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opencc-by-4.0Jul 2017View details →

Plant species distribution survey and its explanatory variables

Ten common herbaceous species were selected based on a survey of a 6.4-km² upstream catchment named « Bourdic » in southern France. Approximately 74 % of the catchment is agricultural (mainly vineyards), and 26 % is semi-natural (mainly woodlands and shrubs). The catchment has a Mediterranean climate with heavy rainfalls causing significant Hortonian runoff. The mean annual temperature is 14°C, and precipitation ranges from 600 to 800 mm per year with a drier period from March to October. Annual potential evapotranspiration is about 1100 mm. The altitude ranges from 55 a.s.l. at the outlet at the northeast to 128 m a.s.l. at the northwest. The surveys were conducted in July-August 2013 according to a non-destructive sampling procedure using GPS with an Android self-developed application; this enabled a location accuracy of 2 m. Agricultural ditches, including roadside ditches, were part of the study. Thirty-five kilometres of the drainage network (46%) were surveyed for presence/absence of the species. The remaining ditches were excluded from the analysis because surveying them was impractical or because recent management practices impaired species identification. After the survey, the georeferenced data were exported in a shapefile data format with line features. Also, explanatory variables of the dataset were reported, such as the geomorphological variables at the landscape scale that included the distance to the outlet (Doutlet), the drained surface area (Drain), the Multiresolution Index of Valley Bottom Flatness (Mrvbf), and the sun exposure of the slopes (Northness). The geomorphological variables at the local (ditch) scale were the slope (Slope) and solar radiation (Solar). All these variables are derived from a Digital Elevation Model (MNT) and a Digital Surface Model (MNS) taken in 2001 using an aerial lidar. We added also the distance to natural lands (Dnat) and distance to roads (Droad) on the basis of the manual classification of an orthophoto of the area taken in 2012.

opencc-by-4.0Dec 2022View details →

The global distribution of plants used by humans datasets: list of utilised species, occurrence data and model outputs at 10 arc-minutes spatial resolution

Datasets and model outputs used to map the global distribution of utilised plants by humans. The folder is composed of two subfolders raw_data and processed_data containing respectively the list of utilised plant species modelled -utilised_plants_species_list.csv-, and their occurrence data -occurrence_data.zip- and predicted distribution -species_proba_per_cell.rds-.   <ul> <li>The file utilised_plants_species_list.csv in the raw_data folder contains a list of 35687 plant species (and hybrids) used by humans and 10 plant use categories with the following 14 fields:</li> </ul> plant_ID: plant identifier number ranging from between 1-35687 binomial_acc_name: binomial accepted name of the plant species author_acc_name:  name of the author(s) is_hybrid: logical TRUE or FALSE indicating whether the species is an hybrid or not. AnimalFood: forage and fodder for vertebrate animals only. EnvironmentalUses: examples include intercrops and nurse crops, ornamentals, barrier hedges, shade plants, windbreaks, soil improvers, plants for revegetation and erosion control, wastewater purifiers, indicators of the presence of metals, pollution, or underground water. Fuels: charcoal, petroleum substitutes, fuel alcohols, etc. Given the importance of energy plants for people, those were distinguished from Materials. GeneSources: wild relatives of major crops which may possess traits associated with biotic or abiotic resistance and may be valuable for breeding programs. HumanFood: food for humans only, including beverages and food additives. InvertebrateFood: plants consumed by invertebrates used by humans, such as bees, silkworms, lac insects and edible grubs. Materials: woods, fibers, cork, cane, tannins, latex, resins, gums, waxes, oils, lipids, etc. and their derived products. Medicines: both human and veterinary. Poisons: plants which are poisonous to both vertebrates and invertebrates, both accidentally and intentionally, e.g., for hunting and fishing, molluscicides, herbicides, insecticides. SocialsUses: plants used for social purposes, which cannot be defined as food or medicine, for instance, masticatories, smoking materials, narcotics, hallucinogens and psychoactive drugs, and plants with ritual or religious significance. Totals: total number of uses recorded for a species   <ul> <li>The zipfile occurrence_data.zip in the processed_data folder contains 35687 Comma Separated Values (CSV) files, one for each species, containing curated geographic occurrence records used to  build species distribution models with the following 14 fields:</li> </ul> Species: the binomial accepted name of the species Fullname:  same as species decimalLongitude: the geographic longitude of the occurrence records of the species in decimal degrees decimalLatitude: the geographic latitude of the occurrence records of the species in decimal degrees countryCode: a three-letter standard abbreviation for the country of the occurrence locality coordinateUncertaintyinMeters: indicator for the accuracy of the coordinate location, described as the radius of a circle around the stated point location year: year of the observation of the occurrence record of the species individualCount: the number of individuals present at the time of the observation gbifID: unique identifier number for the occurrence from the original database basisOfRecords: the type of the individual record, e.g. observation, physical specimen, fossil, living ex-situ, culture collection specimen institutionCode: the name of the institution or organization listed as the data publisher on GBIF establishmentMeans: statement about whether an organism has been introduced to a given place and time through the direct or indirect activity of modern humans is_cultivated_observation: whether or not an organism is cultivated sourceID: name of the source database   <ul> <li>The file species_proba_per_cell.rds in the processed_data folder is a R Data Serialization (RDS) file containing a data.table object with the following 3 fields:</li> </ul> plant_ID: plant identifier number ranging from between 1-35687 proba: species occurrence probability cell: raster grid cell number between 1-2251762 This object can be used in combination with a raster layer to reconstruct the modelled distribution of each species or retrieve species richness and endemism.

