Data Descriptor | Open | Published:

A functional trait database for Mediterranean Basin plants

Scientific Data volume 5, Article number: 180135 (2018) | Download Citation

Abstract

Functional trait databases are emerging as crucial tools for a wide range of ecological studies across the world. Here, we provide a database of functional traits for vascular plant species of the Mediterranean Basin. The database includes 25,764 individual records of 44 traits from 2,457 plant taxa distributed in 119 taxonomic families. This database (BROT 2.0) is an updated and enlarged version of a previous database (BROT 1.0; 8,263 records, 14 traits, 952 taxa). Trait data were obtained from a comprehensive literature review, plus some field and experimental observations. All records are fully referenced and, in many cases, include geographic coordinates. The database is structured to include different levels of accuracy of trait information for each entry. BROT 2.0 should facilitate testing hypotheses on plant functional ecology within the Mediterranean Basin, and comparing this region with other ecosystems worldwide. The BROT 2.0 database and its trait definitions can be used as a template for creating similar trait databases in other regions of the world.

Design Type(s)
  • data integration objective
  • database creation objective
  • biodiversity assessment objective
Measurement Type(s)
  • plant trait
Technology Type(s)
  • data item extraction from journal article
Factor Type(s)
    Sample Characteristic(s)
    • Tracheophyta
    • Mediterranean Region

    ISA-Tab metadata

    Background & Summary

    Plant functional traits determine the response of plant species to environmental factors1 and disturbances2, and are currently used for testing a range of ecological hypotheses3,​4,​5,​6. Trait-based approaches can also be used to understand the mechanisms assembling communities7,​8,​9,​10. Exploring functional (trait) diversity in communities is providing new insights on ecological processes and ecosystem functioning11,12, and has a promising future in the ecology research agenda13. Plant trait databases are also important sources for evolutionary biologists; together with calibrated phylogenies, they are a source of information for understanding the origin and evolution of selective pressures14,​15,​16. Consequently, trait databases are becoming a key research tool in ecology and evolution.

    The Mediterranean Basin harbors around 25 000 plant species, including many endemics17, and has a unique plant genetic diversity within the western Palearctic biogeographic region, mainly attributed to the role of the area as glacial refugium during Pleistocene glacial periods18,19. The presence of many peninsulas (Iberian, Italian, Balkan, and Anatolian) and islands is another driver of plant endemism in the region. Furthermore, the geographical position of the basin at the intersection of three continents (Europe, Asia, and Africa) has shaped a unique plant assembly with plants from the three different biogeographical regions20. At the same time, however, the Mediterranean Basin is also considered one of the global biodiversity hotspots for habitat loss21. This region is the cradle of Western civilization, and has witnessed the rise and fall of many cultures, some with very high population densities, that have led to high levels of habitat degradation and loss for many centuries. Recent threats to plant diversity in Mediterranean Basin include changes in climate, land use and fire regime22,23. Therefore, a description of functional trait structure and variability across the Mediterranean Basin is of critical importance for predicting the possible responses of plant populations, species and communities to future changes.

    The creation of the BROT database24 (hereafter, BROT 1.0) was a major effort to gather plant functional traits for the Mediterranean region. One of the strengths of this database was that it included a range of data types for each trait (e.g., quantitative, semi-quantitative, and binary) so that even coarse information was stored in a useful way within the database, together with high-quality data. It also considered variability within species by including, when available, several trait records for a given taxon. The information included in the database came from many references, including gray literature (reports, theses, and articles in various languages) that are not easily accessible to users. BROT 1.0 was a first step in compiling and organizing trait information in a standardized format for international users. Although BROT 1.0 was focused on fire-related and regeneration traits24, it has been used in many papers published in peer-reviewed journals (more than 150 GoogleScholar citations by December 2017) and was also included in a global plant trait database (TRY25) and in the Encyclopedia of Life (eol.org).

    The increase in functional trait research for the Mediterranean flora, together with the need for a more comprehensive plant trait database for studies on functional ecology and evolution, motivated us to make a major update of the BROT database. Here we introduce BROT 2.0. The great effort performed in compiling regeneration traits in BROT 1.0 was continued in this update, making BROT 2.0 a prominent database on regeneration traits for Mediterranean flora, and in particular for traits related to the regeneration after disturbance. In addition, in this new version of BROT we have increased (tripled) the number of traits and taxa, improved the standardization of some traits, and added geographical coordinates (where possible) for enabling geographically explicit analyses. This new version includes not only regeneration traits, but also vegetative and sexual reproductive traits. Thus BROT 2.0 is the largest source of information on plant traits for the Mediterranean Basin region.

    The BROT 2.0 database is structured on four files (Fig. 1), all connected by unique identifiers. The fact that most information is in the ‘Data file’, and in plain text, simplifies the use of the database. We propose BROT 2.0 as a reference database for functional trait analyses and hypothesis testing within the Mediterranean Basin and for comparing this area with other ecosystems across the globe. It is also a useful tool for identifying knowledge gaps on the functional ecology of plants in the study region. The database and its standardized definitions may also be used as a template for compiling plant trait databases in other regions of the world.

