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FIG. 3 in Stem and caudex anatomy of succulent plant species

FIG. 3. — Transverse sections of stems and caudices: A, B, Pelargonium carnosum (L.) L'Hér.; A, stem, wood; B, stem, bands of libriform fibers; C-E, Moringa drouhardii Jum.; C, stem, diffused fibrous wood, lignification in ray parenchyma cells; D, stem, radial section; E, stem, secondary phloem dilatated; F, Oxalis megalorrhiza Jacq., stem, wood; G-I, Adenia glauca Schinz; G, green stem, cortex and phloem fiber caps; H, green stem, parenchymatous wood; I, caudex, parenchymatous wood. Abbreviations: lf, libriform fibers; r, rays; p, parenchyma cells; fp, fiber cap; sp, secondary phloem. Scale bars: 50 µm.

FIG. 2 in Stem and caudex anatomy of succulent plant species

FIG. 2. — Transverse sections of stems and caudices, unless otherwise noted: A, B, Momordica rostrata Zimm; A, caudex, septate fibers, tangential section; B, caudex, vessels with bordered pits; C-F, Jatropha curcas L.; C, caudex, solitary vessels, wood; D, caudex, fibrous wood; E, caudex, vessels, radial section; F, caudex, thin-walled libriform fibers, parenchyma with amyloplasts,radial section; G, H, Jatropha macrantha Müll. Arg.; G, stem, diffuse fibrous wood, thin-walled libriform fibers, septate and gelatinous fibers; H, stem, axial and ray parenchyma. Abbreviations: ur, uniseriate ray; br, biseriate ray; p, parenchyma; f, fibers; sp, secondary phloem; ct, conjunctive tissue; sf, septate fibers; v, vessel; lf, libriform fibers. Scale bars: A, C-H, 50 µm; B, 10 µm.

FIG. 1 in Stem and caudex anatomy of succulent plant species

FIG. 1. — Transverse sections of stems and caudices, unless otherwise noted: A-C, Adenium obesum (Forssk.) Roem. & Schult.; A, stem, bicollateral bundle; B, caudex, cortex laticifers and fibrous wood; C, caudex, fibrous wood, thin-walled libriform fibers, tangential section; D-F, Ceropegia africana R. Br.; D, stem, bicollateral bundles; E, stem, extraxylary gelatinous fibers; F, caudex, conjunctive tissue, parenchyma cells are proliferated in wood; G-I, Momordica rostrata Zimm; G, stem, wood; H, caudex, wood; I, caudex, conjunctive tissue bordered by secondary phloem. Abbreviations: bc, bicollateral bundle; l, laticifer; p, parenchyma cells; gf, gelatinous fibers; ct, conjunctive tissue; pw, parenchymatous wood; fw, fibrous wood; sp, secondary phloem. Scale bars: 50 µm.

opencc-zeroMar 2022View details →

Introduction history mediates naturalization and invasiveness of cultivated plants

Aim: Species characteristics and cultivation are both associated with alien plant naturalization and invasiveness. Particular species characteristics are favored for cultivation, obscuring the relationship between traits and naturalization success. We sought to better understand the drivers of naturalization and invasiveness by analyzing relationships with species characteristics and cultivation and by disentangling the direct effects of characteristics from the indirect effects mediated by cultivation. Location: Great Britain Time period: c. 1000–present Major taxa studied: Seed plants Methods: We used a comprehensive dataset of 17,396 alien plant taxa introduced to Great Britain before 1850, a country with one of the most well-documented histories of plant introductions. We integrated this with cultivation data from historical and modern records of botanic gardens and commercial nurseries and with trait data. Accounting for time since introduction, we quantified the influences of cultivation and species characteristics on present-day naturalization and invasiveness in Great Britain. Results: Larger native range size, earlier flowering, long-lived herbaceous growth form, and outdoor cultivated habitat were all associated with naturalization. However, these relationships between characteristics and naturalization largely reflected cultivation patterns. The indirect, mediating influence of cultivation on naturalization varied among species characteristics, and was relatively strong for growth form and weak for native range size. Cultivation variables, particularly availability in present-day nurseries, best explained invasiveness, while species characteristics had weaker associations. Main conclusions: Human influence on species introduction and cultivation is associated with increased probability of naturalization and invasiveness, and it has measurable indirect effects by biasing the distribution of species characteristics in the pool of introduced species. Accounting for human cultivation preferences is necessary to make ecological interpretations of the effects of species characteristics on invasion.

