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Dr. Hua-Feng Wang
Hainan University

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0 Phylogenetics
0 urban land use
0 Urban and rural ecosystems
0 Systematics
0 Urban plant diversity

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Systematics
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urban land use
Urban plant diversity

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Original research
Published: 05 August 2021 in Ecology and Evolution
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Within urban green spaces, tree species diversity is believed to correlate with aboveground biomass, though there is some disagreement within the literature on the strength and directionality of the relationship. Therefore, we assessed the relationship between the biodiversity of woody species and the aboveground biomass of woody plant species in the tropical, coastal city of Haikou in southern China. To accomplish this, we obtained comprehensive tree and site data through field sampling of 190 urban functional units (UFUs, or work units) corresponding to six types of land uses governmental-institutional, industrial-commercial, park-recreational, residential, transport infrastructure, and undeveloped area. Based on our field data, we investigated the relationship between tree species diversity and aboveground biomass using multiple regression, which revealed significant relationships across all five types of land uses. Aboveground biomass in green spaces was also correlated with anthropogenic factors, especially time since urban development, or site age, annual maintenance frequency by human caretakers, and human population density. Among these factors, maintenance is the strongest predictor of aboveground biomass in urban green space. Therefore, this study highlights the critical role of maintenance of urban green space in promoting both aboveground biomass and woody biodiversity in urban ecosystems and, consequently, on urban ecosystem services. Our findings contribute to a deeper understanding of the ecosystem services provided by communities of woody plant species in urban areas.

ACS Style

Mir Muhammad Nizamani; Aj Harris; Xia‐Lan Cheng; Zhi‐Xin Zhu; Chi Yung Jim; Hua‐Feng Wang. Positive relationships among aboveground biomass, tree species diversity, and urban greening management in tropical coastal city of Haikou. Ecology and Evolution 2021, 1 .

AMA Style

Mir Muhammad Nizamani, Aj Harris, Xia‐Lan Cheng, Zhi‐Xin Zhu, Chi Yung Jim, Hua‐Feng Wang. Positive relationships among aboveground biomass, tree species diversity, and urban greening management in tropical coastal city of Haikou. Ecology and Evolution. 2021; ():1.

Chicago/Turabian Style

Mir Muhammad Nizamani; Aj Harris; Xia‐Lan Cheng; Zhi‐Xin Zhu; Chi Yung Jim; Hua‐Feng Wang. 2021. "Positive relationships among aboveground biomass, tree species diversity, and urban greening management in tropical coastal city of Haikou." Ecology and Evolution , no. : 1.

Journal article
Published: 15 July 2021 in Mitochondrial DNA Part B
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Bridelia tomentosa is a deciduous shrub in the family of Phyllanthaceae. It grows in the evergreen primary or secondary thickets or forests in the sea level from 1000 to 1500 m. It distributed in.south China (e.g., Fujian, Guangdong, Guangxi, Hainan etc) and other south Asian countries (e.g. Bangladesh, Bhutan, Cambodia etc). Here, we report and characterize the complete plastome of B. tomentosa. The complete plastome is of 149,958 bp in length with a typical structure and gene content of angiosperm plastome, including two inverted repeat (IRs) regions of 26,354 bp, a large single-copy (LSC) region of 81,355 bp and a small single-copy (SSC) region of 15,895 bp. The plastome contains 129 genes, consisting of 84 protein-coding genes, 37 tRNA genes, eight rRNA genes. The overall G/C content in the plastome of B. tomentosa is 36.0%. The complete plastome sequence of B. tomentosa will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Phyllanthaceae.

ACS Style

Yan Chen; Xiu-Rong Ke; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. Complete plastome sequence of Bridelia tomentosa Blume (Phyllanthaceae): a medicinal shrub species in South Asia. Mitochondrial DNA Part B 2021, 6, 2330 -2331.

AMA Style

Yan Chen, Xiu-Rong Ke, Xiao-Feng Zhang, Zhi-Xin Zhu, Hua-Feng Wang. Complete plastome sequence of Bridelia tomentosa Blume (Phyllanthaceae): a medicinal shrub species in South Asia. Mitochondrial DNA Part B. 2021; 6 (8):2330-2331.

Chicago/Turabian Style

Yan Chen; Xiu-Rong Ke; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Complete plastome sequence of Bridelia tomentosa Blume (Phyllanthaceae): a medicinal shrub species in South Asia." Mitochondrial DNA Part B 6, no. 8: 2330-2331.

Journal article
Published: 23 June 2021 in Ecological Modelling
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Individual trait variation has important ecological implications for species populations and communities. In particular, individual variation of metabolic rate links directly with the energy use estimation and scaling patterns in community ecology. Here, we examine the mean-variance relationship of individual metabolic rate by testing Taylor's law (a power-function relationship between mean and variance) for individual rescaled metabolic rate across tree communities in tropical forests. We use a constraint-based model called maximum entropy theory of ecology (METE) to estimate and predict the parameters of Taylor's law. Our results show that, when assuming a universal metabolic scaling between metabolic rate and aboveground biomass, the METE generates the form of Taylor's law but fails to predict its slope. When setting the metabolic scaling exponent as a community-level parameter in the METE model, the estimated and predicted slopes of Taylor's law agree with each other. Our parameterized METE model reveals the positive effect of number of individuals on the metabolic scaling exponent. These results suggest that fluctuation scaling of individual metabolic rate can be explained solely by the macroecological constraints of communities, without relying on the physiological or genetic characters of individual organisms.

