scholarly journals A Generalized Framework for Analyzing Taxonomic, Phylogenetic, and Functional Community Structure Based on Presence–Absence Data

Mathematics ◽  
2018 ◽  
Vol 6 (11) ◽  
pp. 250 ◽  
Author(s):  
János Podani ◽  
Sandrine Pavoine ◽  
Carlo Ricotta
Keyword(s):  
Community Structure ◽  
Beta Diversity ◽  
Point Clouds ◽  
The Other ◽  
Equal Weight ◽  
Ecological Communities ◽  
Dissimilarity Index ◽  
Functional Community ◽  
Generalized Framework ◽  
Vegetation Surveys

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.

scholarly journals Partitioning the temporal changes in abundance-based beta diversity into loss and gain components

2021 ◽  
Author(s):  
Shinichi Tatsumi ◽  
Ryosuke Iritani ◽  
Marc W Cadotte
Keyword(s):  
Community Structure ◽  
Species Composition ◽  
Spatial Variation ◽  
Beta Diversity ◽  
Temporal Dynamics ◽  
Species Abundance ◽  
Temporal Changes ◽  
Ecological Communities ◽  
Multiple Site ◽  
Unified Approach

Spatial variation in species composition, or beta diversity, plays a central role in gauging the structure of ecological communities. Here, we develop a new numerical method to partition the impacts of abundance losses and gains on the temporal changes in spatial beta diversity. We show that the temporal changes in pairwise dissimilarity measures (Ruzka and Bray-Curtis indices) and a multiple-site measure (normalized Whittaker's beta) can be partitioned into six terms that reflect the losses and gains in species abundance. Our new method provides a unified approach to disentangle the temporal dynamics of spatial community structure by means of either incidence- or abundance-based data.

scholarly journals THE ANALYSIS OF OIL CONTENT IN SEDIMENT AND COMMUNITY STRUCTURE OF MACROZOOBENTHOS IN BELAWAN WATERS OF MEDAN CITY, NORTH SUMATERA PROVINCE

2020 ◽  
Vol 3 (2) ◽  
pp. 167-178
Author(s):  
Doli Juna Setia Tanjung ◽  
Bintal Amin ◽  
Syafruddin Nasution
Keyword(s):  
Community Structure ◽  
Linear Regression ◽  
Oil Content ◽  
Diversity Index ◽  
The Other ◽  
Regression Analyses ◽  
Simple Linear Regression ◽  
Dominance Index ◽  
Ocypode Quadrata ◽  
Evenness Index

This research was conducted in March 2019 to determine the oil content in sediment, it’s community structure of macrozoobenthos and it’s a relationship in Belawan Waters of Medan City, North Sumatera. Four sampling stations with five replications in each station were surveyed. The results showed that the average oil content in sediments exceeded the threshold had set by the National Academy of Science. Macrozoobenthos found consists of Ocypode quadrata, Scyla serrate, Rotun dicauda, Penaeus sp, Murex tribulus, and Nassarius olivaccus. The highest abundance was in Station 3 and the lowest was in Station 2. The diversity index in each station was generally very low. Dominance Index in Station 4 was medium, whilst the other stations were high. Evenness index showed in Station 3 and 4 were in high population, Station 1 was in medium population and Station 2 was in low population. Simple linear regression analyses between oil content in sediment with community structure of macrozoobenthos indicated negative correlation ( Y = 10,5-0,0001x , R2 = 0,0004 and r = 0,02 ) which indicated that the higher the oil content, the lower the macrozoobenthos abundance in sediment.

scholarly journals Dynamics of taxonomic and functional community structure in macrozoobenthos and the underlying driving factors in Lake Dongting during 1988 and 2016

2021 ◽  
Vol 33 (1) ◽  
pp. 218-231
Author(s):  
Wang Chouming ◽  
◽  
Zhang Yi ◽  
Tian Qi ◽  
Huang Daizhong ◽  
...  
Keyword(s):  
Community Structure ◽  
Driving Factors ◽  
Functional Community

scholarly journals Gut microbiota composition is associated with narcolepsy type 1

2020 ◽  
Vol 7 (6) ◽  
pp. e896
Author(s):  
Alexandre Lecomte ◽  
Lucie Barateau ◽  
Pedro Pereira ◽  
Lars Paulin ◽  
Petri Auvinen ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Bacterial Communities ◽  
Beta Diversity ◽  
Alpha Diversity ◽  
Amplicon Sequencing ◽  
Rrna Gene ◽  
Differential Abundance ◽  
Alpha And Beta Diversity

ObjectiveTo test the hypothesis that narcolepsy type 1 (NT1) is related to the gut microbiota, we compared the microbiota bacterial communities of patients with NT1 and control subjects.MethodsThirty-five patients with NT1 (51.43% women, mean age 38.29 ± 19.98 years) and 41 controls (57.14% women, mean age 36.14 ± 12.68 years) were included. Stool samples were collected, and the fecal microbiota bacterial communities were compared between patients and controls using the well-standardized 16S rRNA gene amplicon sequencing approach. We studied alpha and beta diversity and differential abundance analysis between patients and controls, and between subgroups of patients with NT1.ResultsWe found no between-group differences for alpha diversity, but we discovered in NT1 a link with NT1 disease duration. We highlighted differences in the global bacterial community structure as assessed by beta diversity metrics even after adjustments for potential confounders as body mass index (BMI), often increased in NT1. Our results revealed differential abundance of several operational taxonomic units within Bacteroidetes, Bacteroides, and Flavonifractor between patients and controls, but not after adjusting for BMI.ConclusionWe provide evidence of gut microbial community structure alterations in NT1. However, further larger and longitudinal multiomics studies are required to replicate and elucidate the relationship between the gut microbiota, immunity dysregulation and NT1.

