'rtry': An R package to support plant trait data preprocessing.

Plant trait data are used to quantify how plants respond to environmental factors and can act as indicators of ecosystem function. Measured trait values are influenced by genetics, trade-offs, competition, environmental conditions, and phenology. These interacting effects on traits are poorly characterized across taxa, and for many traits, measurement protocols are not standardized. As a result, ancillary information about growth and measurement conditions can be highly variable, requiring a flexible data structure. In 2007, the TRY initiative was founded as an integrated database of plant trait data, including ancillary attributes relevant to understanding and interpreting the trait values. The TRY database now integrates around 700 original and collective datasets and has become a central resource of plant trait data. These data are provided in a generic long-table format, where a unique identifier links different trait records and ancillary data measured on the same entity. Due to the high number of trait records, plant taxa, and types of traits and ancillary data released from the TRY database, data preprocessing is necessary but not straightforward. Here, we present the 'rtry' R package, specifically designed to support plant trait data exploration and filtering. By integrating a subset of existing R functions essential for preprocessing, 'rtry' avoids the need for users to navigate the extensive R ecosystem and provides the functions under a consistent syntax. 'rtry' is therefore easy to use even for beginners in R. Notably, 'rtry' does not support data retrieval or analysis; rather, it focuses on the preprocessing tasks to optimize data quality. While 'rtry' primarily targets TRY data, its utility extends to data from other sources, such as the National Ecological Observatory Network (NEON). The 'rtry' package is available on the Comprehensive R Archive Network (CRAN; https://cran.r-project.org/package=rtry) and the GitHub Wiki (https://github.com/MPI-BGC-Functional-Biogeography/rtry/wiki) along with comprehensive documentation and vignettes describing detailed data preprocessing workflows.

Comprehensive leaf size traits dataset for seven plant species from digitised herbarium specimen images covering more than two centuries.

BACKGROUND: Morphological leaf traits are frequently used to quantify, understand and predict plant and vegetation functional diversity and ecology, including environmental and climate change responses. Although morphological leaf traits are easy to measure, their coverage for characterising variation within species and across temporal scales is limited. At the same time, there are about 3100 herbaria worldwide, containing approximately 390 million plant specimens dating from the 16th to 21st century, which can potentially be used to extract morphological leaf traits. Globally, plant specimens are rapidly being digitised and images are made openly available via various biodiversity data platforms, such as iDigBio and GBIF. Based on a pilot study to identify the availability and appropriateness of herbarium specimen images for comprehensive trait data extraction, we developed a spatio-temporal dataset on intraspecific trait variability containing 128,036 morphological leaf trait measurements for seven selected species. NEW INFORMATION: After scrutinising the metadata of digitised herbarium specimen images available from iDigBio and GBIF (21.9 million and 31.6 million images for Tracheophyta; accessed date December 2020), we identified approximately 10 million images potentially appropriate for our study. From the 10 million images, we selected seven species (Salix bebbiana Sarg., Alnus incana (L.) Moench, Viola canina L., Salix glauca L., Chenopodium album L., Impatiens capensis Meerb. and Solanum dulcamara L.) , which have a simple leaf shape, are well represented in space and time and have high availability of specimens per species. We downloaded 17,383 images. Out of these, we discarded 5779 images due to quality issues. We used the remaining 11,604 images to measure the area, length, width and perimeter on 32,009 individual leaf blades using the semi-automated tool TraitEx. The resulting dataset contains 128,036 trait records.We demonstrate its comparability to trait data measured in natural environments following standard protocols by comparing trait values from the TRY database. We conclude that the herbarium specimens provide valuable information on leaf sizes. The dataset created in our study, by extracting leaf traits from the digitised herbarium specimen images of seven selected species, is a promising opportunity to improve ecological knowledge about the adaptation of size-related leaf traits to environmental changes in space and time.

TRY plant trait database - enhanced coverage and open access.

Plant traits-the morphological, anatomical, physiological, biochemical and phenological characteristics of plants-determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait-based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits-almost complete coverage for 'plant growth form'. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait-environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives.

Dispersal limitation drives successional pathways in Central Siberian forests under current and intensified fire regimes.

Fire is a primary driver of boreal forest dynamics. Intensifying fire regimes due to climate change may cause a shift in boreal forest composition toward reduced dominance of conifers and greater abundance of deciduous hardwoods, with potential biogeochemical and biophysical feedbacks to regional and global climate. This shift has already been observed in some North American boreal forests and has been attributed to changes in site conditions. However, it is unknown if the mechanisms controlling fire-induced changes in deciduous hardwood cover are similar among different boreal forests, which differ in the ecological traits of the dominant tree species. To better understand the consequences of intensifying fire regimes in boreal forests, we studied postfire regeneration in five burns in the Central Siberian dark taiga, a vast but poorly studied boreal region. We combined field measurements, dendrochronological analysis, and seed-source maps derived from high-resolution satellite images to quantify the importance of site conditions (e.g., organic layer depth) vs. seed availability in shaping postfire regeneration. We show that dispersal limitation of evergreen conifers was the main factor determining postfire regeneration composition and density. Site conditions had significant but weaker effects. We used information on postfire regeneration to develop a classification scheme for successional pathways, representing the dominance of deciduous hardwoods vs. evergreen conifers at different successional stages. We estimated the spatial distribution of different successional pathways under alternative fire regime scenarios. Under intensified fire regimes, dispersal limitation of evergreen conifers is predicted to become more severe, primarily due to reduced abundance of surviving seed sources within burned areas. Increased dispersal limitation of evergreen conifers, in turn, is predicted to increase the prevalence of successional pathways dominated by deciduous hardwoods. The likely fire-induced shift toward greater deciduous hardwood cover may affect climate-vegetation feedbacks via surface albedo, Bowen ratio, and carbon cycling.