funspace: an R package to build, analyze and plot functional trait spaces

Carmona, Carlos P.; Puglielli, Giacomo

doi:10.1101/2023.03.17.533069

Cited by 6 publications

(7 citation statements)

References 46 publications

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“…Deciduous gymnosperms were excluded from the analysis due to a lack of data for modelling ( n = 14). GAM predictions per each PFT were generated only within the portion of the STS occupied by each PFT to avoid the GAM smoother extrapolating model predictions outside the STS regions occupied by each group (Carmona et al., 2023). The whole analysis was also applied to single traits (see Appendix S5, Figure S5.5a–l).…”

Section: Methodsmentioning

confidence: 99%

Trait dimensions of abiotic stress tolerance in woody plants of the Northern Hemisphere

Pavanetto,

Carmona,

Laanisto

et al. 2023

Global Ecol Biogeogr

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AimTrade‐offs among tolerances to different abiotic stressors limit polytolerance in woody plants. However, the general trait syndromes that underlie large‐scale tolerance patterns of woody plants remain controversial. Here, we tested if the leading trait dimensions that define the global spectrum of plant form and function capture the underlying trait trade‐offs limiting woody plant polytolerance.LocationNorthern Hemisphere.Time PeriodPresent.Major Taxa StudiedWoody plants.MethodsWe used a dataset of 779 species to link the trait dimensions defining the global spectrum of plant form and function with two dimensions summarizing tolerance syndromes to drought, shade, cold and waterlogging. Stress tolerance dimensions were a trade‐off between drought and cold/waterlogging tolerance strategies, and a shade tolerance spectrum. Relationships among trait and stress tolerance dimensions were evaluated using general additive models separately for deciduous and evergreen angiosperms, and evergreen gymnosperms.ResultsDrought‐tolerant angiosperms showed greater specific stem density (SSD) and seed mass (SM), and lower specific leaf area (SLA) and leaf nitrogen content per mass (LN), compared to the cold/waterlogging‐tolerant species. Shade‐tolerant angiosperms displayed greater SSD and SM and lower SLA and LN compared to intolerant angiosperms. Highly contrasting trait adaptations also distinguished drought‐ (greater SSD, SM and lower SLA, LN) from shade‐tolerant evergreen gymnosperms.Main ConclusionsThe ‘SSD–SM’ and the ‘SLA–LN’ dimensions mainly distinguish cold or drought‐tolerant woody angiosperms and shade‐ or drought‐tolerant gymnosperms. Our results also support a conservative trait strategy for shade‐tolerant compared to shade‐intolerant species, with some differences between plant functional types probably due to contrasting leaf lifespans. Overall, our findings identify some leading functional constraints on polytolerance in woody plants and provide a framework to integrate additional trait dimensions to fully elucidate such constraints.

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Section: Methodsmentioning

confidence: 99%

Trait dimensions of abiotic stress tolerance in woody plants of the Northern Hemisphere

Pavanetto,

Carmona,

Laanisto

et al. 2023

Global Ecol Biogeogr

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“…We first defined the above-ground and fine-root trait spaces using principal component analysis (PCA) on imputed trait data (i.e. with completeness of 100% for all the considered traits) by using the 'funspace' R package (Carmona et al, 2023). Overall, the imputation procedure did not alter the definition of the above-ground and fine-root trait spaces (see Appendix S1; Figures S1 and S2).…”

Section: Trait Differences Between Clonal and Non-clonal Perennial Herbsmentioning

confidence: 99%

Unravelling the clonal trait space: Beyond above‐ground and fine‐root traits

Chelli,

Klimešová,

Tsakalos

et al. 2024

Journal of Ecology

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Plant trait variation is constrained by mechanical and energetic trade‐offs as attested by the global spectrum of plant form and function and the fine‐root economics space for above‐ and below‐ground traits. However, traits that are key for fitness maintenance in some plant groups, such as clonal and bud bank traits, have not yet been integrated within the frameworks provided by the above‐ground and the fine‐root economics space. By using an extensive dataset encompassing above‐ground, fine‐root, clonal and bud bank traits of 2000 species of Central European herbs, we asked whether clonal and bud bank traits correspond to the placement of species in the above‐ground or fine‐root trait space. Perennial clonal and non‐clonal herbs show indistinct positioning within the above‐ground and fine‐root trait spaces. This extends and reinforces previous fragmentary evidence of weak correlations between clonal and bud bank traits and above‐ground trait dimensions. Additionally, we identify for the first time a limited correlation between clonal and fine‐root traits as well. This disconnection suggests that clonal traits operate independently from other trait spectra. For this reason, we introduce the concept of a ‘clonal trait space’ for clonal herbs. The first dimension of this space is defined by bud bank size and the persistence of clonal connection, reflecting a gradient of species specialisation for on‐spot persistence and tolerance to disturbance (persistence dimension). The second dimension, defined by multiplication rate and lateral spread, reflects a specialisation axis for clonal multiplication and horizontal size dimension (clonal multiplication dimension). Clonal trait dimensions add non‐redundant information to the above‐ground or fine‐roots trait space. Synthesis: We champion the integration of the persistence and clonal multiplication dimensions from the ‘clonal trait space’ into the frameworks provided by the above‐ground trait and the fine‐root economics spaces, thereby enhancing our comprehension of the multifaceted trait strategies exhibited by plants.

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“…The package and the datasets are also available in Dryad: Carmona et al. (2024). https://doi.org/10.5061/dryad.4tmpg4fg6.…”

Section: Peer Reviewmentioning

confidence: 99%

funspace: An R package to build, analyse and plot functional trait spaces

Carmona,

Pavanetto,

Puglielli

2024

Diversity and Distributions

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AimFunctional trait space analyses are pivotal to describe and compare organisms' functional diversity across the tree of life. Yet, there is no single application that streamlines the many sometimes‐troublesome steps needed to build and analyse functional trait spaces.InnovationTo fill this gap, we propose funspace, an R package to easily handle bivariate and multivariate functional trait space analyses. The six functions that constitute the package can be grouped in three modules: ‘Building and exploring’, ‘Mapping’ and ‘Plotting’. The building and exploring module defines the main features of a functional trait space (e.g. functional diversity metrics) by leveraging kernel density‐based methods. The mapping module uses general additive models to map how a target variable distributes within a trait space. The plotting module provides many options for creating flexible and publication‐ready figures representing the outputs obtained from previous modules. We provide a worked example to demonstrate a complete funspace workflow.Main Conclusionsfunspace will provide researchers working with functional traits across the tree of life with a new tool to easily explore: (i) the main features of any functional trait space, (ii) the relationship between a functional trait space and any other biological or non‐biological factor that might contribute to shaping species' functional diversity.

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funspace: an R package to build, analyze and plot functional trait spaces

Cited by 6 publications

References 46 publications

Trait dimensions of abiotic stress tolerance in woody plants of the Northern Hemisphere

Trait dimensions of abiotic stress tolerance in woody plants of the Northern Hemisphere

Unravelling the clonal trait space: Beyond above‐ground and fine‐root traits

funspace: An R package to build, analyse and plot functional trait spaces

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