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EstablishMed: a dataset of transition probabilities for woody plant establishment in the Mediterranean Region

Cite this dataset

Acevedo-Limón, Lucía; Rumeu, Beatriz; Bracho-Estévanez, Claudio Açai; González-Varo, Juan Pedro (2024). EstablishMed: a dataset of transition probabilities for woody plant establishment in the Mediterranean Region [Dataset]. Dryad. https://doi.org/10.5061/dryad.1c59zw44c

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 To fill this gap, we collated data from a systematic literature review and completed them with new unpublished data to create the EstablishMed dataset.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.

README: EstablishMed: a dataset of transition probabilities for woody plant establishment in the Mediterranean Region

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.

Funding

Universidad de Cádiz, Award: UCA-REC17VPCT-2021

Universidad de Cádiz, Award: UCA-REC13VPCT-2020

Ministerio de Ciencia, Innovación y Universidades, Award: RYC-2017-22095

Ministerio de Ciencia, Innovación y Universidades, Award: PID2019-104922GA-100