ACS Style

Meng Xu; Mengke Jiang; Hua-Feng Wang. Integrating metabolic scaling variation into the maximum entropy theory of ecology explains Taylor's law for individual metabolic rate in tropical forests. Ecological Modelling 2021, 455, 109655 .

AMA Style

Meng Xu, Mengke Jiang, Hua-Feng Wang. Integrating metabolic scaling variation into the maximum entropy theory of ecology explains Taylor's law for individual metabolic rate in tropical forests. Ecological Modelling. 2021; 455 ():109655.

Chicago/Turabian Style

Meng Xu; Mengke Jiang; Hua-Feng Wang. 2021. "Integrating metabolic scaling variation into the maximum entropy theory of ecology explains Taylor's law for individual metabolic rate in tropical forests." Ecological Modelling 455, no. : 109655.

Preprint content
Published: 01 June 2021
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Understanding biological diversity and the mechanisms of Sino-Japanese disjunctions are major challenges in eastern Asian biogeography. The Sino-Japanese flora has been broadly studied as an ideal model, however, few studies have focused on phylogeography and diversification at the genus level utilizing both nuclear and plastid data. Diabelia (Caprifoliaceae) is an East Asian genus, with a disjunctive distribution across the Sino-Japanese flora. However, relationships within Diabelia remain elusive, with none of the previous studies having inferred a species phylogeny using nuclear loci. In this study, we reconstructed the phylogenetic relationships among Diabelia based on nuclear and plastid sequence data by using target enrichment and genome skimming approaches, respectively. We found that the main clades within Diabelia were discordant between nuclear and plastid trees. Both nuclear and plastid phylogenetic analyses supported five main clades: D. serrata, D. tetrasepala, D. spathulata var. sanguinea, D. spathulata var. stenophylla and D. spathulata var. spathulata. Diabelia tetrasepala was inferred to be the result of a hybridization event from the species network analyses. Divergence time estimation and ancestral area reconstructions showed that Diabelia originated in Japan during the early Miocene, with subsequent gene flow between China, Japan and Korea. Overall, our results support the division of Diabelia into five main clades and this research provides new insights in the speciation process and taxonomy of Diabelia.

ACS Style

Xiu-Rong Ke; Diego F. Morales-Briones; Hong-Xin Wang; Qing-Hui Sun; Jacob B. Landis; Jun Wen; Hua-Feng Wang. Nuclear and plastid phylogenomic analyses provide insights into the biogeography and reticulate evolution of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae). 2021, 1 .

AMA Style

Xiu-Rong Ke, Diego F. Morales-Briones, Hong-Xin Wang, Qing-Hui Sun, Jacob B. Landis, Jun Wen, Hua-Feng Wang. Nuclear and plastid phylogenomic analyses provide insights into the biogeography and reticulate evolution of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae). . 2021; ():1.

Chicago/Turabian Style

Xiu-Rong Ke; Diego F. Morales-Briones; Hong-Xin Wang; Qing-Hui Sun; Jacob B. Landis; Jun Wen; Hua-Feng Wang. 2021. "Nuclear and plastid phylogenomic analyses provide insights into the biogeography and reticulate evolution of the Sino-Japanese disjunctive Diabelia (Caprifoliaceae)." , no. : 1.

Journal article
Published: 28 May 2021 in BMC Ecology and Evolution
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Background The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always form sister clades. Perkinsiodendron and Changiostyrax are newly established genera of Styracaceae. However, the phylogenetic relationship of Styracaceae at the generic level needs further research. Results We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, with sequence differences being minor, except for a large 20-kb (14 genes) inversion found in Alniphyllum and Bruinsmia. Seven coding sequences (rps4, rpl23, accD, rpoC1, psaA, rpoA and ndhH) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC + SSC and concatenation of LSC + SSC + one IR) produced similar topologies. In our analyses, all genera were strongly supported as monophyletic. Styrax was sister to the remaining genera. Alniphyllum and Bruinsmia form a clade. Halesia diptera does not cluster with Perkinsiodendron, while Perkinsiodendron and Rehderodendron form a clade. Changiostyrax is sister to a clade of Pterostyrax and Sinojackia. Conclusion Overall, our results demonstrate the power of plastid phylogenomics in improving estimates of phylogenetic relationships among genera. This study also provides insight into plastome evolution across Styracaceae.

ACS Style

Xiu-Lian Cai; Jacob B. Landis; Hong-Xin Wang; Jian-Hua Wang; Zhi-Xin Zhu; Hua-Feng Wang. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC Ecology and Evolution 2021, 21, 1 -16.

AMA Style

Xiu-Lian Cai, Jacob B. Landis, Hong-Xin Wang, Jian-Hua Wang, Zhi-Xin Zhu, Hua-Feng Wang. Plastome structure and phylogenetic relationships of Styracaceae (Ericales). BMC Ecology and Evolution. 2021; 21 (1):1-16.

Chicago/Turabian Style

Xiu-Lian Cai; Jacob B. Landis; Hong-Xin Wang; Jian-Hua Wang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Plastome structure and phylogenetic relationships of Styracaceae (Ericales)." BMC Ecology and Evolution 21, no. 1: 1-16.