opencc-zeroMar 2022View details →

VCF files of common grassland plants from wild collected seeds of 19 common European grassland species with up to 4 consecutive generations grown in monoculture for seed production for restoration

A growing number of restoration projects require large amounts of seeds. As harvesting natural populations cannot cover the demand, wild plants are often propagated in large-scale monocultures. There are concerns that this cultivation process may cause genetic drift and unintended selection, which would alter the genetic properties of the cultivated populations and reduce their genetic diversity. Such changes could reduce the pre-existing adaptation of restored populations, and limit their adaptability to environmental change. We used single nucleotide polymorphism (SNP) markers and a pool-sequencing approach to test for genetic differentiation and changes in gene diversity during cultivation in 19 wild grassland species, comparing the source populations and up to four consecutive cultivation generations. We then linked the magnitudes of genetic changes to the species' breeding systems and seed dormancy, to understand the roles of these traits in genetic change. The propagation changed the genetic composition of the cultivated generations only moderately. The genetic differentiation we observed as a consequence of cultivation was much lower than the natural genetic differentiation between different source regions. The propagated generations harbored even higher gene diversity than wild-collected seeds. Genetic change was stronger in self-compatible than in self-incompatible species, probably as a result of increased outcrossing in the monocultures. Synthesis and applications: Our study indicates that large-scale seed production maintains the genetic integrity of natural populations. Increased genetic diversity may be indicative of increased adaptive potential of propagated seeds, which would make them especially suitable for ecological restoration. Yet, it remains to be tested whether these patterns observed on the level of molecular markers will be mirrored also in plant phenotypes. Further, we used seeds produced in Germany and Austria, where the seed production is regulated and certified. Whether other seed production systems perform equally well remains to be tested.

