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298 results for “plant richness”
Data from: Plant species richness and shrub cover attenuate drought effects on ecosystem functioning across Patagonian rangelands
Drought is an increasingly common phenomenon in drylands as a consequence of climate change. We used 311 sites across a broad range of environmental conditions in Patagonian rangelands to evaluate how drought severity and temperature (abiotic factors) and vegetation structure (biotic factors) modulate the impact of a drought event on the annual integral of normalized difference vegetation index (NDVI-I), our surrogate of ecosystem functioning. We found that NDVI-I decreases were larger with both increasing drought severity and temperature. Plant species richness (SR) and shrub cover (SC) attenuated the effects of drought on NDVI-I. Grass cover did not affect the impacts of drought on NDVI-I. Our results suggest that warming and species loss, two important imprints of global environmental change, could increase the vulnerability of Patagonian ecosystems to drought. Therefore, maintaining SR through appropriate grazing management can attenuate the adverse effects of climate change on ecosystem functioning.
Data from: Predicting spatial patterns of plant species richness: a comparison of direct macroecological and species stacking modelling approaches
PLEASE NOTE, THESE DATA ARE ALSO REFERRED TO IN TWO OTHER PUBLICATIONS. PLEASE SEE http://dx.doi.org/10.1111/j.1365-2486.2008.01766.x AND http://dx.doi.org/10.1111/2041-210X.12222 FOR MORE INFORMATION. Aim: This study compares the direct, macroecological approach (MEM) for modelling species richness (SR) with the more recent approach of stacking predictions from individual species distributions (S-SDM). We implemented both approaches on the same dataset and discuss their respective theoretical assumptions, strengths and drawbacks. We also tested how both approaches performed in reproducing observed patterns of SR along an elevational gradient. Location: Two study areas in the Alps of Switzerland. Methods: We implemented MEM by relating the species counts to environmental predictors with statistical models, assuming a Poisson distribution. S-SDM was implemented by modelling each species distribution individually and then stacking the obtained prediction maps in three different ways – summing binary predictions, summing random draws of binomial trials and summing predicted probabilities – to obtain a final species count. Results: The direct MEM approach yields nearly unbiased predictions centred around the observed mean values, but with a lower correlation between predictions and observations, than that achieved by the S-SDM approaches. This method also cannot provide any information on species identity and, thus, community composition. It does, however, accurately reproduce the hump-shaped pattern of SR observed along the elevational gradient. The S-SDM approach summing binary maps can predict individual species and thus communities, but tends to overpredict SR. The two other S-SDM approaches – the summed binomial trials based on predicted probabilities and summed predicted probabilities – do not overpredict richness, but they predict many competing end points of assembly or they lose the individual species predictions, respectively. Furthermore, all S-SDM approaches fail to appropriately reproduce the observed hump-shaped patterns of SR along the elevational gradient. Main conclusions: Macroecological approach and S-SDM have complementary strengths. We suggest that both could be used in combination to obtain better SR predictions by following the suggestion of constraining S-SDM by MEM predictions.
Current climate overrides historical effects on species richness and range size of freshwater plants in Europe and North America
<p>1. The latitudinal diversity gradient (LDG) hypothesis suggests that species richness should be highest at low latitudes, whereas Rapoport's rule states that largest ranges ought to be found for species at high latitudes. However, there is no consensus over these patterns and their underlying drivers in the freshwater realm.</p> <p>2. We investigated species richness and mean range size of freshwater plants in 50 km × 50 km grid cells across Europe (40°N to 71°N) and North America (25°N to 78°N), supplemented with data based on 1° latitudinal bands for mean range size. We were especially interested to find out whether there are similarities and differences in these ecogeographical patterns and their underlying drivers between the continents due to their contrasting historical characteristics, spatial extent and topography. </p> <p>3. First, we used partial regression to reveal whether species richness and mean range size of freshwater plants have a linear or quadratic relationship with latitude. Second, we employed variation partitioning based on partial regression to model relationships between plant species richness and mean range size and four explanatory variable groups (i.e., environmental features, current climate, historical climate and geographical location). Third, we utilized boosted regression tree analysis to further investigate species richness and mean range size of freshwater plants in relation to a set of explanatory variables. </p> <p>4. Our results revealed that species richness showed relatively similar patterns in relation to latitude between the continents. Similarly, mean range size trends were alike in North America whether we used 50 km x 50 km grid cell data or 1° latitudinal bands. Instead, different patterns in mean range size emerged between the used data sets in Europe. For both of species richness and mean range size, current climate (with different individual predictor variables) was the main driver in both the continents, but historical effects had a small influence on the response variables.</p> <p>5. <i>Synthesis</i>. Our findings indicated that major ecogeographical rules can strongly vary for the same taxonomic group across broad scales between continents. It is also premature to rely solely on well-known terrestrial taxonomic groups when drawing generalizations about ecogeographical rules.</p>
Data from: Fungal pathogen species richness: why do some plant species have more pathogens than others?