Comparative study
Published: 15 May 2021 in BMC Plant Biology
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Background Myrtales is a species rich branch of Rosidae, with many species having important economic, medicinal, and ornamental value. At present, although there are reports on the chloroplast structure of Myrtales, a comprehensive analysis of the chloroplast structure of Myrtales is lacking. Phylogenetic and divergence time estimates of Myrtales are mostly constructed by using chloroplast gene fragments, and the support for relationships is low. A more reliable method to reconstruct the species divergence time and phylogenetic relationships is by using whole chloroplast genomes. In this study, we comprehensively analyzed the structural characteristics of Myrtales chloroplasts, compared variation hotspots, and reconstructed the species differentiation time of Myrtales with four fossils and one secondary calibration point. Results A total of 92 chloroplast sequences of Myrtales, representing six families, 16 subfamilies and 78 genera, were obtained including nine newly sequenced chloroplasts by whole genome sequencing. Structural analyses showed that the chloroplasts range in size between 152,214–171,315 bp and exhibit a typical four part structure. The IR region is between 23,901–36,747 bp, with the large single copy region spanning 83,691–91,249 bp and the small single copy region spanning 11,150–19,703 bp. In total, 123–133 genes are present in the chloroplasts including 77–81 protein coding genes, four rRNA genes and 30–31 tRNA genes. The GC content was 36.9–38.9%, with the average GC content being 37%. The GC content in the LSC, SSC and IR regions was 34.7–37.3%, 30.6–36.8% and 39.7–43.5%, respectively. By analyzing nucleotide polymorphism of the chloroplast, we propose 21 hypervariable regions as potential DNA barcode regions for Myrtales. Phylogenetic analyses showed that Myrtales and its corresponding families are monophyletic, with Combretaceae and the clade of Onagraceae + Lythraceae (BS = 100%, PP = 1) being sister groups. The results of molecular dating showed that the crown of Myrtales was most likely to be 104.90 Ma (95% HPD = 87.88–114.18 Ma), and differentiated from the Geraniales around 111.59 Ma (95% HPD = 95.50–118.62 Ma). Conclusions The chloroplast genome structure of Myrtales is similar to other angiosperms and has a typical four part structure. Due to the expansion and contraction of the IR region, the chloroplast genome sizes in this group are slightly different. The variation of noncoding regions of the chloroplast genome is larger than those of coding regions. Phylogenetic analysis showed that Combretaceae and Onagraceae + Lythraceae were well supported as sister groups. Molecular dating indicates that the Myrtales crown most likely originated during the Albian age of the Lower Cretaceous. These chloroplast genomes contribute to the study of genetic diversity and species evolution of Myrtales, while providing useful information for taxonomic and phylogenetic studies of Myrtales.

ACS Style

Xiao-Feng Zhang; Jacob B. Landis; Hong-Xin Wang; Zhi-Xin Zhu; Hua-Feng Wang. Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. BMC Plant Biology 2021, 21, 1 -19.

AMA Style

Xiao-Feng Zhang, Jacob B. Landis, Hong-Xin Wang, Zhi-Xin Zhu, Hua-Feng Wang. Comparative analysis of chloroplast genome structure and molecular dating in Myrtales. BMC Plant Biology. 2021; 21 (1):1-19.

Chicago/Turabian Style

Xiao-Feng Zhang; Jacob B. Landis; Hong-Xin Wang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Comparative analysis of chloroplast genome structure and molecular dating in Myrtales." BMC Plant Biology 21, no. 1: 1-19.

Article
Published: 14 April 2021
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Background and Aims Abelia (Caprifoliaceae) is a small genus with six species (including one artificial hybrid). The genus has a disjunct distribution across mainland China, Taiwan, and the Ryukyu islands, providing a model system to explore mechanisms of species dispersal in the East Asian flora. However, the current phylogenetic relationships within Abelia remain uncertain. Methods In this study, we reconstructed phylogenetic relationships within Abelia using nuclear loci generated by target enrichment and plastomes from genome skimming. Divergence time estimation, ancestral area reconstruction, and ecological niche modelling (ENM) were used to examine the biogeographic diversification of Abelia. Key Results We found extensive cytonuclear discordance across the genus. Based on nuclear and plastid phylogenies we proposed to merge A. macrotera var. zabelioides into A. uniflora. Network analyses suggested that A chinensis, A. macrotera and A. uniflora are from complex hybrid origins. These hybridization events may explain the complicated taxonomy of the group. Our results show that Abelia originated in southwest China, with the nuclear haplotype network suggesting an ancestral haplotype from southwest and central China. The diversification of Abelia began in the late Eocene, followed by A. chinensis var. ionandra colonizing the island of Taiwan in the Middle Miocene. The ENM results suggested an expansion of climatically suitable areas during the Last Glacial Maximum and range contraction during the Last Interglacial. Disjunction between the Himalayan-Hengduan Mountain region (HHM) and the island of Taiwan is most likely the consequence of topographic isolation and postglacial contraction. Conclusions We used genomic data to reconstruct the phylogeny of Abelia and found a clear pattern of reticulate evolution in the group. Overall, our results supported postglacial range contraction together with topographic heterogeneity resulted in the mainland China-Taiwan island disjunction. This study provides important new insights into the speciation process and taxonomy of Abelia.

ACS Style

Qing-Hui Sun; Diego F. Morales-Briones; Hong-Xin Wang; Jacob B. Landis; Jun Wen; Hua-Feng Wang. Phylogenomic insights into the divergent history and hybridization within the East Asian endemic Abelia (Caprifoliaceae). 2021, 1 .