Using soil eDNA for plant diversity assessments

This data sets corresponds to a publication in Methods in Ecology and Evolution titled: Plant biodiversity assessment through soil eDNA reflects temporal and local diversity In August 2018, a single soil eDNA sample was collected from the centre of each permanent plot (1m2) in the Solhomfjell Forest Reserve stablished by the Sommerfeltia program. The soil eDNA samples were stored in individual plastic bags for transportation to the lab and stored at -20 °C prior to freeze-drying under vacuum. Each soil eDNA sample was separately homogenized with ceramic beads and one gram was used for eDNA extraction. The latter was done in five rounds of two steps: (1) CTAB/chloroform pre-treatment to increase the separation of the organic phase and (2) aqueous phase and using the E.Z.N.A. soil DNA kit following the manufacturer’s protocol (Omega Bio-tek, Norcross, Georgia, USA). The chloroplast marker trnL (UAA) intron P6 loop was chosen as its short sequence can yield amplification of old DNA material degraded in eDNA samples. This marker was amplified for each sample with the g and h primers by PCR, using three technical replicates (Taberlet et al. 2007; 5'-GGGCAATCCTGAGCCAA-3', 5'-CCATTGAGTCTCTGCACCTATC-3'). Forward and reverse primers were tagged with a unique 12 bp oligonucleotide on the 5’ end (Fadrosh et al. 2014). Unique combinations of tagged primers were set up in panels for each PCR reaction for a total of 309 samples (100 samples with 3 PCR replicates each, 5 extractions blanks and 4 PCR negatives). The PCR negatives had no DNA template and were placed on the 96th well position in each panel. Composition of PCR reactions, final volumes and number of cycles can be found in Supporting Information Data S1. The PCR products were run on a 2% agarose gel, and the amplicon concentrations were measured via band intensity using ImageLab software (Bio-Rad, California, USA). The lowest concentration (μM) available for all PCR products and its relative volume was identified and the relative concentrations of the PCR products were adjusted to this same concentration. Amplicons were pooled in one library using a Biomek 4000 automated liquid handler (Beckman Coulter Life Sciences, Indianapolis, Indiana, USA). The library was cleaned using AMPure XP reagent beads (Beckman Coulter Life Sciences, Indianapolis, Indiana, USA). The length for all amplicons in the library was determined using a Fragment Analyzer (Agilent Technologies, Santa Clara, California, USA). The library was sequenced on an Illumina MiSeq platform with 150 bp paired-end reads (Illumina Inc., San Diego, California, USA). Sequence data was analyzed and curated using OBITools 2 (Boyer et al. 2016) following the wolf tutorial with adaptations for demultiplexing dual indexes from QIIME2 (Caporaso et al. 2010). Sequences were retained with both indexes for dereplication for further analysis. Similar sequences were clustered with obiclean (Boyer et al. 2016) only when the read count of the less abundant sequence was below 5% of the most abundant sequence. To reduce multiple identifications of the same sequence, taxonomic assignment of dereplicated and denoised sequences was done by matching to three reference sequences databases containing: (i) only taxa registered in the local Solholmfjell reference library; (ii) the complete arctic boreal database for vascular plants and bryophytes (Sønstebø et al.2010; Willerslev et al. 2014; Soininen et al. 2015); and (iii) taxa available in the EMBL database (downloaded on 7/02/2020) filtered to sequences with trnL (UUA) intron g-h primers using ecoPCR tool from OBITools (Boyer et al. 2016). Resulting identifications from the three databases were merged by sequence and duplicates were eliminated giving priority to reference databases (i), (ii), and (iii) in that order. To minimize erroneous taxonomic assignments, only taxa with a 100% match to a reference sequence were retained. We observed that below this threshold, sequences remained without a taxonomic rank assigned. Further, assigned taxa names were changed to the lowest taxonomic rank possible with trnL (UUA) intron and thus are identical to those registered in vegetation surveys. When different sequences were identified with identical taxa names, a unique entry was retained and the read counts within plots and replicates were summed. Read counts were averaged across all samples and negative controls (extraction + PCR). All analyses are plot-based, and coded using R v 1.4.17 (R Core Team, 2019) and with packages listed in the code. Separate analyses are made for vascular plants and bryophytes, and/or for spruce and pine data subsets, or combinations thereof, when relevant.

opencc-zeroMar 2022View details →

Assessing the vulnerability of plant functional trait strategies to climate change

Aim: Our ability to understand how species may respond to changing climate conditions is hampered by a lack of high-quality data on the adaptive capacity of species. Plant functional traits are linked to many aspects of species life history and adaptation to environment, with different combinations of trait values reflecting alternate strategies for adapting to varied conditions. If the realised climate limits of species can be partially explained by plant functional trait combinations, then a new approach of using trait combinations to predict the expected climate limits of species trait combinations may offer considerable benefits. Location: Australia. Time period: Current and future. Methods: Using trait data for leaf size, seed mass and plant height for 6,747 Australian native species from 27 plant families, we model the expected climate limits of trait combinations and use future climate scenarios to estimate climate change impacts based on plant functional trait strategies. Results: Functional trait combinations were a significant predictor of species climate niche metrics with potentially meaningful relationships with two rainfall variables (R2 = 0.36 & 0.45) and three temperature variables (R2 = 0.21, 0.28, 0.30). Using this method, the proportion of species exposed to conditions across their range that are beyond the expected climate limits of their trait strategies will increase under climate change. Main conclusions: Our new approach, called Trait Strategy Vulnerability, includes three new metrics. For example, the Climate Change Vulnerability (CCV) metric identified a small but important proportion of species (4.3%) that will on average be exposed to conditions beyond their expected limits for summer temperature in the future. These potentially vulnerable species could be high priority targets for deeper assessment of adaptive capacity at the genomic or physiological level. Our methods can be applied to any suite of co-occurring plants globally.

opencc-by-4.0Apr 2022View details →

Data and code from: Geomorphological processes shape plant community traits in the Arctic