opencc-zeroMar 2024View details →

Incorporating plant phenological responses into species distribution models (SDMs) reduces estimates of future species loss and turnover

Anthropogenetic climate change has caused distribution shifts of many species, and species distribution models (SDMs) are central for documenting this relationship. However, most SDMs rarely consider the evolution of climate-sensitive functional traits, such as phenology, which strongly affect species fitness. Using >120,000 herbarium specimens representing 360 plant species across the eastern United States, we developed a novel "phenology-informed" SDM that integrates dynamic phenological responses to changing climates. Compared to standard SDMs, our phenology-informed SDMs forecast lower species habitat loss and less species turnover under climate change. These results suggest that phenotypic plasticity or local adaptation in phenology may help species adjust their ecological niches and persist in their habitats under rapid environmental change. Our findings reveal how phenology variation mediates species distributions and affects regional biodiversity patterns. Our newly developed model also circumvents the need for mechanistic models, facilitating the deployment of trait-based SDMs across unprecedented spatial and taxonomic scales.

opencc-zeroNov 2021View details →

Directional selection shifts trait distributions of planted species in dryland restoration

1. The match between species trait values and local abiotic filters can restrict community membership. An often-implicit assumption of this relationship is that abiotic filters select for a single locally optimal strategy, though difficulty in isolating effects of the abiotic environment from those of dispersal limitation and biotic interactions has resulted in few empirical tests of this assumption. Similar constraints have made it difficult to assess whether the type and intensity of abiotic filters shift along gradients of environmental harshness, as predicted by the stress dominance hypothesis. 2. We planted 9,216 plants of perennial grass and forb species that had a range of functional trait values and were assigned to a warm, intermediate, or cool temperature tolerance pools across eight sites on the Colorado Plateau. We compared the distributions of traits of surviving individuals to null distributions to evaluate whether there were shifts in trait means and variation. Borrowing from phenotypic selection concepts in evolutionary biology, we assessed support for stabilizing, directional, and disruptive abiotic filtering of trait distributions and whether these types of filtering varied with initial species pool. 3. Functional composition was significantly different from null distributions for nearly all traits at all sites, with trait variation more restricted in harsher abiotic conditions, supporting the stress-dominance hypothesis. Contrary to expectations, we primarily found evidence for directional selection, which increased in frequency in warm species pools while disruptive selection was found more often in cool and intermediate species pools. 4. Synthesis: This study provides a controlled experimental approach to test the effect of the abiotic environment on plant trait filtering. We found that opportunistic strategies allowing for rapid water acquisition during favorable periods improved survival at warmer sites. Species with these strategies may be expected to benefit from increasing aridity and may be selected for active management efforts. More generally, the prevalence of directional selection may have important implications for dynamic vegetation models that rely on trait distributions for translating environmental variation into ecosystem processes.

