Find research datasets worth reusing

opencc-by-4.0Oct 2020View details →

Figures 1-9 from: Liu B, Williams DM (2020) From chaos to order: the life history of Hannaea inaequidentata (Lagerstedt) Genkal and Kharitonov (Bacillariophyta), from initial cells to vegetative cells. PhytoKeys 162: 81-112. https://doi.org/10.3897/phytokeys.162.56136

Figures 1-9 Hannaea cf. arcus and Hannaea cf. baicalensis, LM1–7 seven valves showing valve size diminution series for Hannaea cf. arcus8, 9 two valves of Hannaea cf. baicalensis. Scale bar: 10 μm (1, 8).

opencc-by-4.0Oct 2020View details →

Dataset associated to "Unraveling the relative role of light and water competition between lianas and trees in tropical forests: A vegetation model analysis"

This dataset includes all the codes necessary to reproduce the simulations presented in the paper "Unraveling the relative role of light and water competition between lianas and trees in tropical forests: A vegetation model analysis" published in Journal of Ecology. More precisely, it includes the version of the codes used to generate the results for the vegetation model (ED2), the analysis platform (PEcAn), as well as the meterological drivers (Drivers) and the initial conditions (IC) of the model and the priors and posterior parameter distributions.

opencc-zeroOct 2020View details →

Climatic and Vegetational Drivers of Insect Beta Diversity at the Continental Scale

Aim We construct a framework for mapping pattern and drivers of insect diversity at the continental scale, and use it to test whether and which environmental gradients drive insect beta diversity. Location Global; North and Central America; Western Europe Time period 21st century Major taxa studied Insects Methods An informatics system was developed to integrate terrestrial data on insects with environmental parameters. We mined repositories of data for distribution, climatic data was retrieved (WorldClim), and vegetation parameters inferred from remote sensing analysis (MODIS Vegetation Continuous Fields). Beta diversity between sites was calculated and then modelled with two methods, Mantel test with Multiple Regression and Generalized Dissimilarity Modelling. Results Geographic distance was usually the main driver of insect beta diversity. Independent of geographic distance, bioclimate variables explained more variance in dissimilarity than vegetation variables, although the particular variables found to be significant were more consistent in the latter, particularly, tree cover. Tree cover gradients drove compositional dissimilarity at denser coverages, in both continental case studies. For climate, gradients in temperature parameters were significant in driving beta diversity more so than gradients in precipitation parameters. Main conclusions Although environmental gradients drive insect beta diversity independently of geography, the relative contribution of different climatic and vegetational parameters is not expected to be consistent in different study systems. With further incorporation of additional temporal information and variables, this approach will enable development of a predictive framework for conserving insect biodiversity at the global-scale.

opencc-by-4.0Dec 2019View details →

Data from: Living with floating vegetation invasions

Shapefiles of locations of 20 reservoirs and river systems. CSV-files with time series of floating vegetation occurence on 20 reservoirs and river systems based on Landsat imagery

opencc-zeroNov 2021View details →

Vegetation growth and landscape genetics of Tillandsia lomas at its dry limits in the Atacama Desert shows fine-scale response to environmental parameters

1. Ecosystems at its dry limits have been studied while focusing on species biology, fitness and interactions of biotic and abiotic parameters; however, the interactive effects of these parameters remain under-explored and, therefore, information is often lacking about the putative effect of global climate change on these ecosystems. 2. Here, we conducted an analysis of the interplay of fine-scale landscape genetics and biotic and abiotic factors of terrestrial Tillandsia lomas in the hyperarid Atacama Desert, characterized by a fog-dependent vegetation type consisting of almost one single vascular plant species only. 3. We showed that metapopulations of Tillandsia landbeckii are genetically connected over many hundreds of squarekilometres, and despite a large potential to propagate clonally genetic diversity is structured, regionally and locally. On landscape-level genetic diversity correlates well with fitness parameters such as growth, flowering and vegetation density, and we observed also fine-scaled correlation with a 3-D landscape model indicating a positive feedback with saisonal fog occurrence and availability. The various interdependies of biotic and abiotic factors also result in regular linear banding patterns of vegetation arranged orthogonally towards landscape slope. Ex-situ growth experiments indicate that T. landbeckii growths at optimal rates within this extreme, hyperarid environment, and we can extrapolate mean biomass production for this particular ecosystem. 4. Synthesis. Our results suggest that the unique ecosystem of terrestrial Tillandsia lomas in the hyperarid Atacama Desert is an evolutionary balanced and fine-scaled system. Vegetation itself is built up by long-lived and persistent modules. We developed a descriptive model of the various interacting factors, thereby highlighting also a severe threat caused by global climate change.