Aim Geomorphological processes profoundly affect plant establishment and distributions, but their influence on functional traits is insufficiently understood. Here, we unveil trait-geomorphology relationships in Arctic plant communities.   Location High-Arctic Svalbard, low-Arctic Greenland, and sub-Arctic Fennoscandia.   Time period 2011-2018   Major taxa studied Vascular plants   Methods We collected field-quantified data on vegetation, geomorphological processes, microclimate, and soil properties from 5280 plots and 200 species across the three Arctic regions. We combined these data with database trait records to relate local plant community trait composition to dominant geomorphological processes of the Arctic, namely cryoturbation, deflation, fluvial processes, and solifluction. We investigated the relationship between plant functional traits and geomorphological processes using hierarchical generalised additive modelling.   Results Our results demonstrate that community-level traits are related to geomorphological processes, with cryoturbation most strongly influencing both structural and leaf economic traits. These results were consistent across regions, suggesting a coherent biome-level trait response to geomorphological processes.   Main conclusions The results indicate that geomorphological processes shape plant community traits in the Arctic. We provide empirical evidence for the existence of generalisable relationships between plant functional traits and geomorphological processes. The results indicate that the relationships are consistent across these three distinct tundra regions and that geomorphological processes should be considered in future investigations of functional traits.   Kemppinen, Niittynen, Happonen, le Roux, Aalto, Hjort, Maliniemi, Karjalainen, Rautakoski & Luoto. Provisionally accepted. Geomorphological processes shape plant community traits in the Arctic. Global Ecology and Biogeography. These are the data and code from Kemppinen et al. (Provisionally accepted).

opencc-by-4.0Apr 2022View details →

European plant-based foods sales data 2017-2020 (Nielsen Market Track)

<ul> <li>The dataset consists of Excel (.xlsx) files with data on sales of plant-based food products between 2017 and 2020 in a number of European countries (i.e. Austria, Belgium, Denmark, France, Germany, Italy, the Netherlands, Poland, Romania, Spain and the UK.)</li> </ul> <ul> <li>The data are clearly labelled within each file. The key variables (common across datasets) are Value in Euros, Volume in KG/LIT and Volume in Selling Units for a number of meat and dairy substitute food products specific to the retail region.</li> </ul> <ul> <li>The data were originally collected by Nielsen Market Track. They were analysed on the <a href="http://www.smartproteinproject.eu">Smart Protein project</a> in 2021 and used to publish an extensive <a href="https://smartproteinproject.eu/plant-based-food-sector-report/">market data report</a> and to host a <a href="https://www.youtube.com/watch?v=dsIJqvpXXgw">public webinar</a>, both entitled Plant-based foods in Europe: how big is the market?</li> </ul>

opencc-by-4.0Sep 2015View details →

Fig. 1 in Toponyms And Ethnonyms In The Names Of Rovno Amber Animals And Plants

Fig. 1. Liverworts (1) and insects (2–7) from Rovno amber collection of SIZK (table 1, 2): 1— Frullania ucrainica, holotype; 2 — Eohelea gedanica, male and female; 3 — Xenohimatium rovnense, holotype; 4 — Rovnoecus klesovicus, holotype; 5 — Leptoconops rovnensis, holotype; 6 — Bilobomyrma ukrainica, holotype; 7— Gnamptogenys europaea, neotype.

opencc-by-4.0Dec 2020View details →

Fig. 1 in Impact Of Designed Quairokkum Hydropower Plant Reconstruction On The Syr Darya River Ichthyofauna

Fig. 1. Syr Darya River basin with main tributaries, reservoirs and towns. Sampling places: 1. 40.2934, 69.6821; 2. 40.2947, 69.7351; 3. 40.2843, 69.8047; 4. 40.2757, 69.8230; 5. 40.3412, 70.2755

opencc-by-4.0Nov 2016View details →

Fig. 3 in Ornithological Fauna Of The Waste Water Treatment Plants In The Northern Left Bank Ukraine (Chernihiv And Kyiv Regions): Winter Populations And Ecological Structure