scholarly journals Responses of community structure and diversity to nitrogen deposition and rainfall addition in contrasting steppes are ecosystem-dependent and dwarfed by year-to-year community dynamics

2019 ◽  
Vol 124 (3) ◽  
pp. 461-469 ◽  
Author(s):  
Xuejun Yang ◽  
Zhenying Huang ◽  
Ming Dong ◽  
Xuehua Ye ◽  
Guofang Liu ◽  
...  
Keyword(s):  
Species Richness ◽  
Community Structure ◽  
Global Change ◽  
Nitrogen Deposition ◽  
Community Composition ◽  
Community Dynamics ◽  
Environmental Variability ◽  
The Other ◽  
Desert Steppe ◽  
Typical Steppe

Abstract Background and Aims Long-term studies to disentangle the multiple, simultaneous effects of global change on community dynamics are a high research priority to forecast future distribution of diversity. Seldom are such multiple effects of global change studied across different ecosystems. Methods Here we manipulated nitrogen deposition and rainfall at levels realistic for future environmental scenarios in three contrasting steppe types in Mongolia and followed community dynamics for 7 years. Key Results Redundancy analyses showed that community composition varied significantly among years. Rainfall and nitrogen manipulations did have some significant effects, but these effects were dependent on the type of response and varied between ecosystems. Community compositions of desert and meadow steppes, but not that of typical steppe, responded significantly to rainfall addition. Only community composition of meadow steppe responded significantly to nitrogen deposition. Species richness in desert steppe responded significantly to rainfall addition, but the other two steppes did not. Typical steppe showed significant negative response of species richness to nitrogen deposition, but the other two steppes did not. There were significant interactions between year and nitrogen deposition in desert steppe and between year and rainfall addition in typical steppe, suggesting that the effect of the treatments depends on the particular year considered. Conclusions Our multi-year experiment thus suggests that responses of community structure and diversity to global change drivers are ecosystem-dependent and that their responses to experimental treatments are dwarfed by the year-to-year community dynamics. Therefore, our results point to the importance of taking annual environmental variability into account for understanding and predicting the specific responses of different ecosystems to multiple global change drivers.

Feeding ecology of Haloniscus earlei chilton, and Oniscoid Isopod living in Athalassic Saline Waters

1989 ◽  
Vol 40 (3) ◽  
pp. 295 ◽  
Author(s):  
DW Blinn ◽  
SL Blinn ◽  
IAE Bayly
Keyword(s):  
Community Structure ◽  
Feeding Ecology ◽  
The Other ◽  
Diatom Community ◽  
Saline Waters ◽  
Consumption Index ◽  
Periphyton Biomass ◽  
Athalassic Saline Waters

Densities of the oniscoid isopod, Haloniscus searlei Chilton, were orders of magnitude higher on solid substrata than on sediment in the athalassic saline waters of Lake Keilambete and Lake Corangamite, Victoria, Australia. The feeding ecology of H. searlei was examined in the laboratory. Three different grazing densities were employed; one was similar to the estimated density of Haloniscus in the field (c. 212 individuals per m² siderite substratum), and the other two were 3 and 5.5 times higher than field densities, respectively. It was concluded that H. searlei was a very effective grazer. After 2 weeks, treatments with the highest grazing density had 2.5 times less periphyton biomass than treatments at the lowest grazing density and over 3-fold less periphyton than ungrazed controls. Estimated consumption-index values for periphyton were 0.206, 0.124, and 0.096 for treatments ranging from low to high grazing densities. Diatom community structure remained the same in all grazing treatments after 2 weeks. The ability of Haloniscus to use Tanytarsus larvae for food was examined. Cannibalism was also noted.

scholarly journals Iterative K-Closest Point Algorithms for Colored Point Cloud Registration

Sensors ◽  
2020 ◽  
Vol 20 (18) ◽  
pp. 5331
Author(s):  
Ouk Choi ◽  
Min-Gyu Park ◽  
Youngbae Hwang
Keyword(s):  
Real World ◽  
Point Cloud ◽  
Point Clouds ◽  
The Other ◽  
Iterative Closest Point ◽  
Depth Images ◽  
The Cost ◽  
Soft Matching ◽  
Colored Point ◽  
Refinement Algorithm

We present two algorithms for aligning two colored point clouds. The two algorithms are designed to minimize a probabilistic cost based on the color-supported soft matching of points in a point cloud to their K-closest points in the other point cloud. The first algorithm, like prior iterative closest point algorithms, refines the pose parameters to minimize the cost. Assuming that the point clouds are obtained from RGB-depth images, our second algorithm regards the measured depth values as variables and minimizes the cost to obtain refined depth values. Experiments with our synthetic dataset show that our pose refinement algorithm gives better results compared to the existing algorithms. Our depth refinement algorithm is shown to achieve more accurate alignments from the outputs of the pose refinement step. Our algorithms are applied to a real-world dataset, providing accurate and visually improved results.

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