opencc-by-4.0Feb 2022View details →

The distribution and impact of an invasive plant species (Senecio inaequidens) on a dune building engineer (Calamagrostis arenaria)

These data sets are used to run the analyses in the paper 'The distribution and impact of an invasive plant species (Senecio inaequidens) on a dune building engineer (Calamagrostis arenaria)' by Van De Walle et al., 2022, Neobiota (in progress). The presence/absence data (PA) of Senecio inaequidens in European coastal dunes can be found in 'Senecio_PA.xlsx', in the tab 'senecio_PA', together with the country and location where the occurrences were mapped. All coordinates of the samples are available in the tab 'coordinates samples'. 'Marram_growth_experiment.xlsx' contains the data gathered during the growth experiment. The origin of the sand is subdivided in 3 columns: 'Location' represents the location along the Belgian coast where sand was gathered, 'senecio' represents whether sand was gathered from underneath a senecio plant or not  and 'biota' represents whether biota could affect marram grass growth (biota = 0 thus means that the sand was sterilized).   Abstract Disturbance is thought to enhance the probability of invasive species establishment, a prerequisite for naturalization. Coastal dunes are characterized by disturbance in the form of sand dynamics. We studied the effect of this disturbance on the establishment and spread of an invasive plant species (Senecio inaequidens) in European coastal dunes. Local sand dynamics dictate the spatial configuration of marram grass (Calamagrostis arenaria). Therefore, marram grass configuration was used as a reliable proxy for disturbance. As marram grass plays a crucial role in natural dune formation, we evaluated the possible effects S. inaequidens could have on this process, if it would be able to naturalize in European coastal dunes.  We expected the highest probability of S. inaequidens establishment at intermediate marram grass cover because too low cover would increase sand burial, whereas high cover would increase competition. However, our results indicate that S. inaequidens is quite capable of handling higher levels of sand burial. Thus, probability of S. inaequidens establishment was high under low marram cover but slightly lowered when marram cover was high, hinting at the importance of competition. We expected a negative impact of Senecio-altered soils on marram grass growth mediated by soil biota. However, marram grass grew better in sand gathered underneath Senecio plants due to abiotic soil modifications. This enhanced growth may be caused by Senecio leaf litter elevating nutrient concentrations in an otherwise nutrient-poor substrate. If  such increased plant growth is a general phenomenon, further expansion of S. inaequidens could accelerate natural succession in European coastal dunes.

opencc-zeroMay 2022View details →

Soil chemical variables improve models of understory plant species distributions

<div class="page"> <div class="section"> <div class="layoutArea"> <div class="column">Aim</div> <div class="column">To determine the importance of soil variables relative to more commonly used topo-climatic or remotely sensed variables in species distribution models (SDMs) for understory plants.</div> <div class="column"> </div> <div class="column">Location</div> <div class="column">White Mountain National Forest, New Hampshire, U.S.A.</div> <div class="column"> </div> <div class="column">Methods</div> <div class="column">We fit models for presence of 41 forest understory plant species across 158 plots using soil, topographic, and spectral predictors to determine the relative contribution of different predictor types. We determined (a) if the potential importance of soil variables is greater than generally described in SDM literature, (b) which predictors are most important, and (c) if a standard subset of predictors can be used to effectively model all species.</div> <div class="column"> </div> <div class="column">Results</div> <div class="column">Models containing all three predictor types performed best. Soil and topographic variables had comparable importance; spectral variables were of lesser importance. The best predictor variable was B horizon carbon to nitrogen ratio (B C:N), followed by topographic position index, elevation, and B horizon exchangeable calcium (B Ca). No standard subset effectively modeled all species.</div> <div class="column"> </div> <div class="column">Main conclusions</div> <div class="column"> Our results and those of other SDMs that include in-situ soil geochemical data suggest that soil variables are increasingly important with more detailed descriptions of soils. Soil fertility data, such as B C:N and B Ca, are particularly important in acidic, forest soils where pH is a poor indicator of fertility. Commonly used topo-climatic variables provide meaningful predictions but are limited by their use of indirect predictor variables, inhibiting transferability and interpretability. The poor performance of models created using standard subsets of variables highlights the uniqueness of each species' niche and the need to combine flexible model building techniques with a variety of predictor variables.</div> </div> </div> </div>

