23 Works

Data from: DNA methylation as a possible mechanism affecting ability of natural populations to adapt to changing climate

Zuzana Munzbergova, Vit Latzel, Maria Surinova & Vera Hadincova
Environmentally induced epigenetic variation has been recently recognized as a possible mechanism allowing plants to rapidly adapt to novel conditions. Despite increasing evidence on the topic, little is known on how epigenetic variation affects responses of natural populations to changing climate. We studied the effects of experimental demethylation (DNA methylation is an important mediator of heritable control of gene expression) on performance of a clonal grass, Festuca rubra, coming from localities with contrasting temperature and...

Data from: Ecologically diverse and distinct neighbourhoods trigger persistent phenotypic consequences, and amine metabolic profiling detects them

Françoise Hennion, Isabelle Litrico, Igor Bartish, Alexandra Weigelt, Alain Bouchereau & Andreas Prinzing
1.Global change triggers rapid alterations in the composition and diversity of plant communities which may change ecosystem functioning. Do changes in community diversity also change traits persistently, i.e. does coexistence with numerous or functionally or phylogenetically distinct species trigger, in a given focal species, trait shifts that persist? 2.We studied the grass Dactylis glomerata. Dactylis was grown in experimental plots with different species compositions for five years, sampled, cloned and grown in a common garden....

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Bin-Bin Liu, Zhi-Yao Ma, Chen Ren, Richard Hodel, Miao Sun, Xiu-Qun Liu, Guang-Ning Liu, De-Yuan Hong, Elizabeth Zimmer & Jun Wen
With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and...

Data from: European ornamental garden flora as an invasion debt under climate change

Emily Haeuser, Wayne Dawson, Wilfried Thuiller, Stefan Dullinger, Svenja Block, Oliver Bossdorf, Marta Carboni, Luisa Conti, Iwona Dullinger, Franz Essl, Günther Klonner, Dietmar Moser, Tamara Muenkemueller, Madalin Parepa, Matthew V. Talluto, Holger Kreft, Jan Pergl, Petr Pyšek, Patrick Weigelt, Marten Winter, Martin Hermy, Sebastiaan Van Der Veken, Cristina Roquet & Mark Van Kleunen
1.Most naturalized and invasive alien plant species were originally introduced to regions for horticultural purposes. However, many regions now face an invasion debt from ornamental alien species, which have not yet naturalized. In this regard, climate change represents a threat as it may lower the barriers to naturalization for some ornamental alien species. Identifying those species is extremely important for anticipating impending invasions. 2.To identify predictors of naturalization, we modelled the effects of climate, nursery...

Steep topography buffers threatened gymnosperm species against anthropogenic pressures in China

Ditte Arp Jensen, Keping Ma & Jens-Christian Svenning
China is one of the most species-rich countries in the world, harbouring many rare gymnosperms. Following recent human-led loss of forests, China is now experiencing increases in forest cover resulting from efforts of reforestation-schemes. As anthropogenic activities have previously been found to interact with topography in shaping forest cover in China and considering the large human population and the ongoing population increase of the country, it is important to understand the role of anthropogenic pressures...

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: Plant quantity and quality regulate the diversity of arthropod communities in a semi-arid grassland

Xiaoming Lu, Xuezhen Zhao, Taiki Tachibana, Kei Uchida, Takehiro Sasaki & Yongfei Bai
The quantity (e.g. biomass production) and quality (e.g. leaf nutrient content) of plants can strongly influence arthropod diversity, but few studies have tried to disentangle such effects. In this study, we examined the independent effects of plant productivity and leaf traits on the taxon richness and abundance of entire arthropod communities and multiple arthropod orders in replicated monocultures of 15 herbaceous species in the Inner Mongolian grassland. Total taxon richness of arthropod communities increased with...

Evolutionary history and genetic diversity of apomictic allopolyploids in Hieracium s.str. (Asteraceae): morphological versus genomic features

Jindrich Chrtek, Patrik Mraz, Alexander Belyayev, Ladislava Pastova, Viera Mrazova, Petra Caklova, Jirina Josefiova, Danijela Zagorski, Matthias Hartmann, Michaela Jandova, Jan Pinc & Judith Fehrer
Premise of the Study The origin of allopolyploids is believed to shape their evolutionary potential, ecology and geographical ranges. Morphologically distinct apomictic types sharing the same parental species belong to the most challenging groups of polyploids. We evaluated the origins and variation of two triploid taxa (Hieracium pallidiflorum, H. picroides) presumably derived from the same diploid parental pair (H. intybaceum, H. prenanthoides). Methods We used a suite of approaches ranging from morphological, phylogenetic (three unlinked...

Data from: Drivers of plant species’ potential to spread: the importance of demography versus seed dispersal

Lucie Hemrová, James M. Bullock, Danny A.P. Hooftman, Steven M. White, Zuzana Munzbergova & Danny A. P. Hooftman
Understanding the ability of plants to spread is important for assessing conservation strategies, landscape dynamics, invasiveness and ability to cope with climate change. While long-distance seed dispersal is often viewed as a key process in population spread, the importance of inter-specific variation in demography is less explored. Indeed, the relative importance of demography vs seed dispersal in determining population spread is still little understood. We modelled species’ potential for population spread in terms of annual...

