Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

Májeková, Maria; Paal, Taavi; Plowman, Nichola S.; Bryndová, Michala; Kasari, Liis; Norberg, Anna; Weiss, Matthias; Bishop, Tom R.; Luke, Sarah H.; Sam, Kateřina; Bagousse‐Pinguet, Yoann Le; Lepš, Jan; Götzenberger, Lars; Bello, Francesco de

doi:10.1371/journal.pone.0149270

Cited by 107 publications

(85 citation statements)

References 36 publications

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“…Májeková et al . ), even in the highly intensively sampled communities that we investigated, some species might not have been observed. Although this is almost inevitable, as sampling communities truly exhaustively is generally either unfeasible or impossible, it is likely that this may have caused an underestimation of the minimum sampling effort required to reach adequate precision and accuracy.…”

Section: Discussionmentioning

confidence: 89%

“…Májeková et al . (), who studied the effects of missing trait (rather than community) data on the precision of Rao's Quadratic Entropy, Functional Richness and Functional Evenness, found that the former was most robust to missing data and that the latter was least robust, suggesting that precision of the same metrics are consistently the most sensitive to any type of data deficiency.…”

Section: Discussionmentioning

confidence: 99%

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Sensitivity of functional diversity metrics to sampling intensity

et al. 2017

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Summary Functional diversity (FD) metrics are increasingly used in ecological research, particularly in the studies of community assembly and ecosystem functioning. However, studies using the FD metrics vary greatly in the intensity by which ecological communities were sampled and it is largely unknown how sensitive these metrics are to low sampling intensity (undersampling). In this study, we used a combination of simulations with theoretically assembled communities and three comprehensive, independent, empirical datasets on plant, ground beetle, and bird communities to investigate the sensitivity of nine commonly used FD metrics to undersampling. Simulations with both theoretical communities and empirical data showed that in a wide range of contexts, the measurement of various FD metrics requires a much higher sampling effort to reach an ‘adequate’ precision (defined as an r2 of at least 0·7 between different subsets of the same population), than that required for commonly used taxonomic diversity metrics (e.g. species richness), although the ‘accuracy’ (their deviation from the diversity value of a completely sampled community) of their measurements is not more sensitive to undersampling than species richness. We also found that some FD metrics (e.g. Functional Dispersion) are consistently less sensitive to undersampling than others (e.g. nearest neighbour distance‐metrics). Problems of undersampling were generally most severe in datasets with high overall species richness and low overall abundances. We found that the precision of many FD metrics is highly sensitive to undersampling, and more so than commonly used taxonomic diversity metrics. Therefore, to ensure reproducible results in functional biodiversity research, we recommend that thorough sampling designs are used to sample communities and that datasets originally collected for studying taxonomic diversity should only be used for FD when it can be shown that undersampling is not a major issue. In cases where undersampling is suspected or logistically unavoidable, the FD metrics that are relatively insensitive to its effects (e.g. Functional Dispersion) should be prioritized.

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Section: Discussionmentioning

confidence: 89%

Section: Discussionmentioning

confidence: 99%

Sensitivity of functional diversity metrics to sampling intensity

et al. 2017

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“…Finally, we calculated functional trait diversity (FDIS) using the dbFD function in the R package FD (Laliberté, Legendre, Shipley, & Laliberté, ). Both plant height and SLA were log‐transformed before analysis to amplify the probability of detecting functional community patterns (Májeková et al, ). FDIS is a commonly used functional diversity metric and denotes the averaged abundance‐weighted distance between plant species to the community abundance‐weighted functional mean value.…”

Section: Methodsmentioning

confidence: 99%

Intransitivity increases plant functional diversity by limiting dominance in drylands worldwide