opencc-zeroOct 2022View details →

Niche partitioning overrides interspecific competition to determine plant species distributions along a nutrient gradient

Changes in some combination of niche availability, niche overlap and the strength of interspecific interactions are thought to drive changes in plant composition along resource gradients. However, because these processes are difficult to measure in the field, their relative importance in driving compositional change in plant communities remains unclear. In an Australian temperate grassland, we added seeds of three native and three exotic grasses to 1,875 experimental plots in a way that allowed us to simultaneously estimate niche availability, niche overlap and the strength of pairwise interspecific interactions along a gradient of nutrient availability, obtained by adding 0, 5 or 20 g/m2 each of nitrogen, phosphorous and potassium jointly to plots. Niche availability (the proportion of microsites suitable for establishment and growth) was generally low and did not vary in response to nutrient addition. Most species co-occurred along the nutrient gradient by partitioning the available niche space. Where species interacted due to niche overlap, the abundance of one species, the native Chloris truncata, was usually facilitated by other species, with each of the five other species increasing the niche availability to C. truncata under at least one nutrient treatment. Chloris truncata also competitively excluded two species from some but not all sites they could otherwise have occupied. These outcomes did not clearly differ across nutrient treatments. Our results show that fine-scale spatial heterogeneity in establishment microsites can enable species to co-occur via niche partitioning, and competitive exclusion is rare. This finding contributes to an emerging picture that niche partitioning is common and frequently a stronger influence on recruitment outcomes than interspecific competition. The importance of competition in structuring plant communities may be overestimated if recruitment processes are overlooked.

opencc-by-4.0Dec 2023View details →

Plant community formation and species distribution pattern in relation to environmental variables in Endiras Natural Forest, northwest Ethiopia

The study was conducted in Endiras Forest, Northwest Ethiopia, so as to evaluate the effects of environmental variables on the patterns of plant community formation. A systematic random sampling technique was used to collect vegetation data from 56 (20 m x 20 m) plots laid at 100 m intervals on ten transects. In each plot, the species encountered and its percent cover abundance were recorded, which was later transformed into a modified Braun-Blanquet scale. The composite soil samples collected from 15 cm x 15 cm subplots were examined for 13 soil parameters. Communities were determined using cluster analysis. The Shannon-Wiener index was employed to quantify species diversity. The relationships between species and environmental variables were evaluated using Canonical Correspondence Analysis (CCA). Seventy three woody plant species, distributed in 38 families, were documented. Fabaceae was found to be the most species-rich family (21.9%). Five communities were generated from the cluster analyses that vary in diversity. Nine environmental variables were found to be significant in determining patterns of community formation (Pr< 0.05). Organic matter, pH, and altitude, highly correlated with CCA axis 1, are largely shaped the species distribution patterns. Various patterns of community formation demonstrate the need to design different conservation measures.

opencc-by-4.0Dec 2023View details →

Plant community formation and species distribution pattern in relation to environmental variables in Endiras Natural Forest, northwest Ethiopia

