Integrating functional and phylogenetic dimensions of biodiversity into ecological restoration

Functional and phylogenetic diversity are central to most ecological theories applied to ecological restoration. However, because functional and phylogenetic diversity are rarely considered together, the field lacks a universal lens through which to improve restoration science and practice. Here, we demonstrate how simultaneously maximizing functional and phylogenetic diversity in restoration can lead to rapid generation of knowledge about community assembly, the safeguarding of unique evolutionary lineages and functionally distinct species, and the reestablishment of stable and resilient ecosystems. To demonstrate the utility of this approach, we present a species selection framework showing how thoughtful selection of even a limited number of species can result in high levels of functional and phylogenetic diversity in restoration projects. Increasing availability of data on functional traits, phylogenies, and restoration outcomes now enables the explicit incorporation of multiple dimensions of diversity into restoration science and offers new opportunities for integrating ecological theory and restoration practice. ¿p#1 Integrating functional and phylogenetic dimensions of biodiversity into ecological restoration Authors: Magda Garbowski 1, Gustavo Brant Paterno 2, Anna Abrahão 3, Joe Atkinson 4,5, Annalena Mauz 6, Laura Méndez 7,8, Ana Carolina Cardoso de Oliveira 9, Rajat Rastogi 8,10,11,12, Kimberly Thomson 8, Patrick Weigelt 13, Emma Ladouceur 6,14,15 1 Department of Animal and Range Sciences, New Mexico State University, USA. [email protected], ORCID: 0000-0002-4943-4358 2 Biodiversity, Macroecology and Biogeography, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Göttingen, Germany. [email protected], ORCID: 0000-0001-9719-3037 3 Departamento de Biologia, Universidade Federal do Ceará, 60440-900, Fortaleza-CE, Brazil. [email protected], ORCID: 0000-0001-9295-2292 4 School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia. [email protected], ORCID: 0000-0001-9232-4421 6 Department of Biology, University of Prince Edward Island, Charlottetown, Canada. 7 Department of Biology, Philipps-University Marburg, Marburg, Germany [email protected], ORCID: 0000-0001-8155-5929 8 German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany [email protected], ORCID: 0000-0002-9644-3855 9 Departamento de Biologia Vegetal, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil [email protected], ORCID: 0000-0002-2253-2230 10 Department of Community Ecology, Helmholtz Centre for Environmental Research (UFZ), Halle, Germany [email protected], ORCID: 0000-0002-3722-6324 11 Martin Luther University Halle-Wittenberg, Halle, Germany 12 Wildlife Institute of India, Dehradun, India 13 Department of Environmental Science, Radboud Institute for Biological and Environmental Sciences (RIBES), Radboud UniversityNijmegen, The Netherlands. [email protected], ORCID: 0000-0002-2485-3708 14 Canadian Centre for Climate Change and Adaptation, University of Prince Edward Island, St. Peter’s Bay, Canada 15 School of Climate Change and Adaptation, University of Prince Edward Island, Charlottetown, Canada, [email protected], 0000-0002-4943-4358 Running Title: Traits and phylogenetics in restoration

Functional diversity, Phylogenetic diversity, Ecological restoration, Community assembly, Ecosystem stability, Biodiversity Article Type: Viewpoint

150 Main text: 1,839 Number of references: 62 Number of figures: 2 Number of tables: 0 Number of text boxes: 0 Corresponding author: Dr. Magda Garbowski, Assistant Professor of Functional and Restoration Ecology, Department of Animal and Range Sciences, New Mexico State University, Knox Hall, 2980 S. Espina St. 88003, +1 575-646-1805, [email protected] Author contributions: A.A., A.C.O., A.M., E.L., G.B.P., J.A., K.T., L.M., M.G., P.W., and R.R. conceived the ideas. E.L. and M.G. acquired project funding and administered the project. G.B.P. and P.W. contributed data resources and modelling simulations. G.B.P., M.G., and R.R. developed figures. M.G. led writing of the first draft of the manuscript and all authors participated in writing, reviewing, and editing subsequent versions of the manuscript. ¿p#1 Data Accessibility Statement: ¿p#1 Primary data on plant species, phylogenetic trees, and functional traits used in the simulations are available from Paterno et al. (2024) via the GRO. data repository (https://doi.org/10.25625/GUWXUX). All data and R code used to reproduce the simulations, figures, and results of this study will be made available in the GitHub repository https://github.com/paternogbc/ms_phylo_func_restoration upon acceptance of the manuscript. Novelty Statement: Despite serving as the backbone of most ecological theories applied