    Figure 1: Structure of BROT 2.0 database.
    Figure 1

    Yellow boxes are the four files that make up the database, and include the column names of each file and the number of rows (below the box); ID refers to unique identifiers in the corresponding file. Black thick lines indicate the link between files. Gray arrows indicate the manuscript table in which information on a column can be found. (*) “Coordinates” include four columns: latitude, longitude, altitude, and accuracy (see Table 1). (#) “Authority” includes two columns: the authority for the species binomial name, and for the infra-species category (see Table 2).

    Methods

    Database structure

    The structure of BROT 2.0 is very simple and composed of four files (Fig. 1), all included in a single dataset (Data Citation 1: Figshare https://dx.doi.org/10.6084/m9.figshare.c.3843841). The ‘Data file’ includes the main data values for functional traits, the taxon name, and the geographical information associated with each record (Table 1). The ‘Taxa file’ consists of the full scientific name of all taxa, including the authority (Table 2). The ‘Sources file’ includes the full reference for each source used in the database (Table 3). An additional file includes synonymous names for the taxa considered in the database (Table 4). These four files are linked by unique identifiers (Fig. 1). Additional information on the Data file is given in Tables 58 (Fig. 1). The list of traits are provided in Table 9 and a full description and standardization of all traits are given in the ‘Data Records’ section.

    Table 1: Column description of the Data file.
    Table 2: Column description of the Taxa file.
    Table 3: Column description of the Sources file.
    Table 4: Column description of the Synonymous file.
    Table 5: Descriptions of types of data used in the Data file (the ‘DataType’ column).
    Table 6: Descriptions of general methods of published or unpublished data sources (the ‘Method’ column in the Data file).
    Table 7: Descriptions of regions used in the Data file (the ‘Region’ column).
    Table 8: Description of accuracy categories for geographic coordinates used in the Data File (the ‘Accuracy’ column).
    Table 9: List of functional traits included in the database.

    Data compilation

    The geographical scope of the database is the Mediterranean Basin, defined as the land around the Mediterranean Sea with Mediterranean climate, including all Mediterranean islands. Given that the definition of Mediterranean climate is not strict (it has no sharp boundaries at the local scale), and that different Mediterranean species do not share their distribution limits, the border of our study area is also coarse – although as a general geographical reference we follow the limits of the Mediterranean climate by Quézel & Médail26 (Fig. 2). That is, some data come from locations outside of this geographical limit (Fig. 2) but these locations are close and share many species and relevant ecological processes (e.g. summer drought and frequent fires) with ecosystems in the core area of the Mediterranean climate.

    Figure 2: Geographical scope of the database in the Mediterranean Basin.
    Figure 2

    Circles are the locations of the data (for records with geographical coordinates), with colors indicating the number of records. The blue region refers to the Mediterranean climate area following Quézel & Médail26.

    We compiled measurements and observations on plant functional traits from scientific papers, books, reports, theses, and other types of publications for plants from the Mediterranean Basin. In some cases, we also gathered functional trait information from unpublished sources such as expert opinion. The compilation is based on the traits defined in BROT 1.0 (ref. 24), but also includes 30 additional traits; some of the original traits have been redefined in line with the current knowledge. The final 44 plant functional traits considered include 22 general vegetative traits, 15 regeneration traits, and 7 sexual reproductive traits (Table 9). These functional traits reflect the physiological, morphological, reproductive, phenological, and regenerative properties of plants, and determine the ecological role of each plant species in the ecosystem. Many of the functional traits included in the database are known to be important for the response of plants to global changes and disturbances2,6,27,28. For each trait, we provided a standardized definition, and in many cases, this definition includes both quantitative, semi-quantitative and qualitative information (see ‘Data Records’ section), which maximize gathering the available information. In some cases, the data is presented in a conditional form, that is, the data value includes some relevant extra information after a vertical bar (|, ASCII 124; i.e., data|condition; see examples in Table 5).

    For some traits (eight traits, called ‘fixed’ traits in Table 9), only one value for each taxon was compiled; these traits are assumed to be constant across the study area. However, for most traits (36 traits, called ‘variable’ traits in Table 9) we compiled information from multiple sources and localities. This information may include different type (and quality) of data (e.g., quantitative or binary), but may also include different, sometimes even contradictory information. This variability in the data may reflect within-species variability, plasticity or poor knowledge, and thus it is an area for further research. The selection of fixed/variable attribute of the traits was based on the variability observed when gathering the data, and on the general ecological knowledge of the region.

    The database only includes taxa (at least at the species level) native to the Mediterranean Basin. We have tried to avoid information obtained from different publications that were based on the same experiment (in many cases, different publications by the same authors). Functional trait data obtained from inadequate experimental procedures or data that did not fully fit the definition of a particular trait were excluded.

    When available, we provided geographic information data (latitude, longitude, and altitude) for individual records in the database. In many cases, the reference from where the functional trait information was extracted did not include the coordinates, and thus we estimated them from the name of the locality (when possible). Because the studies vary from small plots to large regions, the coordinates of different record differ in the degree of accuracy in relation to the data. Thus we included the variable ‘Accuracy’ in the data to refer to the accuracy of the geographical location (see details in Table 8). Geographical information is provided for the variable traits only as fixed traits are assumed constant across the region.

