75 results on '"Bing-Hong HUANG"'
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2. Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands
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Chih-Kai Yang, Yu-Chung Chiang, Bing-Hong Huang, Li-Ping Ju, and Pei-Chun Liao
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Stone oak ,Continental Asia ,Dispersal–extinction–cladogenesis (DEC) ,Diversification rate ,Endemism ,Greater Sunda Islands ,Botany ,QK1-989 - Abstract
Abstract Background Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus. Results Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate. Conclusions The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events.
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- 2018
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3. Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)
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Chih-Kai Yang, Bing-Hong Huang, Shao-Wei Ho, Meng-Yuan Huang, Jenn-Che Wang, Jian Gao, and Pei-Chun Liao
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Adaptive evolution ,Leaf epicuticular wax ,Lithocarpus ,Physical defenses ,Chemical defenses ,Phylogenetic signal ,Botany ,QK1-989 - Abstract
Abstract Background Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood. Results Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period. Conclusions Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.
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- 2018
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4. Differential genetic responses to the stress revealed the mutation-order adaptive divergence between two sympatric ginger species
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Bing-Hong Huang, Yuan-Chien Lin, Chih-Wei Huang, Hsin-Pei Lu, Min-Xin Luo, and Pei-Chun Liao
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Adaptive divergence ,Divergent time ,Ecological speciation ,Mutation-order mechanism ,Plastic divergence ,Positively selected DEGs ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Divergent genetic responses to the same environmental pressures may lead sympatric ecological speciation possible. Such speciation process possibly explains rapid sympatric speciation of island species. Two island endemic ginger species Zingiber kawagoii and Z. shuanglongensis was suggested to be independently originated from inland ancestors, but their island endemism and similar morphologies and habitats lead another hypothesis of in situ ecological speciation. For understanding when and how these two species diverged, intraspecific variation was estimated from three chloroplast DNA fragments (cpDNA) and interspecific genome-wide SNPs and expression differences after saline treatment were examined by transcriptomic analyses. Results Extremely low intraspecific genetic variation was estimated by cpDNA sequences in both species: nucleotide diversity π = 0.00002 in Z. kawagoii and no nucleotide substitution but only indels found in Z. shuanglongensis. Nonsignificant inter-population genetic differentiation suggests homogenized genetic variation within species. Based on 53,683 SNPs from 13,842 polymorphic transcripts, in which 10,693 SNPs are fixed between species, Z. kawagoii and Z. shuanglongensis were estimated to be diverged since 218~ 238 thousand generations ago (complete divergence since 41.5~ 43.5 thousand generations ago). This time is more recent than the time of Taiwan Island formation. In addition, high proportion of differential expression genes (DEGs) is non-polymorphic or non-positively selected, suggesting key roles of plastic genetic divergence in broaden the selectability in incipient speciation. While some positive selected DEGs were mainly the biotic and abiotic stress-resistance genes, emphasizing the importance of adaptive divergence of stress-related genes in sympatric ecological speciation. Furthermore, the higher proportional expression of functional classes in Z. kawagoii than in Z. shuanglongensis explains the more widespread distribution of Z. kawagoii in Taiwan. Conclusions Our results contradict the previous hypothesis of independent origination of these two island endemic ginger species from SE China and SW China. Adaptive divergent responses to the stress explain how these gingers maintain genetic differentiation in sympatry. However, the recent speciation and rapid expansion make extremely low intraspecific genetic variation in these two species. This study arise a more probable speciation hypothesis of sympatric speciation within an island via the mutation-order mechanism underlying the same environmental pressure.
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- 2018
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5. Environmental disturbance in natural forest and the effect of afforestation methods on timber volume increment in Pinus sylvestris L. var. mongolica Litv.
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Shu-Hong Wu, Chien-Ti Chao, Bing-Hong Huang, Min-Xin Luo, Xiang-Guang Duan, and Pei-Chun Liao
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Afforestation ,Age-dependent selection ,Fire disturbance ,Forest complexity ,Growth increment ,Ecology ,QH540-549.5 - Abstract
The renewal of temperate coniferous forests has a high impact on the global climate, as well as the survival of forest wildlife. As an important native afforestation tree species in northern China, Mongolian pine (Pinus sylvestris L. var. mongolica Litv.) is facing the dilemma of severe regeneration and forest growth. External factors, such as natural disturbances or human intervention, may affect the forest growth potential. Therefore, the present study explores whether environmental factors and afforestation methods affect the growth increment of Mongolian pine. To answer the question mentioned above, natural forest and two kinds of afforestation forests are included in this study. The growth increment is calculated by measuring basic growth parameters. A linear mixed-effect model is used to test whether surface fire, accompanying birch, edge effect, afforestation method, and tree age were determinants of the growth increment. With the model selection, the tree age combined with fire or afforestation is determined as significant effects on the growth increment. The effects of growth position and accompanying plants only influenced young pines. The effects decrease with age, implying the resource competition occurs at young ages only but not affect the adults of dominance trees. Since the growth rate of Mongolian pine varies with age, the environmental selection of timber volume is age-dependent. However, we also found that the growth increment slowdowns if too-fast growth investment in secondary growth at a young. Strengthening the competitive pressure of seedling afforestation is conducive to selecting individuals with a high growth increment and delayed growth cessation. Accordingly, fast-growing trees that survive fires are recommended as sources of seed-harvesting mother trees. Sowing afforestation that is easier to adjust the growth rate of seedlings is recommended than the seedling afforestation. Since external disturbances underlie the age-dependent selection of Mongolian pine growth, competition and environmental pressures at a young age are beneficial for prolonging the growth period and increasing timber volume accumulation. From this study, it can be seen that moderate fire disturbance and the selection of seed from healthy trees for tending are beneficial to the regeneration of temperate coniferous trees and the maintenance of healthy forests.
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- 2020
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6. Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion
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Wuxia Guo, Ying Liu, Wei Lun Ng, Pei-Chun Liao, Bing-Hong Huang, Weixi Li, Chunmei Li, Xianggang Shi, and Yelin Huang
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Invasion ,Eco-adaptation ,Positive selection ,Comparative transcriptomics ,Mikania ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared. Results A total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness. Conclusions We characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha.
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- 2018
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7. Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants
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Bing-Hong Huang, Chih-Wei Huang, Chia-Lung Huang, and Pei-Chun Liao
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Medicine ,Science - Abstract
Abstract Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson’s metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.
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- 2017
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8. The effects of afforestation on soil bacterial communities in temperate grassland are modulated by soil chemical properties
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Shu-Hong Wu, Bing-Hong Huang, Jian Gao, Siqi Wang, and Pei-Chun Liao
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Grassland afforestation ,Microbial composition ,Microbial ecological function ,Soil chemical properties ,Medicine ,Biology (General) ,QH301-705.5 - Abstract
Grassland afforestation dramatically affects the abiotic, biotic, and ecological function properties of the original ecosystems. Interference from afforestation might disrupt the stasis of soil physicochemical properties and the dynamic balance of microbiota. Some studies have suggested low sensitivity of soil properties and bacterial community to afforestation, but the apparent lack of a significant relationship is probably due to the confounding effects of the generalist habitat and rare bacterial communities. In this study, soil chemical and prokaryotic properties in a 30-year-old Mongolia pine (Pinus sylvestris var. mongolica Litv.) afforested region and adjacent grassland in Inner Mongolia were classified and quantified. Our results indicate that the high richness of rare microbes accounts for the alpha-diversity of the soil microbiome. Few OTUs of generalist (core bacteria) and habitat-specialist bacteria are present. However, the high abundance of this small number of OTUs governs the beta-diversity of the grassland and afforested land bacterial communities. Afforestation has changed the soil chemical properties, thus indirectly affecting the soil bacterial composition rather than richness. The contents of soil P, Ca2+, and Fe3+ account for differentially abundant OTUs such as Planctomycetes and subsequent changes in the ecologically functional potential of soil bacterial communities due to grassland afforestation. We conclude that grassland afforestation has changed the chemical properties and composition of the soil and ecological functions of the soil bacterial community and that these effects of afforestation on the microbiome have been modulated by changes in soil chemical properties.
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- 2019
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9. Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea
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Tao Yu, Jian Gao, Bing-Hong Huang, Buddhi Dayananda, Wen-Bao Ma, Yu-Yang Zhang, Pei-Chun Liao, and Jun-Qing Li
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Acer ,sect. Platanoidea ,chloroplast genome ,sequence divergence ,structural variation ,phylogenetics ,Plant ecology ,QK900-989 - Abstract
The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer.
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- 2020
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10. Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity
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Bing-Hong Huang, Chun-Wen Chang, Chih-Wei Huang, Jian Gao, and Pei-Chun Liao
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16S rRNA metagenome ,adult Anura ,functional predictions ,gut microbiota ,agricultural activity ,Microbiology ,QR1-502 - Abstract
The physiological impact of agricultural pollution, habitat disturbance, and food source variability on amphibian remains poorly understood. By comparing the composition and predicted functions of gut microbiota of two frog species from forest and farmland, we quantified the effects of the exogenous environment and endogenous filters on gut microbiota and the corresponding functions. However, compositional differences of the gut microbiota between the frog species were not detected, even when removing roughly 80–88% of the confounding effect produced by common and shared bacteria (i.e., generalists) and those taxa deemed too rare. The habitat effect accounted for 14.1% of the compositional difference of gut microbial specialists, but host and host × habitat effects were not significant. Similar trends of a significant habitat effect, at an even higher level (26.0%), for the physiological and metabolic functions of gut microbiota was predicted. A very obvious skewing of the relative abundance of functional groups toward farmland habitats reflects the highly diverse bacterial functions of farmland frogs, in particular related to pathogenic disease and pesticide degradation, which may be indication of poor adaptation or strong selective pressure against disease. These patterns reflect the impacts of agricultural activities on frogs and how such stresses may be applied in an unequal manner for different frog species.