to ecological restoration, functional and phylogenetic diversity are rarely considered together in restoration science and practice. Here, we show how considering and optimizing for functional and phylogenetic diversity together in restoration projects advances our ability to rapidly generate knowledge of community assembly, safeguard evolutionarily and functionally unique species, and support the reestablishment of stable and resilient ecosystems via restoration efforts. ¿p#1 Abstract Functional and phylogenetic diversity are central to most ecological theories applied to ecological restoration. However, because functional and phylogenetic diversity are rarely considered together, the field lacks a universal lens through which to improve restoration science and practice. Here, we demonstrate how simultaneously maximizing functional and phylogenetic diversity in restoration can lead to rapid generation of knowledge about community assembly, the safeguarding of unique evolutionary lineages and functionally distinct species, and the reestablishment of stable and resilient ecosystems. To demonstrate the utility of this approach, we present a species selection framework showing how thoughtful selection of even a limited number of species can result in high levels of functional and phylogenetic diversity in restoration projects. Increasing availability of data on functional traits, phylogenies, and restoration outcomes now enables the explicit incorporation of multiple dimensions of diversity into restoration science and offers new opportunities for integrating ecological theory and restoration practice. ¿p#1 1 Problem Statement The science and practice of ecological restoration are expanding rapidly and public initiatives such as the United Nations Decade on Ecosystem Restoration have drawn considerable awareness and action to the field. Despite this swift growth, or possibly because of it, Restoration Ecology stands at a crossroads as the field seeks to integrate ecological theory with on-the-ground practice. Because species’ functional and evolutionary characteristics modify which organisms can establish, persist, and co-exist in novel communities, trait-based and phylogenetic approaches serve as the cornerstones of many of the theoretical frameworks being applied to Restoration Ecology (Azevedo & Rother 2025; Barbosa‐Dias et al. 2025; Funk et al. 2008; Laughlin 2024; Silliman et al. 2024). However, even with the increasing application of ecological theory to Restoration Ecology, restoration trajectories remain difficult to predict (Bertuol-Garcia et al. 2023), many restoration efforts fail to recover biodiversity (Shackelford et al. 2021), and additional research is often required to determine which theories are most appropriate for meeting specific restoration goals (Silliman et al. 2024). Further, ecological complexity and unpredictable environmental conditions continue to make testing ecological theory via restoration challenging and complicate our ability to glean generalizable lessons from past and ongoing restoration efforts (Funk et al. 2024). These issues may stem from the fact that multiple facets of biodiversity are rarely considered together when theoretical frameworks are applied to restoration. ¿p#1 2 Restoration and Biodiversity Science Biodiversity is a multidimensional concept that includes “taxonomic, genetic, phenotypic, phylogenetic, and functional variation within and among species, biological communities, and ecosystems” (Diaz et al. 1998). Taxonomic diversity, generally measured as species richness, remains the most commonly used measure for assessing the success of biodiversity-related restoration outcomes (Atkinson et al. 2022; Crouzeilles et al. 2016; Wortley et al. 2013) as it is linked to a range of desirable ecosystem services, such as productivity, carbon sequestration, and the regulation of soil and water dynamics (Edwards & Cerullo 2024; Urgoiti et al. 2022). Functional and phylogenetic diversity are complementary dimensions of the diversity spectrum that can provide a more comprehensive understanding of biodiversity than taxonomic diversity alone. Functional diversity reflects the cumulative variation in morphological, physiological, and phenological characteristics of organisms in a community and provides insight into the diversity of functional roles or niches occupied by species within an ecosystem (Mammola et al. 2021). Phylogenetic diversity quantifies the accumulated evolutionary history represented by species within a community and can be used to identify evolutionarily unique or irreplaceable lineages (Webb et al. 2002). Here, we demonstrate how simultaneously considering and optimizing functional and phylogenetic diversity during restoration can lead to improved understanding of community assembly, the safeguarding of