    Taxa names were homogenized following the European Science Foundation - European Documentation System (ESFEDS)29, which is largely based on Flora Europaea30. When a taxon name was missing in the ESFEDS database, or when some important taxonomic updates were available, generic taxonomical databases31,32, taxonomic databases for specific families33,34, or regional floras35,​36,​37 were used. Finally, all taxa names were checked for up-to-date synonymous names and spelling errors using the Taxonomic Name Resolution Service38. All BROT 2.0 full taxa names, including authority, are provided in the Taxa file. This file also includes the taxonomic family following the APG IV system39. In a separate file (the Synonymous file; Fig. 1), we include synonymous names for the taxa considered; this is not an exhaustive list and only includes some alternative names frequently used in the literature.

    Code availability

    The four files of the database are in ‘CSV’ format and can be easily retrieved from Figshare (Data Citation 1: Figshare https://dx.doi.org/10.6084/m9.figshare.c.3843841) and uploaded to most statistical software, spreadsheets, or database management systems. The Sources, Taxa and Synonymous files have some special characters (e.g., accents on authors and authority names), and thus, for portability, UTF-8 encoding is used; the Data file uses plain text. Missing values are included as empty cells, and only occur in the Data file (in the last 5 columns; i.e., coordinates and comments; Table 1) and Taxa file (in the last two columns; Table 2).

    As an example, we provide below the code to import the data into R and to perform some simple tasks; this code was tested in R (ver. 3.4) under Windows (ver. 7 and 10) and Linux (Ubuntu 16.04) and should work in any of the main computer configurations. Importing the files into a spreadsheet is easy, especially for LibreOffice and OpenOffice; users just need to select 'Unicode UTF-8’ and fields separated by ‘comma’ when opening csv files. Microsoft Excel users may need to first rename the four *.csv files as *.txt, open them via the Import Text Wizard, and then select 'Unicode UTF-8’ with fields separated by ‘comma’.

    Reading the BROT 2.0 files:

    brot <- read.csv("BROT2_dat.csv", row.names=1, stringsAsFactors=F)

    brot.sou <- read.csv("BROT2_sou.csv", row.names=1, stringsAsFactors=F, encoding="UTF-8")

    brot.tax <- read.csv("BROT2_tax.csv", row.names=1, stringsAsFactors=F, encoding="UTF-8")

    brot.syn <- read.csv("BROT2_syn.csv", stringsAsFactors=F, encoding="UTF-8")

    Quantifying the variability (quantiles) of SLA values:

    quantile(as.numeric(brot$Data[brot$Trait=="SLA"]))

    Plotting the number of species by growth forms:

    barplot(sort(table(brot$Data[brot$Trait=="GrowthForm"])), las=2)

    Does Daphne gnidium resprout after fire?

    brot[brot$Taxon=="Daphne gnidium" & brot$Trait=="RespFire", 1:8]

    And what about Quercus species? Do they resprout after fire?

    with(brot[grep("Quercus", brot$Taxon),], table(Data[Trait=="RespFire" & DataType %in% c("boolean", "semi-quantitative")]))

    How many species show their germination stimulated by smoke?

    length(unique(brot$Taxon[brot$Data=="stimulation|smk"]))

    Summarize the role of the different fire-related chemical cues on plant germination:

    with(data.frame(matrix(unlist(strsplit(brot$Data[brot$Trait=="ChemCues"], "|", fixed=T)), ncol=2, byrow=T)), table(X1, X2))

    List the references that provide information on lignotubers:

    sort(brot.sou[unique(brot$Source[brot$Data=="lignotuber"]), ])

    Add families to all records in the main data file:

    brot$Family <- brot.tax[as.character(brot$TaxonID), "Family"]

    List all synonymous used in BROT (two ways with different output formats):

    merge(brot.syn, brot.tax[,-1], by.x="TaxonID", by.y=0)[,-1]

    apply(merge(brot.syn, brot.tax[,-1], by.x="TaxonID", by.y=0)[,-1], 1, function(x) paste(x[1], paste(na.omit(x[-1]), collapse=" "), sep="=" ))

    Data Records

    The data compiled is available in a single dataset (Data Citation 1: Figshare https://dx.doi.org/10.6084/m9.figshare.c.3843841) composed of four ASCII text files, all in CSV format with quoted fields: the ‘Data’ file (BROT2_dat.csv) is the main file; the ‘Taxa’ file includes full taxa names (BROT2_tax.csv), and the ‘Sources’ file includes full references (BROT2_sou.csv). An additional ‘Synonymous’ file (BROT2_syn.csv) includes synonymous names for some of the taxa in the ‘Taxa’ file.