Data from: A prioritised list of invasive alien species to assist the effective implementation of EU legislation

Carles Carboneras, Piero Genovesi, Montserrat Vila, Tim Blackburn, Martina Carrete, Miguel Clavero, Bram D'hondt, Jorge F. Orueta, Belinda Gallardo, Pedro Geraldes, Pablo González-Moreno, Richard D. Gregory, Wolfgang Nentwig, Jean-Yves Paquet, Petr Pysek, Wolfgang Rabitsch, Iván Ramírez, Riccardo Scalera, Jose Tella, Paul Walton, Robin Wynde & Tim M. Blackburn
1. Effective prevention and control of invasive species generally relies on a comprehensive, coherent and representative list of species that enables resources to be used optimally. European Union (EU) Regulation 1143/2014 on invasive alien species (IAS) aims to control or eradicate priority species, and to manage pathways to prevent the introduction and establishment of new IAS; it applies to species considered of Union concern and subject to formal risk assessment. So far, 49 species have...

Community functional structure modulates the responses of net primary productivity to application of various N compounds in a meadow steppe

Jiangping Cai, Wentao Luo, Xue Feng, Guojiao Yang, Xiao-Tao Lü, Mai-He Li, Yong Jiang & Xingguo Han
1. Increasing atmospheric nitrogen (N) deposition influences grassland productivity. The deposited N contains various N forms with different ecological effects on community functions. However, how grassland primary productivity responds to community functional structure in relation to different N compounds remains largely unclear. 2. In this study, we examined the responses of aboveground primary productivity (ANPP) and community function composition to addition of three different N compounds (NH4NO3, (NH4)2SO4, and CO(NH2)2) at the rates of 0,...

The hidden half of the fine root differentiation in herbs: nonacquisitive belowground organs determine fine-root traits

Tomas Herben & Jitka Klimesova
Plants rely on roots for absorption of nutrients from the soil. Differences in traits of fine roots and of the root system in general thus underlie differences among individual species in their ability to live in habitats differing in nutrient status and interactions with other species. Here we examine to what extent structure of the root system is determined by whole-plant parameters, namely the expected life span of the rooting units (either genetic individuals or...

Intraspecific trait variation and species turnover mediate grazing impacts on above- and below-ground functional trait composition of plant communities

Chaonan Wang, Xiang Li, Jiacheng Qin, Yang Wang, Xiaoming Lu, Peizhi Yang & Yongfei Bai
Although grazing has significant impacts on plant functional traits and community composition in grasslands, few studies have simultaneously explored how plant above- and below-ground traits and community functional composition respond to grazing. Using a grazing manipulation experiment with seven levels of grazing intensity (0, 1.5, 3.0, 4.5, 6.0, 7.5, and 9 sheep ha-1) in the Inner Mongolia grassland, we partitioned the roles of intraspecific trait variation (ITV) and species turnover underlying the grazing induced changes...

Shrub encroachment decreases soil inorganic carbon stocks in Mongolian grasslands

Shangshi Liu, Luhong Zhou, He Li, Xia Zhao, Yuanhe Yang, Yankun Zhu, Huifeng Hu, Leiyi Chen, Pujin Zhang, Haihua Shen & Jingyun Fang
1. Widespread shrub encroachment in global drylands may increase plant biomass and change soil organic carbon stocks of grassland ecosystems. However, the response of soil inorganic carbon (SIC), which is a major component of dryland carbon pools, to this vegetation shift remains unknown. 2. We conducted a systematic field survey in 75 pairs of shrub-encroached grassland and control plots at 25 sites in the grasslands of the Inner Mongolia Plateau to evaluate how shrub encroachment...

Assembly of Aegilops comosa chromosomes

Mahmoud Said, Kateřina Holušová, András Farkas, László Ivanizs, Eszter Gaál, Petr Cápal, Michael Abrouk, Mihaela Martis-Thiele, Balázs Kalapos, Jan Bartoš, Bernd Friebe, Jaroslav Doležel & István Molnár
We sequenced and assembled seven chromosomes of Aegilops comosa. The assembly with Meraculous resulted in ~ 50k - 186k scaffolds per chromosome with N50 size 6.4kb - 20.2kb. The scaffold sequences were used for development of molecular markers specific for cDNAs sequences mapped on Ae. comosa chromosomes Pairwise alignment of wheat cDNA-sequences and the chromosomal scaffolds of Ae. comosa identified candidate sequences. In order to analyze the structure and homeology of Aegilops chromosomes, forty-three mapped...