opencc-by-4.0Jan 2021View details →

Dataset: Species presence, trait and philogeny database. Data from: Shift from trait convergence to divergence along old field succession. Journal of Vegetation Science.

This dataset was use in the manuscript "Shift from trait convergence to divergence along old field succession" publish at Journal of Vegetation Science. It contains the data of species presence at three different plots and species trait values (SLA, LDMC, height, seed weight and Phylogeny). We show that at the initial stage of succession, there is a scale-invariant pattern of trait convergence. On the contrary, in the late and intermediate stages of succession we observed that trait divergence became frequent at smaller grains and extents. The trend along the chronosequence is consistent with the theoretical hypothesis that predicts a shift from convergence to divergence along succession.

Data from: Digital photography provides a fast, reliable and non-invasive method to estimate anthocyanin pigment concentration in reproductive and vegetative plant tissues

1. Anthocyanin pigments have become a model trait for evolutionary ecology since they often provide adaptive benefits for plants. Anthocyanins have been traditionally quantified biochemically, or more recently using spectral reflectance. However, both methods require destructive sampling and can be labour intensive and challenging with small samples. Recent advances in digital photography and image processing make it the method of choice for measuring colour in the wild. Here, we use digital images as a quick, non-invasive method to estimate relative anthocyanin concentration among plants exhibiting colour variation. 2. By using a consumer-level digital camera and a free image processing toolbox, we extracted RGB values from digital images to generate colour indices. We tested petals, stems, pedicels and calyces of six species, which contain different types of anthocyanin pigments and exhibit different pigmentation patterns. Colour indices were assessed by their correlation to biochemically determined anthocyanin concentration. For comparison, we also calculated colour indices from spectral reflectance and tested the correlation with anthocyanin concentration. 3. Indices perform differently depending on the nature of the colour variation. For both digital images and spectral reflectance, the most accurate estimates of anthocyanin concentration emerge from anthocyanin content-chroma ratio (ACCR), anthocyanin-chroma basic (ACCB) and strength of green (S green) indices. Some colour indices derived from digital images and spectral reflectance strongly correlate with biochemically determined anthocyanin concentration, but the estimates from digital images performed better than spectral reflectance in terms of 2 and normalized root-mean-square error. This was particularly noticeable in a species with striped petals, but in the case of striped calyces both methods showed a comparable relationship with anthocyanin concentration. 4. Using digital images brings new opportunities to accurately quantify the anthocyanin concentration in both floral and vegetative tissues. This method is efficient, completely non-invasive, applicable to both uniform and patterned colour, and works with samples of any size.

opencc-zeroDec 2015View details →

Data from: Fractal measures of spatial pattern as a heuristic for return rate in vegetative systems

Measurement of population persistence is a long-standing problem in ecology; in particular, whether it is possible to gain insights into persistence without long time-series. Fractal measurements of spatial patterns, such as the Korcak exponent or boundary dimension, have been proposed as indicators of the persistence of underlying dynamics. Here we explore under what conditions a predictive relationship between fractal measures and persistence exists. We combine theoretical arguments with an aerial snapshot and time series from a long-term study of seagrass. For this form of vegetative growth, we find that the expected relationship between the Korcak exponent and persistence is evident at survey sites where the population return rate can be measured. This highlights a limitation of the use of power-law patch-size distributions and other indicators based on spatial snapshots. Moreover, our numeric simulations show that for a single species and a range of environmental conditions that the Korcak–persistence relationship provides a link between temporal dynamics and spatial pattern; however, this relationship is specific to demographic factors, so we cannot use this methodology to compare between species.

