50 Works

Data from: Does reproductive isolation reflect the segregation of color forms in Spiranthes sinensis (Pers.) Ames complex (Orchidaceae) in the Chinese Himalayas?

Zhi-Bin Tao, Zong-Xin Ren, Peter Bernhardt, Huan Liang, Hai-Dong Li, Yan-Hui Zhao, Hong Wang & De-Zhu Li
Isolation between species, or taxa sharing a common lineage, depends primarily on the relative strengths of various reproductive barriers. Previous studies on reproductive isolation between orchids emphasized mechanical and ethological barriers in flowers of species showing food and/or sexual mimicry. In this study, we investigated and quantified a series of pre- and post-pollination barriers between pink and white forms of Spiranthes sinensis sl, a nectar-secreting complex. We generated ML trees based on trnS-G and matK...

The hornwort genome and early land plant evolution

Jian Zhang, Xin-Xing Fu, Rui-Qi Li, Xiang Zhao, Yang Liu, Ming-He Li, Arthur Zwaenepoel, Hong Ma, Bernard Goffinet, Yan-Long Guan, Jia-Yu Xue, Yi-Ying Liao, Qing-Feng Wang, Qing-Hua Wang, Jie-Yu Wang, Guo-Qiang Zhang, Zhi-Wen Wang, Yu Jia, Mei-Zhi Wang, Shan-Shan Dong, Jian-Fen Yang, Yuan-Nian Jiao, Ya-Long Guo, Hong-Zhi Kong, An-Ming Lu … & Zhi-Duan Chen
Hornworts, liverworts, and mosses are three early diverging clades of land plants, together composing the bryophytes. Here we report the draft genome sequence of the hornwort Anthoceros angustus. Phylogenomic inferences confirm the monophyly of bryophytes, with hornworts sister to liverworts and mosses. The simple morphology of hornworts correlates with low genetic redundancy in plant body plan while the basic transcriptional regulation toolkit for plant development has already been established in this early land plant lineage....

Data from: Upward elevation and northwest range shifts for alpine Meconopsis species in the Himalaya-Hengduan Mountains region

Xie He, Kevin Burgess, Xuefei Yang, Antje Ahrends, Lian-Ming Gao & De-Zhu Li
Climate change may impact the distribution of species by shifting their ranges to higher elevations or higher latitudes. The impacts on alpine plant species may be particularly profound due to a potential lack of availability of future suitable habitat. To identify how alpine species have responded to climate change during the past century as well as to predict how they may react to possible global climate change scenarios in the future, we investigate the climatic...

Data from: The topological differences between visitation and pollen transport networks: a comparison in species rich communities of the Himalaya-Hengduan Mountains

Yan-Hui Zhao, Amparo Lazaro, Zong-Xin Ren, Wei Zhou, Hai-Dong Li, Zhi-Bin Tao, Kun Xu, Zhi-Kun Wu, Lorne M. Wolfe, Li De-Zhu & Wang Hong
Pollination networks are usually constructed and assessed by direct field observations which commonly assume that all flower visitors are true pollinators. However, this assumption is often invalid and the use of data based on mere visitors to flowers may lead to a misunderstanding of intrinsic pollination networks. Here, using a large dataset by both sampling floral visitors and analyzing their pollen loads, we constructed 32 networks pairs (visitation vs. pollen transport) across one flowering season...

Amblyanthus chenii, a new species and generic record from Xizang, China

Zhuo Zhou, Yong-Jie Guo, Ji-Pei Yue, Hong-Liang Chen, Yun-Hong Tan & Hang Sun
Amblyanthus chenii (Primulaceae; Myrsinoideae), a new species discovered growing in the understory of primeval forests in Medog County, southeast Xizang, China, is described based on morphological evidence. This is also the first generic record of Amblyanthus in China. The new species is most similar morphologically to A. multiflorus based on its axillary inflorescence and connate filament, but it differs in its 2-4 cm long condensed panicle and up to half adnation of its sepals and...

Phylogeny and biogeography of Fagus (Fagaceae) based on 28 nuclear single/low‐copy loci

Zhi-Yong Zhang, Lu Jiang, Qin Bao, Wei He, Deng‐Mei Fan, Shan‐Mei Cheng, Jordi López-Pujol, Myong Gi Chung, Shota Sakaguchi, Arturo Sánchez-González, Aysun Gedik, De‐Zhu Li & Yi‐Xuan Kou
Fagus L. is a key component in temperate deciduous broadleaf forests of the Northern Hemisphere. However, its biogeographic history has not been examined under the framework of a fully resolved and reasonably time-calibrated phylogeny. In this study, we sequenced 28 nuclear single/low-copy loci (18,555 bp in total) of 11 Fagus species/segregates and seven outgroups. Phylogenetic trees were reconstructed using both concatenation-based (ML, MP, BI) and coalescent-based methods (StarBEAST2, ASTRAL). The monophyly of two subgenera (Fagus...