    In total, we compiled functional trait data from 624 sources, of which 448 are articles published in peer-reviewed journals between 1893 and early 2018 (Fig. 3). The database includes 25,764 records for 2,457 taxa belonging to 2,265 species, 704 genera, and 119 families throughout the Mediterranean Basin. Asteraceae, Fabaceae, Lamiaceae, Poaceae, and Cistaceae are the best represented families in BROT 2.0, with the specific ranking depending on whether we consider the number of records or the number of species (Fig. 4). The top traits in number of records were RespFire (2,668), GrowthForm (2,451), SeedlEmerg (2,417), SeedMass (1,995), and FruitType (1,551 records) (Fig. 5). Data records are geographically distributed throughout the Mediterranean Basin, but some parts of the basin (e.g. the southern rim) are poorly represented (Fig. 2), reflecting the lower number of available studies in this area. Most of the data records (12,132) come from 379 studies conducted in the Iberian Peninsula, following by Greece (2,366 records from 59 sources), Anatolia (1,303 records from 45 sources), Mediterranean France (1,302 records from 38 sources), and Italy (761 records from 27 sources). Considering the numbers of data records, taxa, and sources summarized above, BROT 2.0 represents a significant improvement (both quantitatively and qualitatively) over BROT 1.0 (ref. 24) (Table 10).

    Figure 3: Number of sources included in the database by year of publication.
    Figure 3
    Figure 4: Number of records (left) and number of taxa (right) for the best represented (top 20) families in the database.
    Figure 4
    Figure 5: Number of records in the database for each trait.
    Figure 5

    It includes both fixed (in red) and variable traits (in green). Trait codes as in Table 9.

    Table 10: Main differences between BROT 1.0 and BROT 2.0.

    Definitions, categories, and units of functional traits included in the database are given below, with the trait short names (as in the Data file, Table 1) and whether it is a fixed or variable trait (F, V) in brackets. Traits are ordered following Table 9, that is, first are vegetative traits (1 to 22), then sexual reproductive traits (23 to 29), and finally regeneration traits (30 to 44). Note that the trait short names (in brackets) and all categories (in bold) are written as used in the database (Data file), including the letter case.

    1 Growth form (GrowthForm, F)

    Morphology of the whole plant related with its size (for non-disturbed individuals). Categories are:

    • - tree: very tall woody plant, frequently with one main, primary stem and the green canopy rarely reaching the ground.

    • - large shrub: Large shrub or small tree. Tall woody plant that under optimal conditions may reach arborescence structure.

    • - shrub: woody plants (typically less than 1.5 m), frequently with several shoots growing from the soil level and/or the green canopy reaching the ground.

    • - liana: woody (or slightly ligneous at the base) climber.

    • - subshrub: dwarf woody plant or chamaephytes (typically less than 50 cm), including suffruticose (suffrutescent) plants.

    • - perennial forb: perennial broad-leaved herbaceous plant.

    • - perennial graminoid: perennial grass-like plant.

    • - annual forb: annual broad-leaved herbaceous plant.

    • - annual graminoid: annual grass-like plant.

    • - variable forb: annual, biennial or short-perennial forb.

    • - variable graminoid: annual, biennial or short-perennial grass.

    • - geophyte: herbs that persist during the unfavorable period as bulbs, rhizomes or other subterranean storage organs.

    • - epiphyte: plants growing on other plants for physical support.

    2 Leaf division degree (LeafDivision, F)

    Division degree of leaves (or phyllodes). For species with different stem and basal leaves, it refers to stem leaves. The categories are:

    • - simple: simple leaves.

    • - compound: compound or divided leaves.

    3 Average leaf lifespan (LeafLifespan, V)

    Average time period (months) during which an individual leaf (or phyllodes) of a woody species is alive and physiologically active40 (= leaf longevity). For woody species only.

    4 Leaf phenology (LeafPhenology, F)

    Phenology of leaves (or phyllodes). For woody species only. The categories are:

    • - evergreen: plant that maintains green leaves all year.

    • - winter deciduous: plant that drops all its leaves during the winter.

    • - winter semi-deciduous: plant that drops part of its leaves during the winter, maintaining some brownish leaves in the crown.

    • - drought semi-deciduous: plant that drops part of its leaves during the dry period (excluding species that drop leaves only in very extreme droughts).

    5 Basic leaf shape (LeafShape, F)

    Shape of leaves, phyllodes or leaflets for compound leaves. For species with different stem and basal leaves, it refers to stem leaves. The categories are:

    • - none: without leaves or any functional analogue organ. If leaves are modified as spines, then LeafShape=spines (see below).

    • - broad: plant with broad leaves (for compound leaves, this refers to leaflets).

    • - needle-like: plant with needle-like leaves.

    • - linear: plant with linear leaves (for compound leaves, this refers to leaflets).

    • - scale-like: plant with scale-like leaves.

    • - spines: leaves are modified as spines (which is different from having spines or thorns in the branches).

    • - succulent: plant with succulent (water-stored, thick and fleshy) leaves.

    6 Average leaf area (LeafArea, V)

    Average one-sided projected surface area (mm2) of an individual leaf (or phyllodes)40. For compound leaves, leaflets area×leaflets number. For species with different stem and basal leaves, it refers to stem leaves. Alternatively, one of the following categories:

    • - very small: small needle-like, scale-like, and linear leaves (typically less than 25 mm2).

    • - small: large linear leaves or small broad leaves (typically 25–225 mm2).

    • - medium: moderate broad leaves or divided leaves with moderate leaflets (typically 225–2025 mm2).

    • - large: large broad leaves, or divided leaves with numerous and large broad leaflets (typically 2025–4550 mm2).

    • - very large: very large broad leaves, usually divided (typically more than 4550 mm2).

