Measuring beta‐diversity from taxonomic similarity

Question: The utility of beta (β‐) diversity measures that incorporate information about the degree of taxonomic (dis)similarity between species plots is becoming increasingly recognized. In this framework, the question for this study is: can we define an ecologically meaningful index of β‐diversity that, besides indicating simple species turnover, is able to account for taxonomic similarity amongst species in plots? Methods: First, the properties of existing measures of taxonomic similarity measures are briefly reviewed. Next, a new measure of plot‐to‐plot taxonomic similarity is presented that is based on the maximal common subgraph of two taxonomic trees. The proposed measure is computed from species presences and absences and include information about the degree of higher‐level taxonomic similarity between species plots. The performance of the proposed measure with respect to existing coefficients of taxonomic similarity and the coefficient of Jaccard is discussed using a small data set of heath plant communities. Finally, a method to quantify β‐diversity from taxonomic dissimilarities is discussed. Results: The proposed measure of taxonomic β‐diversity incorporates not only species richness, but also information about the degree of higher‐order taxonomic structure between species plots. In this view, it comes closer to a modern notion of biological diversity than more traditional measures of β‐di‐versity. From regression analysis between the new coefficient and existing measures of taxonomic similarity it is shown that there is an evident nonlinearity between the coefficients. This nonlinearity demonstrates that the new coefficient measures similarity in a conceptually different way from previous indices. Also, in good agreement with the findings of previous authors, the regression between the new index and the Jaccard coefficient of similarity shows that more than 80% of the variance of the former is explained by the community structure at the species level, while only the residual variance is explained by differences in the higher‐order taxonomic structure of the species plots. This means that a genuine taxonomic approach to the quantification of plot‐to‐plot similarity is only needed if we are interested in the residual system's variation that is related to the higher‐order taxonomic structure of a pair of species plots.     

Old and new challenges in using species diversity for assessing biodiversity

Although the maintenance of diversity of living systems is critical for ecosystem functioning, the accelerating pace of global change is threatening its preservation. Standardized methods for biodiversity assessment and monitoring are needed. Species diversity is one of the most widely adopted metrics for assessing patterns and processes of biodiversity, at both ecological and biogeographic scales. However, those perspectives differ because of the types of data that can be feasibly collected, resulting in differences in the questions that can be addressed. Despite a theoretical consensus on diversity metrics, standardized methods for its measurement are lacking, especially at the scales needed to monitor biodiversity for conservation and management purposes. We review the conceptual framework for species diversity, examine common metrics, and explore their use for biodiversity conservation and management. Key differences in diversity measures at ecological and biogeographic scales are the completeness of species lists and the ability to include information on species abundances. We analyse the major pitfalls and problems with quantitative measurement of species diversity, look at the use of weighting measures by phylogenetic distance, discuss potential solutions and propose a research agenda to solve the major existing problems.     

Testing for differences in beta diversity from plot-to-plot dissimilarities

The central role of beta diversity in describing biodiversity patterns has been investigated in many fields of ecology and biogeography. While a variety of measures of beta diversity have been proposed over the past five decades, the question of how to test for differences in beta diversity among different sets of sampling plots has been addressed only rarely. Here, we describe a simple analytical procedure to test for differences in beta diversity among distinct sets of plots. The advantage of this approach compared to methods that have been previously proposed lies in its randomization procedure. Such a procedure creates a distribution of null values of the test statistic that is compatible with the null hypothesis of no significant difference in multivariate dispersion between the groups. The proposed test was illustrated using a large dataset of plant and water beetle (Coleoptera) assemblages collected from 45 farmland ponds in Ireland.     

Scale dependence of plant species richness in a network of protected areas

Despite the widely recognised importance of reserve networks, their effectiveness in encompassing and maintaining biodiversity is still debated. Species diversity is one of the most affordable measures of biodiversity, but it is difficult to survey such data over large scales. This research aimed to perform a sample-based assessment of species richness of groups of plants with different conservation value (alien species, protected species, and all species) within a reserve network, testing the use of partitioning as a tool for assessing diversity at different spatial scales, from the plot to the entire network. Plant diversity patterns differed for the groups of species for most of the investigated spatial scales. Despite these patterns assumed divergent tendencies when different species groups were considered, most of the species richness within the network was given by larger scale β-diversity for both alien and protected species, as well for all species. Diversity partitioning proved an effective tool to quantify the role of spatial scales in structuring the total species richness of the network, and is helpful in planning reserve networks.     