AMA Style

Qing-Hui Sun, Diego F. Morales-Briones, Hong-Xin Wang, Jacob B. Landis, Jun Wen, Hua-Feng Wang. Phylogenomic insights into the divergent history and hybridization within the East Asian endemic Abelia (Caprifoliaceae). . 2021; ():1.

Chicago/Turabian Style

Qing-Hui Sun; Diego F. Morales-Briones; Hong-Xin Wang; Jacob B. Landis; Jun Wen; Hua-Feng Wang. 2021. "Phylogenomic insights into the divergent history and hybridization within the East Asian endemic Abelia (Caprifoliaceae)." , no. : 1.

Research article
Published: 05 April 2021 in Journal of Systematics and Evolution
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The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data, species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we herein recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and chloroplast genomes to reconstruct deep and shallow phylogenies of plants.

ACS Style

Hong‐Xin Wang; Diego F. Morales‐Briones; Michael J. Moore; Jun Wen; Hua‐Feng Wang. A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily. Journal of Systematics and Evolution 2021, 1 .

AMA Style

Hong‐Xin Wang, Diego F. Morales‐Briones, Michael J. Moore, Jun Wen, Hua‐Feng Wang. A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily. Journal of Systematics and Evolution. 2021; ():1.

Chicago/Turabian Style

Hong‐Xin Wang; Diego F. Morales‐Briones; Michael J. Moore; Jun Wen; Hua‐Feng Wang. 2021. "A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily." Journal of Systematics and Evolution , no. : 1.

Mitogenome announcement
Published: 03 April 2021 in Mitochondrial DNA Part B
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Mallotus japonicus is a shrub species in the family of Euphorbiaceae. The study of plastome would be helpful for its phylogenetic study and species identification. The total length of complete plastome for Mallotus japonicus is of 164,912 bp, with typical part-four structure and gene content of angiosperm plastome, including two inverted repeat (IR) regions of 27,829 bp, a large single-copy (LSC) region of 90,319 bp, and a small single-copy (SSC) region of 18,935 bp. The plastome contains 125 genes, consisting of 80 unique protein-coding genes, 31 unique tRNA gene, four unique rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA), and five pseudogenes. The overall G/C content in the plastome of Mallotus japonicus is 40.2%. The phylogenetic analysis indicates that M. japonicus is closer to M. peltatus than other species in this study. The complete plastome sequence is conducive to the exploitation and utilization of Euphorbiaceae resources and the phylogenetic study in future.

ACS Style

Wan-Ping Wu; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. Complete plastome sequence of Mallotus japonicus (Linn. f.) Müll. Arg. (Euphorbiaceae): a medicinal plant species endemic in East Asia. Mitochondrial DNA Part B 2021, 6, 1409 -1410.

AMA Style

Wan-Ping Wu, Xiao-Feng Zhang, Zhi-Xin Zhu, Hua-Feng Wang. Complete plastome sequence of Mallotus japonicus (Linn. f.) Müll. Arg. (Euphorbiaceae): a medicinal plant species endemic in East Asia. Mitochondrial DNA Part B. 2021; 6 (4):1409-1410.

Chicago/Turabian Style

Wan-Ping Wu; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Complete plastome sequence of Mallotus japonicus (Linn. f.) Müll. Arg. (Euphorbiaceae): a medicinal plant species endemic in East Asia." Mitochondrial DNA Part B 6, no. 4: 1409-1410.

Mitogenome announcement
Published: 03 April 2021 in Mitochondrial DNA Part B
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Balakata baccata belongs to the family Euphorbiaceae and is distributed in Yunnan province, China, and other southeast Asian countries, e.g., Bangladesh, Cambodia, India, Indonesia, etc. Here, we report and characterize the complete plastome of B. baccata. The complete plastome is 163,988 bp in length and contains a typical quadripartite structure and gene content found in angiosperms, including two inverted repeat (IR) regions of 27,274 bp, a large single-copy (LSC) region of 90,946 bp and a small single-copy (SSC) region of 18,494 bp. The plastome contains 129 genes, consisting of 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall G/C content in the plastome of B. baccata is 35.6%. Phylogenetic results show that B. baccata is the earliest diverging lineage of Euphorbioideae. Euphorbia helioscopia + E. esula, E. tirucalli + E. milii and B. baccata have a closer phylogenetic relationship than other taxa within Euphorbiaceae. The complete plastome sequence of B. baccata will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.

ACS Style

Lin-Yuan Guo; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. Complete plastome sequence of Balakata baccata (Roxb.) Esser (Euphorbiaceae). Mitochondrial DNA Part B 2021, 6, 1387 -1388.

AMA Style

Lin-Yuan Guo, Xiao-Feng Zhang, Zhi-Xin Zhu, Hua-Feng Wang. Complete plastome sequence of Balakata baccata (Roxb.) Esser (Euphorbiaceae). Mitochondrial DNA Part B. 2021; 6 (4):1387-1388.

Chicago/Turabian Style

Lin-Yuan Guo; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Complete plastome sequence of Balakata baccata (Roxb.) Esser (Euphorbiaceae)." Mitochondrial DNA Part B 6, no. 4: 1387-1388.