    7 Mass-based leaf nitrogen content (LNCm, V)

    Leaf nitrogen content (mass-based) (mg g−1), that is, the ratio of the quantity of nitrogen in the leaf per respective unit dry mass40,41.

    8 Average specific leaf area (SLA, V)

    Average one-sided area of the fresh leaf (or phyllodes) divided by its oven-dry mass40,42, excluding petiole and/or rachis; for mature plants only. Units are mm2 mg−1 (note that mm2 mg−1×10=cm2 g−1).

    9 Average bark thickness (BarkThick, V)

    Average bark thickness (mm) of the main stem at breast height for trees; if available, it should include the diameter (cm) at the height that the bark was measured (as quantitative conditional, i.e., BT|Diam). For woody plants only. Note that in many cases both BT and Diam are mean values of a population (not for an individual tree). Alternatively, one of the following categories:

    • - thin: <= 2 mm.

    • - moderate: 2–15 mm.

    • - thick: >15 mm.

    10 Average height (Height, V)

    Maximum height (m), excluding extremes and reproductive shoots.

    11 Stem specific density (StemDensity, V)

    Oven-dry mass divided by the fresh volume of a section of the main stem40 (excluding bark for woody species; i.e., wood density) (g cm-3).

    12 Coarse:fine fuel (CFFuel, V)

    Coarse to fine fuel biomass ratio (i.e., >=6 mm diameter and<6 mm diameter, respectively), including live and dead material. Alternatively, one of the following categories:

    • - low: without coarse fuel; all fuel is fine.

    • - moderate: abundant fine fuel and low coarse fuel.

    • - high: abundant fine fuel and abundant coarse fuel.

    • - very high: scarce fine fuel and abundant coarse fuel.

    13 Dead fine fuel (DealFuel, V)

    Standing fine (< 6 mm diameter) dead biomass (including twigs, leaves, inflorescences, bark) attached to the plant during the dry season expressed in proportion of the aboveground biomass (for non-senescent individuals) (%). Alternatively, one of the following categories:

    • - low: <=5%

    • - medium: 5-20%

    • - high: >=20%

    14 Leaf dry matter content (LDMC, V)

    Dry matter content of leaves (mg g−1), that is, the ratio of the dry mass of a leaf to its water saturated fresh mass40,41.

    15 Clonality (Clonality, V)

    Ability to colonize the space through vegetative reproduction. Categories considered are:

    • - rhizomes: non-swollen belowground horizontal stem that grows near the soil surface with the ability to produce roots and stems. Rhizomes s.l., i.e., including woody and non-woody rhizomes.

    • - roots: roots normally growing close to the soil surface.

    • - rhizomes or roots: rhizomes and/or roots (not differentiated).

    • - storage organs: non-woody storage organs, normally modified stems (bulbs, corms or stem tubers) or roots (root tubers).

    • - stolons: aboveground horizontal stems.

    • - yes: clonal plant with unknown system.

    • - no: without clonality ability.

    16 Integrated water-use efficiency (d13C, V)

    Delta 13C (δ13C) isotope ratio40.

    17 Lifespan (Lifespan, V)

    Average maximum age (=longevity) for perennials (year). Alternatively, one of the following categories:

    • - very short: <=2 yr

    • - short: 2–5 yr

    • - medium: 5–25 yr

    • - long: 25–150 yr

    • - very long: >150 yr

    18 Nutritional relationships (NutritionalRelat, V)

    Long-term relationship with other species that are implicated in nutrient and/or energy uptake. Categories are:

    • - ectomycorrhizal symbiosis: plant with a mutualistic relationship with ectomycorrhizal fungi.

    • - endomycorrhizal symbiosis: plants with a mutualistic relationship with endomycorrhizal fungi.

    • - nodule bacteria symbiosis: plant with a mutualistic relationship with nitrogen-fixing bacteria.

    • - hemiparasite: photosynthetic plant (hemiparasite) that parasitize another photosynthetic plant (host).

    • - parasite: non-photosynthetic plant that parasitize either a photosynthetic plant (i.e. holoparasites) or a fungus (i.e., myco-heterotrophous).

    • - carnivorous: plant acquiring nutrients by capturing animals or protozoa.

    • - others: plants with other types of nutritional relationships, including a combination of several types of symbiosis (e.g. endo- and ectomycorrhizas).

    • - no: plant without obvious nutritional relationships.

    19 Resistance to xylem cavitation (P50, V)

    Xylem resistance to drought-induced cavitation (in MPa)5.

    20 Maximum rooting depth (RootDepth, V)

    Maximum depth of the roots (m).

    21 Spinescence (Spinescence, F)

    Presence/absence of spines, thorns, prickles and/or spiny leaves in vegetative organs. The categories are:

    • - yes

    • - no

    22 Shoot:root ratio (SRR, V)

    Shoot to root dry mass ratio in saplings (<=3 years old), excluding those from plantations. Alternatively, one of the following categories:

    • - low:<1.5

    • - high: >=1.5

    23 Dispersal mode (DispMode, F)

    The vector(s) used for dispersal (of seeds or any other dispersal unit for sexual reproduction). One or several types, e.g.: GW means that both Gravity and Wind are important); if several, typically the first is the most important. Notation for the different dispersal vectors are:

    • - G: autochory, by Gravity (=unassisted dispersal).

