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opencc-by-4.0Feb 2024View details →

Supplementary Material for "Using Unstructured Crowd-sourced Data to Evaluate Urban Tolerance of Terrestrial Native Animal Species within a California Mega-City"

This data repository is for the publication "Using Unstructured Crowd-sourced Data to Evaluate Urban Tolerance of Terrestrial Native Animal Species within a California Mega-City" and contains all R scripts and data files to reproduce results as well as all supplementary tables and figures.

opencc-by-4.0Nov 2024View details →

Data from 'Tracability of Forest Reproductive Material with the quality label 'Plant van Hier': A DNA database with genetic profiles of native autochthonous tree and shrub species of Flanders, Belgium'

<h2>Background</h2> Indigenous trees and shrubs play an important role in multifunctional forest management. They form a significant part of the biodiversity in our forests. Forest reproductive material (FRM) of autochthonous Flemish origin is sold under the quality label ‘Plant van Hier’, a certification mark of the Agency for Nature and Forests. To ensure the provenance of the seedlings, we developed a DNA-database of genetic profiles of potential parent trees, using species-specific genetic markers. This database enables the traceability of FRM of the ‘Plant van Hier’ label throughout the entire production chain; from seed harvesting and cultivation to planting by the end user. This database contains the genetic profiles of almost all possible parent trees present within 27 Flemish autochthonous seed orchards of eight ecologically important tree and shrub species: Carpinus betulus, Corylus avellana, Frangula alnus, Populus tremula, Sorbus aucuparia, Tilia cordata, Tilia platyphyllos, and Ulmus laevis. The profiles were established using microsatellite markers (11 to 24 markers per species).  New genetic markers were developed for Carpinus betulus and Ulmus laevis. PCR products were run on an ABI 3500 Genetic Analyser (Thermo Fisher Scientific). <h2>Files</h2> The files will be updated when new genotypes are added to the seed orchards. The current data files contain data from genotypes collected in the period 2018-2023.  <h3>Species_genotypes</h3> These files contain the genetic fingerprints of the parent trees of autochthonous Flemish seed orchards. Missing data is indicated as ‘MD’. For Carpinus betulus, an octoploid species, the allelic phenotype is given instead of the genotype as the number of times that an allele occurs on a specific locus is not known. The next metadata is additionally given: - Species: the Latin name of the species - Seed_orchard: the name of the seed orchard in which the genotypes are located - Code_seed_orchard: the code of the seed orchard in which the genotypes are located as given in the Register of Flemish Forest Reproductive Material (‘Register bosbouwkundig uitgangsmateriaal’; inbo.be) - Genotype: the fieldname given to the genotype - Origin: the location where the genotype was collected in Flanders, Belgium. Genotypes were collected from natural stands which are assumed to have an autochthonous origin. When the specific location is unknown, the location ‘Flanders’ is given.  - Year_sampled: the year in which the genotypes were sampled in the respective seed orchard for genetic analysis. <h3>Species_binsets</h3> These files contain the binsets and allele names that are used to score the alleles of the genotypes in the programme Geneious Prime 2019.3.2 (<a href="https://www.geneious.com">https://www.geneious.com</a>). For Tilia platyphyllos and Tilia cordata, the same binsets were used.

opencc-by-4.0Dec 2019View details →

Supplementary Table S27.1: Animal species native to South Africa that have invasive populations elsewhere.

Animal species native to South Africa that have invasive populations elsewhere. Sorted by expected chronological appearance in the first place they were recorded as alien species. Notes are made on whether the introduction is known to be (Y) or not (N) from South Africa (or unknown U). Pathways are according to the CBD pathway classification scheme (Harrower et al. 2017), along with an indication of whether the introduction was intentional or accidental. Species that have multi-continental distributions, and which may in addition have some introduced populations are shown at the end of the table.

opencc-by-4.0Aug 2024View details →

Data from: The thermal limits of native plant species in California Coastal Sage Scrub