Parallel ddRAD and genome skimming analyses reveal a radiative and reticulate evolutionary history of the temperate bamboos

Cen Guo, Peng-Fei Ma, Guo-Qian Yang, Xia-Ying Ye, Ying Guo, Jing-Xia Liu, Yun-Long Liu, Deren Eaton, Zhen-Hua Guo & De-Zhu Li
Rapid evolutionary radiations are among the most challenging phylogenetic problems, wherein different types of data (e.g., morphology, molecular) or genetic markers (e.g., nuclear, organelle) often yield inconsistent results. The tribe Arundinarieae i.e., the temperate bamboos, is a clade of tetraploid originated 22 million years ago and subsequently radiated in East Asia. Previous studies of Arundinarieae have found conflicting relationships and/or low support. Here, we obtain nuclear markers from ddRAD data for 213 Arundinarieae taxa and...

Data from: Correct calculation of CO2 efflux using a closed-chamber linked to a non-dispersive infrared gas analyzer

Gbadamassi G. O. Dossa, Ekananda Paudel, Hongyan Wang, Kunfang Cao, Douglas Schaefer & Rhett D. Harrison
1. Improved understanding of the carbon (C) cycle is essential to model future climates and how this may feedback to affect greenhouse-gas fluxes. 2 .We summarize previous work quantifying respiration rates of organic substrates and briefly discuss how advances in technology, specifically the use of chambers linked to a non-dispersive infra-red gas analyzer (NDIR), can be applied to assess carbon dynamics from short-term field measurements. This technology hastens measurement and is relatively inexpensive, enabling researchers...

Data from: Role of selection and gene flow in population differentiation at the edge vs. interior of the species range differing in climatic conditions

Sergei Volis, Danara Ormanbekova & Irina Shulgina
Evaluating the relative importance of neutral and adaptive processes as determinants of population differentiation across environments is a central theme of evolutionary biology. We applied the QST-FST comparison flanked by a direct test for local adaptation to infer the role of climate-driven selection and gene flow in population differentiation of an annual grass Avena sterilis in two distinct parts of the species range, edge and interior, which represent two globally different climates, desert and Mediterranean....

Data from: Indications for three independent domestication events for the tea plant (Camellia sinensis (L.) O. Kuntze) and new insights into the origin of tea germplasm in China and India revealed by nuclear microsatellites

M. K. Meegahakumbura, M. Wambulwa, K. K. Thapa, M. M. Li, M. Möller, J.C. Xu, J.B. Yang, B.Y. Liu, S. Ranjitkar, J. Liu, D.Z. Li, L.M. Gao, M. C. Wambulwa, D. Z. Li, L. M. Gao, J. B. Yang & J. C. Xu
Background: Tea is the world’s most popular non-alcoholic beverage. China and India are known to be the largest tea producing countries and recognized as the centers for the domestication of the tea plant (Camellia sinensis (L.) O. Kuntze). However, molecular studies on the origin, domestication and relationships of the main teas, China type, Assam type and Cambod type are lacking. Methodology/Principal Findings: Twenty-three nuclear microsatellite markers were used to investigate the genetic diversity, relatedness, and...

Data from: Dianyuea gen. nov. (Salicaceae: Scyphostegioideae) from southwestern China

Ce Shang, Shuai Liao, Yong-Jie Guo & Zhi-Xiang Zhang
Dianyuea C. Shang, S. Liao & Z. X. Zhang, a new monotypic genus of Salicaceae based on Flacourtia turbinata H. J. Dong & H. Peng, is described and illustrated. Morphologically, Dianyuea differs from Flacourtia Comm. ex L'Hér. by having six connate stamens, basal placentation and lobed seed appendages. All those features indicate that Dianyuea is allied with Scyphostegia Stapf. A molecular phylogenetic analysis using plastid trnL-F, matK, and rbcL sequence data for representatives of 16...

Data from: Extraction and separation of active ingredients in Schisandra chinensis (Turcz.) Baill and the study of their antifungal effects

Haijing Yi, Yan Chen, Jun Liu, Jie Zhang, Wei Guo, Weilie Xiao & Yuncong Yao
Schisandra chinensis extracts (SEs) have traditionally been used as an oriental medicine for the treatment of various human diseases, however, their further application in the biocontrol of plant disease remains poorly understood. This study was conducted to develop eco-friendly botanical pesticides from extracts of S. chinensis and assess whether they could play a key role in plant disease defense. Concentrated active fractions (SE-I, SE-II, and SE-III) were obtained from S. chinensis via specific extraction and...

