Biogeographic deconstruction of phylogenetic and functional diversity provides insights into the formation of regional assemblages

Evolutionary history and environmental filtering shape the phylogenetic and functional structure of regional assemblages. However, detecting the footprint of such eco-evolutionary drivers is challenging because these may often counter each other's signature. Here, we examined whether a biogeographic deconstruction approach of phylogenetic (PD) and functional diversity (FD) patterns may help in identifying eco-evolutionary signals in extant regional assemblages. As model system, we used forest understorey angiosperms found in three regions of Italy (Alpine, Mediterranean, Continental). We quantified PD and FD of all species inhabiting the three regions (regional assemblages). Then, we computed PD and FD for the subsets of species restricted to each region (biogeographic elements), also examining diversity patterns of species found across the three regions (widespread element). We used aboveground and belowground traits capturing major plant functions to calculate FD. Additionally, we assessed FD patterns decoupled from phylogeny. We found that species restricted to climatically harsh regions (Alpine and Mediterranean elements) were phylogenetically and functionally clustered, whereas widespread species were characterised by overdispersion. Species confined to the climatically intermediate (Continental) region were randomly sorted. By including all species occurring within a region, the patterns found for the region-restricted species blurred. Phylogenetically decoupled FD patterns were qualitatively similar to non-decoupled ones with the exception of the Alpine element, where we detected a clear signature of functional differentiation between closely related species. This suggests that recent speciation events contributed to shaping the Alpine flora. Compared to the belowground compartment, aboveground traits showed a more coherent pattern with that of all-trait FD – likely because most biomass is allocated aboveground in forest understoreys. This biogeographic deconstruction study illustrates which type of eco-evolutionary insights can be gained by implementing multifaceted and integrated approaches at the macroecological scal

Biogeographic deconstruction of phylogenetic and functional diversity provides insights into the formation of regional assemblages

Evolutionary history and environmental filtering shape the phylogenetic and functional structure of regional assemblages. However, detecting the footprint of such eco-evolutionary drivers is challenging because these may often counter each other's signature. Here, we examined whether a biogeographic deconstruction approach of phylogenetic (PD) and functional diversity (FD) patterns may help in identifying eco-evolutionary signals in extant regional assemblages. As model system, we used forest understorey angiosperms found in three regions of Italy (Alpine, Mediterranean, Continental). We quantified PD and FD of all species inhabiting the three regions (regional assemblages). Then, we computed PD and FD for the subsets of species restricted to each region (biogeographic elements), also examining diversity patterns of species found across the three regions (widespread element). We used aboveground and belowground traits capturing major plant functions to calculate FD. Additionally, we assessed FD patterns decoupled from phylogeny. We found that species restricted to climatically harsh regions (Alpine and Mediterranean elements) were phylogenetically and functionally clustered, whereas widespread species were characterised by overdispersion. Species confined to the climatically intermediate (Continental) region were randomly sorted. By including all species occurring within a region, the patterns found for the region-restricted species blurred. Phylogenetically decoupled FD patterns were qualitatively similar to non-decoupled ones with the exception of the Alpine element, where we detected a clear signature of functional differentiation between closely related species. This suggests that recent speciation events contributed to shaping the Alpine flora. Compared to the belowground compartment, aboveground traits showed a more coherent pattern with that of all-trait FD – likely because most biomass is allocated aboveground in forest understoreys. This biogeographic deconstruction study illustrates which type of eco-evolutionary insights can be gained by implementing multifaceted and integrated approaches at the macroecological scal

A protocol for reproducible functional diversity analyses

The widespread use of species traits in basic and applied ecology, conservation and biogeography has led to an exponential increase in functional diversity analyses, with > 10 000 papers published in 2010-2020, and > 1800 papers only in 2021. This interest is reflected in the development of a multitude of theoretical and methodological frameworks for calculating functional diversity, making it challenging to navigate the myriads of options and to report detailed accounts of trait-based analyses. Therefore, the discipline of trait-based ecology would benefit from the existence of a general guideline for standard reporting and good practices for analyses. We devise an eight-step protocol to guide researchers in conducting and reporting functional diversity analyses, with the overarching goal of increasing reproducibility, transparency and comparability across studies. The protocol is based on: 1) identification of a research question; 2) a sampling scheme and a study design; 3-4) assemblage of data matrices; 5) data exploration and preprocessing; 6) functional diversity computation; 7) model fitting, evaluation and interpretation; and 8) data, metadata and code provision. Throughout the protocol, we provide information on how to best select research questions, study designs, trait data, compute functional diversity, interpret results and discuss ways to ensure reproducibility in reporting results. To facilitate the implementation of this template, we further develop an interactive web-based application (stepFD) in the form of a checklist workflow, detailing all the steps of the protocol and allowing the user to produce a final 'reproducibility report' to upload alongside the published paper. A thorough and transparent reporting of functional diversity analyses ensures that ecologists can incorporate others' findings into meta-analyses, the shared data can be integrated into larger databases for consensus analyses, and available code can be reused by other researchers. All these elements are key to pushing forward this vibrant and fast-growing field of research.Peer reviewe

