Correction: Distance-Based Functional Diversity Measures and Their Decomposition: A Framework Based on Hill Numbers
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PROVIDER: S-EPMC4232602 | biostudies-literature | 2014 Jan
REPOSITORIES: biostudies-literature
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Project description:Hill numbers (or the "effective number of species") are increasingly used to characterize species diversity of an assemblage. This work extends Hill numbers to incorporate species pairwise functional distances calculated from species traits. We derive a parametric class of functional Hill numbers, which quantify "the effective number of equally abundant and (functionally) equally distinct species" in an assemblage. We also propose a class of mean functional diversity (per species), which quantifies the effective sum of functional distances between a fixed species to all other species. The product of the functional Hill number and the mean functional diversity thus quantifies the (total) functional diversity, i.e., the effective total distance between species of the assemblage. The three measures (functional Hill numbers, mean functional diversity and total functional diversity) quantify different aspects of species trait space, and all are based on species abundance and species pairwise functional distances. When all species are equally distinct, our functional Hill numbers reduce to ordinary Hill numbers. When species abundances are not considered or species are equally abundant, our total functional diversity reduces to the sum of all pairwise distances between species of an assemblage. The functional Hill numbers and the mean functional diversity both satisfy a replication principle, implying the total functional diversity satisfies a quadratic replication principle. When there are multiple assemblages defined by the investigator, each of the three measures of the pooled assemblage (gamma) can be multiplicatively decomposed into alpha and beta components, and the two components are independent. The resulting beta component measures pure functional differentiation among assemblages and can be further transformed to obtain several classes of normalized functional similarity (or differentiation) measures, including N-assemblage functional generalizations of the classic Jaccard, Sørensen, Horn and Morisita-Horn similarity indices. The proposed measures are applied to artificial and real data for illustration.
| S-EPMC4085071 | biostudies-literature
Project description:BackgroundDespite the great concern triggered by the environmental crisis worldwide, the loss of temporal key functions and processes involved in biodiversity maintenance has received little attention. Species are restricted in their life cycles by environmental variables because of their physiological and behavioral properties; thus, the timing and duration of species' presence and their activities vary greatly between species within a community. Despite the ecological relevance of such variation, there is currently no measure that summarizes the key temporal aspects of biological diversity and allows comparisons of community phenological patterns. Here, we propose a measure that synthesizes variability of phenological patterns using the Hill numbers-based attribute diversity framework.MethodsWe constructed a new phenological diversity measure based on the aforementioned framework through pairwise overlapping distances, which was supplemented with wavelet analysis. The Hill numbers approach was chosen as an adequate way to define a set of diversity values of different order q, a parameter that determines the sensitivity of the diversity measure to abundance. Wavelet transform analysis was used to model continuous variables from incomplete data sets for different phenophases. The new measure, which we call Phenological Hill numbers (PD), considers the decouplings of phenophases through an overlapping area value between pairs of species within the community. PD was first tested through simulations with varying overlap in phenophase magnitude and intensity and varying number of species, and then by using one real data set.ResultsPD maintains the diversity patterns of order q as in any other diversity measure encompassed by the Hill numbers framework. Minimum PD values in the simulated data sets reflect a lack of differentiation in the phenological curves of the community over time; by contrast, the maximum PD values reflected the most diverse simulations in which phenological curves were equally distributed over time. PD values were consistent with the homogeneous distribution of the intensity and concurrence of phenophases over time, both in the simulated and the real data set.DiscussionPD provides an efficient, readily interpretable and comparable measure that summarizes the variety of phenological patterns observed in ecological communities. PD retains the diversity patterns of order q characteristic of all diversity measures encompassed by the distance-based Hill numbers framework. In addition, wavelet transform analysis proved useful for constructing a continuous phenological curve. This methodological approach to quantify phenological diversity produces simple and intuitive values for the examination of phenological diversity and can be widely applied to any taxon or community's phenological traits.
| S-EPMC9107786 | biostudies-literature
Project description:Bacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (Na), to control the variability associated with rare taxa by differentially weighing them. Here, we investigated Hill number as a framework for microbial diversity measure using a taxa-accmulation curve (TAC) with soil bacterial community data from two distinct studies by 454 pyrosequencing. The reliable biodiversity estimation was obtained when an increase in Hill number arose as the coverage became stable in TACs for a ≥ 1. In silico analysis also indicated that a certain level of sampling depth was desirable for reliable biodiversity estimation. Thus, in order to attain bacterial diversity from second generation sequencing, Hill number can be a good diversity framework with given sequencing depth, that is, until technology is further advanced and able to overcome the under- and random-sampling issues of the current sequencing approaches.
| S-EPMC5128788 | biostudies-literature
Project description:Various methods have been proposed to characterize the functional connectivity between nodes in a network measured with different modalities (electrophysiology, functional magnetic resonance imaging etc.). Since different measures of functional connectivity yield different results for the same dataset, it is important to assess when and how they can be used. In this work, we provide a systematic framework for evaluating the performance of a large range of functional connectivity measures-based upon a comprehensive portfolio of models generating measurable responses. Specifically, we benchmarked 42 methods using 10,000 simulated datasets from 5 different types of generative models with different connectivity structures. Since all functional connectivity methods require the setting of some parameters (window size and number, model order etc.), we first optimized these parameters using performance criteria based upon (threshold free) ROC analysis. We then evaluated the performance of the methods on data simulated with different types of models. Finally, we assessed the performance of the methods against different levels of signal-to-noise ratios and network configurations. A MATLAB toolbox is provided to perform such analyses using other methods and simulated datasets.