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- 2018
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11. Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management
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Bing-Hong Huang, Yu Ruan, Jun-Qing Li, and Pei-Chun Liao
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conservation ,demography ,effective population size ,Kandelia obovata ,restoration ,Plant ecology ,QK900-989 - Abstract
Effective population size (Ne) is a crucial metric for evaluating the current status of genetic diversity and conservation management. Population of Kandelia obovata, a mangrove species that is patchily distributed along the estuaries off Southeastern China, is genetically structured. Here, we applied skyline analyses to infer the demographic history of K. obovata based on Amplified Fragment Length Polymorphisms (AFLP) data. Congruent trends of population growth rate among populations, but concurrent change in Ne estimates, were inferred in all populations. The recent rapid habitat expansion explains the high census population size but small Ne of populations in Northern Taiwan. Our study also revealed lower Ne of reforested populations than their sources. In silico demographic analyses simulate the small or biased sampling of seedlings for reforestation and revealed over 90% and 99% Ne reduction when only 1/2 and 1/10 samples were collected, respectively. These results emphasize the importance of a comprehensive sampling of seeds for restoration. Overall, this study rendered, not only the current Ne of K. obovata populations, but also indicates the importance of Ne estimation on restoration.
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- 2015
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12. Positive Selection and Functional Divergence of R2R3-MYB Paralogous Genes Expressed in Inflorescence Buds of Scutellaria Species (Labiatae)
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Bing-Hong Huang, Erli Pang, Yi-Wen Chen, Huifen Cao, Yu Ruan, and Pei-Chun Liao
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anthocyanin ,evolutionary rate ,functional divergence ,phylogenetic analysis ,positive selection ,R2R3-MYB ,Scutellaria ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Anthocyanin is the main pigment forming floral diversity. Several transcription factors that regulate the expression of anthocyanin biosynthetic genes belong to the R2R3-MYB family. Here we examined the transcriptomes of inflorescence buds of Scutellaria species (skullcaps), identified the expression R2R3-MYBs, and detected the genetic signatures of positive selection for adaptive divergence across the rapidly evolving skullcaps. In the inflorescence buds, seven R2R3-MYBs were identified. MYB11 and MYB16 were detected to be positively selected. The signature of positive selection on MYB genes indicated that species diversification could be affected by transcriptional regulation, rather than at the translational level. When comparing among the background lineages of Arabidopsis, tomato, rice, and Amborella, heterogeneous evolutionary rates were detected among MYB paralogs, especially between MYB13 and MYB19. Significantly different evolutionary rates were also evidenced by type-I functional divergence between MYB13 and MYB19, and the accelerated evolutionary rates in MYB19, implied the acquisition of novel functions. Another paralogous pair, MYB2/7 and MYB11, revealed significant radical amino acid changes, indicating divergence in the regulation of different anthocyanin-biosynthetic enzymes. Our findings not only showed that Scutellaria R2R3-MYBs are functionally divergent and positively selected, but also indicated the adaptive relevance of regulatory genes in floral diversification.
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- 2015
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13. Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach
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Shong Huang, Pei-Chun Liao, Shih-Jie Lai, Yu-Ting Wan, Chun-Wen Chang, Bing-Hong Huang, and Yu-Chung Chiang
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introgression ,AFLP ,Cycas revoluta ,Cycas taitungensis ,horticulture ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - 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. 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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- 2013
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14. Diversification, biogeographic pattern, and demographic history of Taiwanese Scutellaria species inferred from nuclear and chloroplast DNA.
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Yu-Chung Chiang, Bing-Hong Huang, and Pei-Chun Liao
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Medicine ,Science - Abstract
The ragged topography created by orogenesis generates diversified habitats for plants in Taiwan. In addition to colonization from nearby mainland China, high species diversity and endemism of plants is also present in Taiwan. Five of the seven Scutellaria species (Lamiaceae) in Taiwan, for example, are endemic to the island. Hypotheses of multiple sources or in situ radiation have arisen to explain the high endemism of Taiwanese species. In this study, phylogenetic analyses using both nuclear and chloroplast markers revealed the multiple sources of Taiwanese Scutellaria species and confirmed the rapid and recent speciation of endemic species, especially those of the "indica group" composed of S. indica, S. austrotaiwanensis, S. tashiroi, and S. playfairii. The common ancestors of the indica group colonized first in northern Taiwan and dispersed regionally southward and eastward. Climate changes during glacial/interglacial cycles led to gradual colonization and variance events in the ancestors of these species, resulting in the present distribution and genetic differentiation of extant populations. Population decline was also detected in S. indica, which might reflect a bottleneck effect from the glacials. In contrast, the recently speciated endemic members of the indica group have not had enough time to accumulate much genetic variation and are thus genetically insensitive to demographic fluctuations, but the extant lineages were spatially expanded in the coalescent process. This study integrated phylogenetic and population genetic analyses to illustrate the evolutionary history of Taiwanese Scutellaria of high endemism and may be indicative of the diversification mechanism of plants on continental islands.
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- 2012
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15. Local adaptation and migratory habits balance spatial‐genetic structure between continental and insular chestnut tiger butterflies in East Asia
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Min‐Xin Luo, Hsin‐Pei Lu, Bing‐Hong Huang, Chia‐Lung Huang, Yu‐Feng Hsu, and Pei‐Chun Liao
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Habits ,Asia, Eastern ,Genetics ,Animals ,Genetic Variation ,Bayes Theorem ,Butterflies ,DNA, Mitochondrial ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Microsatellite Repeats - Abstract
Geographic and climatic differences between islands and continents may affect the evolution of their biota, and promote divergent selection in species distributed in both landscapes. To assess spatial-genetic structure, we genotyped 18 expressed sequence tag-simple sequence repeat (EST-SSR) loci and sequenced two mtDNA markers (ND5 and COI) and one nuclear marker (EF1α) in two subspecies of the butterfly Parantica sita. Compared with nuclear markers, mtDNA had a stronger signal of population structure. Approximate Bayesian computation (ABC) suggested that a continuous-gene-flow model best described the data. According to this model, the two subspecies diverged approximately 23.1 kya, with 10 times more introgression from the continental (ssp. sita) to the insular subspecies (ssp. niphonica) than vice versa. Ecological niche modelling was performed to predict the paleo- and current potential distributions and elucidate the geohistorical process, which revealed a northeastern, insular origin. Winter precipitation and annual temperature range were the main determinants of the subspecies distributions. Maximum-likelihood population-effects models showed that the population differentiation of the insular and continental subspecies was primarily affected by environmental resistance and local climate. Sex-biased migration capacity and long-term precipitation-driven divergence between the continental and insular lineages shaped the current genetic structure of P. sita. Evidence from the nuclear markers confirmed intersubspecific gene flow despite adaptive divergence between the subspecies. These results imply that the continental subspecies is still capable of returning to the island and introgressing with the insular subspecies.
- Published
- 2022
16. Heterocarpy diversifies diaspore propagation of the desert shrub <scp> Ammopiptanthus mongolicus </scp>
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Yong Zhi Yang, Run Hong Gao, Min Wei Chai, Rong Zhang, Bing Hong Huang, Pei Chun Liao, and Min Xin Luo
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Diaspore (botany) ,Ecology ,Botany ,Selective advantage ,Ammopiptanthus mongolicus ,Biological dispersal ,Plant Science ,Biology ,Deserts and xeric shrublands ,Ecology, Evolution, Behavior and Systematics - Published
- 2020
17. Tissue-specific bioaccumulation of heavy metals in Ammopiptanthus mongolicus, the only evergreen shrub in the desert of Northwest China
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Yong-Zhi Yang, Run-Hong Gao, Min-Xin Luo, Bing-Hong Huang, and Pei-Chun Liao
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ammopiptanthus mongolicus ,bioaccumulation ,lcsh:Biology (General) ,bioavailability ,heavy metals ,translocation efficiency ,complex mixtures ,mobilization ,lcsh:QH301-705.5 - Abstract
The concentration of heavy metals (HMs) in plants is determined by the background values in soil and/or the expression of genes related to HM metabolism. To determine if the bioaccumulation of HMs in Ammopiptanthus mongolicus, an evergreen desert shrub commonly used as a traditional medicine, is related to environmental background and/or tissue (organ) specific, the HM concentrations (As, Cd, Cr, Cu, Hg, Pb, Ni, and Zn) in the soil, roots, stems, and leaves of A. mongolicus in the desert of northwestern China were measured. Efficiencies of bioconcentration, bioaccumulation, and translocation to different portions of the plant were calculated. A linear mixed-effects model was used to test the effects of environmental background and tissue specificity on bioaccumulation. The results showed that most HMs did not exceed the pollution threshold in the soil samples, and the accumulation in plants did not meet the standard of worldwide averages. The phytoaccumulation of HMs was independent of the background concentration in soil but was related to plant tissues, which reflects the low mobility of HMs in the desert, and suggesting that the phytoaccumulation is related to the metabolic capacity and/or differential expression of HM-related genes in tissues of A. mongolicus. The high translocation efficiency of mercury from the underground portion to the leaves makes A. mongolicus a potential phytoremediator for mercury contamination. However, the removal efficiency in high-dose contamination soil still needs to be further examined. This study suggests that the desert environment may lack appropriate microorganisms to decompose immobile HMs effectively. In addition, when using A. mongolicus as a medicinal plant, special attention should be paid to the accumulation of HMs in different tissues, even if they have not reached the risk threshold.