Field and laboratory data for Goldsmith et al. (In Review) entitled, "The thermal limits of native plant species in California Coastal Sage Scrub." Four data files are included:  Goldsmithetal_PlantFunctionalTraitMetaData-18July24.xlsx -Provides metadata (header, description, units, measurement type, and expample) for each column of the file entitled "Goldsmithetal_PlantFunctionalTraitData-18July24.csv."  Goldsmithetal_PlantFunctionalTraitData-18July24.csv - Provides raw data for field and lab observations of plant functional traits as described in the methods section of this data record.  Goldsmithetal_PlantFvFmLabData-29March24.csv - Provides raw data for experimental lab observations of leaf fv/fm following experimental heat treatments as described in the methods section of this data record.  Goldsmithetal_PlantFvFmLabMetaData-2Aug23.xlsx - Provides metadata (header, description, units, measurement type, and expample) for each column of the file entitled "Goldsmithetal_PlantFvFmLabData-29March24.csv."    Contact Greg Goldsmith (goldsmith at chapman dot edu) for additional information.

opencc-by-4.0Oct 2023View details →

SInAS: A global dataset of native and alien distributions of alien species

The SInAS dataset represents a collection of regional lists of alien (also called non-native or non-indigenous) species and includes information about their native ranges, alien ranges, invasion status for alien ranges, habitats and year of first record. This dataset has been generated by standardising and integrating large global databases of alien species occurrences using the SInAS workflow version 2.0.  The SInAS dataset is described in more detail in the following scientific article, which need to be cited when using this dataset: Gómez-Suárez, M., Laeseke, P., and Seebens, H. (submitted) A global dataset of native and alien distributions of alien species  The code to generate the dataset is stored on Github (https://github.com/hseebens/SInAS) with releases available on Zenodo (https://doi.org/10.5281/zenodo.3763221).

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Invasive grass litter suppresses a native grass species and promotes disease

Plant litter can alter ecosystems and promote plant invasions by altering resource availability, depositing phytotoxins, and transmitting microorganisms to living plants. Transmission of microorganisms from invasive plant litter to live plants may gain importance as invasive plants, which often escape pathogens upon introduction to a new range, acquire new pathogens over time. It is unclear, however, if invasive plant litter affects native plant communities by promoting disease. Microstegium vimineum is an invasive grass that suppresses native populations, in part through litter production, and has acquired new fungal leaf spot diseases since its introduction to the United States. In a greenhouse experiment, we evaluated how M. vimineum litter and its pathogens mediated competition with the native grass Elymus virginicus. Microstegium vimineum litter promoted disease on E. virginicus and suppressed establishment and biomass of both species. Litter had stronger negative effects on E. virginicus than M. vimineum, increasing the relative biomass of M. vimineum. Live plant competition reduced biomass of both species and live M. vimineum increased disease incidence on E. virginicus. Altogether, invasive grass litter suppressed both species, ultimately favoring the invasive species in competition, and increased disease incidence on the native species.

openCC (other)Nov 2021View details →

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Baltimore Ecosystem Study: Increased diversity of the regional species pool via seeding augments establishment of native species in experimental vacant lot restorations

The harsh geophysical template characterized by the urban environment combined with people’s choices has led ecologists to invoke environmental filtering as the main ecological phenomena explaining urban biodiversity patterns. Yet, dispersal is often overlooked as a driving factor, especially on expanding vacant land. Does overcoming dispersal limitation by seeding native species in urban environments and increasing the functional or phylogenetic diversity of the seeding pool increase native plant species diversity and abundance in urban vacant land? We took an experimental approach to learn how different dimensions of plant biodiversity within an augmented regional species pool, via seed additions, can explain variation in community structure over a 3-year period. Vacant lots were cleared and manipulated with seeding treatments of high or low phylogenetic and functional diversities from a pool of 28 native species. Establishment success, total native cover and native species richness were followed and compared to cleared, unseeded control lots as well as un-manipulated lots. Seeding increased native plant abundance and richness over uncleared plots, as well as cleared and unseeded control plots. Phylogenetically diverse seed mixtures had greater establishment success than mixtures composed of closely related species. Diversifying seed mixtures increased the likelihood of including species that are better able to establish on vacant land. However, there were no differences in varying levels of either functional or phylogenetic diversity. Augmenting the regional species pool via diverse seed mixtures can enhance native plant cover and richness under the harsh environmental conditions conferred by land abandonment.

openCC (other)Oct 2022View details →

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Short-term disappearance of foliar litter of three tree species native to rain forest of Puerto Rico