Journal article
Published: 27 March 2021 in Urban Forestry & Urban Greening
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Relatively little is known about the dynamics of tropical urban forests, their phylogenetic diversity, as well as the socioeconomic and ecological factors that influence overall diversity across the urban landscape. However, permanent forest inventory and monitoring plot networks are increasingly being established across forests and cities of the world to monitor structural and functional attributes of urban forests, as well as ecosystem services. We analyzed a tropical, coastal urban forest in San Juan, Puerto Rico using metrics of phylogenetic diversity (PD), plant diversity, and available permanent plot data from an urban forest inventory and monitoring system. In total, we found that there were 152 species belonging to 119 genera and 44 families in San Juan. PD tended to be highest in forest remnants. We also explored correlations between socioeconomic factors and taxonomic diversity and found that plant species richness was correlated with population density and housing price. We found marginally significant relationships between housing price, population density, and several PD metrics. Our results further suggest mixed evidence of luxury and legacy effects, two factors that have been linked to the plant diversity of anthropogenic ecosystems in other research. Overall, despite centuries of human influence, the existing urban forest diversity in San Juan - although perhaps not the particular species composition - is likely to be primarily the result of climate, biome, and multi-scale socioeconomic contexts and not legacy effects. The approach used and findings from this study could be used to better understand the application of PD metrics for assessing urban biodiversity and other beneficial attributes of urban forests.

ACS Style

Zhi-Xin Zhu; Francisco J. Escobedo; Liam J. Revell; Thomas Brandeis; Jun Xie; Hua-Feng Wang. Using phylogenetic diversity to explore the socioeconomic and ecological drivers of a tropical, coastal urban forest. Urban Forestry & Urban Greening 2021, 61, 127111 .

AMA Style

Zhi-Xin Zhu, Francisco J. Escobedo, Liam J. Revell, Thomas Brandeis, Jun Xie, Hua-Feng Wang. Using phylogenetic diversity to explore the socioeconomic and ecological drivers of a tropical, coastal urban forest. Urban Forestry & Urban Greening. 2021; 61 ():127111.

Chicago/Turabian Style

Zhi-Xin Zhu; Francisco J. Escobedo; Liam J. Revell; Thomas Brandeis; Jun Xie; Hua-Feng Wang. 2021. "Using phylogenetic diversity to explore the socioeconomic and ecological drivers of a tropical, coastal urban forest." Urban Forestry & Urban Greening 61, no. : 127111.

Mitogenome announcement
Published: 04 March 2021 in Mitochondrial DNA Part B
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Macaranga tanarius (L.) Muell. Arg. is a tree species within Euphorbiaceae, which can be used for building timber and its extract can be used to treat diabetes. In this report, we describe the complete plastome sequence of Macaranga tanarius. The complete plastome of Macaranga tanarius (L.) Muell. Arg. is of 165,362 bp in length, and it is with typical plastome structure and gene content of angiosperm plastome, including two reverse repeat regions (IRs) of 27,503 bp, large single copy region (LSC) of 91,443 bp, and small single copy (SSC) region of 18,913 bp. The plastome contains 131 genes, including 85 protein coding genes, 38 tRNA genes, eight rRNA genes (i.e., 5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). The total G/C content of Macaranga tanarius (L.) Muell. Arg.plastome is 35.6%. The complete plastome sequence is conducive to the development and utilization of Euphorbiaceae resources and the phylogenetic study.

ACS Style

Jiang-Qu Tang; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. Complete plastome sequence of Macaranga tanarius (L.) Muell. Arg. (Euphorbiaceae): a fast-growing timber species. Mitochondrial DNA Part B 2021, 6, 929 -930.

AMA Style

Jiang-Qu Tang, Xiao-Feng Zhang, Zhi-Xin Zhu, Hua-Feng Wang. Complete plastome sequence of Macaranga tanarius (L.) Muell. Arg. (Euphorbiaceae): a fast-growing timber species. Mitochondrial DNA Part B. 2021; 6 (3):929-930.

Chicago/Turabian Style

Jiang-Qu Tang; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Complete plastome sequence of Macaranga tanarius (L.) Muell. Arg. (Euphorbiaceae): a fast-growing timber species." Mitochondrial DNA Part B 6, no. 3: 929-930.

Mitogenome announcement
Published: 04 March 2021 in Mitochondrial DNA Part B
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Xylosma longifolia is a tree species within Salicaceae and is distributed in Guizhou, Yunnan, Fujian, Guangxi, Guangdong, and Hainan provinces of China as well as in Vietnam, Laos, and India. There are no studies utilizing the complete plastome of Xylosma longifolia in the current literature. Therefore, this report provides a reference for the plastid gene sequence of Xylosma longifolia, and it contributes to the phylogenetic placement and species identification. In this report, we described the complete plastome sequence of Xylosma longifolia. The complete plastome length of Xylosma longifolia is 156,938 bp and has the typical quadripartite structure and gene content of angiosperms, including two inverted repeat (IR) regions of 27,514 bp, a large single-copy (LSC) region of 85,221 bp and a small single-copy (SSC) region of 16,689 bp. The plastome contains 130 genes, including 86 protein coding genes, 36 tRNA genes, eight rRNA genes (5S rRNA, 4.5S rRNA, 16S rRNA, and 23S rRNA). The GC content of the plastome is 36.8%. The complete plastome sequence will be a valuable resource for studies involving the phylogenetic inference of Salicaceae.