- Published
- 2020
18. Genetic evidence of the southward founder speciation of Cycas taitungensis from ancestral C. revoluta along the Ryukyu Archipelagos
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Jui Tse Chang, Bing Hong Huang, and Pei Chun Liao
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0106 biological sciences ,0301 basic medicine ,Genetic diversity ,Population size ,Biology ,Cycas ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Phylogeography ,030104 developmental biology ,Effective population size ,Evolutionary biology ,Cycas taitungensis ,Genetic algorithm ,Genetics ,Ecology, Evolution, Behavior and Systematics ,Founder effect - Abstract
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.
- Published
- 2019
19. Deviation from the Brownian motion expectation implies episodic adaptive divergences in traits of Lithocarpus species in Taiwan
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Min-Xin Luo, Meng-Yuan Huang, Chih-Kai Yang, Yi-Zhou He, Bing-Hong Huang, and Pei-Chun Liao
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Phylogenetic constraint ,Adaptive divergence ,lcsh:Biology (General) ,Trait evolution ,Lithocarpus ,Brownian motion model ,lcsh:QH301-705.5 ,Continuous trait - Abstract
Adaptive trait divergence is usually episodic rather than universal in a phylogeny. To determine whether trait divergence reaches an extreme level (i.e. deviation from neutrality), the evolutionary rate of the species and intraspecific variation must be taken into account. Accordingly, we attempt to explore the trend of trait divergence over divergence times conditioned on the genetic distance. The Brownian motion (BM) model, a commonly used random-walk process for describing the neutral evolution of traits, is used to simulate the distribution of trait divergence under neutrality. The observed trait divergences are then compared to the BM expectations to detect outliers, which are considered to be selected. We assessed the ability of this method to characterize trait divergence under selection among 14 Lithocarpus species in Taiwan. The results are consistent with the previous inference of phylogenetic constraint based on tests of the phylogenetic signal, but further signals of adaptive and conserved trait divergences are detected between some lineages derived from particular nodes (common ancestors), indicating differential investments in growth rate and chemical defense among some endemic species in Taiwan. These results show that the adaptive divergence of environment-related traits is transient, episodic, and punctuated. Under strong selection pressure, the trait divergence after standard deviation correction will be more significant because the trait variance within the population decreases. However, it tends to be an overestimation of conservative evolution in older common ancestors due to the larger standard deviation produced from diverse descendants. Nevertheless, this study still provides a simple approach to detect adaptive divergence in a phylogenetic framework.
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- 2019
20. Niche partitioning among three snail-eating snakes revealed by dentition asymmetry and prey specialisation
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Min Xin Luo, Hung Ngoc Nguyen, Kai Xiang Chang, Si Min Lin, Bing Hong Huang, Chih Wei Huang, and Shu Ping Wu
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0106 biological sciences ,Ecological niche ,Squamata ,010604 marine biology & hydrobiology ,media_common.quotation_subject ,Niche ,Snails ,Niche differentiation ,Land snail ,Taiwan ,Zoology ,Snakes ,Biology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Competition (biology) ,Sympatric speciation ,Character displacement ,Animals ,Dentition ,Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics ,Ecosystem ,media_common - Abstract
The level of dentition asymmetry in snail-eating snakes may reflect their prey choice and feeding efficiency on asymmetric land snails. The three species of Pareas snakes (Squamata: Pareidae) in Taiwan, which form partially sympatric distribution on the island, provide a potential case to test the hypothesis of niche partitioning and character displacement with regard to dentition asymmetry and specialisation in feeding behaviour. In this study, behavioural experiments confirmed that P. formosensis feeds exclusively on slugs, whereas P. atayal and P. komaii consumed both. However, P. atayal more efficiently preys on land snails than P. komaii, exhibiting a shorter handling time and fewer mandibular retractions. Micro-CT and ancestral character reconstruction demonstrated the lowest asymmetry in P. formosensis (the slug specialist), the highest dentition asymmetry in P. atayal (the land snail specialist) and flexibility in P. komaii (the niche switcher): increased dentition asymmetry when sympatrically distributed with the slug eater (character displacement), and decreased asymmetry when living alone (ecological niche release). Ecological niche modelling showed that the distribution of P. formosensis is associated with the presence of slugs, while that of P. atayal could be explained by the land snails. Combining the results from morphology, phylogeny, behavioural experiments and ecological niche modelling, we showed that competition in the sympatric region might have facilitated character displacement among congeners, while the absence of competition in allopatric region has led to ecological niche release.
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- 2020
21. Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea
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Wen Bao Ma, Buddhi Dayananda, Yuyang Zhang, Jun Qing Li, Tao Yu, Pei Chun Liao, Jian Gao, and Bing Hong Huang
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0106 biological sciences ,0303 health sciences ,Phylogenetic tree ,structural variation ,Forestry ,lcsh:QK900-989 ,Biology ,Acer ,010603 evolutionary biology ,01 natural sciences ,Genome ,DNA sequencing ,Structural variation ,phylogenetics ,03 medical and health sciences ,sequence divergence ,Chloroplast DNA ,Phylogenetics ,Genetic marker ,Evolutionary biology ,GenBank ,lcsh:Plant ecology ,chloroplast genome ,030304 developmental biology ,sect. Platanoidea - Abstract
The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer.
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- 2020
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22. Historical biogeography of Acer L. (Sapindaceae): genetic evidence for Out-of-Asia hypothesis with multiple dispersals to North America and Europe
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Bing Hong Huang, Pei Chun Liao, Jian Gao, Jun Qing Li, Tao Yu, and Yuyang Zhang
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0106 biological sciences ,0301 basic medicine ,Time Factors ,Biogeography ,Biodiversity ,Acer ,Subspecies ,010603 evolutionary biology ,01 natural sciences ,Models, Biological ,Article ,03 medical and health sciences ,Genus ,Seed Dispersal ,Likelihood Functions ,Multidisciplinary ,Base Sequence ,Land bridge ,Ecology ,Maximum parsimony ,Phylogenetics ,Phylogeography ,030104 developmental biology ,Geography ,Biological dispersal - Abstract
Biogeography is the study of where, when, and how modern species evolved and diversified. Acer L. (maple) is one of the most diverse and widespread genera in the Northern Hemisphere. It comprises 124–156 species in the world, approximately 80% species of Acer are native in Asia. The current diversity center of Acer is not congruent with the distribution of the oldest fossils of the genus. Therefore, we herein used 84 species and subspecies to reconstruct the phylogeny and investigate the biogeographic history of Acer using nuclear ITS and three cpDNA fragments (psbA-trnH spacer, rpl16 intron, and trnL-trnF spacer) with maximum likelihood, maximum parsimony, and Bayesian inference methods. The analyses showed that the current diversity center and the origin center of Acer is Asia. Additionally, the North American and Euro-Mediterranean species originated from multiple sources from Asia via the North Atlantic Land Bridge and the Bering Land Bridge, and intercontinental migration has mainly occurred since the Miocene. This study not only provides a novel insight of the origin and dispersal routes of Acer but also exemplifies how past climatic changes affect the diversification-rates of Northern Hemisphere forest trees.
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- 2020
23. Taxonomic notes on Scutellaria taipeiensis (Lamiaceae) from morphological and molecular data
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Jui Tse Chang, Chien Ti Chao, Bing Hong Huang, and Pei Chun Liao
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Synonym ,Scutellaria ,Taiwan ,Plant Science ,plant taxonomy ,DNA sequencing ,Magnoliopsida ,Genus ,lcsh:Botany ,Botany ,Plantae ,Ecology, Evolution, Behavior and Systematics ,Lamiaceae ,Phylogenetic tree ,biology ,Scutellaria taipeiensis ,Lamiaceae Scutellarioideae plant taxonomy Taiwan ,biology.organism_classification ,Plant taxonomy ,Scutellarioideae ,lcsh:QK1-989 ,Lamiales ,Tracheophyta ,Herbarium - Abstract
The genus Scutellaria comprises eight species distributed from 50 to 2000 m in Taiwan. Amongst them, S. barbata and S. taipeiensis are very similar on the basis of morphological and plastid DNA sequence information. Therefore, a comprehensive study of the taxonomic status of S. taipeiensis is necessary. We reviewed the herbarium sheets, related literature and protologues and compared morphologies of these two species, as well as their phylogenetic relationships. All evidence, including the diagnostic characters between S. taipeiensis and S. barbata, suggest that they belonged to a single species rather than two. As a result, S. taipeiensis is treated as a synonym of S. barbata.