    • - W: anemochory, by Wind (with wind dispersal adaptations).

    • - H: Hydrochory, by water.

    • - B: Ballistichory, by launching (=ballochory).

    • - M: Myrmecochory, by ants.

    • - N: eNdozoochory, internal animal transport.

    • - P: ePizoochory, external animal transport (=exozoochory).

    • - O: hOarding, scatter and hoarding diaspores by animals (others than ants).

    • - Z: Zoochory, dispersal mediated by animals (unknown transport system).

    24 Diaspore (Diaspore, F)

    Dispersal unit for sexual reproduction. The categories are:

    • - seed: including some single-seeded fruits such as achenes or caryopsis.

    • - fruit: single or aggregated fruit.

    • - spore

    25 Fruit dry mass (FruitMass, V)

    Average dry mass (mg) of single or aggregated fruits (excluding some single-seeded fruits such as achenes or caryopsis, that are typically considered as "seeds"). Alternatively, one of the following categories:

    • - very light:<3 mg

    • - light: 3–30 mg

    • - medium: 30–300 mg

    • - heavy: 300–3000 mg

    • - very heavy: >3000 mg

    26 Fruit type (FruitType, F)

    Type of the fruit. Including single or aggregated fruits (dispersal unit). Categories are:

    • - dry: dry fruit.

    • - fleshy: fleshy fruit, including fruit in which the fleshy part is the floral cup (hypanthium) (e.g. Rosa).

    27 Seed dry mass (SeedMass, V)

    Average dry mass of seeds (including some single-seeded fruits such as achenes or caryopsis) (mg). Alternatively, one of the following categories:

    • - very light:<3 mg

    • - light: >=3 and<30 mg

    • - medium: >=30 and<300 mg

    • - heavy: >=300 mg

    28 Annual seed production (SeedProd, V)

    Average number of seeds per plant produced every year (# seeds). Alternatively, one of the following categories:

    • - rarely: rarely, if ever, produces seeds in the study area.

    • - few: <=50 seeds.

    • - medium: 50–500 seeds.

    • - many: > 500 seeds.

    29 Basic seed shape (SeedShape, V)

    Ratio between the two maximum diameters: first maximum divided by the second maximum, excluding structures attached to the seed coat as wings or pappus. Alternatively, one of the following categories:

    • - regular: close to 1 (spherical or lens-shaped seeds).

    • - irregular: far to 1 (elongated seeds).

    30 Bud source (BudSource, V)

    Location of the bud bank for resprouting species43. The categories are:

    • - epicormic buds: stem buds (protected by the bark).

    • - apex: buds in the stem apex protected from fire by leaf bases.

    • - root crown: transition point between stem and root.

    • - lignotuber: woody swelling below or just above the soil, ontogenetically programmed (i.e., inherited character). Based on embryological and/or anatomical features.

    • - thickened root-crown: woody swelling below or just above the soil non-ontogenetically programmed (e.g. stem coalescence). Thickened root crown.

    • - burl: woody swelling below or just above the soil with the unspecified origin (no distinction between lignotuber and burl is reported).

    • - rhizomes: belowground horizontal stem (non-swollen).

    • - woody rhizomes: woody belowground horizontal stem.

    • - non-woody rhizomes: non-woody belowground horizontal stem.

    • - roots

    • - rhizomes or roots: rhizomes and/or roots (unspecified).

    • - storage organs: non-woody storage organs, i.e., modified stems (bulbs, corms or stem tubers) or roots (root tubers).

    • - others: other bud sources, including those not clearly specified (e.g. stump).

    31 Fire-stimulated flowering (FireStimFlower, V)

    Fire-stimulated flowering in post-fire resprouters. The categories are:

    • - no: lower or similar flowering post-fire than in unburned vegetation.

    • - yes: higher flowering post-fire than in unburned vegetation (includes facultative and obligate post-fire flowering); these are mostly geophytes.

    32 Resprouting capacity after clipping (RespClip, V)

    Resprouting capacity one year after clipping 100% of the plant as average proportion of adult plants that resprout (percentage). Not reported for annual plants (which can be assumed to be RespClip=no). Alternatively, one of the following categories:

    • - no: without resprouting capacity.

    • - low: few individuals resprouting and/or weak resprouts.

    • - high: most individuals resprouting and/or vigorous resprouts.

    • - yes: with resprouting capacity (not quantified).

    • - variable: very high variability observed in the sampling area.

    33 Resprouting capacity after disturbances (RespDist, V)

    Resprouting capacity after undefined disturbances (average proportion of adult plants that resprout as percentage). Not reported for annual plants (which can be assumed to be RespDist=no). Alternatively, one of the following categories:

    • - no: without resprouting capacity.

    • - low: few individuals resprouting and/or weak sprouts.

    • - high: most individuals resprouting and/or vigorous sprouts.

    • - yes: with resprouting capacity (not quantified).

    • - variable: very high variability observed in the sampling area.

    34 Resprouting capacity after fire (RespFire, V)

    Resprouting capacity after one year when most of the plant has been scorched (average proportion of adult plants that resprout as percentage). Not reported for annual plants (which can be assumed to be RespFire=no). Alternatively, one of the following categories:

    • - no: without resprouting capacity.