Variation among plant species in the number of associated herbivore and pathogen species is predicted to fit a species-area relationship in which the area or biomass embodied by a plant species is a function of individual size and geographic range size. This hypothesis is tested using published estimates of geographic range, individual size, and species richness of fungal-pathogens for 490 plant species occurring in the United States and controlling for sampling intensity and phylogenetic effects. The number of pathogens found on a plant species increases with the metrics of plant species' area and/or habitat diversity and their effects are similar between gymnosperm and angiosperm lineages. The strength of this pattern across a diverse set of plant lineages suggests that accumulation and persistence of pathogen species on plant species are governed by the same processes among temperate plants.
Water availability drives above-ground biomass and bird richness in forest restoration plantings to achieve carbon and biodiversity co-benefits
<p>To combat global warming and biodiversity loss we require effective forest restoration that encourages recovery of species diversity and ecosystem function to deliver essential ecosystem services, such as biomass accumulation. Further, understanding how and where to undertake restoration to achieve carbon sequestration and biodiversity conservation would provide an opportunity to finance ecosystem restoration under carbon markets. We surveyed 30 native mixed-species plantings in subtropical forests and woodlands in Australia, and used structural equation modelling to determine vegetation, soil and climate variables most likely driving above-ground biomass accrual and bird richness, and investigate the relationships between plant diversity, above-ground biomass accrual and bird diversity. We focussed on woodland and forest-dependent birds, and functional groups at risk of decline (insectivorous, understorey-nesting, and small-bodied birds). We found that mean moisture availability strongly limits above-ground biomass accrual and bird richness in restoration plantings, indicating potential synergies in choosing sites for carbon and biodiversity purposes. Counter to theory, woody plant richness was a poor direct predictor of above-ground biomass accrual, but was indirectly related via significant, positive effects of stand density. We also found no direct relationship between above-ground biomass accrual and bird richness, likely because of the strong effects of moisture availability on both variables. Instead, moisture availability and patch size strongly and positively influenced the richness of woodland and forest dependent birds. For understorey-nesting birds, however, shrub cover and patch size predicted richness. Stand age or area of native vegetation surrounding the patch did not influence bird richness. Our results suggest that in subtropical biomes, planting larger patches to higher densities, ideally using a diversity of trees and shrubs (characteristics of ecological plantings) in more mesic locations will enhance the provision of carbon and biodiversity co-benefits. Further, ecological plantings will aid the rapid recovery of woodland and forest bird richness, with comparable above-ground biomass accrual to less diverse forestry plantations.</p>
Data from: Plant species richness promotes soil carbon and nitrogen stocks in grasslands without legumes
1. The storage of carbon (C) and nitrogen (N) in soil are important ecosystem functions. Grassland biodiversity experiments have shown a positive effect of plant diversity on soil C and N storage. However, these experiments all included legumes, which constitute an important N input through N2-fixation. Indeed, the results of these experiments suggest that N2-fixation by legumes is a major driver of soil C and N storage. 2. We studied whether plant diversity affects soil C and N storage in the absence of legumes. In an 11-years grassland biodiversity experiment without legumes, we measured soil C and N stocks. We further determined above-ground biomass productivity, standing root biomass, soil organic matter decomposition and N mineralization rates to understand the mechanisms underlying the change in soil C and N stocks in relation to plant diversity and their feedbacks to plant productivity. 3. We found that soil C and N stocks increased by 18 and 16% in eight-species mixtures compared to the average of monocultures of the same species, respectively. Increased soil C and N stocks were mainly driven by increased C input and N retention, resulting from enhanced plant productivity, which surpassed enhanced C loss from decomposition. Importantly, higher soil C and N stocks were associated with enhanced soil N mineralization rates, which can explain the strengthening of the positive diversity-productivity relationship observed in the last years of the experiment. 4. Synthesis: We demonstrated that also in the absence of legumes plant species richness promotes soil carbon (C) and nitrogen (N) stocks via increased plant productivity. In turn, enhanced soil C and N stocks showed a positive feedback to plant productivity via enhanced N mineralization, which could further accelerate soil C and N storage in the long term.
