322,944 research outputs found
Rarefy: Rarefaction Method
No full textRarefy includes functions for the calculation of spatially and non-spatially explicit rarefaction curves using different indices of taxonomic, functional and phylogenetic diversity. The user can also rarefy any biodiversity metric as provided by a self-written function (or an already existent one) that gives as output a vector with the values of a certain index of biodiversity calculated per plot (Ricotta, C., Acosta, A., Bacaro, G., Carboni, M., Chiarucci, A., Rocchini, D., Pavoine, S. (2019) ; Bacaro, G., Altobelli, A., Cameletti, M., Ciccarelli, D., Martellos, S., Palmer, M. W., . . . Chiarucci, A. (2016) ; Bacaro, G., Rocchini, D., Ghisla, A., Marcantonio, M., Neteler, M., & Chiarucci, A. (2012)
A new look at functional beta diversity
No full textThe variability in species composition among a set of sampling sites, or beta diversity, is considered a key signature of the ecological processes that shape the spatial structure of species assemblages. In this paper, we propose to decompose this variability into three additive components: i) the standard similarity in the (relative) abundances of species among sites, ii) the degree of functional dissimilarity between individuals of distinct species among sites, and iii) the degree of functional similarity between individuals of distinct species among sites, or beta redundancy. These three components can be used to portray the functional resemblance among sites on a ternary diagram. With the resulting ternary diagram of ‘functional resemblance’ we can relate various aspects of taxonomic and functional variability among sites to community assembly processes more completely than just looking at individual components. The potential of this method is shown with real data on the functional turnover of Alpine species along a primary succession on glacial deposits in northern Italy
A new parametric measure of functional dissimilarity. Bridging the gap between the Bray-Curtis dissimilarity and the Euclidean distance
No full textCommunity ecologists usually consider the Euclidean distance inappropriate to explore the multivariate structure of species abundance data. This is because the Euclidean distance may lead to the counterintuitive result for which two sample plots with no species in common may be more similar to each other than two plots that share the same species list. To overcome this paradoxical situation, the species abundances need to be normalized in some way. Among the many coefficients used by ecologists for the analysis of assemblage data, the Bray-Curtis dissimilarity is certainly the most commonly used. This measure entails normalization of species-wise differences between two plots by the total species abundance in both plots. By highlighting the relationship between the Bray-Curtis dissimilarity and the Euclidean distance, we propose a parametric dissimilarity measure that is appropriate for handling data on community composition. We also show how the new parametric measure can be generalized to the measurement of functional dissimilarity between two plots. A small dataset on the species functional turnover along a chronosequence on Alpine grasslands is used to illustrate the behavior of the proposed measure
Identifying functionally distinctive and threatened species
No full textFunctional traits determine species' responses to environmental change and/or determine species' effects on ecosystem functions. When species with distinctive functional traits are threatened, there is a risk that ecosystem properties are also threatened. This is because functionally distinctive species may be those that have irreplaceable roles in an ecosystem and/or those that would be able to survive unusual environmental disturbances. To include functional distinctiveness as a criterion in conservation strategies, we need formal quantification of species' degree of distinctiveness while incorporating extinction risk. Based on previously developed quantitative methods, we develop a framework that links different metrics of functional distinctiveness and accounts for all species' extinction probabilities. Our framework is particularly relevant at the local scale, where species extinctions impact ecosystem functioning and where conservation policies are developed. As a case study, we thus applied our framework to the mammals of Indian dry forests known to be threatened with a drastic decrease in functional diversity and identified top-priority species as the threatened, most functionally distinctive species. We notably highlight that although some of the top-priority species we identified are charismatic and targeted by conservation actions, others are not. On the basis of this case study, we note that less charismatic, less known species that may be key for ecosystems could be revealed by applying our framework to a range of ecosystems and taxa
A family of functional dissimilarity measures for presence and absence data
No full textPlot-to-plot dissimilarity measures are considered a valuable tool for understanding the complex ecological mechanisms that drive community composition. Traditional presence/absence coefficients are usually based on different combinations of the matching/mismatching components of the 2 9 2 contingency table. However, more recently, dissimilarity measures that incorporate information about the degree of functional differences between the species in both plots have received increasing attention. This is because such "functional dissimilarity measures" capture information on the species' functional traits, which is ignored by traditional coefficients. Therefore, functional dissimilarity measures tend to correlate more strongly with ecosystem-level processes, as species influence these processes via their traits. In this study, we introduce a new family of dissimilarity measures for presence and absence data, which consider functional dissimilarities among species in the calculation of the matching/mismatching components of the 2 9 2 contingency table. Within this family, the behavior of the Jaccard coefficient, together with its additive components, species replacement, and richness difference, is examined by graphical comparisons and ordinations based on simulated data