Fig. 3. Similarity clusters of bird populations' species composition in winter according to the water treatment facilities' biotopic zones: 1 — zone of water bodies; 2 — dam zone; 3 — technological zone 4 — meadows agricultural zone.

opencc-by-4.0Jul 2014View details →

Fig. 1 in Species Composition And Structure Of The Communities Of Plant-Parasitic And Free-Living Soil Nematodes In The Greenhouses Of Botanical Gardens Of Ukraine

Fig. 1. Dendrogram of similarity of the nematode communities in the greenhouses of botanical gardens of Ukraine (amalgamation by the method of complete linkage). Explanation of the abbreviations is given in table 2. Рис. 1. Дендрограмма сходства нематодных сообществ в оранжереях ботанических садов Украины (объединение по методу полной связи). Расшифровка сокращений дана в таблице 2.

opencc-by-4.0Jul 2014View details →

Fig. 2 in Species Composition And Structure Of The Communities Of Plant-Parasitic And Free-Living Soil Nematodes In The Greenhouses Of Botanical Gardens Of Ukraine

Fig. 2. Dendrogram of similarity of plant-parasitic nematodes' communities in the greenhouses of botanical gardens of Ukraine (amalgamation by the method of complete linkage). Explanation of the abbreviations is given in table 2.

Data from: Restoration of native saltmarshes can reverse arthropod assemblages and trophic interactions changed by a plant invasion

Plant invasions profoundly impact both natural and managed ecosystems, and removal of the invasive plants addresses only part of the problem of restoring impacted areas. The rehabilitation of diverse communities and their ecosystem functions following removal of invasive plants is an important goal of ecological restoration. Arthropod assemblages and trophic interactions are important indicators of the success of restoration, but have largely been overlooked in saltmarshes. We determined how arthropod assemblages and trophic interactions changed with the invasion of the exotic plant Spartina alterniflora and with the restoration of the native plant Phragmites australis following Spartina removal in a Chinese saltmarsh. We investigated multiple biotic and abiotic variables to gain insight into the factors underlying the changes in arthropod assemblages and trophic structure. We found that although Spartina invasion had changed arthropod diversity, community structure, feeding-guild composition, and the diets of arthropod natural enemies in the saltmarsh, these changes could be reversed by the restoration of native Phragmites vegetation following removal of the invader. The variation in arthropod assemblages and trophic structure were critically associated with four biotic and abiotic variables (aboveground biomass, plant density, leaf N, and soil salinity). Our findings demonstrate the positive effects of controlling invasive plants on biodiversity and nutrient cycling, and provide a foundation for assessing the efficacy of ecological restoration projects in saltmarshes.

opencc-by-4.0Apr 2022View details →

Dataset for "Alien plants tend to occur in species-poor communities"

This dataset contains the list of plant species, their abundances, vegetation types, and the area of the vegetation plots analyzed in the paper titled “Alien plants tend to occur in species-poor communities” by Padullés Cubino et al. (2022; Neobiota).  These data were obtained from the Czech National Phytosociological Database (Chytrý and Rafajová, 2003) (<a href="https://botzool.cz/vegsci/phytosociologicalDb">https://botzool.cz/vegsci/phytosociologicalDb</a>). The dataset contains 2 tables: <ol> <li>“Metadata.xlsx”: It includes a description of the fields found in "plot_species.csv".</li> <li>“plot_species.csv”: It includes the list of angiosperm plant taxa, their abundance cover, associated vegetation type, and the area of each vegetation plot.</li> </ol> References:  Chytrý M, Rafajová M (2003) Czech National Phytosociological Database: basic statistics of the available vegetation-plot data. Preslia 75: 1–15.