ACS Style

Peng Chen; Xiao-Feng Zhang; Jacob B. Landis; Zhi-Xin Zhu; Hua-Feng Wang. Complete plastome sequence of Xylosma longifolia Clos. (Salicaceae). Mitochondrial DNA Part B 2021, 6, 1085 -1086.

AMA Style

Peng Chen, Xiao-Feng Zhang, Jacob B. Landis, Zhi-Xin Zhu, Hua-Feng Wang. Complete plastome sequence of Xylosma longifolia Clos. (Salicaceae). Mitochondrial DNA Part B. 2021; 6 (3):1085-1086.

Chicago/Turabian Style

Peng Chen; Xiao-Feng Zhang; Jacob B. Landis; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Complete plastome sequence of Xylosma longifolia Clos. (Salicaceae)." Mitochondrial DNA Part B 6, no. 3: 1085-1086.

Mitogenome announcement
Published: 04 March 2021 in Mitochondrial DNA Part B
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Vernicia montana Lour. is a deciduous tree species belonging to the family of Euphorbiaceae, distributed in southeast Asia. Here, we report and characterize the complete plastome of Vernicia montana Lour. The complete plastome is of 164,506 bp in length with a typical structure and gene content of angiosperm plastome, including two inverted repeat (IRs) regions of 27,965 bp, a large single-copy (LSC) region of 91,427 bp and a small single-copy (SSC) region of 17,149 bp. The plastome contains 130 genes, consisting of 81 protein-coding genes (six of which are repetitive in IR), 38 tRNA genes (seven of which are repetitive in IR), seven rRNA genes (5S rRNA, 4.5S rRNA, 23S rRNA and 16S rRNA) (three of which are repetitive in the IR), and four pseudogenes. The overall G/C content in the plastome of Vernicia montana Lour. is 35.8%. The complete plastome sequence of montana Lour. will provide a useful resource for the conservation genetics of this species as well as for phylogenetic studies in Euphorbiaceae.

ACS Style

Jian-Feng Yao; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. Complete plastome sequence of Vernicia Montana Lour. (Euphorbiaceae): a deciduous tree species in southeast Asia. Mitochondrial DNA Part B 2021, 6, 1075 -1076.

AMA Style

Jian-Feng Yao, Xiao-Feng Zhang, Zhi-Xin Zhu, Hua-Feng Wang. Complete plastome sequence of Vernicia Montana Lour. (Euphorbiaceae): a deciduous tree species in southeast Asia. Mitochondrial DNA Part B. 2021; 6 (3):1075-1076.

Chicago/Turabian Style

Jian-Feng Yao; Xiao-Feng Zhang; Zhi-Xin Zhu; Hua-Feng Wang. 2021. "Complete plastome sequence of Vernicia Montana Lour. (Euphorbiaceae): a deciduous tree species in southeast Asia." Mitochondrial DNA Part B 6, no. 3: 1075-1076.

Original research
Published: 01 February 2021 in Ecology and Evolution
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To better identify biodiversity hotspots for conservation on Hainan Island, a tropical island in southern China, we assessed spatial variation in phylogenetic diversity and species richness using 18,976 georeferenced specimen records and a newly reconstructed molecular phylogeny of 957 native woody plants. Within this framework, we delineated bioregions based on vegetation composition and mapped areas of neoendemism and paleoendemism to identify areas of priority for conservation. Our results reveal that the southwest of Hainan is the most important hot spot for endemism and plant diversity followed by the southeast area. The distribution of endemic species showed a scattered, rather than clustered, pattern on the island. Based on phylogenetic range‐weighted turnover metrics, we delineated three major vegetational zones in Hainan. These largely correspond to natural secondary growth and managed forests (e.g., rubber and timber forests) in central Hainan, old‐growth forests and natural secondary growth forest at the margins of Hainan, and nature reserves on the island (e.g., Jianfeng and Diaoluo National Nature Reserves). Our study helps to elucidate potential botanical conservation priorities for Hainan within an evolutionary, phylogenetic framework.

ACS Style

Zhi‐Xin Zhu; Aj Harris; Mir Muhammad Nizamani; Andrew H. Thornhill; Rosa A. Scherson; Hua‐Feng Wang. Spatial phylogenetics of the native woody plant species in Hainan, China. Ecology and Evolution 2021, 11, 2100 -2109.

AMA Style

Zhi‐Xin Zhu, Aj Harris, Mir Muhammad Nizamani, Andrew H. Thornhill, Rosa A. Scherson, Hua‐Feng Wang. Spatial phylogenetics of the native woody plant species in Hainan, China. Ecology and Evolution. 2021; 11 (5):2100-2109.

Chicago/Turabian Style

Zhi‐Xin Zhu; Aj Harris; Mir Muhammad Nizamani; Andrew H. Thornhill; Rosa A. Scherson; Hua‐Feng Wang. 2021. "Spatial phylogenetics of the native woody plant species in Hainan, China." Ecology and Evolution 11, no. 5: 2100-2109.