Data from: Spatial variability in soil organic carbon in a tropical montane landscape: associations between soil organic carbon and land use, soil properties, vegetation, and topography vary across plot to landscape scales

Marleen De Blécourt, Marife D. Corre, Ekananda Paudel, Rhett D. Harrison, Rainer Brumme & Edzo Veldkamp
Presently, the lack of data on soil organic carbon (SOC) stocks in relation to land-use types and biophysical characteristics prevents reliable estimates of ecosystem carbon stocks in montane landscapes of mainland SE Asia. Our study, conducted in a 10 000 ha landscape in Xishuangbanna, SW China, aimed at assessing the spatial variability in SOC concentrations and stocks, as well as the relationships of SOC with land-use types, soil properties, vegetation characteristics and topographical attributes at...

Nuclear phylogenomic analyses of asterids conflict with plastome trees and support novel relationships among major lineages

Gregory Stull, Pamela S. Soltis, Douglas E. Soltis, Matthew A. Gitzendanner & Stephen A. Smith
Premise : Discordance between nuclear and organellar phylogenies (cytonuclear discordance) is a well-documented phenomenon at shallow evolutionary levels, but has been poorly investigated at deep levels of plant phylogeny. Determining the extent of cytonuclear discordance across major plant lineages is essential not only for elucidating evolutionary processes but also for evaluating the currently used framework of plant phylogeny, which is largely based on the plastid genome. Methods : We present a phylogenomic examination of a...

The impact of a native dominant plant, Euphorbia jolkinii, on plant-flower visitor networks and pollen deposition on stigmas of co-flowering species in sub-alpine meadows of Shangri-La, SW China

Yan-Hui Zhao, Jane Memmott, Ian Vaughan, Hai-Dong Li, Zong-Xin Ren, Amparo Lazaro, Wei Zhou, Xin Xu, Wei-Jia Wang, Huan Liang, De-Zhu Li & Hong Wang
1. Anthropogenic activity can modify the distribution of species abundance in a community leading to the appearance of new dominant species. While many studies report that an alien plant species which becomes increasingly dominant can change species composition, plant-pollinator network structure and the reproductive output of native plant species, much less is known about native plant species which become dominant in their communities. 2. Euphorbia jolkinii Boissier (Euphorbia, hereafter) has become a dominant native plant...

Data from: Factors determining forest diversity and biomass on a tropical volcano, Mt. Rinjani, Lombok, Indonesia

Gbadamassi G. O. Dossa, Ekananda Paudel, Junichi Fujinuma, Haiying Yu, Wanlop Chutipong, Yuan Zhang, Sherryl Paz, Rhett D. Harrison & Nathan G. Swenson
Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetation over an altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modeled alpha- (plot) and beta- (among plot) diversity (Fisher’s alpha), compositional change, and biomass against elevation and selected covariates. We also examined community phylogenetic structure across the...

Sexual dimorphism, temporal niche differentiation and evidence for the Jack Sprat effect in an annual dioecious plant

Qian Yu, Qian Yu, Spencer Barrett, Xin-Jia Wang, Li Zhong, Hong Wang, De-Zhu Li & Wei Zhou
Sexual dimorphism in dioecious plants often occurs as a consequence of the different resource requirements of females and males, especially during reproduction. The contrasting reproductive roles of the sexes can influence the phenology of growth, plant size and flowering time, with implications for the intensity of competitive interactions within and between the sexes. Here, we investigate the influence of contrasting nutrient regimes and intra-sexual and inter-sexual competition on the expression of sexual dimorphism in life-history...

Phylogeny and biogeography of the hollies (Ilex L., Aquifoliaceae)

Xin Yao, Yu Song, Jun-Bo Yang, Yun-Hong Tan & Richard Corlett
The holly genus, Ilex L., in the monogeneric Aquifoliaceae, is the largest woody dioecious genus (>664 spp.), with a near‐cosmopolitan distribution in mesic environments. We constructed a phylogeny based on two nuclear genes, representing 177 species spread across the geographical range, and dated using macrofossil records. The five main clades had a common ancestor in the early Eocene, much earlier than previously suggested. Ilex originated in subtropical Asia and extant clades colonized South America by...

Evolutionary and ecological processes influence a plant-bumble bee network

Huan Liang
Species interactions, such as those between plants and pollinators, are known to be shaped by both evolutionary history and ecological factors. However, the relative importance of neutral- and niche-based ecological processes is still under debate, and little is known about which ecological factors are most important for explaining phylogenetic patterns in interaction networks. Using a plant-bumble bee network comprising 2428 interactions between 29 plant species and 12 bumble bee species in the Himalaya-Hengduan mountains, we...