Litter disappearance was examined before (1989) and after (1990) Hurricane Hugo in the Luquillo Experimental Forest, Puerto Rico using mesh litterbags containing abscised Cyrilla racemiflora or Dacryodes excelsa leaves or fresh Prestoea montana leaves. Biomass and nitrogen dynamics were compared among: i) species; ii) mid- and high-elevation forest types; iii) riparian and upland sites; and iv) among pre- and post-hurricane disturbed environments. Biomass disappearance was compared using multiple regression and negative exponential models in which the slopes were estimates of the decomposition rates subsequent to apparent leaching losses and the y-intercepts were indices of initial mass losses (leaching). C. racemiflora leaves with low nitrogen (0.39 %) and high lignin (22.1 %) content decayed at a low rate and immobilized available nitrogen. D. excelsa leaves had moderate nitrogen (0.67 %) and lignin (16.6 %) content, decayed at moderate rates, and maintained the initial nitrogen mass. P. montana foliage had high nitrogen (1.76 %) and moderate lignin (16.7 %) content and rapidly lost both mass and nitrogen. There were not significant differences in litter disappearance and nitrogen dynamics among forest types and slope positions. Initial mass loss of C. racemiflora leaves was lower in 1990 but the subsequent decomposition rate did not change. Initial mass losses and the overall decomposition rates were lower in 1990 than in 1989 for D. excelsa. D. excelsa and C. racemiflora litter immobilized nitrogen in 1990 but released 10-15% of their initial N in 1989, whereas P. montana released nitrogen in both years (25-40 %). Observed differences in litter disappearance rates between years may have been due to differences in the timing of precipitation. Foliar litter inputs during post-hurricane recovery of vegetation in Puerto Rico may serve to immobilize and conserve site nitrogen. Support for this work was provided by grants BSR-8811902, DEB-9411973, DEB-9705814 , DEB-00

openCC (other)Nov 2023View details →

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Distribution of functionally distinct native and non-indigenous species within marine urban habitats

This data file (.xls) is composed of 5 sheets: <ol> <li>The “Taxon labels”: Taxon code, full name, authority and status/type (Abiotic, Unassigned, Native, Cryptogenic, Non-Indigenous Species)</li> <li>The “Trait labels”: Trait modality and labels and correspondences.</li> <li>The “Taxon-by-Trait matrix”: Fuzzy coded scores for each trait modality and taxon</li> <li>The “Taxon-by-sample matrix”: Abundance data of retained taxa in samples</li> <li>The “Sample labels and description”: Site and experimental factors (Habitat, Age, Experimental Unit, Replicate, nested within site) corresponding to each sample.</li> </ol> Sheets 4 and 5 are extracted from a published dataset, which cannot be shared at this stage of revision without revealing the name of several of the manuscript authors. This is done in respect with the journal guidelines about data storage.

opencc-by-4.0Mar 2023View details →

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Distribution of functionally distinct native and non-indigenous species within marine urban habitats

opencc-by-4.0Mar 2023View details →

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Effects of experimental manipulation of light and nutrients on establishment of seedlings of native and invasive woody species in Long Island, NY, USA forests 2000 - 2003

While several studies on the process of invasion often focused on single factors or on the general explanation of ‘disturbance,' recent work has attempted to move towards a more mechanistic understanding of the factors that promote plant community invasion. Manipulative experiments provide a means for discerning causal relationships and interactive effects of environmental factors in promoting invasion. This dataset contains the results of multifactor manipulative experiments in forest communities, which compared factors influencing early seedling establishment for native and invasive woody plants. In an earlier study, we found that in Long Island, NY, invasion patterns are correlated with forest community type (pine barrens or hardwood), light availability, and soil N and Ca. Therefore, we conducted manipulative field experiments in two different years to determine the relative importance and interaction of experimental gaps and N and Ca addition in pine barrens and hardwood forests in promoting invasion. We used seedlings of seven common native and invasive species in the first experiment, and 16 native and invasive species paired phylogenetically in the second experiment. This was done in the years 2000 and 2003 respectively.

openCC (other)Jun 2020View details →

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Emerging fungal pathogen of an invasive grass: Implications for competition with native plant species

This data package includes data and code from an experiment testing the effects of a leaf spot fungal infection and competition from the invasive (to the U.S.) grass Microstegium vimineum on the performance of three native grass species: Dichanthelium clandestinum, Elymus virginicus, and Eragrostis spectabilis. The experiment was performed between June and September of 2019 in a greenhouse on the University of Florida campus in Gainesville, FL, USA. The leaf spot infection is caused by the fungal pathogen Bipolaris gigantea, which has recently emerged on populations of M. vimineum in the U.S. We tested the hypothesis that infection of B. gigantea would both directly and indirectly affect the native grass species by measuring the change in biomass of each species with and without pathogen inoculation (direct effects) and by measuring the effect of pathogen inoculation on M. vimineum competition through changes in native grass biomass across a density gradient of M. vimneum (indirect effects). The code includes statistical analyses and figures. The code was run using R (version 4.0.1).

