Biology subjects

Pavoine, S.

Publications and source records attributed to Pavoine, S..

7 recordsLinked to original sources

bioRxiv2025

Formalizing biodiversity measures and guiding through them

Facing the myriad of indices claimed to be biodiversity indices that have been proposed by the scientific community, it becomes critical to analyze the mathematical properties that determine whether any index respond to biological necessities about biodiversity quantification. In ecology, species richness, the number of species, was a pioneer simple formula still currently most widely used as a biodiversity index. Species, functional, phylogenetic diversity indices then emerged from the feeling that combining species richness with the distribution of species abundances, functional and/or phylogenetic characteristics could provide indices that are more linked to ecological phenomena than species richness alone. Although there are theoretically an infinite number of potential biodiversity indices, I show here that some widely used indices of biodiversity actually take on large values in the absence of diversity. I thus claim for stricter definition of mathematical formulas that can be classified as biodiversity indices and for the use of parametric guiding indices that generalize and connect existing indices, tracing paths through the jungle of indices. As a case study I develop a parametric guiding index, and applying it on bat diversity, I show that analyzing the mathematical properties of potential biodiversity indices is critical to evaluate their relevance as regards a study objective in ecology. I come to the conclusions that to improve applications of biodiversity indices in ecology we need to: stop claiming for a single best formula; acknowledge that biodiversity indices are above all diversity indices, with the particularity that they are applied to biological data; agree on a set of minimal conditions that any biodiversity index must fulfill; integrate a large panel of diversity indices in software packages to enable ecologists to select and apply the most relevant index for their study. I propose a set of minimal conditions as a first step in this direction.

ecology↗

bioRxiv2024

A new look at functional beta diversity

O_LIThe 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. C_LIO_LIIn this paper, we propose to decompose this variability into three additive components: i) the standard compositional similarity between individuals of the same 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. These three components can be used to portray the functional resemblance among sites on a ternary diagram. C_LIO_LIThe 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. C_LIO_LISynthesis. 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. C_LI

ecology↗

bioRxiv2023

Functional and phylogenetic β diversities and their link with clustering/overdispersion and uniqueness/redundancy

In the recent decades, research on biodiversity in community ecology has been marked by the consideration of species evolutionary histories and biological traits, including those said functional as they relate to the functions a species has in ecosystems. Among the different spatial levels at which FP diversity can be quantified, less attention has been given to the definition of the general concept of between-communities ({beta}) FP diversity than to those of local, within-communities () and regional, merged-communities ({gamma}) FP diversities. Here we develop a new way for partitioning FP {beta} diversity into elementary components to underline how and why FP {beta} diversity differs from species {beta} diversity, the latter reflecting only differences in species abundances between communities. As a reference example, we consider two distinct measures of FP {beta} diversity: Raos dissimilarity coefficient (Q{beta}) that expresses an average dissimilarity between communities, and its transformation into an equivalent number of communities (D{beta}). Thanks to analytical partitioning and simulations, we show that Q{beta} and D{beta} are connected differently with typical patterns of community structure. The search for the ecological and evolutionary processes that drive community assembly and the assessment of community resilience and stability have indeed revealed typical community structures: the local clustering of species with similar traits or shared evolutionary histories; and the local () or regional ({gamma}) presence of functionally or phylogenetically redundant versus unique species. While Q{beta} and D{beta} are both increasing functions of species {beta} diversity and {gamma} FP uniqueness, Q{beta} increases with FP clustering while D{beta} increases with FP redundancy. The selection of an index of {beta} diversity for a given study depends on its objective, such as communication to conservation policy makers or theoretical study of the ecological and evolutionary processes of community assembly. To facilitate and secure this selection, we call, through our study, for the development of formal and precise definition(s) for FP {beta} diversity in light of the concepts of clustering versus overdispersion, and redundancy versus uniqueness. In particular, we call for further research on when and why FP {beta} diversity should increase with FP clustering.

ecology↗

bioRxiv2022

Identifying functionally distinctive and threatened species

Functional 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 the degree of distinctiveness and threat a species exhibits. Starting with previous quantification attempts, we develop a framework that links different viewpoints on 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. We notably highlight that although some of the functionally distinctive and threatened species we identified, such as the tiger, are charismatic and considered by conservation actions, others are not. This is the case for some rat species and pangolins, whose negative image in the media during the COVID-19 pandemic could be detrimental to attracting public interest in their preservation. From this case study, we note that noncharismatic, less known species that may be key for ecosystems could be revealed by applying our framework to a range of ecosystems and taxa.

ecology↗

bioRxiv2021

On the relationships between rarity, uniqueness, distinctiveness, originality and functional/phylogenetic diversity

Rarity reflects the low abundance of a species while distinctiveness reflects its quality of being easy to recognize because it has unique functional characteristics and/or an isolated phylogenetic position. As such, the assemblage-level rarity of a species functional and phylogenetic characteristics (that we name effective originality) results from both the rarity and the distinctiveness of this species. The functional and phylogenetic diversity of an assemblage then results from a compromise between the abundances and the effective originalities of the species it contains. Although the distinctiveness of a species itself depends on the abundance of the other species in the assemblage, distinctiveness indices that are available in the ecological literature scarcely consider abundance data. We develop a unifying framework that demonstrates the direct connections between measures of diversity, rarity, distinctiveness and effective originality. While developing our framework, we discovered a family of distinctiveness indices that permit a full control of the influence one wants to give to the strict uniqueness of a species (=its smallest functional or phylogenetic distance to another species in the assemblage). Illustrating our framework with bat phylogenetic diversity along a disturbance gradient in Mexico, we show how each component of rarity, distinctiveness and originality can be controlled to obtain efficient indicators for conservation. Overall our framework is aimed to improve conservation actions directed towards highly diverse areas and/or towards species whose loss would considerably decrease biodiversity by offering flexible quantitative tools where the influence of abundant versus rare, and ordinary versus original, species is understood and controlled.

ecology↗

bioRxiv2021

Towards a unifying framework for diversity and dissimilarity coefficients

Diversity and dissimilarity within and between species assemblages have now been studied for more than half a century by community ecologists in relation to their connections with ecosystem functioning. However, a generalized framework that puts diversity and dissimilarity coefficients under the same formal umbrella is still lacking. In this paper, we show that generalized means represent an effective tool to develop a unifying formulation for the construction of a large array of parametric diversity and dissimilarity measures. These measures include some of the classical diversity coefficients, such as the Shannon entropy, the Gini-Simpson index or the parametric diversity of Patil and Taillie, together with a large number of dissimilarity coefficients of the Bray-Curtis family and can be further extended to the measurement of functional and phylogenetic differences within and between plots.

ecology↗

bioRxiv2017

Mammal extinctions and the increasing isolation of humans on the tree of life

A sixth great mass extinction is ongoing due to the direct and indirect effects of human pressures. However, not all lineages are impacted equally. As humans, we frequently believe that we hold a unique place on Earth. Here, we show that our current impacts on the natural world risk to heighten that expectation. Evolutionary proximity to Homo sapiens emerges as a powerful predictor of extinction risk among mammals. Our analysis shows that the species most closely related to H. sapiens are exposed to a large variety of threat types and that they may also have greater intrinsic sensitivity to threats. Pruning back the tree of life around us will lead to our species being among those with the fewest close relatives. We will erase our evolutionary history, forcing its uniqueness. If no action is taken, we will lose crucial biodiversity for the preservation of Earth ecosystems, and a key reference to what makes us human.

ecology↗