    • - low: few individuals resprouting and/or weak sprouts.

    • - high: most individuals resprouting and/or vigorous sprouts.

    • - yes: with resprouting capacity (not quantified).

    • - variable: very high variability observed in the sampling area.

    35 Chemical germination cues (ChemCues, V)

    Germinative response to smoke (smk), ash (ash), charcoal (cha), nitrogenous compounds like KNO3 (NC1), NaNO2 (NC2), NH4Cl (NC3), NH4HOC3 (NC4), NH4NO3 (NC5), or response to karrikins (KAR), cyanohydrins (CYN, including several cyanides, mandelonitrile, and glyceronitrile). The response in indicated before the vertical bar, and the chemical cue tested, after the vertical bar (e.g. stimulation|smk). The categories are:

    • - stimulation|###: germination of the treated seeds higher than the control.

    • - unaffected|###: germination of the treated seeds equal to the control.

    • - inhibition|###: germination of the treated seeds lower than the control.

    36 Heat-stimulated germination (HeatStimGerm, V)

    The highest intensity in heat treatments (i.e., seed exposition to dry heat >=50 °C) that produce higher germination than the control (i.e., stimulated germination). Heat intensity defined as: Low (L:<100 °C during <=5 min.), Moderate (M:<100 °C during >5 min. or >=100 °C during <= 5 min.), High (H: >=100 °C during >5 min.) or unknown (unk). Note that in many cases, post-treatment seed viability is not considered or not specified. The heat intensities tested for each experiment are indicated after the vertical bar (category|LMH), with an underscore when the corresponding heat intensity is not tested (e.g., category|L_H). The categories are:

    • - yes|unk: stimulated germination is produced after unspecified heat intensity exposition.

    • - high|###: stimulated germination after exposition to High-intensity treatments (### refers to L, M and H respectively).

    • - moderate|###: the highest heat intensity that produces stimulated germination is Moderate (### refers to L, M and H respectively).

    • - low|###: the highest heat intensity that produces stimulated germination is Low (### refers to L, M and H respectively).

    • - unaffected|###: germination is not stimulated after any heat intensity tested and at least one of the treatments does not affect seed germination (### refers to L, M and H respectively; unk if unknown).

    • - inhibition|###: inhibited germination (i.e., lower germination than control) in all heat treatments tested (### refers to L, M and H respectively; unk if unknown).

    37 Other germination cues (OtherCues, V)

    Germination response to exposition to boiling water (blw), mechanical scarification (mec), summer temperature (tsu), temperature fluctuation (tfu), light (lgt). The response is indicated before the bar and the cue tested is indicated after the vertical bar (category|cue, e.g., stimulation|blw). Categories are:

    • - stimulation|###: germination of the treated seeds higher than the control.

    • - unaffected|###: germination of the treated seeds equal to the control.

    • - inhibition|###: germination of the treated seeds lower than the control.

    38 Canopy seed bank longevity (CanopySeedBank, V)

    Presence and longevity of the stored seeds in the canopy. The categories are:

    • - yes: seeds stored in the canopy is present (no information on longevity)

    • - no: no stored seeds in the canopy.

    • - short: 2 or 3 years

    • - mid: 4–10 yr

    • - long: >10 yr

    39 Serotiny level (SerotinyLevel, V)

    Average proportion of serotinous (closed) cones in the canopy (%)44.

    40 Soil seed bank longevity (SoilSeedBank, V)

    Period that seeds remain viable in the soil seed bank inferred from: soil and vegetation comparisons (veg), experimental seed burial (bur), seed dormancy (dor) or unknown methods (unk). The method used is indicated after the vertical bar (response|method, e.g., persistent|veg). The categories are:

    • - transient|###: no soil seed bank; seeds germinate in the first favorable season after dispersal. Normally seed bank longevity <=1 yr (no persistent seed bank).

    • - persistent|###: seeds do not germinate in the first favorable season after dispersal. Normally seed bank longevity >1 yr (could be longer but it is unknown).

    • - short-persistent|###: >1 and <=5 yr

    • - at least short-persistent|###: at least>1 and <=5 yr (could be longer but it is unknown).

    • - mid-persistent|###: at least>5 yr (could be longer but it is unknown)

    • - long-persistent|###: at least>15 yr

    • - very long-persistent|###: >=30 yr

    41 Age at maturity of resprouts (MatResp, V)

    Average age of resprouts at the first successful reproduction (yr), i.e. when most of the resprouted plants produce the first seed crop. Alternatively, one of the following categories:

    • - early:<5 yr

    • - medium: 5–10 yr

    • - late: >10 yr

    42 Age at maturity of saplings (MatSap, V)

    Average age of saplings at the first successful reproduction (yr), i.e. when most of the saplings produce the first seed crop, excluding saplings from plantations. Alternatively, one of the following categories:

    • - early:<5 yr

    • - medium: 5–10 yr

    • - late: >10 yr

    43 Post-fire seedling emergence (SeedlEmerg, V)

    Average density of seedlings per pre-fire mature individuals emerged during the first year after fire. This is a ratio (number of seedlings / number of mature plants), or alternatively, one of the following categories:

    • - no: no post-fire seedlings emergence.