| S-EPMC4260483 | biostudies-literature
Project description:MotivationDifferentiating ecosystems poses a complex, high-dimensional problem constrained by capturing relevant variation across species profiles. Researchers use pairwise distances and subsequent dimensionality reduction to highlight variation in a few dimensions. Despite popularity in analysis of ecological data, these low-dimensional visualizations can contain geometric abnormalities such as "arch" and "horseshoe" effects, potentially obscuring the impact of environmental gradients. These abnormalities appear in ordination but are in fact a product of oversaturated large pairwise distances.ResultsWe present Local Manifold distance (LMdist), an unsupervised algorithm which adjusts pairwise beta diversity measures to better represent true ecological distances between samples. Beta diversity measures can have a bounded dynamic range in depicting long environmental gradients with high species turnover. Using a graph structure, LMdist projects pairwise distances onto a manifold and traverses the manifold surface to adjust pairwise distances at the upper end of the beta diversity measure's dynamic range. This allows for values beyond the range of the original measure. Not all datasets will have oversaturated pairwise distances, nor will capture variation that resembles a manifold, so LMdist adjusts only those pairwise values which may be undervalued in the presence of a sampled gradient. The adjusted distances serve as input for ordination and statistical testing. We demonstrate on real and simulated data that LMdist effectively recovers distances along known gradients and along complex manifolds such as the Swiss roll dataset. LMdist enables more powerful statistical tests for gradient effects and reveals variation orthogonal to the gradient.Availability and implementationAvailable on GitHub at https://github.com/knights-lab/LMdist.
| S-EPMC10713119 | biostudies-literature
Project description:The aim of this paper is to develop Cook's distance measures for assessing the influence of both atypical curves and observations under varying coefficient model for functional responses. Our Cook's distance measures include Cook's distances for deleting multiple curves and for deleting multiple grid points, and their scaled Cook's distances. We systematically investigate some theoretical properties of these diagnostic measures. Simulation studies are conducted to evaluate the finite sample properties of these Cook's distances under different scenarios. A real diffusion tensor tract data set is analyzed to illustrate the use of our diagnostic measures.
| S-EPMC4524573 | biostudies-literature
Project description:The essential biological properties of proteins-folding, biochemical activities, and the capacity to adapt-arise from the global pattern of interactions between amino acid residues. The statistical coupling analysis (SCA) is an approach to defining this pattern that involves the study of amino acid coevolution in an ensemble of sequences comprising a protein family. This approach indicates a functional architecture within proteins in which the basic units are coupled networks of amino acids termed sectors. This evolution-based decomposition has potential for new understandings of the structural basis for protein function. To facilitate its usage, we present here the principles and practice of the SCA and introduce new methods for sector analysis in a python-based software package (pySCA). We show that the pattern of amino acid interactions within sectors is linked to the divergence of functional lineages in a multiple sequence alignment-a model for how sector properties might be differentially tuned in members of a protein family. This work provides new tools for studying proteins and for generally testing the concept of sectors as the principal units of function and adaptive variation.
| S-EPMC4890866 | biostudies-literature
Project description:In this paper, we derive interrelations of graph distance measures by means of inequalities. For this investigation we are using graph distance measures based on topological indices that have not been studied in this context. Specifically, we are using the well-known Wiener index, Randić index, eigenvalue-based quantities and graph entropies. In addition to this analysis, we present results from numerical studies exploring various properties of the measures and aspects of their quality. Our results could find application in chemoinformatics and computational biology where the structural investigation of chemical components and gene networks is currently of great interest.
| S-EPMC3997355 | biostudies-literature
Project description:Although microbial participation in litter decomposition is widely known within terrestrial soils, the role and significance of microorganisms during the aerial standing litter phase of decomposition remains poorly investigated. We examined the fungi inhabiting standing leaf litter of Schizachyrium scoparium and Schizachyrium tenerum in a Longleaf Pine savanna ecosystem and estimated their contribution to litter decomposition. We identified fungal phylotypes associated with leaf litter and quantified leaf C mass loss, fungal biomass production, and microbial respiration during decomposition. These data were used to construct budgets estimating C flow into and through fungi. Significant losses in S. scoparium (55%) and S. tenerum (67%) leaf C mass were observed during standing decomposition along with concomitant increases in fungal biomass, which reached a maximum of 36 and 33 mgC/g detrital C, respectively. Cumulative fungal production during decomposition totaled 99 ± 6 mgC/g initial detrital C in S. scoparium and 73 ± 5 mgC/g initial detrital C in S. tenerum, indicating that 18 and 11% of the litter C was converted into fungal biomass, respectively. Corresponding estimates of cumulative fungal respiration totaled 106 ± 7 and 174 ± 11 mgC/g initial detrital C in S. scoparium and S. tenerum, respectively. Next generation sequencing identified several fungal phylotypes, with the majority of sequences belonging to the Ascomycota (Dothideomycetes) and Basidiomycota (Agaricomycetes). Fungal phylotypes were similar between litter species and changed over time, showing a successional pattern. These findings extend our understanding of fungal processes to standing litter in terrestrial ecosystems, and highlight the quantitative importance of fungi in C cycling processes.
| S-EPMC8959008 | biostudies-literature
Project description:ObjectiveThis study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions.MethodsThe experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene.ResultsA total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms.ConclusionThis study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.
| S-EPMC10472150 | biostudies-literature