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- 2020
24. Chloroplast genome of an extremely endangered conifer Thuja sutchuenensis Franch.: gene organization, comparative and phylogenetic analysis
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Tao Yu, Yuyang Zhang, Jun Qing Li, Bing Hong Huang, and Pei Chun Liao
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0106 biological sciences ,0301 basic medicine ,biology ,Phylogenetic tree ,Physiology ,Thuja sutchuenensis ,Plant Science ,biology.organism_classification ,01 natural sciences ,Genome ,Thuja ,03 medical and health sciences ,030104 developmental biology ,Gymnosperm ,Evolutionary biology ,Phylogenomics ,Thujopsis ,Molecular Biology ,GC-content ,010606 plant biology & botany ,Research Article - Abstract
Thuja sutchuenensis is a critically endangered tertiary relict species of Cupressaceae from southwestern China. We sequenced the complete chloroplast (cp) genome of T. sutchuenensis, showing the genome content of 129,776 bp, 118 unique genes including 82 unique protein-coding genes, 32 tRNA genes, and 4 rRNA genes. The genome structures, gene order, and GC content are similar to other typical gymnosperm cp genomes. Thirty-eight simple sequence repeats were identified in the T. sutchuenensis cp genome. We also found an apparent inversion between trnT and psbK between genera Thuja and Thujopsis. In addition, positive selection signals were detected in seven genes with high Ka/Ks ratios. The reconstructed phylogeny based on locally collinear blocks of cp genomes among 21 gymnosperms species is similar to previous inferences. We also inferred a Late-Miocene divergence between T. sutchuenensis and T. standishii, according to the dating of ~ 11.05 Mya by cp genomes. These results will be helpful for future studies of Cupressaceae phylogeny as well as studies in population genetics, systematics, and cp genetic engineering. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12298-019-00736-7) contains supplementary material, which is available to authorized users.
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- 2020
25. Taxonomic notes on
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Chien-Ti, Chao, Bing-Hong, Huang, Jui-Tse, Chang, and Pei-Chun, Liao
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Lamiaceae ,Cenozoic ,Taiwan ,plant taxonomy ,Plantae ,Scutellarioideae ,Research Article ,Taxonomy ,Lamiales - Abstract
The genus Scutellaria comprises eight species distributed from 50 to 2000 m in Taiwan. Amongst them, S. barbata and S. taipeiensis are very similar on the basis of morphological and plastid DNA sequence information. Therefore, a comprehensive study of the taxonomic status of S. taipeiensis is necessary. We reviewed the herbarium sheets, related literature and protologues and compared morphologies of these two species, as well as their phylogenetic relationships. All evidence, including the diagnostic characters between S. taipeiensis and S. barbata, suggest that they belonged to a single species rather than two. As a result, S. taipeiensis is treated as a synonym of S. barbata.
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- 2019
26. Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion
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Weixi Li, Bing Hong Huang, Xianggang Shi, Wuxia Guo, Yelin Huang, Pei Chun Liao, Chunmei Li, Ying Liu, and Wei Lun Ng
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0301 basic medicine ,lcsh:QH426-470 ,lcsh:Biotechnology ,Niche ,Plant Weeds ,Mikania ,Invasive species ,Evolution, Molecular ,03 medical and health sciences ,Invasion ,Comparative transcriptomics ,lcsh:TP248.13-248.65 ,Botany ,Genetics ,Selection, Genetic ,Mikania micrantha ,Gene ,Phylogeny ,Eco-adaptation ,biology ,Phylogenetic tree ,Gene Expression Profiling ,Molecular Sequence Annotation ,Asteraceae ,biology.organism_classification ,Positive selection ,lcsh:Genetics ,030104 developmental biology ,Weed ,Introduced Species ,Biotechnology ,Research Article - Abstract
Background Mikania micrantha H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative M. cordata, the only Mikania species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader M. micrantha and its native congener M. cordata in China, to unravel the genetic basis underlying the strong invasiveness of M. micrantha. For a more robust comparison, another non-invasive congener M. cordifolia was also sequenced and compared. Results A total of 52,179, 55,835, and 52,983 unigenes were obtained for M. micrantha, M. cordata, and M. cordifolia, respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between M. micrantha and M. cordata, i.e., approximately 4.81 million years ago (MYA), after their divergence with M. cordifolia (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in M. micrantha than in M. cordata or M. cordifolia. Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of M. micrantha. Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in M. micrantha could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of M. micrantha to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness. Conclusions We characterized the transcriptomes of the invasive species M. micrantha and its non-invasive congeners, M. cordata and M. cordifolia. A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of M. micrantha. Electronic supplementary material The online version of this article (10.1186/s12864-018-4784-9) contains supplementary material, which is available to authorized users.
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- 2018
27. Functional divergence and intron variability during evolution of angiosperm TERMINAL FLOWER1 (TFL1) genes
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Bing Hong Huang, Jenyu Chang, Yu Ting Wan, Jun Qing Li, Pei Chun Liao, and Jian Gao
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0301 basic medicine ,Arabidopsis ,lcsh:Medicine ,Biology ,Genes, Plant ,Basal angiosperms ,Article ,Evolution, Molecular ,Magnoliopsida ,03 medical and health sciences ,Exon ,Gene Expression Regulation, Plant ,Phylogenetics ,lcsh:Science ,Gene ,Phylogeny ,Regulation of gene expression ,Genetics ,Multidisciplinary ,Arabidopsis Proteins ,fungi ,lcsh:R ,Intron ,Genetic Variation ,food and beverages ,Meristem ,Introns ,030104 developmental biology ,lcsh:Q ,Functional divergence - Abstract
The protein encoded by the TERMINAL FLOWER1 (TFL1) gene maintains indeterminacy in inflorescence meristem to repress flowering, and has undergone multiple duplications. However, basal angiosperms have one copy of a TFL1-like gene, which clusters with eudicot TFL1/CEN paralogs. Functional conservation has been reported in the paralogs CENTRORADIALIS (CEN) in eudicots, and ROOTS CURL IN NPA (RCNs) genes in monocots. In this study, long-term functional conservation and selective constraints were found between angiosperms, while the relaxation of selective constraints led to subfunctionalisation between paralogs. Long intron lengths of magnoliid TFL1-like gene contain more conserved motifs that potentially regulate TFL1/CEN/RCNs expression. These might be relevant to the functional flexibility of the non-duplicate TFL1-like gene in the basal angiosperms in comparison with the short, lower frequency intron lengths in eudicot and monocot TFL1/CEN/RCNs paralogs. The functionally conserved duplicates of eudicots and monocots evolved according to the duplication-degeneration-complementation model, avoiding redundancy by relaxation of selective constraints on exon 1 and exon 4. These data suggest that strong purifying selection has maintained the relevant functions of TFL1/CEN/RCNs paralogs on flowering regulation throughout the evolution of angiosperms, and the shorter introns with radical amino acid changes are important for the retention of paralogous duplicates.
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- 2017
28. The Aboveground Vegetation Type and Underground Soil Property Mediate the Divergence of Soil Microbiomes and the Biological Interactions
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Gang Li, Shu Hong Wu, Chia Lung Huang, Pei Chun Liao, and Bing Hong Huang
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DNA, Bacterial ,0301 basic medicine ,Soil Science ,Forests ,Biology ,Poaceae ,complex mixtures ,Trees ,Soil ,03 medical and health sciences ,Microbial ecology ,RNA, Ribosomal, 16S ,Vegetation type ,Soil ecology ,Ecosystem ,Soil Microbiology ,Ecology, Evolution, Behavior and Systematics ,Rhizosphere ,Biotic component ,Bacteria ,Ecology ,Microbiota ,Soil organic matter ,Vegetation ,030104 developmental biology ,Soil water - Abstract
The composition of the soil microbiome is influenced by environmental (abiotic) variables and biological interactions (biotic factors). To determine whether the aboveground vegetation and soil physicochemical properties were the main determinant of beta-diversity and biological interaction of soil microbial community, we sampled soils from the temperate coniferous forest and grassland. Clustering of operational taxonomic units was conducted using 16S rRNA gene. We found that the microbial composition of the rhizospheres, in which root exudates influence the microbial environment, show lower alpha-diversity than that of nonroot soils. The nonsignificant rhizosphere effect suggested other undetermined factors or stochastic processes accounted for microbial diversity in the rhizosphere. More significant microbe-microbe interactions were observed in forest and rhizosphere soils relative to the grassland soils. The elevated number of positive correlations for relative abundances in forest soil implied beneficial associations being common among bacteria, in particular within the rhizosphere environment. The particular soil properties generated by root exudates also alter the physicochemical properties of soil such as K and pH value, and might in turn favor the adoption of teamwork-cooperation strategies for microbe-microbe interactions, represented as large clusters of positive associations among bacterial taxa. Specific biological interactions differentiated the microbiomes within forest soils. Thus, the environmental selection pressure of aboveground vegetation accounts for differences between soil microbiomes while biotic factors are responsible for fine-scale differences of the microbial community in forest soils.
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- 2017
29. Continuation of the genetic divergence of ecological speciation by spatial environmental heterogeneity in island endemic plants
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Chia Lung Huang, Bing Hong Huang, Chih Wei Huang, and Pei Chun Liao
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0106 biological sciences ,0301 basic medicine ,Sympatry ,Heteropatric speciation ,Genetic Speciation ,Scutellaria ,Science ,Allopatric speciation ,Taiwan ,Biology ,010603 evolutionary biology ,01 natural sciences ,Article ,Ecological speciation ,03 medical and health sciences ,Genetic algorithm ,Cluster Analysis ,Ecosystem ,Phylogeny ,Islands ,Multidisciplinary ,Ecology ,Genetic Variation ,Bayes Theorem ,Incipient speciation ,Biological Evolution ,Genetic divergence ,030104 developmental biology ,Genetics, Population ,Logistic Models ,Sympatric speciation ,Evolutionary biology ,Multivariate Analysis ,Medicine ,Microsatellite Repeats - Abstract
Divergent selection plays a critical role not only as a speciation driver but also in maintaining post-speciation divergence. In the absence of direct evidence, ancestral interspecific gene flow between incipient species can reflect ancient selective pressure for ecological speciation. In the present study, two late-Pleistocene diverged species endemic to Taiwan, Scutellaria playfairii and S. tashiroi, were spatially and ecologically partitioned with partial overlap. Multilocus genome-scan analyses and in silico evaluation revealed ancestral interspecific gene flow but distinct genetic compositions, implying that adaptive divergence contributed to their speciation. Ecological niche modeling and principal component analysis suggested incomplete divergent niches between the two species; the species distribution is therefore consistent with Hutchinson’s metaphor of multidimensional hypervolume niches rather than attributable to a single factor. Constraint ordination analysis supported this inference of a combination of variables explaining the genetic structure. The rare occurrence of hybrids in the sympatric population suggested hybrid breakdown, providing further evidence of divergent selection blocking gene flow. The correlation of environmental variables with integrated genetic components demonstrated that environmental heterogeneity maintains the species and population differentiation. This study highlights the importance of environmental heterogeneity and divergent selection for the rapid speciation and recent diversification of island plants.