    • - low: number of seedlings lower than the number of pre-fire mature individuals.

    • - high: number of seedlings higher than the number of pre-fire mature individuals.

    • - yes: post-fire seedling emergence observed (quantitative data not available).

    • - variable: high variability observed between populations or sampled areas.

    44 Post-fire seedling survival (SeedlSurv, V)

    Proportion of seedlings surviving the first dry season after fire (%). Alternatively, one of the following categories:

    • - no: no post-fire seedlings survival.

    • - low: survival<25%

    • - high: survival >=25%

    Technical Validation

    Most of the records included in the database (79%) are based on published material in peer-reviewed scientific journals (46%), books (27%), or theses (5%), and thus most data should be accurate. In addition, each specific data value has the original references, and so users can evaluate the validity and accuracy of the original source. The data has been checked for possible redundancies and errors, and some published data were excluded from the final database; data considered doubtful (e.g., very extreme values, or data that did not fully fit the definition of the trait, or that were obtained with a questionable sampling) were not included. Also note that for each species and trait, the BROT 2.0 database includes different values from different sources, and so users can make their own decisions on data usage; for example, using the mean trait value, or excluding extreme values. This feature of BROT 2.0 database is especially important because it provides information on trait variability.

    The spatial scope of the database is the Mediterranean Basin (Fig. 2). The differences in the number of records among sub-regions of the Basin (for example, the north and the south of the Basin, Fig. 2) reflect the spatial heterogeneity of knowledge across the Basin.

    The integrity of the files can be verified by the following md5 checksums:

    BROT2_dat.csv "797222960172b5ca587173f061a5f629"

    BROT2_sou.csv "302c8f6bbaa2f1a49c95f6706941941c"

    BROT2_tax.csv "758a4c23a30b080333face4c6689c47b"

    BROT2_syn.csv "c756db95e433283b6c2bdca51a11a5e3"

    Usage Notes

    To properly use the data, it is important to consider the following fields in the Data file: ‘Method’, ‘Accuracy’, and ‘DataType’. The first provides information on the origin of the data, and is related to quality; data with Method= ‘measure’ is likely to be of the highest quality (Table 6). ‘Accuracy’ provides an indicator of the accuracy of the geographical location (Table 8). Users can use these fields to select the data that best suits their requirement, or to weight their analysis. The ‘DataType’ column is also informative, as different types of data (quantitative, semi-quantitative, etc.) are linked to the quality and accuracy of the data (Table 5). Because quantitative data can be converted to qualitative or semi-quantitative (following the trait definitions given in the section ‘Data Records’), users can choose between using more data of low quality or less data of high quality.

    Note that there may be variability in a given trait, and the more information (more records from different sources), the more certain is the value of the trait for a given species. For instance, resprouting is a key trait in fire-prone ecosystems, and for some (few) species, we may find records for both ‘yes’ and ‘no’ in the ability to resprout. This may be due to variability, but it could also be due to a poor sampling. The number of records, together with the field ‘Methods’, may provide an estimation of the level of confidence in the information. Moreover, given that all records are referenced, it is always possible to go to the original reference to search for additional information.

    Note also that some traits are poorly known and prone to mistakes. For instance, the type of underground resprouting (trait: ‘BudSource’) is not always easy to observe, and many researchers, especially in the past, tended to confuse structures like ‘lignotubers’ with any other underground resprouting organ43,45. When the mistake was clear from the reference, it was not included in the database, but in many instances, it is impossible to know, as variability exists among populations and geographical locations.

    Additional information

    How to cite this article: Tavşanoğlu, Ç. & Pausas, J. G. A functional trait database for Mediterranean Basin plants. Sci. Data 5:180135 doi: 10.1038/sdata.2018.135 (2018).

    Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

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    Data Citations

    1. 1.

      Tavşanoğlu, Ç., & Pausas, J. G. Figshare https://dx.doi.org/10.6084/m9.figshare.c.3843841 (2018)

    Acknowledgements

    We thank Susana Paula for her contribution to BROT. We also thank Jose Navarro-Cano who shared unpublished trait data for the current update. The Scientific Research Unit of Hacettepe University funded several mutual visits by the authors (FBB-2015-7251, FBD-2017-13864, FBB-2017-14948). BROT 2.0 was performed under the framework of the FILAS (CGL2015-64086-P, Spanish government) and PROMETEO/2016/021 (Valencia Government) projects.

    Author information

    Affiliations

    1. Division of Ecology, Department of Biology, Hacettepe University, Beytepe 06800, Ankara, Turkey

      • Çağatay Tavşanoğlu
    2. Centro de Investigaciones sobre Desertificación, Consejo Superior de Investigaciones Científicas (CIDE-CSIC), 46113, Valencia, Spain

      • Juli G. Pausas

    Authors

    1. Search for Çağatay Tavşanoğlu in:

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    Contributions

    J.G. provided the idea and the design of the database. Ç.T. compiled most of the new data of BROT 2.0 and wrote the first version of the manuscript. Ç.T. and J.G. wrote the final version.

    Competing interests

    The authors declare no competing interests.

    Corresponding author

    Correspondence to Juli G. Pausas.

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    DOI

    https://doi.org/10.1038/sdata.2018.135