A generalized framework for analyzing taxonomic, phylogenetic, and functional community structure based on presence-absence data

Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the lack of common conceptual basis behind index definitions. A new framework is needed which allows such comparisons, thus facilitating evaluation of the importance of the three sources of extra information in relation to conventional species-based representations. We define taxonomic, phylogenetic and functional beta diversity of species assemblages based on the generalized Jaccard dissimilarity index. This coefficient does not give equal weight to species, because traditional site dissimilarities are lowered by taking into account the taxonomic, phylogenetic or functional similarity of differential species in one site to the species in the other. These, together with the traditional, taxon- (species-) based beta diversity are decomposed into two additive fractions, one due to taxonomic, phylogenetic or functional excess and the other to replacement. In addition to numerical results, taxonomic, phylogenetic and functional community structure is visualized by 2D simplex or ternary plots. Redundancy with respect to taxon-based structure is expressed in terms of centroid distances between point clouds in these diagrams. The approach is illustrated by examples coming from vegetation surveys representing different ecological conditions. We found that beta diversity decreases in the following order: taxon-based, taxonomic (Linnaean), phylogenetic and functional. Therefore, we put forward the beta-redundancy hypothesis suggesting that this ordering may be most often the case in ecological communities, and discuss potential reasons and possible exceptions to this supposed rule. Whereas the pattern of change in diversity may be indicative of fundamental features of the particular community being studied, the effect of the choice of functional traits—a more or less subjective element of the framework—remains to be investigated

Of beta diversity, variance, evenness, and dissimilarity

The amount of variation in species composition among sampling units or beta diversity has become a primary tool for connecting the spatial structure of species assemblages to ecological processes. Many different measures of beta diversity have been developed. Among them, the total variance in the community composition matrix has been proposed as a single-number estimate of beta diversity. In this study, I first show that this measure summarizes the compositional variation among sampling units after nonlinear transformation of species abundances. Therefore, it is not always adequate for estimating beta diversity. Next, I propose an alternative approach for calculating beta diversity in which variance is substituted by a weighted measure of concentration (i.e., an inverse measure of evenness). The relationship between this new measure of beta diversity and so-called multiple-site dissimilarity measures is also discussed

Seasonal changes in avian communities living in an extensively used farmland of Western Poland

To study the seasonal changes in avian communities, we collected data in an extensively used farmland in Western Poland during 2006-2013. Generalized additive mixed models were used in order to study the effects of seasonality and protected areas on the overall bird species richness. A similarity percentage analysis was also conducted in order to identify the species that contribute most strongly to dissimilarity among each bird according to the phenological season. Furthermore, the differences in bird communities were investigated applying the decomposition of the species richness in season, trend, and remainder components. Each season showed significant differences in bird species richness (seasonality effect). The effect of the protected areas was slightly positive on the overall species richness for all seasons. However, an overall negative trend was detected for the entire period of eight years. The bird community composition was different among seasons, showing differences in terms of dominant species. Greater differences were found between breeding and wintering seasons, in particular, the spatial pattern of sites with higher bird richness (hotspots) were different between breeding and wintering seasons. Our findings showed a negative trend in bird species richness verified in the Polish farmlands from 2006. This result mirrors the same negative trend already highlighted for Western Europe. The role of protected areas, even if slightly positive, was not enough to mitigate this decline process. Therefore, to effectively protect farmland birds, it is necessary to also consider inter-seasons variation, and for this, we suggest the use of medium-term temporal studies on bird communities’ trends

A statistical reduced-reference method for color image quality assessment

Although color is a fundamental feature of human visual perception, it has been largely unexplored in the reduced-reference (RR) image quality assessment (IQA) schemes. In this paper, we propose a natural scene statistic (NSS) method, which efficiently uses this information. It is based on the statistical deviation between the steerable pyramid coefficients of the reference color image and the degraded one. We propose and analyze the multivariate generalized Gaussian distribution (MGGD) to model the underlying statistics. In order to quantify the degradation, we develop and evaluate two measures based respectively on the Geodesic distance between two MGGDs and on the closed-form of the Kullback Leibler divergence. We performed an extensive evaluation of both metrics in various color spaces (RGB, HSV, CIELAB and YCrCb) using the TID 2008 benchmark and the FRTV Phase I validation process. Experimental results demonstrate the effectiveness of the proposed framework to achieve a good consistency with human visual perception. Furthermore, the best configuration is obtained with CIELAB color space associated to KLD deviation measure

DISTANCE: a framework for software measure construction.

In this paper we present a framework for software measurement that is specifically suited to satisfy the measurement needs of empirical software engineering research. The framework offers an approach to measurement that builds upon the easily imagined, detected and visualised concepts of similarity and dissimilarity between software entities. These concepts are used both to model the software attributes of interest and to define the corresponding software measures. Central to the framework is a process model that embeds constructive procedures for attribute modelling and measure construction into a goal-oriented approach to empirical software engineering studies. The underlying measurement theoretic principles of our approach ensure the construct validity of the resulting measures. The approach was tested on a popular suite of object-oriented design measures. We further show that our measure construction method compares favourably to related work.Software;

Quartet consistency count method for reconstructing phylogenetic trees

Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry picking with tie breaking. We show that the success rate of the new algorithm is almost equal to that of neighbor-joining. This gives an explanation of the qualitative nature of neighbor-joining and that of dissimilarity maps from DNA sequence data. Moreover, the new algorithm always reconstructs correct trees from quartet consistent dissimilarity maps.Comment: 11 pages, 5 figure

Semiparametric estimation of (constrained) ultrametric trees

This paper introduces a general, formal treatment of dynamic constraints, i.e., constraints on the state changes that are allowed in a given state space. Such dynamic constraints can be seen as representations of "real world" constraints in a managerial context. The notions of transition, reversible and irreversible transition, and transition relation will be introduced. The link with Kripke models (for modal logics) is also made explicit. Several (subtle) examples of dynamic constraints will be given. Some important classes of dynamic constraints in a database context will be identified, e.g. various forms of cumulativity, non-decreasing values, constraints on initial and final values, life cycles, changing life cycles, and transition and constant dependencies. Several properties of these dependencies will be treated. For instance, it turns out that functional dependencies can be considered as "degenerated" transition dependencies. Also, the distinction between primary keys and alternate keys is reexamined, from a dynamic point of view.

Comparison and contrast in perceptual categorization

People categorized pairs of perceptual stimuli that varied in both category membership and pairwise similarity. Experiments 1 and 2 showed categorization of 1 color of a pair to be reliably contrasted from that of the other. This similarity-based contrast effect occurred only when the context stimulus was relevant for the categorization of the target (Experiment 3). The effect was not simply owing to perceptual color contrast (Experiment 4), and it extended to pictures from common semantic categories (Experiment 5). Results were consistent with a sign-and-magnitude version of N. Stewart and G. D. A. Brown's (2005) similarity-dissimilarity generalized context model, in which categorization is affected by both similarity to and difference from target categories. The data are also modeled with criterion setting theory (M. Treisman & T. C. Williams, 1984), in which the decision criterion is systematically shifted toward the mean of the current stimuli