EstablishMed: a dataset of transition probabilities for woody plant establishment in the Mediterranean Region
Data files
Jun 13, 2024 version files 1.60 MB
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establishmed.csv
1.57 MB
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mediterranean_traits.csv
9.04 KB
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README.md
21.74 KB
Abstract
Motivation: Plant establishment is the result of sequential demographic processes, namely post-dispersal seed survival, seed germination, seedling survival and sapling survival. These processes can be quantified as transition probabilities between life stages through field experiments, and their product provides an overall establishment probability. This information is essential to understand demography within populations and plant colonization potential under global change scenarios. The Mediterranean Region constitutes a biodiversity hotspot characterised by severe summer droughts, which suppose a critical demographic bottleneck for perennial plant establishment. Despite many studies have quantified transition probabilities of woody species in this region, information is scattered through literature and has not yet been compiled. To fill this gap, we collated data from a systematic literature review and completed them with new unpublished data to create the EstablishMed dataset.
Main types of variables contained: EstablishMed is a compilation of 4728 records of transition probabilities that quantify demographic processes operating during plant establishment. All records belong to native species and were obtained in situ under field conditions. Each record includes information about the specific spatiotemporal context of the study (i.e., year, site, population, habitat and microhabitat) and the experimental procedures employed (e.g., degree of protection against natural enemies). In addition, we included taxonomic and trait information of the study species (i.e., seed mass, dispersal syndrome and life form), and the bioclimate of the study sites.
Spatial location and grain: The dataset covers the whole Mediterranean Region. The finest spatial resolution corresponds to microhabitat types within populations.
Time period and grain: Data were extracted from 271 studies originated between 1991 and 2024.
Major taxa and level of measurement: 134 woody species from 80 genera and 39 families.
Software format: EstablishMed is available in .csv format in Dryad repository.
Global Ecology and Biogeography (https://doi.org/10.1111/geb.13879)
Lucía Acevedo-Limón, Beatriz Rumeu, Claudio A. Bracho-Estévanez, Juan P. González-Varo.
Correspondence and request for materials should be addressed to Lucía Acevedo Limón (lucia.acevedo@uca.es).
establishmed.csv
Transition probability data of demographic processes operating during the establishment of 134 woody species from the Mediterranean Region. The dataset comprises 4728 transition probability records (rows) accompanied by variables of the spatiotemporal context (i.e., year, site, population, habitat and microhabitat) and experimental procedures employed to obtain the transition probability (e.g., degree of protection against natural enemies), as well as additional information on taxonomy, plant traits and bioclimate.
| Variable name | Description |
|---|---|
| species | Species name according to World Flora Online (WFO) and World Checklist of Vascular Plants (WCVP). |
| subspecies_taxonomy | Subspecies and variety level for those species with higher taxonomic resolution according to WFO and WCVP. |
| genus | Genus according to WFO and WCVP. |
| family | Family according to WFO and WCVP. |
| process | Demographic processes during establishment, including post-dispersal seed survival, seed germination, seedling survival and sapling survival. |
| transition_probability | Transition probability value obtained from the reviewed study (i.e., percentage or probability) and standardized as a probability (range: 0 - 1). |
| sampling_year | Temporal replicates are included in this variable as the year when the experiment was set up. When the experiment was replicated through several years, but results were reported as an average, we used a range that included the first and last sampling years separated by “-” symbol; e.g., seed predation probability evaluated over three consecutive years would be 2002-2004 (Gómez et al., 2008). When sampling years were not consecutive, the years were separated by “_” symbol; e.g., seed predation experiment conducted in 2009 and 2011 would be 2009_2011 (Pías et al., 2014). |
| site | Geographic location where the study was conducted. |