Data from: Urine is an important nitrogen source for plants irrespective of vegetation composition in an Arctic tundra: insights from a 15N-enriched urea tracer experiment

1. Mammalian herbivores can strongly influence nitrogen (N) cycling and herbivore urine could be a central component of the N cycle in grazed ecosystems. Despite its potential role for ecosystem productivity and functioning, the fate of N derived from urine has rarely been investigated in grazed ecosystems. 2. This study explored the fate of 15N-enriched urea in tundra sites that have been either lightly or intensively grazed by reindeer for more than 50 years. We followed the fate of the 15N applied to the plant canopy, at 2 weeks and 1 year after tracer addition, in the different ecosystem N pools. 3. 15N-urea was rapidly incorporated in cryptogams and in aboveground parts of vascular plants, while the soil microbial pool and plant roots sequestered only a marginal proportion. Further, the litter layer constituted a large sink for the 15N-urea, at least in the short term, indicating a high biological activity in the litter layer and high immobilization in the first phases of organic matter decomposition. 4. Mosses and lichens still constituted the largest sink for the 15N-urea 1 year after tracer addition at both levels of grazing intensity demonstrating their large ability to capture and retain N from urine. Despite large fundamental differences in their traits, deciduous and evergreen shrubs were just as efficient as graminoids in taking up the 15N-urea. The total recovery of 15N-urea was lower in the intensively grazed sites, suggesting that reindeer reduce ecosystem N retention. 5. Synthesis The rapid incorporation of the applied 15N-urea indicates that arctic plants can take advantage of a pulse of incoming N from urine. In addition, δ 15N values of all taxa in the heavily grazed sites converged towards the δ 15N values for urine, bringing further evidence that urine is an important N source for plants in grazed tundra ecosystems.

Data from: Genome dynamics of hybrid Saccharomyces cerevisiae during vegetative and meiotic divisions

Mutation and recombination are the major sources of genetic diversity in all organisms. In the baker's yeast, all mutation rate estimates are in homozygous background. We determined the extent of genetic change through mutation and loss of heterozygosity (LOH) in a heterozygous Saccharomyces cerevisiae genome during successive vegetative and meiotic divisions. We measured genome wide LOH and base mutation rates during vegetative and meiotic divisions in a hybrid (S288c/YJM789) S. cerevisiae strain. The S288c/YJM789 hybrid showed nearly complete reduction in heterozygosity within 31 generations of meioses and improved spore viability. LOH in the meiotic lines was driven primarily by the mating of spores within the tetrad. The S288c/YJM789 hybrid lines propagated vegetatively for the same duration as the meiotic lines, showed variable LOH (from 2-3% and up to 35%). Two of the vegetative lines with extensive LOH, showed frequent and large internal LOH tracts that suggest a high frequency of recombination repair. These results suggest significant LOH can occur in the S288c/YJM789 hybrid during vegetative propagation presumably due to return to growth events. The average base substitution rates for the vegetative lines (1.82 x 10-10 per base per division) and the meiotic lines (1.22 x 10-10 per base per division), are the first genome wide mutation rate estimates for a hybrid yeast. This study therefore provides a novel context for the analysis of mutation rates (especially in the context of detecting LOH during vegetative divisions), compared to previous mutation accumulation studies in yeast that used homozygous backgrounds.

Data from: Removal of an apex predator initiates a trophic cascade that extends from herbivores to vegetation and the soil nutrient pool

It is widely assumed that organisms at low trophic levels, particularly microbes and plants, are essential to basic services in ecosystems, such as nutrient cycling. In theory, apex predators' effects on ecosystems could extend to nutrient cycling and the soil nutrient pool by influencing the intensity and spatial organization of herbivory. Here, we take advantage of a long-term manipulation of dingo abundance across Australia's dingo-proof fence in the Strzelecki Desert to investigate the effects that removal of an apex predator has on herbivore abundance, vegetation and the soil nutrient pool. Results showed that kangaroos were more abundant where dingoes were rare, and effects of kangaroo exclusion on vegetation, and total carbon, total nitrogen and available phosphorus in the soil were marked where dingoes were rare, but negligible where dingoes were common. By showing that a trophic cascade resulting from an apex predator's lethal effects on herbivores extends to the soil nutrient pool, we demonstrate a hitherto unappreciated pathway via which predators can influence nutrient dynamics. A key implication of our study is the vast spatial scale across which apex predators' effects on herbivore populations operate and, in turn, effects on the soil nutrient pool and ecosystem productivity could become manifest.