Computing diversity from dated phylogenies and taxonomic hierarchies: does it make a difference to the conclusions?

Recently, dated phylogenies have been increasingly used for ecological studies on community structure and conservation planning. There is, however, a major impediment to a systematic application of phylogenetic methods in ecology: reliable phylogenies with time-calibrated branch lengths are lacking for a large number of taxonomic groups and this condition is likely to continue for a long time. A solution for this problem consists in using undated phylogenies or taxonomic hierarchies as proxies for dated phylogenies. Nonetheless, little is known on the potential loss of information of these approaches compared to studies using dated phylogenies with time-calibrated branch lengths. The aim of this study is to ask how the use of undated phylogenies and taxonomic hierarchies biases a very simple measure of diversity, the mean pairwise phylogenetic distance between community species, compared to the diversity of dated phylogenies derived from the freely available software Phylomatic. This is illustrated with three sets of data on plant species sampled at different scales. Our results show that: (1) surprisingly, the diversity computed from dated phylogenies derived from Phylomatic is more strongly related to the diversity computed from taxonomic hierarchies than to the diversity computed from undated phylogenies, while (2) less surprisingly, the strength of this relationship increases if we consider only angiosperm species.     

Sampling intraspecific variability in leaf functional traits: Practical suggestions to maximize collected information

The choice of the best sampling strategy to capture mean values of functional traits for a species/population, while maintaining information about traits’ variability and minimizing the sampling size and effort, is an open issue in functional trait ecology. Intraspecific variability (ITV) of functional traits strongly influences sampling size and effort. However, while adequate information is available about intraspecific variability between individuals (ITV_BI) and among populations (ITV_POP), relatively few studies have analyzed intraspecific variability within individuals (ITV_WI). Here, we provide an analysis of ITV_WI of two foliar traits, namely specific leaf area (SLA) and osmotic potential (π), in a population of Quercus ilex L. We assessed the baseline ITV_WI level of variation between the two traits and provided the minimum and optimal sampling size in order to take into account ITV_WI, comparing sampling optimization outputs with those previously proposed in the literature. Different factors accounted for different amount of variance of the two traits. SLA variance was mostly spread within individuals (43.4% of the total variance), while π variance was mainly spread between individuals (43.2%). Strategies that did not account for all the canopy strata produced mean values not representative of the sampled population. The minimum size to adequately capture the studied functional traits corresponded to 5 leaves taken randomly from 5 individuals, while the most accurate and feasible sampling size was 4 leaves taken randomly from 10 individuals. We demonstrate that the spatial structure of the canopy could significantly affect traits variability. Moreover, different strategies for different traits could be implemented during sampling surveys. We partially confirm sampling sizes previously proposed in the recent literature and encourage future analysis involving different traits.     

A New Measure of Functional Evenness and Some of Its Properties

Functional evenness is increasingly considered an important facet of functional diversity that sheds light on the complex relationships between community assembly and ecosystem functioning. Nonetheless, in spite of its relevant role for ecosystem functioning, only a few measures of functional evenness have been proposed. In this paper we introduce a new measure of functional evenness that reflects the regularity in the distribution of species abundances, together with the evenness in their pairwise functional dissimilarities. To show how the proposed measure works, we focus on changes in functional evenness calculated from Grime’s classification of plant strategies as competitors (C), stress-tolerators (S) and ruderals (R) along a post-fire successional gradient in temperate chestnut forests of southern Switzerland.     

Beta diversity reconsidered

A simple analytical procedure to test for differences in beta diversity among sets of plots has been recently presented. Here, we describe an improved randomization procedure that replaces the one previously proposed. This procedure consists of shuffling within-group dissimilarities among groups and disregarding between-group dissimilarities. By repeating this operation many times, a distribution of the test statistics under the null hypothesis of no differences in the mean plot-to-plot dissimilarities within groups is obtained. This procedure ensures that the correct null model is selected. To describe this new procedure, we used plant and water beetle (Coleoptera) data collected from 45 permanent ponds. Beta diversity was compared between plant and water beetle (Coleoptera) assemblages.