unique evolutionary lineages and functionally distinct species, and the reestablishment of diverse plant communities that support stable and resilient ecosystem functions. To demonstrate the utility of the approach, we present a species selection framework for ecosystem restoration based on both species’ functional traits and evolutionary histories. Although our arguments are largely centered on functional and phylogenetic diversity in terrestrial plant-based restoration, the ideas presented are relevant to restoration across diverse systems and scales. ¿p#1 3 Community (dis)assembly For a species to occur in a given area, propagules of that species must overcome a series of dispersal, abiotic, and biotic filters. The ability to overcome these filters and persist in communities depends on a species’ phylogenetic background and its functional traits. For instance, evolutionary history can influence whether a species occurs in a regional species pool, whether it relies on specific biotic interactions for regeneration and whether it is able to coexist with other species in an assemblage (Campbell et al. 2019; Chamberlain et al. 2014; Gleiser et al. 2025). Similarly, plants of a given species must possess traits that allow them to disperse to a local community, withstand specific abiotic conditions at a site, and tolerate competition from co-occurring species (Laughlin 2024; Leger et al. 2021). Despite both being shaped by community assembly processes, phylogenetic and functional diversity are often decoupled in communities (Hähn et al. 2024). For example, some grassland ecosystems have low phylogenetic diversity while exhibiting high functional diversity due to local environmental filters (Tan et al. 2012; Večeřa et al. 2023), whereas many forests exhibit high phylogenetic diversity but low functional diversity because they retain distantly related taxa in distinct layers of forest strata (Hähn et al. 2024). This decoupling highlights the importance of considering phylogenetic and functional dimensions of diversity together to better elucidate how past and current forces shape the abundance and composition of species in communities. Natural and anthropogenic disturbances influence the processes driving community assembly and modify which species can establish and persist in communities (González-Orozco et al. 2016; Le Bagousse-Pinguet et al. 2025; Uchida et al. 2019). For example, increasing land-use intensity has led to a consistent decline in pollinator-dependent plants across European grasslands (Clough et al. 2014), and nutrient enrichment disproportionately reduces the abundance of species from certain plant families (Nelson et al. 2025) or with certain photosynthetic pathways (Garbowski et al. 2023). Clarifying how global changes and local disturbances lead to the non-random loss of functional strategies and evolutionary lineages is essential for understanding how novel filters shape community (re)assembly in restoration (Figure 1). ¿p#1 4 Benefits of maximizing functional and phylogenetic diversity in ecological restoration ¿p#1 4.1 Safeguarding functional and evolutionary uniqueness Maximizing functional and phylogenetic diversity in native plant development and restoration may provide a precautionary approach to safeguarding diversity even without complete knowledge of the unique roles and interactions supported by species (Figure 2). A growing body of evidence suggests that rare species disproportionately contribute to vulnerable ecosystem functions and services (Leitão et al. 2016; Soliveres et al. 2016) such as resistance to invaders (Zavaleta & Hulvey 2004), recreational value (Booth et al. 2011), and the maintenance of unique co-evolutionary relationships across trophic levels (Vieira et al. 2013). Further, unlike more dominant species that primarily interact with co-occurring species via negative associations, rare species tend to form positive associations in assemblages supporting small but persistent interaction networks in plant communities (Calatayud et al. 2020). Because of their disproportionate contributions to communities and ecosystems, targeting functionally and phylogenetically distinct species in restoration would help maintain unique ecological functions and complex networks in restored ecosystems. A multi-faceted diversity approach would also allow researchers and practitioners to identify species that are functionally and phylogenetically similar to one another to guide species substitutions in the native plant development and the restoration process. This would be particularly important for identifying substitutes for desirable species that are difficult to collect in the field or challenging to produce in agricultural settings. ¿p#1 4.2 Restoring ecosystem functionality and stability Phylogenetic and functional diversity underpin