Data from: Livestock activity increases exotic plant richness, but wildlife increases native richness, with stronger effects under low productivity
1.Grazing by domestic livestock is one of the most widespread land uses worldwide, particularly in rangelands, where it co-occurs with grazing by wild herbivores. Grazing effects on plant diversity are likely to depend on intensity of grazing, herbivore type, coevolution with plants and prevailing environmental conditions. 2.We collected data on climate, plant productivity, soil properties, grazing intensity and herbivore type; and measured their effects on plant species richness from 451 sites across 0.4 M km2 of semi-arid rangelands in eastern Australia. We used structural equation modelling to examine the direct and indirect effects of increasing grazing intensity by different herbivores (cattle, sheep, kangaroos, rabbits) on native and exotic plant species richness across all sites, and in subsets focusing on three woodland communities spanning a gradient in productivity. 3.Direct effects of grazing by all herbivores were strongest under low productivity but waned with increasing productivity. Increases in the intensity of recent and historic livestock grazing corresponded with greater exotic plant richness under low productivity and less native plant richness under both low and moderate productivity. Rabbit effects were greatest under moderate productivity. Overall effects of kangaroos were benign. Grazing indirectly affected native and exotic plant richness by increasing soil phosphorus and reducing soil health (i.e., nutrient cycling). 4.Synthesis and applications. Our study shows that livestock grazing increases exotic species richness but reduces native richness, while kangaroo grazing increases native richness in environments with low productivity. The results provide clear messages for land managers and policy makers: (1) the coexistence of livestock grazing and plant diversity is only possible within more productive environments and (2) grazing under low or moderate productivity will impact upon native and exotic plant richness.
Data from: A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change
Plant-herbivore interactions provide critical insights into the mechanisms that govern the spatiotemporal distributions of organisms. These interactions are crucial to understanding the impacts of climate change, which are likely to have an effect on the population dynamics of alpine herbivores. The Royle's pika (Ochotona roylei, hereafter pika) is a lagomorph found in the western Himalaya, and is dependent on alpine plants that are at risk from climate change. As the main prey of many carnivores in the region, the pika plays a crucial role in trophic interactions. We examined topographical features, plant genera presence, and seasonal dynamics as drivers of the plant richness in the pika's diet across an elevational gradient (2600−4450 m). We identified 79 plant genera in the faecal pellets of pikas, of which 89% were forbs, > 60% were endemic to the Himalaya and 97.5% of the plant genera identified followed the C3 photosynthetic pathway. We found that during the pre-monsoon season, the plant richness of the pika's diet decreased with increasing elevation. We demonstrate that a large area of talus supports greater plant diversity and, not surprisingly, results in higher species richness in the pika's diet. However, in talus habitat with deep crevices, pikas consumed fewer plant genera suggesting they may be foraging sub-optimally due to predation risk. The continued increase in global temperature is expected to have an effect on the distribution dynamics of C3 plants and consequently influence pika diet and distribution, resulting in a significant negative cascading effect on the Himalayan ecosystem.
Data from: Plant communities on nitrogen‐rich soil are less sensitive to soil moisture than plant communities on nitrogen‐poor soil
1.Plant species composition and diversity are known to change across local gradients of light, moisture, and nutrients, but ecologists still have a relatively limited understanding of how communities respond to multiple limiting resources. 2.We used a trait‐based approach to investigate how the functional composition and diversity of forest understory plant communities change along gradients in light, soil moisture and nitrogen availability. We used a total of seven leaf, root, and whole‐plant traits for 55‐78 species, and estimated the effects of the three resources on the mean and dispersion of these traits in understory plant communities across 50 forest sites. 3.Soil moisture and nitrogen availability (C/N ratio) both influenced plant community traits, but light availability (canopy openness) did not. Generally, increases in moisture and nitrogen both resulted in shifts towards more acquisitive resource use strategies, including greater leaf area, specific leaf area and maximum plant height, and lower leaf dry matter content, root dry matter content and rooting depth. Functional diversity of most traits also increased with increasing soil moisture and nitrogen. Although most traits varied with soil moisture on nitrogen‐poor sites, moisture did not influence of the distribution of any traits on nitrogen‐rich sites. 4.Synthesis: Independent co‐limitation of soil moisture and nitrogen appeared to influence the functional composition and diversity of understory vegetation in our study area. The co‐occurrence of species with resource acquisitive and conservative strategies on nitrogen‐rich sites may make plant communities relatively resistant to changes to soil moisture. These results suggest that altered precipitation regimes under climate change could lead to greater changes in the composition and diversity of plant communities on nutrient‐poor soils than on nutrient‐rich soils.