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- 2017
30. Multilocus Genome Evidence for a Paraphyletic Relationship and Past Interspecific Gene Flow Between Species of Cycas Section Asiorientales
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Bing-Hong Huang, Yu-Chung Chiang, Hsien-Hui Shen, Nan Li, Shong Huang, Pei Chun Liao, and Yi-Qing Gong
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Paraphyly ,biology ,Section (archaeology) ,Evolutionary biology ,Interspecific competition ,Cycas ,biology.organism_classification ,Genome ,Gene flow - Published
- 2018
31. Nuclear and chloroplast DNA phylogeography suggests an Early Miocene southward expansion of Lithocarpus (Fagaceae) on the Asian continent and islands
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Bing Hong Huang, Chih-Kai Yang, Pei Chun Liao, Li Ping Ju, and Yu-Chung Chiang
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0106 biological sciences ,0301 basic medicine ,Stone oak ,Pleistocene ,Biogeography ,Population ,Lithocarpus ,Plant Science ,Southeast asian ,010603 evolutionary biology ,01 natural sciences ,Historical biogeography ,Coalescent theory ,03 medical and health sciences ,lcsh:Botany ,education ,Phylogeny ,education.field_of_study ,biology ,Ecology ,Indochina ,biology.organism_classification ,lcsh:QK1-989 ,Fagaceae ,Diversification rate ,Phylogeography ,030104 developmental biology ,Continental Asia ,Dispersal–extinction–cladogenesis (DEC) ,Greater Sunda Islands ,Original Article ,Endemism - Abstract
Background Most genera of Fagaceae are thought to have originated in the temperate regions except for the genus Lithocarpus, the stone oaks. Lithocarpus is distributed in subtropical and tropical Asia, and its ancestral population is hypothesized to be distributed in tropical regions in Borneo and Indochina. Borneo and the nearby islands (the Greater Sunda Islands) were connected to the Malay Peninsula and Indochina prior to the Pliocene epoch and formed the former Sundaland continent. The Southeast Asian Lithocarpus, is thought to have dispersed between continental Asia and the present Sundaland. The drastic climate changes during the Pliocene and Pleistocene epochs which caused periodic sea-level changes is often used to explain the cause of its diversity. The aim of this study was to establish phylogenetic relationships by analyzing nuclear (nrDNA) and chloroplast (cpDNA) DNA in order to describe and analyze the origin, causes of diversification and historical biogeography of Lithocarpus. Results Phylogeny reconstructed through the multiple-species coalescent method with nrDNA and cpDNA revealed that the continental-Asian taxa were clustered at the basal lineages. The derived lineages of tropical Lithocarpus, with the inference of a subtropical ancestral state, imply a southward migration in the Early Miocene period with subsequent in situ diversification in the Greater Sunda Islands. The gradual decrease in temperature since the Middle Miocene period is proposed as a cause of the increase in the net diversification rate. Conclusions The historical ancestral origin of Lithocarpus has been suggested to be mainland Asia. Southward migration in the Early Miocene period with subsequent in situ diversification could explain the current diversity of stone oaks in Southeast Asia. This study also considered the multiple origins of stone oaks currently indigenous to the subtropical islands offshore and near mainland China. Our results provide phylogenetic evidence for a subtropical origin of Asian stone oaks and reveal the process of diversification and how it fits into the timeline of major geologic and climatic events rather than local, episodic, rate-shifting events. Electronic supplementary material The online version of this article (10.1186/s40529-018-0244-8) contains supplementary material, which is available to authorized users.
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- 2018
32. Genetic diversity analysis of Jatropha curcas L. accessions cultivated in Taiwan using inter simple sequence repeats (ISSR) markers
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Fure-Chyi Chen, Su-Ju Lin, Yong-Pei Wu, Bing-Hong Huang, and Celimphilo Mavuso
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0106 biological sciences ,0301 basic medicine ,Germplasm ,Veterinary medicine ,Genetic diversity ,biology ,UPGMA ,Jatropha ,Forestry ,biology.organism_classification ,01 natural sciences ,Analysis of molecular variance ,03 medical and health sciences ,030104 developmental biology ,Genetic marker ,Botany ,Genetic variation ,Agronomy and Crop Science ,Jatropha curcas ,010606 plant biology & botany - Abstract
The study of genetic diversity in different Jatropha curcas L. accessions cultivated in Taiwan comprises a necessary first step in germplasm evaluation towards improving this plant species. Genetic variations of 78 Jatropha curcas L. accessions representing origin of eight countries, cultivated in two locations in Taiwan were determined using inter simple sequence repeats (ISSR) markers. Out of 22 screened UBC primers set No. 9, ten primers amplified a total of 27 loci with 23 be polymorphic (85.19 %). Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis indicated two main clusters with the Dice coefficient of similarity ranging from 0.62 to 1.00. Although the grouping was not related to cultivation locations, there was close genetic relationship among the Jatropha populations. Analysis of molecular variance revealed 31.23 % of the variability attributable to among populations with the remaining 68.77 % within Jatropha populations. The overall analysis of different populations suggests less variation of cultivated Jatropha populations in Taiwan.
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- 2015
33. Molecular genetic and biochemical evidence for adaptive evolution of leaf abaxial epicuticular wax crystals in the genus Lithocarpus (Fagaceae)
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Bing Hong Huang, Chih-Kai Yang, Jenn Che Wang, Meng-Yuan Huang, Pei Chun Liao, Jian Gao, and Shao Wei Ho
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0106 biological sciences ,Adaptive evolution ,Adaptation, Biological ,Lithocarpus ,Physical defenses ,Secondary Metabolism ,Phylogenetic signal ,Plant Science ,Photosynthesis ,Fagaceae ,010603 evolutionary biology ,01 natural sciences ,Epicuticular wax ,Evolution, Molecular ,Phylogenetics ,lcsh:Botany ,Botany ,Hydroxybenzoates ,Selection, Genetic ,Chemical defenses ,Leaf epicuticular wax ,Gene ,Phylogeny ,Plant Proteins ,Wax ,biology ,biology.organism_classification ,Trichome ,lcsh:QK1-989 ,Plant Leaves ,visual_art ,Waxes ,visual_art.visual_art_medium ,Microscopy, Electron, Scanning ,010606 plant biology & botany - Abstract
Background Leaf epicuticular wax is an important functional trait for physiological regulation and pathogen defense. This study tests how selective pressure may have forced the trait of leaf abaxial epicuticular wax crystals (LAEWC) and whether the presence/absence of LAEWC is associated with other ecophysiological traits. Scanning Electron Microscopy was conducted to check for LAEWC in different Lithocarpus species. Four wax biosynthesis related genes, including two wax backbone genes ECERIFERUM 1 (CER1) and CER3, one regulatory gene CER7 and one transport gene CER5, were cloned and sequenced. Ecophysiological measurements of secondary metabolites, photosynthesis, water usage efficiency, and nutrition indices were also determined. Evolutionary hypotheses of leaf wax character transition associated with the evolution of those ecophysiological traits as well as species evolution were tested by maximum likelihood. Results Eight of 14 studied Lithocarpus species have obvious LAEWC appearing with various types of trichomes. Measurements of ecophysiological traits show no direct correlations with the presence/absence of LAEWC. However, the content of phenolic acids is significantly associated with the gene evolution of the wax biosynthetic backbone gene CER1, which was detected to be positively selected when LAEWC was gained during the late-Miocene-to-Pliocene period. Conclusions Changes of landmass and vegetation type accelerated the diversification of tropical and subtropical forest trees and certain herbivores during the late Miocene. As phenolic acids were long thought to be associated with defense against herbivories, co-occurrence of LAEWC and phenolic acids may suggest that LAEWC might be an adaptive defensive mechanism in Lithocarpus.