openCC (other)Feb 2021View details →

Figure 3 in You are what you eat: native versus exotic Crotalaria species (Fabaceae) as host plants of the Ornate Bella Moth, Utetheisa ornatrix (Lepidoptera: Erebidae: Arctiinae)

Figure 3. Rates of development of Utetheisa ornatrix larvae on different species of native and exotic Crotalaria in Florida and effect of leaves versus beans in the diet (see text for details): (A) partial development of larvae on the native C. rotundifolia versus exotic C. lanceolata; (B, C) partial development of larvae on the native C. pumila versus exotic C. lanceolata; (D, E) development of larvae on the exotic C. spectabilis/retusa versus exotic C. lanceolata; (F) development of larvae on C. incana (native to U. ornatrix range in the Neotropics, but introduced to Florida) versus exotic C. lanceolata. (F – based on data from Sourakov and Locascio 2013).

Figure 4 in You are what you eat: native versus exotic Crotalaria species (Fabaceae) as host plants of the Ornate Bella Moth, Utetheisa ornatrix (Lepidoptera: Erebidae: Arctiinae)

Figure 4. Fore wing size of Utetheisa ornatrix raised on different species of native and exotic Crotalaria and effect of leaves versus beans in the diet (see text for details): (A) Fore wing size of

Figure 2 in You are what you eat: native versus exotic Crotalaria species (Fabaceae) as host plants of the Ornate Bella Moth, Utetheisa ornatrix (Lepidoptera: Erebidae: Arctiinae)

Figure 2. (A) Understorey of the Florida hammock habitat occupied with invasive exotic Crotalaria spectabilis; (B) a clearing in a secondary Florida habitat, overgrown with exotic Crotalaria pallida; (C, D) mature larvae of U. ornatrix prefer pods of C. spectabilis over leaves; (E) carpenter ants are attracted to the extrafloral nectaries of C. lanceolata; (F, G) larva of U. ornatrix on C. pumila and a pod destroyed by it; (H) mature larva of U. ornatrix inside a pod of C. incana; (I, J) pods of C. pallida are numerous and large and provide ample food and shelter for U. ornatrix; (K) empty pods of C. spectabilis in December with all of their seeds consumed by U. ornatrix larvae; (L) in December, C. retusa becomes the preferred hostplant of U. ornatrix in the C. spectabilis-dominated habitat, when the latter declines; similarly, C. pumila becomes preferred for oviposition in C. lanceolata-dominated habitat; (M) the seeds of C. retusa are well protected by thick walls of the pod; here, a third instar larva is unable to penetrate it; (N) onset of the ultimate instar; (O–Q) prepupa-to-pupa development of U. ornatrix.

Figure 1 in You are what you eat: native versus exotic Crotalaria species (Fabaceae) as host plants of the Ornate Bella Moth, Utetheisa ornatrix (Lepidoptera: Erebidae: Arctiinae)

Figure 1. (A) In the wild population of U. ornatrix, adult moth landing on the flower of exotic Crotalaria retusa, Micanopy, Florida; (B) a typical size of a moth from a wild population at Cross Creek, Florida, resulting from larval feeding on C. rotundifolia leaves (top) and its offspring raised in the laboratory on beans of C. spectabilis (bottom) (fore wing length = 20 mm); (C) a single egg batch split in two (experimental and control groups) prior to hatching; (D) hostplant preference test using mature larvae of U. ornatrix inside a tray; (E) differences in pod size and seed volume in six Crotalaria species found in Florida; (F) difference in sprouting rate under similar conditions: native Crotalaria pumila shows much slower sprouting rate than introduced invasive Crotalaria species; (G) upland pine habitat on the University of Florida campus overtaken by thousands of exotic Crotalaria lanceolata plants with a sporadic native C. pumila in the midst (October 2014); (H) U. ornatrix eggs on C. lanceolata; (I) first instar larvae; (J) third instar larva.

opencc-by-4.0Jun 2014View details →

Figure 3 in Population structure of a native and an alien species of snail in an urban area of the Atlantic Rainforest

Figure 3. Detectability probability (A), abundance (B) and recruitment (C) estimated for Achatina fulica during the study. The error bars show 90% confidence intervals.