Data from: Shrubs as ecosystem engineers across an environmental gradient: effects on species richness and exotic plant invasion
Ecosystem-engineering plants modify the physical environment and can increase species diversity and exotic species invasion. At the individual level, the effects of ecosystem engineers on other plants often become more positive in stressful environments. In this study, we investigated whether the community-level effects of ecosystem engineers also become stronger in more stressful environments. Using comparative and experimental approaches, we assessed the ability of a native shrub (Ericameria ericoides) to act as an ecosystem engineer across a stress gradient in a coastal dune in northern California, USA. We found increased coarse organic matter and lower wind speeds within shrub patches. Growth of a dominant invasive grass (Bromus diandrus) was facilitated both by aboveground shrub biomass and by growing in soil taken from shrub patches. Experimental removal of shrubs negatively affected species most associated with shrubs and positively affected species most often found outside of shrubs. Counter to the stress-gradient hypothesis, the effects of shrubs on the physical environment and individual plant growth did not increase across the established stress gradient at this site. At the community level, shrub patches increased beta diversity, and contained greater rarified richness and exotic plant cover than shrub-free patches. Shrub effects on rarified richness increased with environmental stress, but effects on exotic cover and beta diversity did not. Our study provides evidence for the community-level effects of shrubs as ecosystem engineers in this system, but shows that these effects do not necessarily become stronger in more stressful environments.
Data from: Fire may mediate effects of landscape connectivity on plant community richness in prairie remnants
Following the predictions of island biogeography and metapopulation theory, efforts to understand and maintain plant communities have focused on spatial attributes such as patch size and connectivity. However, despite a large body of literature, the effects of these spatial attributes remain uncertain, and accumulating evidence suggests that they may interact with local patch characteristics. Here, we assess the role of spatial attributes (patch size and connectivity at two time periods) and of patch quality (indicated by number of years since last fire, as this is a fire-dependent system) in determining plant species richness at 63 remnant prairie sites in Wisconsin, USA. Our results demonstrate significant main effects of patch size, with larger patches being richer than small patches, and of fire, with recent-fire sites being richer than fire-excluded sites. We also report a novel interaction between number of years since fire and patch connectivity. Historical (1950) connectivity was negatively related to species richness at recent-fire sites, but positively related to species richness at fire-excluded sites, while current (2000) connectivity and species richness were positively correlated at recent-fire sites, but unrelated at fire-excluded sites. Our findings indicate that measures of patch quality such as time since last fire can alter the association between spatial attributes such as patch size or connectivity and species richness.
Data from: Patterns of modern pollen and plant richness across northern Europe
1. Sedimentary pollen offers excellent opportunities to reconstruct vegetation changes over past millennia. Number of different pollen taxa or pollen richness is used to characterise past plant richness. To improve the interpretation of sedimentary pollen richness, it is essential to understand the relationship between pollen and plant richness in contemporary landscapes. This study presents a regional-scale comparison of pollen and plant richness from northern Europe and evaluates the importance of environmental variables on pollen and plant richness. 2. We use a pollen dataset of 511 lake-surface pollen samples ranging through temperate, boreal, and tundra biomes. To characterise plant diversity, we use a dataset formulated from the two largest plant atlases available in Europe. We compare pollen and plant richness estimates in different groups of taxa (wind-pollinated vs non-wind-pollinated, trees and shrubs vs herbs and grasses) and test their relationships with climate and landscape variables. 3. Pollen richness is significantly positively correlated with plant richness (r=0.53). The pollen–plant richness correlation improves (r=0.63) when high pollen-producers are downweighted prior to estimating richness minimising the influence of pollen-production on the pollen richness estimate. This suggests that methods accommodating pollen-production differences in richness estimates deserve further attention and should become more widely used in Quaternary pollen diversity studies. 4. The highest correlations are found between pollen and plant richness of trees and shrubs (r=0.83) and of wind-pollinated taxa (r=0.75) suggesting that these are the best measures of broad-scale plant richness over several thousands of square kilometres. 5. Mean annual temperature is the strongest predictor of both pollen and plant richness. Landscape openness is positively associated with pollen richness but not with plant richness. Pollen-richness values from extremely open and/or cold areas where pollen production is low, should be interpreted with caution because low local pollen production increases the proportion of extra-regional pollen. 5. Synthesis. Our results confirm that pollen data can provide insights into past plant richness changes in northern Europe, and with careful consideration of pollen production differences and spatial scale represented, pollen data make it possible to investigate vegetation diversity trends over long timescales and under changing climatic and habitat conditions.