Data from: Phylogenetic marker development for target enrichment from transcriptome and genome skim data: the pipeline and its application in southern African Oxalis (Oxalidaceae)

Roswitha Schmickl, Aaron Liston, Vojtěch Zeisek, Kenneth Oberlander, Kevin Weitemier, Shannon C. K. Straub, Richard C. Cronn, Léanne L. Dreyer & Jan Suda
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low-copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to select hundreds of LCN loci by a comparison between transcriptome and genome skim data. We used our script to obtain LCN genes for southern African...

Data from: Taming the wild: resolving the gene pools of non-model Arabidopsis lineages

Nora Hohmann, Roswitha Schmickl, Tzen-Yuh Chiang, Magdalena Lučanová, Filip Kolář, Karol Marhold & Marcus A. Koch
Background: Wild relatives in the genus Arabidopsis are recognized as useful model systems to study traits and evolutionary processes in outcrossing species, which are often difficult or even impossible to investigate in the selfing and annual Arabidopsis thaliana. However, Arabidopsis as a genus is littered with sub-species and ecotypes which make realizing the potential of these non-model Arabidopsis lineages problematic. There are relatively few evolutionary studies which comprehensively characterize the gene pools across all of...

Influence of elevation on bioregionalisation: A case study of the Sino-Himalayan flora

Yun Liu, Jianfei Ye, Haihua Hu, Danxiao Peng, Lina Zhao, Limin Lu, Wajid Zaman & Zhiduan Chen
Aim: Elevation is an important factor that influences bioregionalisation in mountainous areas, but its effects are not well known. Taking the Sino-Himalayan flora as a case, we aimed to test the effect of elevation on bioregionalisation and provide a regionalisation scheme of the Sino-Himalayan flora. Location: The Sino-Himalaya (East Himalaya, the Hengduan Mountains and the Yunnan Plateau in China). Taxon: Angiosperms. Methods: We compiled distribution data and elevation ranges of angiosperms in the Sino-Himalaya and...

Low-intensity cattle grazing is better than cattle exclusion to drive secondary savannas towards the features of native Cerrado vegetation

Giselda Durigan
Although livestock have been historically associated with land conversion and biodiversity loss, well-managed cattle grazing has been reported to contribute to conservation of open ecosystems. Knowing the balance between positive and negative effects of livestock (presence or exclusion) on different ecosystems is, therefore, crucial to support management decisions. We conducted an experiment in a secondary savanna with exotic grasses, used as pasture, to assess the effect of cattle presence in low density and cattle exclusion...

Data from: Extensive yellow crusts below limestone overhangs: a new taxon close to a minute epiphytic lichen

Jan Vondrak, Mahroo Haji Moniri, Jiri Malicek & Jiri Kosnar
A conspicuous yellow crust forming extensive covers on some dry and shaded limestone rocks in Europe is described here as Caloplaca substerilis subsp. orbicularis M. Haji Moniri, Vondrák & Malíček subsp. nov. Based on nuITS rDNA, 28S nuLSU rDNA and mtSSU rDNA sequence data, the new taxon is closely related to Caloplaca sterilis and C. ulcerosa. The three taxa form a supported clade in the subfamily Xanthorioideae (Teloschistaceae), but none of the recent genera are...

Data from: Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (Senecio carniolicus, Asteraceae)

Pedro Escobar García, Manuela Winkler, Ruth Flatscher, Michaela Sonnleitner, Jana Krejčíková, Jan Suda, Karl Hülber, Gerald M. Schneeweiss & Peter Schönswetter
Recent evidence suggests that survival of arctic-alpine organisms in peripheral or interior glacial refugia are not mutually exclusive and may both be involved in shaping an organisms’ Pleistocene history, yet potentially at different time levels. Here, we test this hypothesis in a high-mountain plant (diploid lineage of Senecio carniolicus, Asteraceae) from the Eastern European Alps, in which patterns of morphological variation and current habitat requirements suggest survival in both types of refugia. To this end,...

Data from: Vertical root distribution of individual species in a mountain grassland community: does it respond to neighbours?

Tomas Herben, Tereza Vozábová, Věra Hadincová, František Krahulec, Hana Mayerová, Sylvie Pecháčková, Hana Skálová & Karol Krak
1.Vertical differentiation in root placement is one of the potential mechanisms of plant niche differentiation. It can be due to the remarkable plasticity of roots in response to nutrients and neighbours, but most data on it come from pot or garden experiments. The roles of vertical differentiation and of plasticity in it in the field are thus not well known. 2.We examined species-specific root vertical distribution in a montane grassland using quantitative Real-Time PCR. We...

Data from: Functional traits determine why species belong to the dark diversity in a dry grassland fragmented landscape

Rocío Belinchón, Lucie Hemrová & Zuzana Münzbergová
A challenge for nature conservation is to know why many species are absent from suitable habitats and whether they might be able to disperse and to establish. Here, we used 272 dry grassland patches within a fragmented landscape to investigate the role of local abiotic conditions and dispersal filtering in determining the likelihood of vascular plants to belong to the dark diversity (i.e. absent portion of the species pool). First, we quantified the species (SD),...

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