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- 2017
34. Recurrent positive selection and heterogeneous codon usage bias events leading to coexistence of divergent pigeon circoviruses
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Shinn Shyong Tsai, Pei Chun Liao, Bing Hong Huang, Kuo Pin Chuang, Kung Kai Wang, and Hung-Jen Liu
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Circovirus ,Genetics ,Genotype ,Phylogenetic tree ,Bird Diseases ,Molecular Sequence Data ,Genome, Viral ,Biology ,Genome ,Evolution, Molecular ,Open Reading Frames ,Open reading frame ,Phylogenetics ,Virology ,Codon usage bias ,GenBank ,Animals ,Coding region ,Capsid Proteins ,Circoviridae Infections ,Codon ,Columbidae ,Clade ,Phylogeny - Abstract
The capsid genes from 14 pigeon circovirus (PiCV) sequences, collected from Taiwan between 2009 and 2010, were sequenced and compared with 14 PiCV capsid gene sequences from GenBank. Based on pairwise comparison, PiCV strains from Taiwan shared 73.9-100% nucleotide identity and 72-100% amino acid identity with those of the 14 reported PiCV sequences. Phylogenetic analyses revealed that Taiwanese PiCV isolates can be grouped into two clades: clade 1 comprising isolates from Belgium, Australia, USA, Italy and China, and clade 2 showing close relation to isolates from Germany and France. Recurrent positive selection was detected in clade 1 PiCV lineages, which may contribute to the diversification of predominant PiCV sequences in Taiwan. Further observations suggest that synonymous codon usage variations between PiCV clade 1 and clade 2 may reflect the adaptive divergence on translation efficiency of capsid genes in infectious hosts. Variation in selective pressures acting on the evolutionary divergence and codon usage bias of both clades explains the regional coexistence of virus sequences congeners prevented from competitive exclusion within an island such as Taiwan. Our genotyping results also provide insight into the aetiological agents of PiCV outbreak in Taiwan and we present a comparative analysis of the central coding region of PiCV genome. From the sequence comparison results of 28 PiCVs which differs in regard to the geographical origin and columbid species, we identified conserved regions within the capsid gene that are likely to be suitable for primer selection and vaccine development.
- Published
- 2015
35. Applying Effective Population Size Estimates of Kandelia obovata Sheue, Liu and Yong to Conservation and Restoration Management
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Yu Ruan, Pei Chun Liao, Bing Hong Huang, and Jun Qing Li
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Genetic diversity ,education.field_of_study ,demography ,restoration ,Demographic history ,Ecology ,Population size ,Population ,conservation ,Forestry ,lcsh:QK900-989 ,Biology ,biology.organism_classification ,Effective population size ,Habitat ,Kandelia obovata ,lcsh:Plant ecology ,education ,effective population size ,Sampling bias - Abstract
Effective population size (Ne) is a crucial metric for evaluating the current status of genetic diversity and conservation management. Population of Kandelia obovata, a mangrove species that is patchily distributed along the estuaries off Southeastern China, is genetically structured. Here, we applied skyline analyses to infer the demographic history of K. obovata based on Amplified Fragment Length Polymorphisms (AFLP) data. Congruent trends of population growth rate among populations, but concurrent change in Ne estimates, were inferred in all populations. The recent rapid habitat expansion explains the high census population size but small Ne of populations in Northern Taiwan. Our study also revealed lower Ne of reforested populations than their sources. In silico demographic analyses simulate the small or biased sampling of seedlings for reforestation and revealed over 90% and 99% Ne reduction when only 1/2 and 1/10 samples were collected, respectively. These results emphasize the importance of a comprehensive sampling of seeds for restoration. Overall, this study rendered, not only the current Ne of K. obovata populations, but also indicates the importance of Ne estimation on restoration.
- Published
- 2015
36. Local Climate Heterogeneity Shapes Population Genetic Structure of Two Undifferentiated Insular Scutellaria Species
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Yao Moan Huang, Huan Yi Hsiung, Jui Tse Chang, Chih Wei Huang, Pei Chun Liao, and Bing Hong Huang
- Subjects
0106 biological sciences ,0301 basic medicine ,Scutellaria ,Population ,Plant Science ,Biology ,precipitation ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,taxonomy ,Genetic variation ,climate heterogeneity ,Endemism ,education ,Original Research ,Ecological niche ,education.field_of_study ,Ecology ,Regression ,030104 developmental biology ,typhoon ,Typhoon ,Genetic structure ,genetic variation ,Taxonomy (biology) - Abstract
Spatial climate heterogeneity may not only affect adaptive gene frequencies but could also indirectly shape the genetic structure of neutral loci by impacting demographic dynamics. In this study, the effect of local climate on population genetic variation was tested in two phylogenetically close Scutellaria species in Taiwan. Scutellaria taipeiensis, which was originally assumed to be an endemic species of Taiwan Island, is shown to be part of the widespread species S. barbata based on the overlapping ranges of genetic variation and climatic niches as well as their morphological similarity. Rejection of the scenario of “early divergence with secondary contact” and the support for multiple origins of populations of S. taipeiensis from S. barbata provide strong evolutionary evidence for a taxonomic revision of the species combination. Further tests of a climatic effect on genetic variation were conducted. Regression analyses show nonlinear correlations among any pair of geographic, climatic, and genetic distances. However, significantly, the bioclimatic variables that represent the precipitation from late summer to early autumn explain roughly 13% of the genetic variation of our sampled populations. These results indicate that spatial differences of precipitation in the typhoon season may influence the regeneration rate and colonization rate of local populations. The periodic typhoon episodes explain the significant but nonlinear influence of climatic variables on population genetic differentiation. Although, the climatic difference does not lead to species divergence, the local climate variability indeed impacts the spatial genetic distribution at the population level.
- Published
- 2017
- Full Text
- View/download PDF
37. Imbalanced positive selection maintains the functional divergence of duplicated DIHYDROKAEMPFEROL 4-REDUCTASE genes
- Author
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Pei Chun Liao, Jian Gao, Chia Lung Huang, Bing Hong Huang, and Yi Wen Chen
- Subjects
0301 basic medicine ,Scutellaria ,Pseudogene ,Paralogous Gene ,Biology ,Article ,Evolution, Molecular ,03 medical and health sciences ,Magnoliopsida ,Gene Expression Regulation, Plant ,Genes, Duplicate ,Gene Duplication ,Gene duplication ,Regulatory Elements, Transcriptional ,Selection, Genetic ,Codon ,Gene ,Phylogeny ,Plant Proteins ,Regulation of gene expression ,Multidisciplinary ,Models, Genetic ,Gene Expression Profiling ,Genetic Variation ,Gene expression profiling ,Alcohol Oxidoreductases ,030104 developmental biology ,Evolutionary biology ,Subfunctionalization ,Functional divergence - Abstract
Gene duplication could be beneficial by functional division but might increase the risk of genetic load. The dynamics of duplicated paralogs number could involve recombination, positive selection, and functional divergence. Duplication of DIHYDROFLAVONOL 4-REDUCTASE (DFR) has been reported in several organisms and may have been retained by escape from adaptive conflict (EAC). In this study, we screened the angiosperm DFR gene focusing on a diversified genus Scutellaria to investigate how these duplicated genes are retained. We deduced that gene duplication involved multiple independent events in angiosperms, but the duplication of DFR was before the divergence of Scutellaria. Asymmetric positive selective pressures resulted in different evolutionary rates between the duplicates. Different numbers of regulatory elements, differential codon usages, radical amino acid changes, and differential gene expressions provide evidences of functional divergence between the two DFR duplicates in Scutellaria, implying adaptive subfunctionalization between duplicates. The discovery of pseudogenes accompanying a reduced replacement rate in one DFR paralogous gene suggested possibly leading to “loss of function” due to dosage imbalance after the transient adaptive subfunctionalization in the early stage of duplication. Notwithstanding, episodic gene duplication and functional divergence may be relevant to the diversification of ecological function of DFR gene in Scutellaria.
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- 2016
- Full Text
- View/download PDF
38. Population genetic structure, local adaptation, and conservation genetics of Kandelia obovata
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Yu Ruan, Yu Ting Wan, Jun Qing Li, Shong Huang, Shih Jie Lai, Pei Chun Liao, and Bing Hong Huang
- Subjects
Conservation genetics ,education.field_of_study ,Ecology ,Population ,Forestry ,Horticulture ,Biology ,biology.organism_classification ,Gene flow ,Effective population size ,Kandelia obovata ,Genetic structure ,Genetics ,Biological dispersal ,education ,Molecular Biology ,Local adaptation - Abstract
Topographic changes during the Pleistocene glacial/interglacial cycles affected the distribution of coastline mangroves and influenced their population genetic structure. The submergence of the continental shelf off southeast China during the postglacial age caused coastline expansions and resulted in the colonization of mangroves. Here, we performed multilocus genome scans using amplified fragment-length polymorphisms to explore the effects of topography and natural selection in structuring Kandelia obovata populations. Long-term isolation by the Taiwan Strait since the end of the last glacial maximum, which obstructed gene flow, differentiated the Taiwanese and Chinese populations. Founders that colonized from both outlets of the Taiwan Strait were sourced from the northern South China Sea and the Ryukyus, thereby creating a melting pot in the Taiwan Strait. Inner-strait currents played roles as vectors for propagule dispersal among populations. Upon examination of the allele-frequency distributions of outlier loci, most negative outliers reflected the widespread polymorphisms shared by common ancestors. Furthermore, significant differentiation in the genetic components of positive outliers between this and other populations and the negative correlation with geographic distance suggested the presence of geography- or latitude-independent population divergence. Restored populations were compared with their sources and revealed biased sampling of nursery seedlings, which caused within-population substructures and reduced effective population sizes. This study indicated that multiple factors affect the population structure of the mangroves off southeast China.
