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Abstract Quantifying the structure and dynamics of species interactions in ecological communities is fundamental to studying ecology and evolution. While there are numerous approaches to analysing ecological networks, there is not yet an approach that can (1) quantify dissimilarity in the global structure of ecological networks that range from identical species and interaction composition to zero shared species or interactions and (2) map species between such networks while incorporating additional ecological information, such as species traits or abundances.To address these challenges, we introduce the use of optimal transport distances to quantify ecological network dissimilarity and functionally equivalent species between networks. Specifically, we describe the Gromov–Wasserstein (GW) and Fused Gromov–Wasserstein (FGW) distances. We apply these optimal transport methods to synthetic and empirical data, using mammal food webs throughout sub‐Saharan Africa for illustration. We showcase the application of GW and FGW distances to identify the most functionally similar species between food webs, incorporate additional trait information into network comparisons and quantify food web dissimilarity among geographic regions.Our results demonstrate that GW and FGW distances can effectively differentiate ecological networks based on their topological structure while identifying functionally equivalent species, even when networks have different species. The FGW distance further improves node mapping for basal species by incorporating node‐level traits. We show that these methods allow for a more nuanced understanding of the topological similarities in food web networks among geographic regions compared to an alternative measure of network dissimilarity based on species identities.Optimal transport distances offer a new approach for quantifying functional equivalence between networks and a measure of network dissimilarity suitable for a broader range of uses than existing approaches. OT methods can be harnessed to analyse ecological networks at large spatial scales and compare networks among ecosystems, realms or taxa. Optimal transport‐based distances, therefore, provide a powerful tool for analysing ecological networks with great potential to advance our understanding of ecological community structure and dynamics in a changing world.
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A roadmap for sampling and scaling biological nitrogen fixation in terrestrial ecosystems
Abstract Accurately quantifying rates and patterns of biological nitrogen fixation (BNF) in terrestrial ecosystems is essential to characterize ecological and biogeochemical interactions, identify mechanistic controls, improve BNF representation in conceptual and numerical modelling, and forecast nitrogen limitation constraints on future carbon (C) cycling.While many resources address the technical advantages and limitations of different methods for measuring BNF, less systematic consideration has been given to the broader decisions involved in planning studies, interpreting data, and extrapolating results. Here, we present a conceptual and practical road map to study design, study execution, data analysis and scaling, outlining key considerations at each step.We address issues including defining N‐fixing niches of interest, identifying important sources of temporal and spatial heterogeneity, designing a sampling scheme (including method selection, measurement conditions, replication, and consideration of hotspots and hot moments), and approaches to analysing, scaling and reporting BNF. We also review the comparability of estimates derived using different approaches in the literature, and provide sample R code for simulating symbiotic BNF data frames and upscaling.Improving and standardizing study design at each of these stages will improve the accuracy and interpretability of data, define limits of extrapolation, and facilitate broader use of BNF data for downstream applications. We highlight aspects—such as quantifying scales of heterogeneity, statistical approaches for dealing with non‐normality, and consideration of rates versus ecological significance—that are ripe for further development.
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- Award ID(s):
- 1754126
- PAR ID:
- 10451097
- Publisher / Repository:
- Wiley-Blackwell
- Date Published:
- Journal Name:
- Methods in Ecology and Evolution
- Volume:
- 12
- Issue:
- 6
- ISSN:
- 2041-210X
- Format(s):
- Medium: X Size: p. 1122-1137
- Size(s):
- p. 1122-1137
- Sponsoring Org:
- National Science Foundation
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