Preprint content
Published: 29 January 2021
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Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax and Sinojackia are monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the Large Single-Copy (LSC) region. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always form sister clades . Perkinsiodendron and Changiostyrax were newly established genera of Styracaceae. However, the phylogenetic relationship of Styracaceae at the genera level needs further research.Results: We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available complete plastome sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, and the sequence difference is small, except for the large 20-kb (14 genes) inversion region found in Alniphyllum and Bruinsmia. Seven coding sequences (rps4, rpl23, accD, rpoC1, psaA, rpoA and ndhH) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC+SSC and concatenation of LSC+SSC+one IR) produced similar topologies. In our analyses, all genera were strongly supported as monophyletic. Styrax was sister to the remaining genera. Alniphyllum and Bruinsmia form a clade. Halesia diptera does not cluster with Perkinsiodendron, while Perkinsiodendron and Rehderodendron form a clade. Changiostyrax is sister to a clade of Pterostyrax and Sinojackia,Conclusion: Our results clearly indicate that Pterostyrax is monophyletic, and the establishment of Perkinsiodendron and Changiostyrax are supported. A 20-kb reverse sequence was also found in the newly published sequence of Alniphyllum fortunei, which confirmed the existence of large inversion sequence in Alniphyllum and Bruinsmia.

ACS Style

Xiu-Lian Cai; Jacob B. Landis; Hong-Xin Wang; Jian-Hua Wang; Zhi-Xin Zhu; Huafeng Wang. Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales). 2021, 1 .

AMA Style

Xiu-Lian Cai, Jacob B. Landis, Hong-Xin Wang, Jian-Hua Wang, Zhi-Xin Zhu, Huafeng Wang. Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales). . 2021; ():1.

Chicago/Turabian Style

Xiu-Lian Cai; Jacob B. Landis; Hong-Xin Wang; Jian-Hua Wang; Zhi-Xin Zhu; Huafeng Wang. 2021. "Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales)." , no. : 1.

Preprint content
Published: 29 October 2020
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The use of diverse datasets in phylogenetic studies aiming for understanding evolutionary histories of species can yield conflicting inference. Phylogenetic conflicts observed in animal and plant systems have often been explained by hybridization, incomplete lineage sorting (ILS), or horizontal gene transfer. Here, we employed target enrichment data, species tree and species network approaches to infer the backbone phylogeny of the family Caprifoliaceae, while distinguishing among sources of incongruence. We used 713 nuclear loci and 46 complete plastome sequence data from 43 samples representing 38 species from all major clades to reconstruct the phylogeny of the family using concatenation and coalescence approaches. We found significant nuclear gene tree conflict as well as cytonuclear discordance. Additionally, coalescent simulations and phylogenetic species network analyses suggested putative ancient hybridization among subfamilies of Caprifoliaceae, which seems to be the main source of phylogenetic discordance. Ancestral state reconstruction of six morphological characters revealed some homoplasy for each character examined. By dating the branching events, we inferred the origin of Caprifoliaceae at approximately 66.65 Ma in the late Cretaceous. By integrating evidence from molecular phylogeny, divergence times, and morphology, we herein recognize Zabelioideae as a new subfamily in Caprifoliaceae. This work shows the necessity of using a combination of multiple approaches to identify the sources of gene tree discordance. Our study also highlights the importance of using data from both nuclear and chloroplast genomes to reconstruct deep and shallow phylogenies of plants.

ACS Style

Hong-Xin Wang; Diego F. Morales-Briones; Michael J. Moore; Jun Wen; Hua-Feng Wang. A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily. 2020, 1 .

AMA Style

Hong-Xin Wang, Diego F. Morales-Briones, Michael J. Moore, Jun Wen, Hua-Feng Wang. A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily. . 2020; ():1.

Chicago/Turabian Style

Hong-Xin Wang; Diego F. Morales-Briones; Michael J. Moore; Jun Wen; Hua-Feng Wang. 2020. "A phylogenomic perspective on gene tree conflict and character evolution in Caprifoliaceae using target enrichment data, with Zabelioideae recognized as a new subfamily." , no. : 1.

Article
Published: 22 October 2020 in Remote Sensing
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Urban green spaces provide a host of ecosystem services, the quantity and structure of which play an important role in human well-being. Rapid urbanization may modify urban green spaces, having various effects on plant diversity. Tropical coastal cities have urbanized rapidly in recent decades, but few studies have been conducted with a focus on their green spaces. We studied the responses of cultivated and spontaneous plants, both key components of urban flora, to the landscape structure of urban green spaces and possible social drivers. We analyzed existing relationships between plant diversity indices, urban green space landscape metrics (using Systeme Probatoire d’Observation de la Terre (SPOT) data,), and social factors, including the type, population density, construction age, and GPS coordinates of each Urban Functional Unit, or UFU. We found that UFUs with more green space patches had higher cultivated and spontaneous species richness than those with fewer green space patches. Spontaneous species richness decreased when green space patches became fragmented, and it increased when green space patches were more connected (e.g., via land bridges). Conversely, cultivated species richness increased with green space patch fragmentation. The phylogenetic diversity of both cultivated and spontaneous plants were weakly associated with green space structure, which was strongly driven by land use. Old UFUs and those with larger populations had more green space patches overall, although they tended to be small and fragmented. Green space patch density was found to increase as the UFU age increased. From the viewpoint of knowledge transfer, understanding the effects and drivers of landscape patterns of urban green spaces could inform the development of improved policies and management of urban green space areas.

ACS Style

Xia-Lan Cheng; Mir Muhammad Nizamani; C.Y. Jim; Kelly Balfour; Liang-Jun Da; Salman Qureshi; Zhi-Xin Zhu; Hua-Feng Wang. Using SPOT Data and FRAGSTAS to Analyze the Relationship between Plant Diversity and Green Space Landscape Patterns in the Tropical Coastal City of Zhanjiang, China. Remote Sensing 2020, 12, 3477 .