opencc-zeroDec 2014View details →

Data from: Linkage of plant trait space to successional age and species richness in boreal forest understory vegetation

Determining the changes in within- and between-species functional diversity in plant communities, and their contribution to overall species trait overlap, can enhance efforts at understanding mechanisms of species coexistence. However, little is known about how variation in species functional diversity influences variation in species trait overlap among contrasting environments. Here, we studied the understorey vegetation in a well-characterized 5000-year-old chronosequence involving 30 forested islands that differ greatly in size, soil fertility, and species diversity. Across this chronosequence we expected consistent changes in both within- and between-species functional diversity that would lead to decreasing overall species trait overlap with increasing successional age, species richness, understorey vegetation density and spatial heterogeneity of soil resources. For each island we measured specific leaf area (SLA) of each of ten individuals of each plant species present. Using a variance decomposition method, we partitioned the total community functional diversity of SLA on each island into within- and between-species functional diversity. Further, we estimated overall species trait overlap as the ratio of within-species functional diversity to total functional diversity. Using regression analyses we then explored relationships of within- and between-species functional diversity, and of overall species trait overlap, with several environmental variables across the 30 islands. Consistent with our hypotheses, overall species trait overlap decreased with successional age due to a statistically significant decrease in within-species functional diversity, and decreased with species richness due to a simultaneous decrease in within-species functional diversity and increase in between-species functional diversity. Against our predictions, overall species trait overlap increased in more competitive environments and did not change with increasing spatial heterogeneity of soil N or P. Synthesis: Our study suggests niche packing as a key mechanism for species coexistence in plant communities. Using SLA as an integrator of plant ecological strategy we show that community successional age and species richness are significantly linked to trait space distribution of plant individuals of boreal forest understorey vegetation and therefore to local species coexistence. Our results also suggest that the trait space of dominant and subordinate species may respond differently to local environmental variables.

Data from: A theoretical foundation for multi-scale regular vegetation patterns

Self-organized regular vegetation patterns are widespread1 and thought to mediate ecosystem functions such as productivity and robustness, but the mechanisms underlying their origin and maintenance remain disputed. Particularly controversial are landscapes of overdispersed (evenly spaced) elements, such as North American Mima mounds, Brazilian murundus, South African heuweltjies, and, famously, Namibian fairy circles. Two competing hypotheses are currently debated. On the one hand, models of scale-dependent feedbacks, whereby plants facilitate neighbours while competing with distant individuals, can reproduce various regular patterns identified in satellite imagery. Owing to deep theoretical roots and apparent generality, scale-dependent feedbacks are widely viewed as a unifying and near-universal principle of regular-pattern formation, despite scant empirical evidence. On the other hand, many overdispersed vegetation patterns worldwide have been attributed to subterranean ecosystem engineers such as termites, ants, and rodents. Although potentially consistent with territorial competition, this interpretation has been challenged theoretically and empirically and (unlike scale-dependent feedbacks) lacks a unifying dynamical theory, fuelling scepticism about its plausibility and generality. Here we provide a general theoretical foundation for self-organization of social-insect colonies, validated using data from four continents, which demonstrates that intraspecific competition between territorial animals can generate the large-scale hexagonal regularity of these patterns. However, this mechanism is not mutually exclusive with scale-dependent feedbacks. Using Namib Desert fairy circles as a case study, we present field data showing that these landscapes exhibit multi-scale patterning—previously undocumented in this system—that cannot be explained by either mechanism in isolation. These multi-scale patterns and other emergent properties, such as enhanced resistance to and recovery from drought, instead arise from dynamic interactions in our theoretical framework, which couples both mechanisms. The potentially global extent of animal-induced regularity in vegetation—which can modulate other patterning processes in functionally important ways—emphasizes the need to integrate multiple mechanisms of ecological self-organization.