- Published
- 2013
39. From shoot to leaf: step-wise shifts in meristem and KNOX1 activity correlate with the evolution of a unifoliate body plan in Gesneriaceae
- Author
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Michael Möller, Bing-Hong Huang, Chun-Neng Wang, and Kanae Nishii
- Subjects
0106 biological sciences ,0301 basic medicine ,food.ingredient ,Meristem ,Lamiales ,Biology ,Calceolariaceae ,010603 evolutionary biology ,01 natural sciences ,Gesneriaceae ,03 medical and health sciences ,Magnoliopsida ,food ,Botany ,Genetics ,Plantaginaceae ,Amino Acid Sequence ,Phylogeny ,Plant Proteins ,Homeodomain Proteins ,Antirrhinum ,biology.organism_classification ,Biological Evolution ,Plant Leaves ,030104 developmental biology ,Streptocarpus ,Sequence Alignment ,Cotyledon ,Developmental Biology - Abstract
Typical dicots possess equal-sized cotyledons and leaf-bearing shoots topped with a shoot apical meristem (SAM), the source of lateral organs, and where KNOX1 homeobox genes act as key regulators. New World Gesneriaceae show typical cotyledons, whereas Old World Gesneriaceae show anisocotyly, the unequal post-germination growth of cotyledons, and include unifoliate (one-leaf) plants. One-leaf plants show an extremely reduced body plan: the adult above-ground photosynthetic tissue consisting of a single cotyledon, a macrocotyledon enlarged by the basal meristem (BM), but lacking a SAM. To investigate the origin and evolution of the BM and one-leaf plants, the meristem activity and KNOX1 SHOOTMERISTEMLESS (STM) expression in cotyledons and leaves were systematically studied by RT-PCR and in situ hybridization across the family Gesneriaceae, Jovellana in Calceolariaceae (sister family to Gesneriaceae), and Antirrhinum in Plantaginaceae, all families of order Lamiales (asterids), in comparison to Arabidopsis (Brassicales, rosids). In all examined Lamiales samples, unlike Arabidopsis, BM activity accompanied by STM expression was found in both cotyledons in early stages. Foliage leaves of Gesneriaceae and Jovellana also showed the correlation of BM and STM expression. An extension of BM activity was found following a phylogenetic trajectory towards one-leaf plants where it is active throughout the lifetime of the macrocotyledon. Our results suggest that KNOX1 involvement in early cotyledon expansion originated early on in the diversification of Lamiales and is proposed as the prerequisite for the evolution of vegetative diversity in Gesneriaceae. Step-wise morphological shifts, driven by transfers of meristematic activity, as evidenced by shifts in KNOX1 expression, may be one mechanism by which morphological diversity evolves in plants.
- Published
- 2016
40. Changes of diet and dominant intestinal microbes in farmland frogs
- Author
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Bing Hong Huang, Pei Chun Liao, Chia Lung Huang, Si Min Lin, and Chun Wen Chang
- Subjects
0106 biological sciences ,0301 basic medicine ,Microbiology (medical) ,Fejervarya limnocharis ,Richness ,Male ,Firmicutes ,Gut microbiota ,Gut flora ,Generalist and specialist species ,010603 evolutionary biology ,01 natural sciences ,Microbiology ,03 medical and health sciences ,Abundance ,Animals ,Ecosystem ,Phylogeny ,biology ,Bacteria ,Ecology ,Bacteroidetes ,biology.organism_classification ,Custom farming ,Animal Feed ,Diet ,Gastrointestinal Microbiome ,Intestines ,030104 developmental biology ,Microbial population biology ,Female ,Species richness ,Anura ,Acidobacteria ,Research Article - Abstract
Background Agricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems. Results The occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes. Conclusions This study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife. Electronic supplementary material The online version of this article (doi:10.1186/s12866-016-0660-4) contains supplementary material, which is available to authorized users.
- Published
- 2016
41. Microbial Community Composition of the Danshui River Estuary of Northern Taiwan and the Practicality of the Phylogenetic Method in Microbial Barcoding
- Author
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Bing Hong Huang, Pei Chun Liao, and Shong Huang
- Subjects
Molecular Sequence Data ,Taiwan ,Biodiversity ,Soil Science ,Biology ,Comamonadaceae ,Diversity index ,Rivers ,Microbial ecology ,RNA, Ribosomal, 16S ,Proteobacteria ,Ecosystem ,Rhodobacteraceae ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Genetic diversity ,Geography ,Ecology ,Community structure ,Genetic Variation ,Sequence Analysis, DNA ,Microbial population biology ,Species evenness ,Water Microbiology ,human activities ,Gammaproteobacteria - Abstract
In this study, the microbial community in a mangrove ecosystem was surveyed and used to test the eligibility of 16S rDNA library and neighbor-joining method for the purpose of estimating microbial composition. Genetic diversity (pi) and four other diversity indices (Simpson's unbiased, Shannon-Wiener, Evenness, and Chao1 indices) were applied to estimate the adaptive lineages of microorganisms in the mangrove ecosystem. The results indicated that gamma-Proteobacteria is the most diverse taxon, while the most abundant family is Rhodobacteraceae (alpha-Proteobacteria), followed by Comamonadaceae (beta-Proteobacteria). This result may imply the existence of a graded distribution of microbial diversity across a spectrum of different salinities in the waterbody of this estuary ecosystem. Furthermore, at least 500-1,000 bps of the posterior portion of 16S rDNA is required as a marker to profile the microbial diversity in a microcosm of interest using phylogenetic methods, according to the results of our sliding window analyses for the measurements of pi, consistency index, and retention index.
- Published
- 2007
42. Inferences of demographic history and fine-scale landscape genetics in Cycas panzhihuaensis and implications for its conservation
- Author
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Yong Qiong Yang, Bing Hong Huang, Zhi Xiang Yu, and Pei Chun Liao
- Subjects
education.field_of_study ,Genetic diversity ,Ecology ,Demographic history ,Population ,Forestry ,Horticulture ,Biology ,Ex situ conservation ,Effective population size ,Genetic structure ,Threatened species ,Genetics ,education ,Cycas panzhihuaensis ,Molecular Biology - Abstract
Understanding the population genetic structure and demographic history helps in the management and restoration of endangered species. Cycas panzhihuaensis (Panzihihua sago palm) is narrowly distributed in the eastern Sichuan Basin of China. The only extant population is in the Panzhihua Cycad Nature Reserve (PCNR), which is close to Panzhihua City, and is threatened by the mining industry and slash-and-burn agriculture. To protect this rare species, the local government implemented an ex situ conservation project. In this study, amplified fragment length polymorphism (AFLP) was used to explore the genetic diversity of wild and cultivated populations. Two evolutionarily significant units (ESUs) in PCNR were determined based on significant differences in genetic diversity and demographic histories. The western ESU has low genetic diversity and shares common genotypes with a part of the eastern ESU. The founder effect is suggested as the best-fit scenario to explain the current genetic distribution among the eastern and western ESUs. Small carrying capacity limits both census and effective population sizes, and the gene surfing hypothesis explains the high frequency of fixed alleles without private alleles in multiple loci in the western subpopulation. Every cultivated population, established for either conservation or horticultural purposes, has only genotypes from a single ESU. Supplementary collection for ex situ conservation is suggested to preserve the genetic features of C. panzhihuaensis.
- Published
- 2015
43. 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
- Subjects
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
44. Development of transferable expressed sequence tag-simple sequence repeat (EST-SSR) markers for delimitating two recently diverged gingers endemic to Taiwan.
- Author
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Yi-Ting TSENG, Min-Xin LUO, Bing-Hong HUANG, and Pei-Chun LIAO
- Subjects
PRINCIPAL components analysis ,MICROSATELLITE repeats ,GINGER ,DISCRIMINANT analysis ,GENETIC markers ,BAYESIAN analysis - Abstract
Species delimitation may be difficult for recently divergent species, particularly those with few distinguishable morphological characteristics. Zingiber kawagoii and Z. shuanglongensis are two recently divergent species endemic to Taiwan whose extremely similar vegetative characteristics hinder their distinction during non-flowering seasons. Given their recent divergence, the speciation process and introgressions between these two gingers warrant exploration. However, such studies are hampered by the absence of appropriate molecular markers. To solve this dilemma, we developed 20 transferable expressed sequence tag-simple sequence repeat loci (EST-SSR). Seven highly differentiated loci were further identified for rapid species delimitation. A preliminary test using discriminant analysis of principal components (DAPC) validated the effective discrimination of these EST-SSR loci, while Bayesian clustering analysis (BCA) revealed obvious introgression events between species, particularly on positive-outlier loci. These results imply adaptive introgressions between these species. However, more sampling and further experiments are necessary to validate this inference and resolve questions regarding the introgression and speciation mechanisms. The development of genetic markers in this study provides appropriate experimental conditions and a basis for further research. [ABSTRACT FROM AUTHOR]
- Published
- 2019
- Full Text
- View/download PDF
45. Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals
- Author
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Pei Chun Liao and Bing Hong Huang
- Subjects
Primates ,Plasmodium ,Immunology ,Microbiology ,Evolutionary arms race ,parasitic diseases ,medicine ,Animals ,Humans ,Codon ,Molecular Biology ,Immune gene ,Phylogeny ,Genetics ,Mammals ,Recombination, Genetic ,biology ,Positive selection ,Cell Biology ,medicine.disease ,biology.organism_classification ,Biological Evolution ,Immunity, Innate ,Malaria ,Infectious Diseases ,Amino Acid Substitution ,Evolutionary biology ,Functional divergence ,Signal Transduction - Abstract
Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens.