The study was conducted in Endiras Forest, Northwest Ethiopia, so as to evaluate the effects of environmental variables on the patterns of plant community formation. A systematic random sampling technique was used to collect vegetation data from 56 (20 m x 20 m) plots laid at 100 m intervals on ten transects. In each plot, the species encountered and its percent cover abundance were recorded. The composite soil samples collected from 15 cm x 15 cm subplots were examined for 13 soil parameters. Communities were determined using cluster analysis. The Shannon-Wiener index was employed to quantify species diversity. The relationships between species and environmental variables were evaluated using CCA. Seventy three woody plant species, distributed in 38 families, were documented. Fabaceae was found to be the most species-rich family (21.9%). Five communities were generated from the cluster analysis. Nine environmental variables were found to be significant in determining patterns of community formation (Pr< 0.05). Organic matter, pH, and altitude are largely shaped the species distribution patterns. Various patterns of community formation demonstrate the need to design different conservation measures.

opencc-zeroMay 2024View details →

Assessing the links between pollinators and the genetic and epigenetic features of plant species with contrasting distribution ranges

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long-term dimensions of plant-pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation-sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity.

opencc-by-4.0Aug 2024View details →

Sequencing data from: Divergent lineages in a young species: the case of Datilillo (Yucca valida), a broadly distributed plant from the Baja California Peninsula

<div> <div> Premise: Globally, barriers triggered by climatic changes have caused habitat fragmentation and population allopatric divergence. Across North America, oscillations during the Quaternary have played important roles in the distribution of wildlife. Notably, diverse plant species from the Baja California Peninsula in western North America, isolated during the Pleistocene glacial–interglacial cycles, exhibit strong genetic structure and highly concordant divergent lineages across their ranges. A representative plant genus of the peninsula is Yucca, with Y. valida having the widest range. Although a dominant species, it has an extensive distribution discontinuity between 26° N and 27° N, suggesting restricted gene flow. Moreover, historical distribution models indicate the absence of an area with suitable conditions for the species during the Last Interglacial, making it an interesting model for studying genetic divergence. Methods: We assembled 4411 SNPs from 147 plants of Y. valida throughout its range to examine its phylogeography to identify the number of genetic lineages, quantify their genetic differentiation, reconstruct their demographic history and estimate the age of the species. Results: Three allopatric lineages were identified based on the SNPs. Our analyses support that genetic drift is the driver of genetic differentiation among these lineages. We estimated an age of less than 1 million years for the common ancestor of Y. valida and its sister species. Conclusions: Habitat fragmentation caused by climatic changes, low dispersal, and an extensive geographical range gap acted as cumulative mechanisms leading to allopatric divergence in Y. valida. </div> </div>

Image 5 in Distribution of six little known plant species from Arunachal Pradesh, India

Image 5. Plectocomia himalayana Griff.

Image 1 in Distribution of six little known plant species from Arunachal Pradesh, India

Image 1. Begonia silhetensis (A. DC.) C.B. Clarke

Image 3. Larsenianthus arunachalensis M in Distribution of six little known plant species from Arunachal Pradesh, India

Image 3. Larsenianthus arunachalensis M.Sabu, Sanoj & T. Rajesh Kumar

Image 4. Larsenianthus assamensis S in Distribution of six little known plant species from Arunachal Pradesh, India

Image 4. Larsenianthus assamensis S.Dey, Mood & S. Choudhury

Image 2 in Distribution of six little known plant species from Arunachal Pradesh, India

Image 2. Dalbergia thomsonii Benth.

Image 6 in Distribution of six little known plant species from Arunachal Pradesh, India

Image 6. Tricarpelema glanduliferum (J. Joseph & R.S. Rao) R.S. Rao

opencc-by-4.0Jun 2021View details →

Potential distributional shifts in North America of allelopathic invasive plant species under climate change models

Occurrence data for invaive species used in ecological niche modeling for predictive studies. These data are cleaned to removed data with duplicates, incomplete coordinates, unlikely coordinates (e.g., 0,0), or those lacking environmental data were removed using the scrubr v.0.1.1 package in R (Chamberlain, 2016). Points falling outside of the respective training region for each species were also removed. These data represent downloads from iDigBio and GBIF.

opencc-by-4.0Dec 2018View details →

Fig. 4 in Wild bees (Anthophila) of Porto Santo (Madeira Archipelago) and their habitats: species diversity, distribution patterns and bee-plant network *

Fig. 4: Bipartite graph of the bee-plant network of Porto Santo.