Data from: Mountain building, climate cooling and the richness of cold-adapted plants in the northern hemisphere
Aim The summits of mountain ranges at mid-latitude in the Northern Hemisphere and the Arctic share many ecological properties including comparable climate and similar floras. We hypothesise that the orogeny during the Oligocene-Miocene combined with global cooling allowed the origin and early diversification of cold-adapted plant lineages in these regions. Before establishment of the Arctic cryosphere, adaptation and speciation in high elevation areas of these mountains ranges may have led to higher species richness when compared to the Arctic. Subsequent colonisation from mid-latitude mountain ranges to the Arctic may explain similar but poorer flora. Location Arctic-Alpine regions of the Northern Hemisphere. Methods We mapped the cold climate in the Northern Hemisphere for most of the Cenozoic (60 Ma until present) based on paleoclimate proxies coupled with paleoelevations. We generated species distribution maps from occurrences and regional atlases for 5464 cold-adapted plant species from 756 genera occupying cold climates. We fitted a generalised linear model to evaluate the association between cold-adapted plant species richness and environmental as well as geographic variables. We performed a meta-analysis of studies, which inferred and dated the ancestral geographic origin of cold-adapted lineages using phylogenies. Results We found that the subalpine-alpine areas of the mid-latitude mountain ranges comprise higher cold-adapted plant species richness than the Palearctic and Nearctic polar regions. The topo-climatic reconstructions indicated that the cold climatic niche occurred first in mid-latitude mountain ranges (42-38 Ma), specifically in the Himalayan region, and only later in the Arctic (22-18 Ma). The meta-analysis of the dating of the origin of cold-adapted lineages indicated that most clades originated in central Asia between 39 and 7 Ma. Main conclusions Our results support the hypothesis that the orogeny and the progressive cooling in the Oligocene-Miocene generated cold climates in mid-latitude mountain ranges, before the appearance of cold climates in most of the Arctic. Early, cold mountainous regions likely allowed for the evolution and diversification of cold-adapted plant lineages followed by the subsequent colonisation of the Arctic. Our results are in line with Humboldt's vision of integrating biological and geological context in order to better understand the processes underlying the origin of arctic-alpine plant assemblages.
Data from: Persistence at the final stage of volcanic island ontogeny: abiotic predictors explain native plant species richness on 111 remote Pacific atolls
Aim: The final island ontogeny of the General Dynamic Model (GDM) (i.e. before island submergence) in tropical oceans corresponds to the coral atoll stage. Here, we examined whether the species richness of native vascular plants (indigenous and endemic species) on atolls is controlled by spatial and/or physical processes. We also predicted that atolls strongly affected by anthropogenic disturbance would have lower native species richness than predicted by spatial and physical processes. Location: Marshall Islands, Kiribati Islands, Nauru, Niue, Johnston, Cook Islands, French Polynesia and Pitcairn Islands (Pacific Ocean). Taxon: Native vascular plants Methods: We used stepwise regression to test the relative influence of five biogeographic variables on native species richness. Relationships were assessed for the full set of 111 Pacific coral atolls, as well as for atoll subsets ranging from 9 to 45 atolls. An index of human impact was then estimated, and residuals in the regression model predicting species richness from biogeographic variables were compared with the level of human impact. Results: A regression model including atoll area, highest atoll elevation, the stepping stone distances from the nearest raised atoll and volcanic island explained native species richness on the 111 Pacific coral atolls. Regression models for different archipelagos and atoll subsets were also significant. Endemic species richness was significantly linked with highest atoll elevation and the stepping stone distances from the nearest raised atoll. Residuals in the biogeographic regression model were barely related to human impact across the 111 atolls but were significantly related to human impact in the Kiribati atolls. Main conclusions: Native species richness on atolls is mainly controlled by physical and spatial characteristics. However, anthropogenic disturbances have altered the predicted pattern of native species richness leading to a lower model fit in some atoll subsets.