- Published
- 2014
46. Asymmetric Introgression in the Horticultural Living Fossil Cycas Sect. Asiorientales Using a Genome-Wide Scanning Approach
- Author
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Yu Ting Wan, Pei Chun Liao, Shih Jie Lai, Bing Hong Huang, Chun Wen Chang, Shong Huang, and Yu-Chung Chiang
- Subjects
Cycas ,Gene Flow ,introgression ,AFLP ,Cycas revoluta ,Cycas taitungensis ,horticulture ,DNA, Plant ,Population ,Taiwan ,Allopatric speciation ,Introgression ,Article ,Catalysis ,Gene flow ,Inorganic Chemistry ,lcsh:Chemistry ,Species Specificity ,Amplified Fragment Length Polymorphism Analysis ,Physical and Theoretical Chemistry ,education ,Molecular Biology ,Cycad ,lcsh:QH301-705.5 ,Ecosystem ,Phylogeny ,Spectroscopy ,Principal Component Analysis ,education.field_of_study ,biology ,Fossils ,Ecology ,Organic Chemistry ,Genetic Variation ,Bayes Theorem ,General Medicine ,biology.organism_classification ,Computer Science Applications ,lcsh:Biology (General) ,lcsh:QD1-999 ,Evolutionary biology ,Hybridization, Genetic ,Lod Score ,Genome, Plant - 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. 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.
- Published
- 2013
- Full Text
- View/download PDF
47. Diversification, biogeographic pattern, and demographic history of Taiwanese Scutellaria species inferred from nuclear and chloroplast DNA
- Author
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Bing Hong Huang, Yu-Chung Chiang, and Pei Chun Liao
- Subjects
Gene Flow ,Evolutionary Genetics ,Plant Phylogenetics ,Evolutionary Processes ,Plant Evolution ,DNA, Plant ,Demographic history ,Scutellaria ,Speciation ,Population ,Molecular Sequence Data ,Population Dynamics ,Taiwan ,Population genetics ,lcsh:Medicine ,Plant Science ,Biology ,Species Specificity ,Effective Population Size ,Genetics ,Endemism ,education ,lcsh:Science ,Phylogeny ,Cell Nucleus ,education.field_of_study ,Evolutionary Biology ,Multidisciplinary ,Phylogenetic tree ,Population Biology ,Models, Genetic ,Ecology ,lcsh:R ,DNA, Chloroplast ,Species diversity ,Paleogenetics ,Genetic Variation ,food and beverages ,Bayes Theorem ,Phylogeography ,Haplotypes ,Genetic Polymorphism ,lcsh:Q ,Population Genetics ,Research Article - Abstract
The ragged topography created by orogenesis generates diversified habitats for plants in Taiwan. In addition to colonization from nearby mainland China, high species diversity and endemism of plants is also present in Taiwan. Five of the seven Scutellaria species (Lamiaceae) in Taiwan, for example, are endemic to the island. Hypotheses of multiple sources or in situ radiation have arisen to explain the high endemism of Taiwanese species. In this study, phylogenetic analyses using both nuclear and chloroplast markers revealed the multiple sources of Taiwanese Scutellaria species and confirmed the rapid and recent speciation of endemic species, especially those of the “indica group” composed of S. indica, S. austrotaiwanensis, S. tashiroi, and S. playfairii. The common ancestors of the indica group colonized first in northern Taiwan and dispersed regionally southward and eastward. Climate changes during glacial/interglacial cycles led to gradual colonization and variance events in the ancestors of these species, resulting in the present distribution and genetic differentiation of extant populations. Population decline was also detected in S. indica, which might reflect a bottleneck effect from the glacials. In contrast, the recently speciated endemic members of the indica group have not had enough time to accumulate much genetic variation and are thus genetically insensitive to demographic fluctuations, but the extant lineages were spatially expanded in the coalescent process. This study integrated phylogenetic and population genetic analyses to illustrate the evolutionary history of Taiwanese Scutellaria of high endemism and may be indicative of the diversification mechanism of plants on continental islands.
- Published
- 2012
48. Characterization of 24 transferable microsatellite loci in four skullcaps (Scutellaria, Labiatae)
- Author
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Tsai Wen Hsu, Huei Chuan Shih, Pei Chun Liao, Chun Wen Chang, Bing Hong Huang, and Yu-Chung Chiang
- Subjects
Genetic Markers ,Heterozygote ,DNA, Plant ,Scutellaria ,Population structure ,Molecular Sequence Data ,Taiwan ,Introduced species ,Plant Science ,Biology ,Polymerase Chain Reaction ,Loss of heterozygosity ,Genetics ,Allele ,Ecology, Evolution, Behavior and Systematics ,Alleles ,DNA Primers ,Polymorphism, Genetic ,Base Sequence ,Scutellaria indica ,Genetic Variation ,Sequence Analysis, DNA ,Mating system ,biology.organism_classification ,Genetic Loci ,Microsatellite ,Microsatellite Repeats - Abstract
Premise of the study: Transferable polymorphic microsatellite loci for four skullcaps, Scutellaria indica , S. taiwanensis , S. austrotaiwanensis , and S. playfairii , were developed for future studies of the mating system and population structure of these species. Interspecifi c amplifi cation was also tested in various Scutellaria species. Methods and Results: Twelve novel polymorphic microsatellite loci were isolated from four S. taiwanensis specimens, and seven are interspecifi cally transferable. Microsatellite loci developed from S. austrotaiwanensis in a previous study were also analyzed in the other three species, and 12 loci were found to be transferable. Allele numbers of the total 24 loci for S. indica , S. taiwanensis , S. playfairii , and S. austrotaiwanensis are two to four, two, two to fiand two to three, respectively, with an expected heterozygosity ranging from 0.114 – 0.661, 0.062 – 0.499, 0.280 – 0.730, and 0.268 – 0.662, respectively. The interspecies transferability of these 24 loci was further tested in another 10 Scutellaria species, including three species native to Taiwan. Seventeen loci were found to be interspecifi cally amplifi able, especially among the Taiwan native species. Conclusions: These highly polymorphic and transferable loci will be useful for future studies of the mating system of closely related Scutellaria species.
- Published
- 2011
49. Diversifying selection of the anthocyanin biosynthetic downstream gene UFGT accelerates floral diversity of island Scutellaria species.
- Author
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Bing-Hong Huang, Yi-Wen Chen, Chia-Lung Huang, Jian Gao, and Pei-Chun Liao
- Subjects
- *
PLANT diversity , *SCUTELLARIA , *POLLINATION , *FLOWERS , *INFLORESCENCES , *GENETIC mutation , *NATURAL selection , *BIOLOGICAL evolution , *PLANTS - Abstract
Background: Adaptive divergence, which usually explains rapid diversification within island species, might involve the positive selection of genes. Anthocyanin biosynthetic pathway (ABP) genes are important for floral diversity, and are related to stress resistance and pollination, which could be responsible for species diversification. Previous studies have shown that upstream genes of ABP are subject to selective constraints and have a slow evolutionary rate, while the constraints on downstream genes are lower. Results: In this study, we confirmed these earlier observations of heterogeneous evolutionary rate in upstream gene CHS and the downstream gene UFGT, both of which were expressed in Scutellaria sp. inflorescence buds. We found a higher evolutionary rate and positive selection for UFGT. The codons under positive selection corresponded to the diversified regions, and the presence or absence of an α-helix might produce conformation changes in the Rossmann-like fold structure. The significantly high evolutionary rates for UFGT genes in Taiwanese lineages suggested rapid accumulation of amino acid mutations in island species. The results showed positive selection in closely related species and explained the high diversification of floral patterns in these recently diverged species. In contrast, non-synonymous mutation rate decreases in long-term divergent species could reduce mutational load and prevent the accumulation of deleterious mutations. Conclusions: Together with the positive selection of transcription factors for ABP genes described in a previous study, these results confirmed that positive selection takes place at a translational level and suggested that the high divergence of ABP genes is related to the floral diversity in island Scutellaria species. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
50. Changes of diet and dominant intestinal microbes in farmland frogs.
- Author
-
Chun-Wen Chang, Bing-Hong Huang, Si-Min Lin, Chia-Lung Huang, and Pei-Chun Liao
- Subjects
- *
DIET , *MICROORGANISMS , *HABITATS , *HABITAT selection , *AGRICULTURAL ecology - Abstract
Background: Agricultural activities inevitably result in anthropogenic interference with natural habitats. The diet and the gut microbiota of farmland wildlife can be altered due to the changes in food webs within agricultural ecosystems. In this work, we compared the diet and intestinal microbiota of the frog Fejervarya limnocharis in natural and farmland habitats in order to understand how custom farming affects the health of in vivo microbial ecosystems. Results: The occurrence, abundance, and the numbers of prey categories of stomach content were significantly different between the frogs inhabiting natural and farmland habitats. In addition, differences in the abundance, species richness, and alpha-diversity of intestinal microbial communities were also statistically significant. The microbial composition, and particularly the composition of dominant microbes living in intestines, indicated that the land use practices might be one of factors affecting the gut microbial community composition. Although the first three dominant microbial phyla Bacteroidetes, Firmicutes, and Proteobacteria found in the intestines of frogs were classified as generalists among habitats, the most dominant gut bacterial phylum Bacteroidetes in natural environments was replaced by the microbial phylum Firmicutes in farmland frogs. Increased intestinal microbial richness of the farmland frogs, which is mostly contributed by numerous microbial species of Proteobacteria, Actinobacteria, Acidobacteria, and Planctomycetes, not only reflects the possible shifts in microbial community composition through the alteration of external ecosystem, but also indicates the higher risk of invasion by disease-related microbes. Conclusions: This study indicates that anthropogenic activities, such as the custom farming, have not only affected the food resources of frogs, but also influenced the health and in vivo microbial ecosystem of wildlife. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
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