Large contribution of woody plant expansion to recent vegetative greening of the Northern Great Plains

Aim: Extensive portions of high-latitude grasslands worldwide have recently experienced increased vegetative productivity (i.e., greening) and have undergone a rapid transition towards woody plant dominance via the process of woody plant expansion (WPE). This raises the underlying question: To what degree are WPE and greening spatiotemporally linked? Given that these vegetative changes are predicted to continue, we seek to understand how recent changes in vegetation extent and productivity have interacted under recent climate change and anthropogenic disturbance to provide insights surrounding the future trajectory of temperate grasslands broadly. Location: Northern Great Plains (NGP), North America Taxon: Woody plants Methods: Greening was measured as the significant increase in three metrics between 2000 and 2019: leaf area index (LAI), annual maximum normalized difference vegetative index (NDVI), and annual mean NDVI. WPE was measured as the significant proportional increase in percent tree cover change between 2000 and 2019 in grasslands. We then examine these variables across a host of 26 potential driving variables. Results: We show that average proportional greening increased by 0.2-1.3% yr -1 (depending on metric), and proportional WPE increased by 6.9% yr -1 since 2000 across the NGP. Both changes are largely driven by the absence of wildfire and changing climate. Furthermore, WPE was spatially coherent and positively associated with a large component of recent greening, as revealed by their coupling across 34.1-40.6% of grassland area and as evidenced by the 9.7-19.7% of the variability in greening explained by WPE. Main conclusions: WPE and greening are spatiotemporally coupled across large portions of the NGP. Under continued climate change and wildfire suppression, WPE and greening are likely to continue across large swathes of grasslands globally. Furthermore, our results show that using a single greening metric may be insufficient to capture the large-scale vegetative changes such as the expansion of woody vegetation.

Eco-evolutionary causes and consequences of rarity in plants: a meta-analysis

Species differ dramatically in their prevalence in the natural world, with many species characterized as rare due to restricted geographic distribution, low local abundance, and/or habitat specialization. We investigated eco-evolutionary causes and consequences of rarity with phylogenetically-controlled meta-analyses of population genetic diversity, fitness, and functional traits in rare and common congeneric plant species. Our syntheses included 252 rare species and 267 common congeners reported in 153 peer-reviewed articles published from 1978-2020 and one manuscript in press. Rare species have reduced population genetic diversity, depressed fitness, and smaller reproductive structures than common congeners. Rare species also could suffer from inbreeding depression and reduced fertilization efficiency. By limiting their capacity to adapt and migrate, these characteristics could influence contemporary patterns of rarity and increase the susceptibility of rare species to rapid environmental change. We recommend that future studies present more nuanced data on the extent of rarity in focal species, expose rare and common species to ecologically-relevant treatments, including reciprocal transplants, and conduct quantitative genetic and population genomic analyses across a greater array of systems. This research could elucidate the processes that contribute to rarity and generate robust predictions of extinction risks under global change.

openother-openApr 2022View details →

Gene/Protein BridgeDb ID Mapping Database (Ensembl Plants 49)

Ensembl Plants 49 derived ID mapping database for use with BridgeDb. The scripts used to create these databases based on Ensembl BioMart can be found at <a href="https://github.com/bridgedb/create-bridgedb-genedb">https://github.com/bridgedb/create-bridgedb-genedb</a>. This work was funded by the <a href="https://fairplus-project.eu/">FAIRplus project</a> (grant agreement no 802750) and <a href="https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants">NWO Open Science Fund</a> (grant no <a href="https://www.nwo.nl/en/projects/203001121">203.001.121</a>).

Data supporting: Success of post-fire plant recovery strategies varies with shifting fire seasonality

Wildfires are increasing in size and severity and fire seasons are lengthening, largely driven by climate and land use change. Many plant species from fire prone ecosystems are adapted to specific fire regimes corresponding to historical conditions and shifts beyond these bounds may have severe impacts on vegetation recovery and long-term species persistence. Here, we conduct a meta-analysis of field-based studies across different vegetation types and climate regions to investigate how post-fire plant recruitment, reproduction and survival are affected by fires that occur outside of the historical fire season. We find that fires outside of the historical fire season may lead to decreased post-fire recruitment for many species, particularly obligate seeding species. Conversely, we find a general increase of post-fire survival in resprouting species. Our results highlight the trade-offs that exist when considering the effects of changes in the seasonal timing of fire, an already present aspect of climate-related global fire regime change.