Bacterial community richness shifts the balance between volatile organic compound-mediated microbe-pathogen and microbe-plant interactions
Even though bacteria are important in determining plant growth and health via volatile organic compounds (VOCs), it is unclear how these beneficial effects emerge in multi-species microbiomes. Here we studied this using a model plant-bacteria system, where we manipulated bacterial community richness and composition and determined the subsequent effects on VOC production and VOC-mediated pathogen suppression and plant growth-promotion. We assembled VOC-producing bacterial communities in different richness levels ranging from one to twelve strains using three soil-dwelling bacterial genera (Bacillus, Paenibacillus and Pseudomonas) and investigated how the composition and richness of bacterial community affect the production and functioning of VOCs. We found that VOC production correlated positively with pathogen suppression and plant growth-promotion and that all bacteria produced a diverse set of VOCs. However, while pathogen suppression was maximized at intermediate community richness levels when the relative amount and the number of VOCs were the highest, plant growth-promotion was maximized at low richness levels and was only affected by the relative amount of plant growth-promoting VOCs. The contrasting effects of richness could be explained by differences in the amount and number of produced VOCs and by opposing effects of community productivity and evenness on pathogen suppression and plant-growth promotion along the richness gradient. Together, these results suggest that the number of interacting bacterial species and the structure of the rhizosphere microbiome drive the balance between VOC-mediated microbe-pathogen and microbe-plant interactions potentially affecting plant disease outcomes in natural and agricultural ecosystems.
Data from: Habitat diversity associated with island size and environmental filtering control the species richness of rock-savanna plants in neotropical inselbergs
Disentangling the multiple factors controlling species diversity is a major challenge in ecology. Island biogeography and environmental filtering are two influential theories emphasizing respectively island size and isolation, and the abiotic environment, as key drivers of species richness. However, few attempts have been made to quantify their relative importance and investigate their mechanistic basis. Here, we applied structural equation modelling, a powerful method allowing test of complex hypotheses involving multiple and indirect effects, on an island-like system of 22 French Guianan neotropical inselbergs covered with rock-savanna. We separated the effects of size (rock-savanna area), isolation (density of surrounding inselbergs), environmental filtering (rainfall, altitude) and dispersal filtering (forest-matrix openness) on the species richness of all plants and of various ecological groups (terrestrial versus epiphytic, small-scale versus large-scale dispersal species). We showed that the species richness of all plants and terrestrial species was mainly explained by the size of rock-savanna vegetation patches, with increasing richness associated with higher rock-savanna area, while inselberg isolation and forest-matrix openness had no measurable effect. This size effect was mediated by an increase in terrestrial-habitat diversity, even after accounting for increased sampling effort. The richness of epiphytic species was mainly explained by environmental filtering, with a positive effect of rainfall and altitude, but also by a positive size effect mediated by enhanced woody-plant species richness. Inselberg size and environmental filtering both explained the richness of small-scale and large-scale dispersal species, but these ecological groups responded in opposite directions to altitude and rainfall, that is positively for large-scale and negatively for small-scale dispersal species. Our study revealed both habitat diversity associated with island size and environmental filtering as major drivers of neotropical inselberg plant diversity and showed the importance of plant species growth form and dispersal ability to explain the relative importance of each driver.