et al. 2018

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101. Biotic interactions are a key determinant of plant community structure. Indirect interactions 11 such as intransitivity (i.e. the absent of competitive hierarchies among species) have been 12 hypothesized to benefit diversity within plant communities. However, their effect on functional 13 diversity remains scarcely explored in real communities. Here we develop a novel approach to 14 infer intransitivity from plant spatial patterns and functional traits (maximum plant height and 15 specific leaf area), and quantify its effect on functional diversity along environmental gradients 16 in 100 drylands from all continents except Antarctica. 17 2. We first calculated the spatial association pattern for all perennials to infer competition 18 between species. Trait values were used as a proxy of competitive hierarchies to infer the 19 direction of these interactions. We used multiple regression models to evaluate how 20 intransitivity responds to abiotic variables (mean annual temperature and precipitation, 21 precipitation seasonality, soil pH and sand content). We also evaluated the effects of 22 intransitivity on functional diversity, quantified using metrics focusing on either subordinate 23 (FDIS) or dominant (FDISw) species. 24 3. Intransitivity mostly responded to climatic variables, and significantly increased with 25 precipitation scarcity and seasonality. We found that intransitivity had significant effects on 26 functional diversity, and was the main driver explaining changes in FDIS. However, this 27 response was only observed under high precipitation seasonality. 28Synthesis. Intransitivity increased the diversity of drylands under high rainfall seasonality by 29 favoring the abundance of subordinate species with contrasted trait values. Our findings specify 30 how intransitivity structures the functional diversity of dryland vegetation worldwide. 31Intransitivity may be particularly important in ecosystems where the availability of abiotic 32 resources changes over time, thereby breaking down inherent competitive hierarchies between 33 plant species. Neglecting intransitivity will bias our estimation of the impacts of biotic 34 interactions on plant communities, a key issue to fully understand how plant communities will 35 respond to ongoing environmental changes. 36

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“…However, the results encourage the use of a local trait dataset as the priority choice in a trait-based analysis, if one is available. Otherwise, as missing trait data should be avoided (Májeková et al, 2016), a continental trait dataset (and thus Palearctic literature)…”

Section: Consequences Of Trait Variability On Community-weighted Mementioning

confidence: 99%

Intraspecific body size variability in soil organisms at a European scale: Implications for functional biogeography

et al. 2018

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Investigating the functional facet of biodiversity provides ecologists with a deeper understanding of community assembly and ecosystem processes, from local to biogeographical scales. A central assumption in functional ecology is that interspecific trait variability is higher than intraspecific variability. The “stable species hierarchy” hypothesis states that for similar species found in different environmental conditions, their species trait ranking is conserved. In this study, we applied this trait hierarchy concept prevalent in plant ecology to the growing field of soil functional ecology, for which newly developed trait databases are being increasingly used. However, to date there have been few attempts to test for patterns of intraspecific trait variability (ITV) in these databases. We thus aimed to characterize how such patterns might influence (a) a species hierarchy based on trait values and (b) the conclusions of a trait‐based analysis at a community level. To examine this, we used Collembola body size data (extracted from the BETSI database) as model trait. The source consisted of four regional trait datasets (Poland, Scandinavia, Spain and UK) and one dataset for which species traits are defined at a continental (European) scale. We found that, firstly, species were consistently ranked in all the trait datasets, although slight differences were observed between continental and northern European (i.e. Scandinavia and UK) trait datasets. In the two northern datasets, body size was higher (ca. 10%), indicating an intraspecific body size gradient from temperate to colder northern regions that we assumed could be explained by latitudinal patterns. Secondly, using selected published species abundance matrices (from experimental studies), we calculated the community‐weighted mean body size using various trait datasets. The findings showed that the slight discrepancies observed between trait datasets can lead to different conclusions. This work confirms that properly defining the extent of ITV in databases is of primary importance to ensure robust conclusions. This is particularly important for databases hosting large‐scale data that might be influenced by biogeographical patterns as latitudinal gradients. We recommend using a local regional trait dataset when available or, if not, a continental trait dataset. As trait databases are now commonly used tools for performing trait‐based analyses, it is crucial to carefully select the data used to make inferences. A http://onlinelibrary.wiley.com/doi/10.1111/1365-2435.13194/suppinfo is available for this article.

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Evaluating Functional Diversity: Missing Trait Data and the Importance of Species Abundance Structure and Data Transformation

Cited by 107 publications

References 36 publications

Sensitivity of functional diversity metrics to sampling intensity

Sensitivity of functional diversity metrics to sampling intensity

Intransitivity increases plant functional diversity by limiting dominance in drylands worldwide

Intraspecific body size variability in soil organisms at a European scale: Implications for functional biogeography

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