Data from: Biodiversity explain maximum variation in productivity under experimental warming, nitrogen addition and grazing in mountain grasslands

Jiajia Liu, Detuan Liu, Kun Xu, Lian-Ming Gao, Xuejun Ge, Kevin S. Burgess, Marc W. Cadotte & Xue-Jun Ge
Anthropogenic global warming, nitrogen addition and over-grazing alter plant communities and threaten plant biodiversity, potentially impacting community productivity, especially in sensitive mountain grassland ecosystems. However, it still remains unknown whether the relationship between plant biodiversity and community productivity varies across different anthropogenic influences, and especially how changes in multiple biodiversity facets drive these impacts on productivity. Here we measured different facets of biodiversity including functional and phylogenetic richness and evenness in mountain grasslands along an...

Data from: Joint effect of phylogenetic relatedness and trait selection on the elevational distribution of Rhododendron species

Jiayun Zou, Yahuang Luo, Kevin S. Burgess, Shaolin Tan, Wei Zheng, Kun Xu, Chaonan Fu & Lianming Gao
Congeneric species may coexist at fine spatial scales through niche differentiation, however, the magnitude to which the effects of functional traits and phylogenetic relatedness contribute to their distribution along elevational gradients remains understudied. To test the hypothesis that trait and elevational range overlap can affect local speciesʼ coexistence, we first compared phylogenetic relatedness and trait (including morphological traits and leaf elements) divergence among closely related species of Rhododendron L. on Yulong Mountain, China. We then...

Data from: Identification of putative orthologous genes for the phylogenetic reconstruction of temperate woody bamboos (Poaceae: Bambusoideae)

Li-Na Zhang, Xian-Zhi Zhang, Yu-Xiao Zhang, Chun-Xia Zeng, Peng-Fei Ma, Lei Zhao, Zhen-Hua Guo & De-Zhu Li
The temperate woody bamboos (Arundinarieae) are highly diverse in morphology but lack a substantial amount of genetic variation. The taxonomy of this lineage is intractable, and the relationships within the tribe have not been well resolved. Recent studies indicated that this tribe could have a complex evolutionary history. Although phylogenetic studies of the tribe have been carried out, most of these phylogenetic reconstructions were based on plastid data, which provide lower phylogenetic resolution compared to...

Data from: Shifting baselines on a tropical forest frontier: extirpations drive declines in local ecological knowledge

Zhong Kai, Teoh Shu Woan, Li Jie, Eben Goodale, Kaoru Kitajima, Robert Bagchi, Rhett D. Harrison & Zhang Kai
The value of local ecological knowledge (LEK) to conservation is increasingly recognised, but LEK is being rapidly lost as indigenous livelihoods change. Biodiversity loss is also a driver of the loss of LEK, but quantitative study is lacking. In our study landscape in SW China, a large proportion of species have been extirpated. Hence, we were interested to understand whether species extirpation might have led to an erosion of LEK and the implications this might...

Data from: Structure of the epiphyte community in a tropical montane forest in SW China

Mingxu Zhao, Nalaka Geekiyanage, Jianchu Xu, Myo Myo Khin, Dian Ridwan Nurdiana, Ekananda Paudel & Rhett Daniel Harrison
Vascular epiphytes are an understudied and particularly important component of tropical forest ecosystems. However, owing to the difficulties of access, little is known about the properties of epiphyte-host tree communities and the factors structuring them, especially in Asia. We investigated factors structuring the vascular epiphyte-host community and its network properties in a tropical montane forest in Xishuangbanna, SW China. Vascular epiphytes were surveyed in six plots located in mature forests. Six host and four micro-site...

Data from: A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny

, Anne Bruneau, Nasim Azani, Marielle Babineau, Edeline Gagnon, Carole Sinou, Royce Steeves, Erin Zimmerman, C. Donovan Bailey, Lynsey Kovar, Madhugiri Nageswara-Rao, Hannah Banks, RuthP. Clark, Manuel De La Estrella, Peter Gasson, GeoffreyC. Kite, BenteB. Klitgaard, GwilymP. Lewis, Danilo Neves, Gerhard Prenner, María De Lourdes Rico-Arce, ArianeR. Barbosa, Maria Cristina López-Roberts, Luciano Paganucci De Queiroz, PétalaG. Ribeiro … & Tingshuang Yi
The classification of the legume family proposed here addresses the long-known non-monophyly of the traditionally recognised subfamily Caesalpinioideae, by recognising six robustly supported monophyletic subfamilies. This new classification uses as its framework the most comprehensive phylogenetic analyses of legumes to date, based on plastid matK gene sequences, and including near-complete sampling of genera (698 of the currently recognised 765 genera) and ca. 20% (3696) of known species. The matK gene region has been the most...

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