Dataset and code for the manuscript "Plant indirect interactions reduce species richness but increase phylogenetic diversity"
<p>This Zenodo repository contains the original data set and code for replicating the result published in the paper "<strong>Plant indirect interactions reduce species richness but increase phylogenetic diversity</strong>"</p><p> </p><ol><li>The "BD.xlsx" data frame contains the original data. The first column, "ID," is an ID for each one of the patches (i.e., vegetation units containing one or more individuals for the same or different species separated from other patches by bare ground). The second and third columns, "localidad" and "suelo", inform about the location where patches are found. The "species" column identifies the different species present at each patch.</li><li> The "Comb1.xlsx" data frame contains the possible combination of 4 species for each ID (concatenation of "localidad" and "suelo") for all the species found in the sampling. Besides "ID", there is one column for each of the species included in interactions ("spA", "spB", "spC", "spD") that contains the name of the species.</li><li>The "phylo.xlsx" data frame contains the taxonomic information of the species found during the sampling. For each species recorded in column "species" we assign its genus (column "genus") and family (column "family")</li><li> "ALL_IN.xlsx" is a data frame containing for each "ID" (proxy of location), the species involved in interactions ("spA", "spB", "spC" & "spD"), the "interaction sign" indicating if a given interaction is positive or negative (results based on simulation) and "Order" indicating the number of species involved in the interactions(from two to four).</li><li>"Code.R" provides the R code necessary to obtain the results. As statistics is based on simulation, every run can provide slightly different results, although differences do not affect interpretation. Please note that running time can be elevated depending on the computer used.</li></ol><p> </p>
Changes in plant species richness due to land use and nitrogen deposition across the globe
<p>Data and scripts corresponding to the article "Combined effects of land use and nitrogen deposition on plant species richness worldwide". In the article, we quantified the combined effects of land use and nitrogen deposition on terrestrial plant species richness at a 0.25º spatial resolution across the globe. We first determined the proportional changes in plant species richness for different land-use types and N deposition values through meta-analyses of local monitoring data obtained from the literature. We then combined the site-level responses with global land use and N deposition maps in a new multi-pressure species-area relationship (mp-SAR) model to provide estimates of changes in plant species richness at a resolution of 0.25º (about 25 km at the equator) worldwide.</p> <p>In this repository you will find all the data necessary to get the final results and the code in R to guide you through out the analysis.</p>
Key roles for the freezing line and disturbance in driving the low plant species richness of temperate regions
<p><b>Aim</b>: At the macroscale, climate strongly correlates with species richness gradients, resulting from differences in <i>in-situ</i> diversification and dispersal. One historical explanation for the pattern is that regions spanning temperate climates contain few species because past disturbances have generated high extinction rates, and species from tropical regions are unable to easily colonize temperate regions. We test these postulates for Himalayan plants, which span subtropical to temperate climates over steep elevational gradients.</p> <p><b>Location: </b>Himalaya</p> <p><b>Time period:</b> Present day</p> <p><b>Major taxa studied:</b> Angiosperms</p> <p><b>Methods: </b>We use<b> </b>a comprehensive survey of 31 floras to document the elevational and geographical distributions of native Himalayan plants, augmented by field studies of trees in both the east and west Himalaya. We use grade of membership models to cluster species according to locations shared and phylogenetic analysis to evaluate diversification rates.</p> <p><b>Results: </b>Species fall into four cohesive biotas, organized by climate. Points of turnover between biotas occur where the mean minimum temperature of the coldest month is approximately 0<sup>o</sup>C (2,000 m - 2,500 m), and at the point of occasional annual freezing (1,000 m - 1,500 m); these boundaries run the length of the Himalaya. The patterns are retained when we consider whole clades rather than species. All plants (and the subsets trees, herbs and shrubs) belonging to the biota above the 2,000 m - 2,500 m line have higher recent speciation rates than those lower down.</p> <p><b>Main conclusions:</b> We attribute the high rate of recent speciation in temperate climates to high rates of turnover, creating ecological and geographical opportunity. The high elevation biota has few species, but spans the largest area, implying species numbers are far from any carrying capacity, at least with respect to accumulation of allopatric forms. This study thus links climatic restrictions of clades to differences in diversification rates, and by inference species numbers.</p>
Plant circadian clock control of Medicago truncatula nodulation involving regulation of Nodule Cysteine-Rich genes
<p>Legumes house nitrogen-fixing endosymbiotic rhizobia in specialized polyploid cells within root nodules, which undergo tightly regulated metabolic activity. By carrying out expression analysis of transcripts over time in Medicago truncatula nodules we found that the circadian clock enables coordinated control of metabolic and regulatory processes linked to nitrogen fixation. This involves the circadian clock-associated transcriptional factor LATE ELONGATED HYPOCOTYL (LHY), with lhy mutants being affected in nodulation. Rhythmic transcripts in root nodules include a subset of Nodule-specific Cysteine Rich peptides (NCRs) that have the LHY-bound conserved Evening Element in their promoters. Until now, studies have suggested that NCRs act to regulate bacteroid differentiation and keep the rhizobial population in check. However, these conclusions came from the study of a few members of this very large gene family that has complex diversified spatio-temporal expression. We suggest that rhythmic expression of NCRs may be important for temporal coordination of bacterial activity with the rhythms of the plant host, in order to ensure optimal symbiosis.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.