gnetifer or gnepines hypothesis is valid and to generate solid structural evidence for the monophyly of extant gymnosperms.
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a phylogeny of cycads cycadales inferred from chloroplast matk gene trnk intron and nuclear rdna its region
Molecular Phylogenetics and Evolution, 2005Co-Authors: Shu Miaw Chaw, Terrence W Walters, Chienchang Chang, Shinhsiao ChenAbstract:Phylogenetic relationships among the three families and 12 living genera of cycads were reconstructed by distance and parsimony criteria using three markers: the chloroplast matK gene, the chloroplast trnK intron and the nuclear ITS/5.8S rDNA sequence. All datasets indicate that Cycadaceae (including only the genus Cycas) is remotely related to other cycads, in which Dioon was resolved as the basal-most clade, followed by Bowenia and a clade containing the remaining nine genera. Encephalartos and Lepidozamia are closer to each other than to Macrozamia. The African genus Stangeria is embedded within the New World subfamily Zamiodeae. Therefore, Bowenia is an unlikely sister to Stangeria, contrary to the view that they form the Stangeriaceae. The generic status of DyeroCycas and Chigua is unsupportable as they are paraphyletic with Cycas and the Zamia, respectively. Nonsense mutations in the matK gene and indels in the other two datasets lend evidence to reinforce the above conclusions. According to the phylogenies, the past geography of the genera of cycads and the evolution of character states are hypothesized and discussed. Within the suborder Zamiieae, Stangeria, and the tribe Zamieae evolved significantly faster than other genera. The matK gene and ITS/5.8S region contain more useful information than the trnK intron in addressing phylogeny. Redelimitations of Zamiaceae, Stangeriaceae, subfamily Encephalartoideae and subtribe Macrozamiineae are necessary.
Mark W Duncan - One of the best experts on this subject based on the ideXlab platform.
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quantification of the neurotoxin 2 amino 3 methylamino propanoic acid bmaa in cycadales
Phytochemistry, 1992Co-Authors: Timothy S Charlton, Sanford P Markey, Ann M Marini, Knut Norstog, Mark W DuncanAbstract:Abstract Cycads have been recognized as toxic for many years and are known to cause hind limb ataxia in grazing animals. The l -isomer of 2-amino-3-(methylamino)propanoic acid (BMAA; β-methyldiaminopropanonic acid), a constituent of cycads, has recently been implicated in the onset of human neurologic disorders. We have used combined gas chromatography-mass spectrometry (GC-MS) to determine the BMAA content of the leaves ( n = 30) and female gametophyte ( n = 11) of a variety of cycads. A stable isotopomer of BMAA (i.e. [ 2 H 3 ] BMAA) was used as an internal standard to optimize specificity and precision. BMAA content is greater in members of the genus Cycas (i.e. up to 1800 μg g −1 fr. wt) whereas smaller amounts (i.e. −1 ) are present in members of the six other genera tested. Where BMAA content of both leaves and seeds was determined in the same species ( n = 4), values were comparable. Based on our results we estimate that grazing animals are exposed to exceedingly low doses of BMAA. These data would tend to exclude BMAA as the etiologic agent in hind limb ataxia in grazing animals.
Knut Norstog - One of the best experts on this subject based on the ideXlab platform.
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quantification of the neurotoxin 2 amino 3 methylamino propanoic acid bmaa in cycadales
Phytochemistry, 1992Co-Authors: Timothy S Charlton, Sanford P Markey, Ann M Marini, Knut Norstog, Mark W DuncanAbstract:Abstract Cycads have been recognized as toxic for many years and are known to cause hind limb ataxia in grazing animals. The l -isomer of 2-amino-3-(methylamino)propanoic acid (BMAA; β-methyldiaminopropanonic acid), a constituent of cycads, has recently been implicated in the onset of human neurologic disorders. We have used combined gas chromatography-mass spectrometry (GC-MS) to determine the BMAA content of the leaves ( n = 30) and female gametophyte ( n = 11) of a variety of cycads. A stable isotopomer of BMAA (i.e. [ 2 H 3 ] BMAA) was used as an internal standard to optimize specificity and precision. BMAA content is greater in members of the genus Cycas (i.e. up to 1800 μg g −1 fr. wt) whereas smaller amounts (i.e. −1 ) are present in members of the six other genera tested. Where BMAA content of both leaves and seeds was determined in the same species ( n = 4), values were comparable. Based on our results we estimate that grazing animals are exposed to exceedingly low doses of BMAA. These data would tend to exclude BMAA as the etiologic agent in hind limb ataxia in grazing animals.
Pei-chun Liao - One of the best experts on this subject based on the ideXlab platform.
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genetic evidence of the southward founder speciation of Cycas taitungensis from ancestral c revoluta along the ryukyu archipelagos
Conservation Genetics, 2019Co-Authors: Juitse Chang, Bing-hong Huang, Pei-chun LiaoAbstract:Cycas taitungensis and its sister species, C. revoluta (Cycas sect. Asiorientalis), are distributed peripatrically. Previous studies have revealed their phylogeographic pattern and, based on certain plastid DNA markers, have established that they diverged recently. However, the speciation process involving the genomic divergence has not been well clarified. In this study, based on their geographical distribution and estimates of their genetic diversity, two speciation models are proposed: (1) the founder and (2) the bottleneck speciation mode. Using approximate Bayesian computation (ABC) in combination with their estimated genetic diversity and population structure, we infer that the ancestral C. taitungensis populations diverged and southward colonized southeastern Taiwan from ancestral C. revoluta since the middle Pleistocene. These founders preserved ancestral polymorphism, resulting in small differences in genetic diversity and effective population size (Ne), despite a large difference in census population size (Nc) between two species. Based on this case of island cycad species offshore of continental Asia, this study provides new insight into how the speciation process influences the genetic diversity pattern of species with small Nc and Ne.
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Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach
MDPI AG, 2013Co-Authors: Shong Huang, Pei-chun Liao, Shih-jie Lai, Yu-ting Wan, Chun-wen Chang, Bing-hong Huang, Yu-chung ChiangAbstract:The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. Consistent results tested by all neutral loci, and the species-associated loci, specify the recent introgression from the paradox of sharing of ancestral polymorphisms. Phenomenon of introgression of cultivated cycads implies niche conservation among two geographic-isolated cycads, even though the habitats of the extant wild populations of two species are distinct
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Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach
2013Co-Authors: Yu-chung Chiang, Shong Huang, Shih-jie Lai, Yu-ting Wan, Chun-wen Chang, Bing-hong Huang, Pei-chun LiaoAbstract:Abstract: The Asian cycads are mostly allopatric, distributed in small population sizes. Hybridization between allopatric species provides clues in determining the mechanism of species divergence. Horticultural introduction provides the chance of interspecific gene flow between allopatric species. Two allopatrically eastern Asian Cycas sect. Asiorientales species, C. revoluta and C. taitungensis, which are widely distributed in Ryukyus and Fujian Province and endemic to Taiwan, respectively, were planted in eastern Taiwan for horticultural reason. Higher degrees of genetic admixture in cultivated samples than wild populations in both cycad species were detected based on multilocus scans by neutral AFLP markers. Furthermore, bidirectional but asymmetric introgression by horticultural introduction of C. revoluta is evidenced by the reanalyses of species associated loci, which are assumed to be diverged after species divergence. Partial loci introgressed from native cycad to the invaders were also detected at the loci of strong species association. ConsistentInt. J. Mol. Sci. 2013, 14 822