Functional rarefaction for species abundance data
No full text1. Recently a number of rarefaction curves including information on species' functional traits were proposed for those measures of functional diversity that monotonically increase with species richness. 2.Building on these methods, in this paper, we propose a functional rarefaction curve for species abundance data that is obtained using the classical diversity decomposition of the Rao quadratic diversity into alpha, beta and gamma diversity. 3.The proposed abundance-based functional rarefaction is illustrated with one dedicated case study in sand dune communities in Italy. 4.Although we put emphasis on functional diversity only, because of its mathematical generality, the proposed method can be extended to virtually any abundance-weighted concave measure for comparing diversity among habitats sampled with different effort
The ternary diagram of functional diversity
No full textAmong the many diversity indices in the ecologist toolbox, measures that can be partitioned into additive terms are particularly useful as the different components can be related to different ecological processes shaping community structure. In this paper, an additive diversity decomposition is proposed to partition the diversity structure of a given community into three complementary fractions: functional diversity, functional redundancy and species dominance. These three components sum up to one. Therefore, they can be used to portray the community structure in a ternary diagram. Since the identification of community-level patterns is an essential step to investigate the main drivers of species coexistence, the ternary diagram of functional diversity can be used to relate different facets of diversity to community assembly processes more exhaustively than looking only at one index at a time. The value of the proposed diversity decomposition is demonstrated by the analysis of actual abundance data on plant assemblages sampled in grazed and ungrazed grasslands in Tuscany (Central Italy)
Quantifying the extent of plant functional specialization using Grime's CSR strategies
No full textSpecialization refers to a species adaptation to a restricted range of environmental conditions. While generalist species are able to exploit a wide variety of resources in a broad range of habitats, specialist species tend to have narrower niche breadths. From an evolutionary perspective, specialization is the result of a functional syndrome in which a suite of traits covary to allow the effective exploitation of specific resources. Accordingly, the measurement of specialization should be based on a multi-trait approach. In plant ecology, a well-known classification of the adaptive strategies of plants is Grime's competitor, stress tolerator, ruderal (CSR) theory in which the three principal strategies represent relatively easily measurable trait combinations from the global spectrum of plant form and function arising under conditions of competition, abiotic restriction to growth or periodic disturbance, respectively. In this paper, we thus introduce a method to summarize the functional specialization of plant species and communities by applying inequality measures to Grime's CSR strategies. The general idea is that a plant species that can be exclusively assigned to one CSR strategy can be considered a specialist (as it adopts only one adaptive strategy to access resources), while species that share functional characteristics of multiple CSR strategies can be considered more generalist. The behavior of the proposed measures is shown with one case study on the functional changes of six Alpine vegetation types ordered along a gradient, from pioneer to more stable communities
On two dissimilarity-based measures of functional beta diversity
No full textIn this paper, we propose two related versions of a dissimilarity-based measure of functional beta diversity, together with the associated tests for differences in beta diversity among different groups of samples. Both measures are based on the optimal functional matching between the species in two samples. As such, they are tightly connected to Hurlbert's seminal work on encounter-based diversity measures. The behavior of the proposed measures is illustrated with one worked example on the functional turnover of Alpine species along a successional gradient. Results show that both measures proved able to detect the functional turnover of vegetation along the chronosequence. The method, for which we provide a simple R function, further allows to evaluate the functional contribution of single sampling units to the overall beta diversity of any kind of species assemblages
Diffusive author(s), cohesive author: Analysis of S/N (1994)
No full textThis study indicates the ways in which various aspects of the author(s) are brought forth in Dumb type’s performance art, the S/N production. Previous research has suggested a non-hierarchical organization of Dumb type and the absence of a “privileged author” in Dumb type’s collaborative work, S/N. However, the results that I have investigated from member’s interviews on the creative process of S/N along with my analysis of the recorded images of S/N, indicate a different aspect of the author(s). First, S/N was created through, so to speak, the collective ideas of the members of Dumb type. Further, S/N has at least nine quotations from previous performances, installations, and printed writings, besides the work-in-progress technique. Explicating one of the “author functions” as given by Michel Foucault, each text has plural subjects of the author. However, it has been revealed from members’ interviews that Teiji Furuhashi had a decision-making role in selecting the members’ ideas within the performance. Since then, S/N has had plural subjects of creation; however, Furuhashi is one of the subjects of creation along with the “privileged author.” S/N has plural authors (diffusive authors) yet at the same time, it has a “privileged author,” Teiji Furuhashi (cohesive author)
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