opencc-zeroOct 2019View details →

The origin and genetic variability of vegetatively propagated clones identified from old planted trees and plantations of Thujopsis dolabrata var. hondae in Ishikawa Prefecture, Japan

<a name="_Hlk10084612">Clonal plantations of Thujopsis dolabrata var. hondae have been established in Ishikawa Prefecture, Japan, since at least the 1800s. Historical planting of the species has led to the development of vegetatively propagated local cultivars, which originated from 'donor' trees that have often been conserved in sacred groves or avenues at shrines and temples. These donor trees must have been selected from natural populations. In this study we estimated the origin and genetic variability of clones identified among old planted trees and clonal plantations of T. dolabrata var. hondae, using 19 microsatellite markers. We discovered 12 clones among old planted trees, including five identical to members of a set of 14 we previously identified in plantations (giving 21 clones in total). Based on analyses combining assignment and exclusion tests, we inferred origins of eight of those 21 clones: six may have originated from a natural population distributed in Ishikawa, one from Hokkaido & Aomori, and the other from Iwate & Yamagata, suggesting the clones constituting cultivars have multiple origins. The clones identified in plantations have significantly lower genetic variability, and higher relatedness, indicating that clones of cultivars have a much narrower genetic base than those of natural populations. We suggest new clones selected from natural populations</a> elsewhere, as well as Ishikawa, are needed for future breeding of T. dolabrata var. hondae to develop clonal forestry for this species.

Data from: Both trait-neutrality and filtering effects are validated by the vegetation patterns detected in the functional recovery of sand grasslands

Neutral theory of species assembly means that species assembly is governed by stochastic dispersal processes and fluctuations in established populations. An alternative theory suggests that assembly is strongly determined by functional trait filtering governed by abiotic and biotic filtering selecting species from the local species pool. To test these assumptions, in the current paper we analysed vegetation changes in the first 12 years of succession after heavy goose grazing on acidic sand. With trait-based analyses using permanent plots we addressed the following hypotheses: (i) High fluctuations in the trait values are typical in the first years; later a temporally divergent change in the trait patterns of sites with different vertical position became characteristic. (ii) In the functional diversity of regenerative and vegetative traits we expected different temporal patterns. We confirmed the first hypothesis, as in the first few years most traits displayed high fluctuations with no clear patterns. Our findings weakly supported the second hypothesis; while there were distinct patterns detected in the functional richness of traits, functional divergence and evenness displayed no clear distinctive patterns. We can conclude that both trait neutrality and filtering effects operate in the vegetation changes of the first period of secondary succession.

Data from: Positive size-speed relationships in gametes and vegetative cells of Chlamydomonas reinhardtii; implications for the evolution of sperm.

It is commonly held that differences in gametes of the two sexes (anisogamy) evolved from ancestors whose gametes were similar in size and behaviour (isogamy). Underlying many hypotheses explaining anisogamy are assumed relationships between cell size and speed in the ancestral isogamous population. Using the isogamous alga Chlamydomonas reinhardtii, we explored size-speed distributions in vegetative and gamete cells of ten cell lines, and clonal data from within two cell lines. We applied an independent speed selection approach to gamete populations of C. reinhardtii, monitoring correlated responses in size following selection for high speed. We demonstrate positive size-speed relationships in clones, cell lines and artificially selected speed selection lines. We found different size-speed relationships in the two cell types of C. reinhardtii even though they overlap in size, suggesting that cell composition and/or programs of gene expression are capable of altering this relationship, and that the relationship is evolvable. The positive genetic size-speed correlation means that the division of parent vegetative cells into numerous gametes trades off against not only size but also speed, a trade-off that has not received previous attention. Our results support re-evaluating the role of speed selection in the evolution of anisogamy.

opencc-zeroDec 2015View details →

Data from: Precipitation mediates the effect of human disturbance on the Brazilian Caatinga vegetation