AMA Style

Xia-Lan Cheng, Mir Muhammad Nizamani, C.Y. Jim, Kelly Balfour, Liang-Jun Da, Salman Qureshi, Zhi-Xin Zhu, Hua-Feng Wang. Using SPOT Data and FRAGSTAS to Analyze the Relationship between Plant Diversity and Green Space Landscape Patterns in the Tropical Coastal City of Zhanjiang, China. Remote Sensing. 2020; 12 (21):3477.

Chicago/Turabian Style

Xia-Lan Cheng; Mir Muhammad Nizamani; C.Y. Jim; Kelly Balfour; Liang-Jun Da; Salman Qureshi; Zhi-Xin Zhu; Hua-Feng Wang. 2020. "Using SPOT Data and FRAGSTAS to Analyze the Relationship between Plant Diversity and Green Space Landscape Patterns in the Tropical Coastal City of Zhanjiang, China." Remote Sensing 12, no. 21: 3477.

Journal article
Published: 01 September 2020 in Gene
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Malvaceae s.l. is the largest family of Malvales, comprising more than 4225 species. Within Malvaceae, the phylogenetic relationships among subfamilies remain controversial. To resolve these relationships and explore plastome evolution in Malvaceae, we assembled a complete plastome data set of 39 Malvales species, including newly reported sequences for 13 Malvaceae and two Dipterocarpaceae species. All species possessed the typical quadripartite structure of angiosperm plastomes, but significant independent expansions of the Inverted Repeat regions were detected in Abelmoschus esculentus and Durio zibethinus. Nine coding sequences were identified with positively selected sites in Malvaceae. Several highly variable Non-CDS and coding regions were identified in the plastomes of Malvaceae that may be valuable for phylogenetic reconstruction at lower taxonomic levels. Phylogenetic reconstructions based on 78 protein-coding genes strongly supported nearly all relationships among Malvaceae subfamilies. The diversification of the subfamilies of Malvaceae was dated to the late Cretaceous and early Eocene, during a time of global warmth.

ACS Style

Jian-Hua Wang; Michael J. Moore; Hongxin Wang; Zhi-Xin Zhu; Hua-Feng Wang. Plastome evolution and phylogenetic relationships among Malvaceae subfamilies. Gene 2020, 765, 145103 .

AMA Style

Jian-Hua Wang, Michael J. Moore, Hongxin Wang, Zhi-Xin Zhu, Hua-Feng Wang. Plastome evolution and phylogenetic relationships among Malvaceae subfamilies. Gene. 2020; 765 ():145103.

Chicago/Turabian Style

Jian-Hua Wang; Michael J. Moore; Hongxin Wang; Zhi-Xin Zhu; Hua-Feng Wang. 2020. "Plastome evolution and phylogenetic relationships among Malvaceae subfamilies." Gene 765, no. : 145103.

Preprint content
Published: 25 August 2020
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Background: The Styracaceae are a woody, dicotyledonous family containing 12 genera and an estimated 160 species. Recent studies have shown that Styrax is monophyletic, Alniphyllum and Bruinsmia cluster into a clade with an approximately 20-kb inversion in the LSC. Halesia and Pterostyrax are not supported as monophyletic, while Melliodendron and Changiostyrax always from a clade sister to the rest of the family. However, the phylogenetic relationship of Styracaceae at the level of genera remains ambiguous. Results: We collected 28 complete plastomes of Styracaceae, including 12 sequences newly reported here and 16 publicly available complete plastome sequences, comprising 11 of the 12 genera of Styracaceae. All species possessed the typical quadripartite structure of angiosperm plastomes, and the sequence difference is small, except for the large 20-kb (14 genes) inversion region found in Alniphyllum and Bruinsmia . Seven coding sequences ( rps4 , rpl23 , accD , rpoC1 , psaA , rpoA and ndhH ) were identified to possess positively selected sites. Phylogenetic reconstructions based on seven data sets (i.e., LSC, SSC, IR, Coding, Non-coding, combination of LSC+SSC and concatenation of LSC+SSC+one IR) produced similar topologies and most relationships are consistent with previous findings. In our study, Pterostyrax was strongly supported as monophyletic; Melliodendron and Changiostyrax as successively sister to the rest of the family. Conclusion: Our results clearly indicate that Pterostyrax is monophyletic, and the establishment of Perkinsiodendron and Changiostyrax are supported. A 20-kb reverse sequence was found in the newly published sequence of Alniphyllum fortunei , which confirmed the existence of large inversion sequence in Alniphyllum and Bruinsmia .

ACS Style

Hua-Feng Wang; Xiu-Lian Cai; Jacob B. Landis; Hong-Xin Wang; Jian-Hua Wang; Zhi-Xin Zhu. Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales). 2020, 1 .

AMA Style

Hua-Feng Wang, Xiu-Lian Cai, Jacob B. Landis, Hong-Xin Wang, Jian-Hua Wang, Zhi-Xin Zhu. Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales). . 2020; ():1.

Chicago/Turabian Style

Hua-Feng Wang; Xiu-Lian Cai; Jacob B. Landis; Hong-Xin Wang; Jian-Hua Wang; Zhi-Xin Zhu. 2020. "Plastome Structure and Phylogenetic Relationships of Styracaceae (Ericales)." , no. : 1.