| population | Identity of the studied population within the site, where experiments were conducted. |
| bioclimate | Bioclimatic belts of the Mediterranean Region where the study was conducted, which were oro-Mediterranean, supra-Mediterranean, meso-Mediterranean, termo-Mediterranean and infra-Mediterranean. |
| coordinates | Spatial coordinates of the studied population expressed in decimal degrees. When not provided, we searched coordinates in other publications of the same authors or we considered the coordinates of a reference location (i.e., the nearest town). In those cases where the data was expressed as an average of multiple populations, we calculated the centroid of all population coordinates. |
| habitat | Type of habitat where experiments were conducted (i.e., pine-oak forest, juniper woodland, coastal shrubland, etc.). It also includes landscape or macrohabitat features (i.e., forest edge, forest gap, etc.). |
| habitat_id | Standardization of the habitat variable in a limited number of levels: abandoned cropland, afforested, burned area, cropland, degraded, dehesa, forest, grassland, heathland, marsh, scrubland, shrubland, sttepe, woodland. |
| microhabitat | Name of the microhabitat as reported in the study. |
| microhabitat_id | Standardization of the microhabitat variable into a limited number of levels: tree, shrub, conspecific, open and shaded. The latter one corresponds to artificially shaded areas. |
| protection | Degree of protection against natural enemies of the field experiment. This variable had six levels: |
| exp_period | Monitoring time period. Expressed in number of days for seed predation experiments and number of months for germination experiments. |
| viability_filter | Whether seeds were subjected to some viability filter, such as a flotation test (“yes”) or not (“no”). |
| viability_value | When seed were subjected to some viability test, the probability that seeds were viable. |
| seedling_origin | For seedling survival process, this variable refers to the origin of the monitored plant, if it was emerged from a seed (“emerged”) or grow up in controlled conditions and later transplanted to the field (“planted”). |
| seedling_age | The number of years-old of transplanted plants. |
| seed_treatment | Pre-sowing treatment applied to experimental seeds. This variable has the following levels: buried, depulped, dewinged, dispersed, dry fruit (heterocarpy), fleshy fruit (heterocarpy), heat, naked_embryo, partially_depulped, red_morph, scarification, seed_bank, small_seeds_discarded, soaked, stratification, unburied, whole_fruit, yellow_morph, NA. |
| seed_mass_mg | Mean seed mass (mg) of the species according to the specific seed mass value reported on the study, TRY and BROT2. |
| dispersal_syndrome | The dispersal syndrome of the species accounts for morphological traits of the diaspore, which predicts a single dispersal mode (i.e., anemochory, autochory, dyszoochory, epizoochory, frugivory and thalassochory). The dataset includes one heterocarpy species (i.e., Thymelaea velutina) that simultaneously produce dry and fleshy fruits, so both frugivory and autochory would correspond in this case. |
| life_form | Classification of the studied species according to its life form: tree, shrub and vine. |
| study | Identification code of each study, expressed as the first author’s name, publication year and journal name. |
| name_submitted | Species name (at species, subspecies or variety level) as it was on the original study. |
| publication_year | Year of publication of the study. |
| country | Name of the country where the study was conducted. |
mediterranean_traits.csv
Chorological type (geographic distribution), deciduousness and endemicity of the taxa included in EstablishMed to characterise the representation of typical Mediterranean flora. The dataset includes 140 taxa (rows), comprising species and subspecific taxa, like subspecies and varieties.
| Variable name | Description |
|---|---|
| species | Species name according to World Flora Online (WFO) and World Checklist of Vascular Plants (WCVP). |
| subspecific_taxonomy | Subspecies and variety level for those species with higher taxonomic resolution according to WFO and WCVP. |
| deciduousness | Deciduousness of each species as ‘evergreen’, ‘summer deciduous’ and ‘winter deciduous’ (López-González 2004). |
| chorology | Chorological type of the taxa based on its geographic distribution within the Western Palearctic as either predominantly ‘Mediterranean’ or ‘Mediterranean-Eurosiberian’ (Castroviejo 2020). |
| endemic_region | Endemicity of the taxa for a geographic area within the Mediterranean Region. |