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

Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters

CITATION: Ottaviani, G., et al. 2017. Quantifying the effects of ecological constraints on trait expression using novel trait-gradient analysis parameters. Ecology and Evolution, 8(1):435-440, doi:10.1002/ece3.3541.The original publication is available at https://onlinelibrary.wiley.comComplex processes related to biotic and abiotic forces can impose limitations to assembly and composition of plant communities. Quantifying the effects of these constraints on plant functional traits across environmental gradients, and among communities, remains challenging. We define ecological constraint (Ci) as the combined, limiting effect of biotic interactions and environmental filtering on trait expression (i.e., the mean value and range of functional traits). Here, we propose a set of novel parameters to quantify this constraint by extending the trait‐gradient analysis (TGA) methodology. The key parameter is ecological constraint, which is dimensionless and can be measured at various scales, for example, on population and community levels. It facilitates comparing the effects of ecological constraints on trait expressions across environmental gradients, as well as within and among communities. We illustrate the implementation of the proposed parameters using the bark thickness of 14 woody species along an aridity gradient on granite outcrops in southwestern Australia. We found a positive correlation between increasing environmental stress and strength of ecological constraint on bark thickness expression. Also, plants from more stressful habitats (shrublands on shallow soils and in sun‐exposed locations) displayed higher ecological constraint for bark thickness than plants in more benign habitats (woodlands on deep soils and in sheltered locations). The relative ease of calculation and dimensionless nature of Ci allow it to be readily implemented at various scales and make it widely applicable. It therefore has the potential to advance the mechanistic understanding of the ecological processes shaping trait expression. Some future applications of the new parameters could be investigating the patterns of ecological constraints (1) among communities from different regions, (2) on different traits across similar environmental gradients, and (3) for the same trait across different gradient types.https://onlinelibrary.wiley.com/doi/10.1002/ece3.3541Publisher's versio

A multifaceted approach for beech forest conservation: environmental drivers of understory plant diversity

Studies addressing multiple aspects of biodiversity simultaneously (i.e., multifaceted approaches) can quantify plant diversity-environment links comprehensively, however they are scant in forests. This is because of the multidimensional nature of plant diversity. We studied taxonomic, functional and phylogenetic diversity patterns in 19 beech forest understory plots in two areas belonging to a biodiversity monitoring plan in Tuscany, Italy. We performed linear-mixed-effect models to quantify the influence of elevation (proxy for macroclimate), aspect (affecting microclimate), and basal area (related to microclimate and stand maturity) on diversity facets of vascular plants. Elevation played a major role in shaping diversity: high-elevation plots were less rich in species and had a reduced functional diversity of storage organs that may promote cold-tolerance. Conversely, the diversity of flowering phenology increased with elevation, thus low-elevation vegetation converged functionally towards a common, short blooming period. This strategy may be advantageous for understory plants in the deciduous beech forests experiencing longer growing seasons, hence more extended canopy closure at lower elevations. Basal area negatively affected foliar and multiple-trait functional diversity which may be associated with highly selective and competitive environment for light capture in closed canopy, mature stands. Slope aspect did not exert any significant effect on diversity facets, neither did interactions among predictors. Overall, these results confirm the usefulness of implementing multifaceted approaches to i) better understand the influence of environmental drivers on different aspects of plant diversity, and ii) inform the biodiversity monitoring plan that is in place in the study forests by systematically including functional diversity instead of taxonomic metrics only

Trait hypervolumes based on natural history collections can detect ecological strategies that are distinct to biogeographic regions

specimen_localities_for_mapping_trait_hypervolumes.csv Point localities of specimens held in natural history collections for a random sample of 575 angiosperm species that all occur in the continent of Africa. Some of the localities were georeferenced as part of this research. Localities were spatially disaggregated using the R package ecospat prior to use in Species Distribution Models that were then used to spatially project biodiversity metrics. Fields: 1. Source How the specimen locality data was obtained: GBIF = from the Global Biodiversity Information Facility, TROPICOS = from  Tropicos.org. Missouri Botanical Garden, Taxonomic_literature = specimens cited in published taxonomic literature, Kew_herbarium = specimens seen by authors in the herbarium of the Royal Botanic Gardens, Kew, London. RAINBIO = RAINBIO species checklist of tropical African vascular plants, LMA_herbarium = specimens seen by authors in the herbarium of the Agricultural Research Institute of Mozambique, Maputo, Mozambique, Kitwe_herbarium =   specimens seen by authors in the herbarium of the Division of Forest Research Forestry Department, Kitwe, Zambia, Edinburgh_herbarium = specimens seen by authors in the herbarium of the Royal Botanic Garden Edinburgh, Windhoek_herbarium = specimens seen by authors in the herbarium of the National Herbarium of Namibia, UPS_herbarium = specimens seen by authors in the herbarium of the Museum of Evolution, Uppsala, Sweden. 2. Identitiy_number Identity number applied by GBIF to the specimen record 3. scientificName Binomial species name 4. Country Country in which the specimen was made 5. locality  Textual description of the locality in which the specimen was made 6. habitat Textual description of the habitat in which the specimen was made 7. day Day of the month on which the specimen was made 8. month Month of the year on which the specimen was made 9. year Year in which the specimen was made 10. recordedBy Person or people who made the specimen 11. rec.Number Number given by collector to collection 12. Error.Diam. Spatial error of georefencing (km) 13. Min_Elev.M. Minimum altitude (m) 14. Max_Elev.M. Maximum altitude (m)       15. decimalLatitude Coordinates of latitude 16. decimalLongitude Coordinates of longitude 17. Label..notes Additional information recorded about the location of specimen collection 18. Georeferenced  Whether each specimen record was (1) or was not (0) georeferenced (i.e. coordinates inferred from a textual description of locality) during this research taxonomic_references_from_which_trait_values_obtained.docx Taxonomic publications from which trait values were extracted. </p