many ecosystem properties ecologists aim to reestablish with restoration including, but not limited to, productivity (Brun et al. 2019; Cadotte et al. 2009), carbon sequestration (Ding et al. 2024; Wang et al. 2022) and pollinator networks (Dehling et al. 2022). The positive effects of functional and phylogenetic diversity on these and other ecosystem properties stem from similar mechanisms, largely niche partitioning among distantly related or functionally dissimilar species. However, this is not always the case; some studies have found individual traits to be stronger drivers of specific ecosystem functions than functional diversity (Conti & Díaz 2013). Yet, because the field still lacks clarity on trait-function relationships and their context dependence (Funk et al. 2024), maximizing functional and phylogenetic diversity may provide the best avenue for ensuring that species associated with specific functions are included in restored plant communities. In addition, because considerable trade-offs and synergies exist among ecosystem functions (Ladouceur et al. 2021), maximizing functional and phylogenetic diversity may be key to reestablishing plant communities capable of supporting numerous ecosystem functions simultaneously (Fiedler et al. 2021). Maximizing functional and phylogenetic diversity may also promote ecosystem stability, or the ability of communities to maintain ecosystem properties under variable conditions. This is because functionally and phylogenetically diverse communities are more likely to contain species with diverse functional strategies that support asynchronous responses to stressors and disturbances (de Bello et al. 2021). Indeed, functional diversity underpins biomass stability in response to grazing (Hallett et al. 2017; Kang et al. 2020) and drought (Luo et al. 2023; Pérez-Ramos et al. 2017), while both phylogenetic (Pu et al. 2014) and functional (Ceulemans et al. 2019) diversity shape ecosystem responses to perturbations. However, whether functional and phylogenetic diversity support stability may depend on phylogenetic conservatism of specific traits. Some plant traits (e.g., hydraulic traits, wood density, leaf mass per area) are phylogenetically conserved, whereas others (e.g., CAM, C4 pathways) have evolved independently in different lineages (Flores et al. 2014; Li et al. 2024). If traits are strongly conserved, functional and phylogenetic diversity are expected to have similar, generally positive effects on stability. But, phylogenetic diversity can also capture unmeasured traits that confer asynchronous responses among species, leading to higher stability even when functional diversity shows no direct relationship with stability. Given this variation in phylogenetic signal, restoration should balance phylogenetic and functional diversity, recognizing potential trade-offs when traits lack phylogenetic structure (S2 vs. S3, Figure 2B). ¿p#1 4.3 Diversifying restoration planning and assessment Diverse goals and site-specific conditions necessitate tailored approaches to most restoration projects. Simultaneously, the decisions made during the planning phase of restoration are shaped by scarce resources forcing practitioners to make tough choices about which species to include in seed mixes and plantings. Given that many restoration projects include less than 10 species (Shackelford et al. 2021), it is difficult to imagine adequate recovery of biodiversity through restoration efforts. Indeed, taxonomic diversity of restored communities is often lower than that of reference sites or seed mixes (Holl et al. 2022). However, assessing restoration success solely in relation to taxonomic diversity may obscure the recovery of other facets of diversity and ecosystem properties regularly targeted in restoration (Gann et al. 2019). Recent research suggests that planting or seeding with functionally or phylogenetically diverse assemblages at the onset of restoration results in restored communities with high levels of functional and phylogenetic diversity at later stages, even if taxonomic richness declines (Barak et al. 2023). Given that functional and phylogenetic diversity underpin many of the ecosystem attributes targeted in restoration such as structural diversity and ecosystem function, considering restoration outcomes in relation to functional and phylogenetic diversity may provide an alternative yet informative way of assessing restoration success. Luckily, attaining high levels of functional and phylogenetic diversity in restoration projects does not require exorbitant numbers of species to be included in seed mixes or plantings, and can be prioritized alongside other goals (Ladwig et al. 2020) (Figure 2). ¿p#1 5 Future directions for biodiversity-driven restoration Ample and immediate opportunities exist to integrate functional