Seasonally dry tropical forests (SDTFs) are one of the most threatened forests worldwide. These species-rich forests not only cope with several acute (e.g. forest loss) and chronic (e.g. overgrazing and firewood extraction) human disturbances, but also with climate change (e.g. longer and more severe droughts); yet, the isolated and combined effects of climate and acute and chronic human disturbances on SDTF vegetation are poorly known. Given the environmental filter imposed by drought in SDTFs, the composition and structure of vegetation is expected to be strongly associated with annual precipitation, and thus the effects of human disturbances on vegetation may also depend on precipitation (i.e. interacting effect). We tested these hypotheses in the Brazilian Caatinga – a SDTF threatened by climate change and human disturbances. We evaluated the isolated and combined (both additive and multiplicative) effect of precipitation, a chronic disturbance index and acute disturbance (landscape forest cover) on the diversity, stem density, evenness, taxonomic composition and aboveground biomass of adult trees and shrubs across 19 0.1-ha plots distributed along a disturbance and precipitation gradients. We recorded 5541 stems from 129 species. Precipitation showed a stronger (positive) effect on species diversity than acute and chronic disturbances and, as expected, the effect of disturbance depended on precipitation (interacting effect): i.e. species diversity (especially the number of rare species) was negatively related to forest loss but positively related to chronic disturbance in wetter sites, whereas in drier sites, species diversity was weakly related to forest cover, but strongly and negatively related to chronic disturbance. Contrary to species diversity, community evenness, stem density and biomass were weakly related to all predictors. Synthesis. Precipitation appears to be a strong environmental filter determining the distribution of water-demanding plant species. Chronic disturbance in wetter (high-productive) forests may favour species diversity by increasing ecosystem heterogeneity (intermediate disturbance hypothesis). Yet, the biodiversity costs of chronic disturbance are higher in drier (low-productive) forests; i.e. there is a co-limitation imposed by drought and disturbance in drier forests. Overall, our findings indicate that rapid climatic changes in the region will probably have strong negative effects on this SDTF.

Data from: Resident species with larger size metrics do not recruit more offspring from the seed bank in old-field meadow vegetation

1. According to the traditional 'Size Advantage' (SA) hypothesis, plant species with larger body size are expected to be more successful when competition is intense, i.e. within severely crowded vegetation. Recent studies in old-field habitats, however, have shown that those species with greater numerical abundance as resident plants generally have a relatively small minimum reproductive threshold size (MIN), not a relatively large maximum potential body size (MAX). 2. In this study, we test for a size advantage in terms of species abundance representation in the soil seed bank, and we extend the SA hypothesis to include two additional size metrics: leaf size and seed size. Specifically, we ask, for resident species within a crowded old-field meadow: is larger seed size, leaf size, and/or body size associated with greater reproductive / recruitment success (i.e. number of germinable seeds within — and establishing plants emerging from — the soil seed bank)? We collected soil cores for a greenhouse experiment to record relative species abundances of germinable seeds in the seed bank, and we used a field experiment to record local abundances of species emerging from the resident seed bank within denuded plant neighbourhoods over three subsequent field seasons. 3. We found no general support for the SA hypothesis involving any of the size metrics, and none of the latter was a strong predictor of the number of germinable seeds emerging from soil cores in the greenhouse experiment. However, for species establishing in the field experiment from the seed bank over the three-year survey period, more abundant species in years 2 and 3 tended to be those with smaller MIN, and thus smaller MAX. In addition, within more crowded neighbourhoods, representation of reproductive plants was generally greater for species with relatively small MIN (and hence small MAX). 4. Synthesis. Our results extend support for the 'Reproductive Economy Advantage' hypothesis in old field habitats, to include not just established, largely undisturbed vegetation, but also very early stages of recruitment from seed within locally crowded plant neighbourhoods. Specifically, more successful species here are not those with relatively large potential body size (MAX); they are species capable of producing at least some offspring despite severe body size suppression, because they have a relatively small MIN.

opennotspecifiedDec 2005View details →

FIGURE 25 in " Cerrado " vegetation, with descriptions of three new species

FIGURE 25. Tarsonemus longisetae sp. nov. (male). Dorsal surface.