and phylogenetic diversity into restoration science. Trait coverage is ever-growing (Kattge et al. 2020) and phylogenetic data are available for increasing numbers of species across the Tree of Life (Baker et al. 2022). These data, along with more readily accessible data on the outcomes of restoration projects (Ladouceur et al. 2022) can be leveraged to retroactively assess how functional and phylogenetic diversity change throughout the restoration process and to determine if high initial levels of taxonomic, phylogenetic, and functional diversity beget high levels of multiple facets of diversity at later stages (Paterno et al. 2024). Research that applies a diversity-driven framework in restoration could also expedite our ability to link traits and phylogenetic identities to population fitness and ecosystem function. These are key shortfalls of restoration ecology (Funk et al. 2024), functional ecology (Chacón-Labella et al. 2023; de Bello et al. 2025), and phylogenetic ecology (Swenson 2019), yet are central to predicting how all ecosystems, including restored ones, will respond to stressors and disturbances. Further, given the continued unpredictability of restoration outcomes, elucidating whether high functional and phylogenetic diversity increase restoration success and reduce variability in restoration outcomes, particularly in relation to targeted ecosystem functions, would be of great relevance to restoration research and practice. ¿p#1 6 Conclusion Decades of attempts to base restoration practice on ecological theory have fallen short and restoration outcomes continue to be unpredictable. However, the current rate of ecological degradation necessitates an approach to restoration research and practice that hedges bets against uncertainty and provides avenues for the rapid generation of new knowledge. 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Each row represents a different stage of restoration: the reference community (top row, lightest shade); the degraded community (second row, white); the species pool available for restoration (third row, medium shade); and the restored community after abiotic and biotic filtering (bottom row, darkest shade). Symbols represent unique plant species and parallelograms depict interacting anthropogenic (e.g., market availability of species), abiotic (e.g., aridity), and biotic (e.g., grazing) filters that shape restored communities. Shown from left to right are changes in taxonomic diversity, functional diversity, and phylogenetic diversity, with species lost from communities shown in light gray in functional trait space and in a phylogenetic tree. ¿p#1 Figure 2: Optimizing restoration outcomes by maximizing functional and phylogenetic diversity. Data are from 51 native woody species occurring in a restoration experiment in Sumatra, Indonesia (Paterno et al. 2024). Simulated degradation removed 44 species (85%) biased toward tall and dense-wood taxa, reducing functional diversity (FD; functional richness based on maximum height, and wood density) by 95% and phylogenetic diversity (PD; Faith’s PD) by 77% (panel C, reference vs. degraded community). (A) Species-level standardized contributions (z-scores) to FD and PD, calculated by sequentially reintroducing each lost species into the degraded community. (B) Standardized PD and FD for 100,000 simulated restored communities, each representing the recovery of 30% of the species pool (7 persisting plus 8 reintroduced species). Colors indicate the top 5% of communities for PD (blue), FD (green), or both (pink); S1–S4 highlight four restoration scenarios. (C) For the reference, degraded, and scenarios S1–S4, phylogenetic trees (top row), trait space (maximum height vs. wood density; bottom row), and relative PD and FD (bar plots to the right; scaled to the reference) illustrate restoration outcomes. S1 (locally available species biased toward low height and wood density) recovered 32% of PD and 28% of FD. S2 (maximizing FD) recovered FD to PD) recovered ~52% of PD and ~71% of FD. S4 (jointly maximizing PD and FD) achieved ~49% of PD and algorithms can effectively identify species combinations that simultaneously enhance FD and PD by prioritizing taxa with the greatest functional and phylogenetic contributions. Information & Authors Information Version history Copyright This work is licensed under a Non Exclusive No Reuse License.

Authors Metrics & Citations Metrics Article Usage 462views 155downloads Citations Download citation Magda Garbowski, Gustavo Paterno, Anna Abrahão, et al. Integrating functional and phylogenetic dimensions of biodiversity into ecological restoration. Authorea. 17 November 2025. DOI: https://doi.org/10.22541/au.176339926.60650912/v1 DOI: https://doi.org/10.22541/au.176339926.60650912/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu.