scholarly journals Variation partitioning in canonical ordination reveals no effect of soil but an effect of co-occurring species on translocation success in Iris atrofusca

2010 ◽  
Vol 48 (1) ◽  
pp. 265-273 ◽  
Author(s):  
Sergei Volis ◽  
Michael Dorman ◽  
Michael Blecher ◽  
Yuval Sapir ◽  
Lev Burdeniy
Keyword(s):  
Variation Partitioning ◽  
Canonical Ordination

scholarly journals Statistical methods for temporal and space–time analysis of community composition data

2014 ◽  
Vol 281 (1778) ◽  
pp. 20132728 ◽  
Author(s):  
Pierre Legendre ◽  
Olivier Gauthier
Keyword(s):  
Statistical Methods ◽  
Community Composition ◽  
Beta Diversity ◽  
Variation Partitioning ◽  
Regression Tree ◽  
Space Time ◽  
Time Variability ◽  
Ecological Data ◽  
Canonical Ordination ◽  
Temporal Beta Diversity

This review focuses on the analysis of temporal beta diversity, which is the variation in community composition along time in a study area. Temporal beta diversity is measured by the variance of the multivariate community composition time series and that variance can be partitioned using appropriate statistical methods. Some of these methods are classical, such as simple or canonical ordination, whereas others are recent, including the methods of temporal eigenfunction analysis developed for multiscale exploration (i.e. addressing several scales of variation) of univariate or multivariate response data, reviewed, to our knowledge for the first time in this review. These methods are illustrated with ecological data from 13 years of benthic surveys in Chesapeake Bay, USA. The following methods are applied to the Chesapeake data: distance-based Moran's eigenvector maps, asymmetric eigenvector maps, scalogram, variation partitioning, multivariate correlogram, multivariate regression tree, and two-way MANOVA to study temporal and space–time variability. Local (temporal) contributions to beta diversity (LCBD indices) are computed and analysed graphically and by regression against environmental variables, and the role of species in determining the LCBD values is analysed by correlation analysis. A tutorial detailing the analyses in the R language is provided in an appendix.

scholarly journals Examining residual spatial correlation in variation partitioning of beta diversity in a subtropical forest

2019 ◽  
Vol 12 (4) ◽  
pp. 636-644 ◽  
Author(s):  
Ke Cao ◽  
Xiangcheng Mi ◽  
Liwen Zhang ◽  
Haibao Ren ◽  
Mingjian Yu ◽  
...  
Keyword(s):  
Spatial Correlation ◽  
Beta Diversity ◽  
Variation Partitioning ◽  
Subtropical Forest ◽  
Residual Variance ◽  
Spatial Structures ◽  
Data Set ◽  
Strong Argument ◽  
Canonical Ordination ◽  
Spatial Variables

Abstract Aims The relative roles of ecological processes in structuring beta diversity are usually quantified by variation partitioning of beta diversity with respect to environmental and spatial variables or gamma diversity. However, if important environmental or spatial factors are omitted, or a scale mismatch occurs in the analysis, unaccounted spatial correlation will appear in the residual errors and lead to residual spatial correlation and problematic inferences. Methods Multi-scale ordination (MSO) partitions the canonical ordination results by distance into a set of empirical variograms which characterize the spatial structures of explanatory, conditional and residual variance against distance. Then these variance components can be used to diagnose residual spatial correlation by checking assumptions related to geostatistics or regression analysis. In this paper, we first illustrate the performance of MSO using a simulated data set with known properties, thus making statistical issues explicit. We then test for significant residual spatial correlation in beta diversity analyses of the Gutianshan (GTS) 24-ha subtropical forest plot in eastern China. Important Findings Even though we used up to 24 topographic and edaphic variables mapped at high resolution and spatial variables representing spatial structures at all scales, we still found significant residual spatial correlation at the 10 m × 10 m quadrat scale. This invalidated the analysis and inferences at this scale. We also show that MSO provides a complementary tool to test for significant residual spatial correlation in beta diversity analyses. Our results provided a strong argument supporting the need to test for significant residual spatial correlation before interpreting the results of beta diversity analyses.

scholarly journals Mobile Genetic Elements Drive the Antibiotic Resistome Alteration in Freshwater Shrimp Aquaculture

Water ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1461
Author(s):  
Hao Fang ◽  
Nan Ye ◽  
Kailong Huang ◽  
Junnan Yu ◽  
Shuai Zhang
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Procambarus Clarkii ◽  
Variation Partitioning ◽  
Antibiotic Resistance Genes ◽  
Mobile Genetic Elements ◽  
Shrimp Aquaculture ◽  
Sediment Samples ◽  
Genetic Elements ◽  
Freshwater Aquaculture

Shrimp aquaculture environments are a natural reservoir of multiple antibiotic resistance genes (ARGs) due to the overuse of antibiotics. Nowadays, the prevalence of these kinds of emerging contaminants in shrimp aquaculture environments is still unclear. In this study, high-throughput sequencing techniques were used to analyze the distribution of ARGs and mobile genetic elements (MGEs), bacterial communities, and their correlations in water and sediment samples in two types of typical shrimp (Procambarus clarkii and Macrobrachium rosenbergii) freshwater aquaculture environments. A total of 318 ARG subtypes within 19 ARG types were detected in all the samples. The biodiversity and relative abundance of ARGs in sediment samples showed much higher levels compared to water samples from all ponds in the study area. Bacitracin (17.44–82.82%) and multidrug (8.57–49.70%) were dominant ARG types in P. clarkii ponds, while sulfonamide (26.33–39.59%) and bacitracin (12.75–37.11%) were dominant ARG types in M. rosenbergii ponds. Network analysis underlined the complex co-occurrence patterns between bacterial communities and ARGs. Proteobacteria, Cyanobacteria, and Actinobacteria exhibited a high abundance in all samples, in which C39 (OTU25355) and Hydrogenophaga (OTU162961) played important roles in the dissemination of and variation in ARGs based on their strong connections between ARGs and bacterial communities. Furthermore, pathogens (e.g., Aeromonadaceae (OTU195200) and Microbacteriaceae (OTU16033)), which were potential hosts for various ARGs, may accelerate the propagation of ARGs and be harmful to human health via horizontal gene transfer mediated by MGEs. Variation partitioning analysis further confirmed that MGEs were the most crucial contributor (74.76%) driving the resistome alteration. This study may help us to understand the non-ignorable correlations among ARGs, bacterial diversity, and MGEs in the shrimp freshwater aquaculture environments.

scholarly journals Ecotones and gradient as determinants of herpetofaunal community structure in the primary forest of Mount Kupe, Cameroon

2000 ◽  
Vol 16 (4) ◽  
pp. 517-533 ◽  
Author(s):  
Ulrich Hofer ◽  
Louis-Félix Bersier ◽  
Daniel Borcard
Keyword(s):  
Forest Type ◽  
Variation Partitioning ◽  
Null Model ◽  
Elevational Gradient ◽  
Community Response ◽  
Primary Forest ◽  
Minor Importance ◽  
Breeding Sites ◽  
Physiological Tolerance ◽  
The Individual

The relative effects of the elevational gradient and of environmental discontinuities (ecotones) on the structure of a herpetofaunal assemblage in a tropical upland forest were contrasted by means of canonical correspondence analysis. Qualitative descriptors were used to define the elevational positions of the ecotones of interest, namely transitions in forest type and presence/absence of water bodies. The elevational gradient was coded in a form that accommodated different types of community response. Analyses were run for four subsets of the entire assemblage: (1) reptiles, (2) amphibians, (3) amphibians dependent on streams for reproduction, and (4) amphibians that do not use streams for reproduction. All subsets showed a significant relationship with the gradient, which suggested that most species respond to the physical continuum associated with the change in elevation. A response to ecotones was revealed for the amphibian subset only and associated with the presence or absence of watercourses. However, this response disappeared within subsets 3 and 4. A variation partitioning analysis was used to assess the individual and common contributions of gradient and ecotone descriptors to the elevational variation in the structure of subsets 1 and 2. The gradient descriptors explained more variation in the reptile subset than did ecotones, while the reverse was found in the amphibian subset. The dependence of most amphibians on aquatic breeding sites that were not available at all elevations reduced the relative importance of the gradient on the species distributions in subset 2 and accounted for the difference to the reptiles. In all, these findings add to the results of previous null model tests on the same four subsets, where competitive interactions were assigned a minor importance in limiting elevational distributions. The response patterns revealed by the present approach, with ecotones and gradient contrasted in a single analysis, emphasised the role of individual responses to the gradient according to the species' physiological tolerance limits.

scholarly journals Deciphering Main Climate and Edaphic Components Driving Oat Adaptation to Mediterranean Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Francisco J. Canales ◽  
Gracia Montilla-Bascón ◽  
Luis M. Gallego-Sánchez ◽  
Fernando Flores ◽  
Nicolas Rispail ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Agronomic Traits ◽  
Interaction Analysis ◽  
Variation Partitioning ◽  
Environment Interaction ◽  
Edaphic Factors ◽  
Mediterranean Environments ◽  
Wide Range ◽  
Northern Regions ◽  
Edaphic Variables

Oat, Avena sativa, is an important crop traditionally grown in cool-temperate regions. However, its cultivated area in the Mediterranean rim steadily increased during the last 20 years due to its good adaptation to a wide range of soils. Nevertheless, under Mediterranean cultivation conditions, oats have to face high temperatures and drought episodes that reduce its yield as compared with northern regions. Therefore, oat crop needs to be improved for adaptation to Mediterranean environments. In this work, we investigated the influence of climatic and edaphic variables on a collection of 709 Mediterranean landraces and cultivars growing under Mediterranean conditions. We performed genotype–environment interaction analysis using heritability-adjusted genotype plus genotype–environment biplot analyses to determine the best performing accessions. Further, their local adaptation to different environmental variables and the partial contribution of climate and edaphic factors to the different agronomic traits was determined through canonical correspondence, redundancy analysis, and variation partitioning. Here, we show that northern bred elite cultivars were not among the best performing accessions in Mediterranean environments, with several landraces outyielding these. While all the best performing cultivars had early flowering, this was not the case for all the best performing landraces, which showed different patterns of adaption to Mediterranean agroclimatic conditions. Thus, higher yielding landraces showed adaptation to moderate to low levels of rain during pre- and post-flowering periods and moderate to high temperature and radiation during post-flowering period. This analysis also highlights landraces adapted to more extreme environmental conditions. The study allowed the selection of oat genotypes adapted to different climate and edaphic factors, reducing undesired effect of environmental variables on agronomic traits and highlights the usefulness of variation partitioning for selecting genotypes adapted to specific climate and edaphic conditions.

scholarly journals Species Richness of the Family Ericaceae along an Elevational Gradient in Yunnan, China

Forests ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 511 ◽  
Author(s):  
Ji-Hua Wang ◽  
Yan-Fei Cai ◽  
Lu Zhang ◽  
Chuan-Kun Xu ◽  
Shi-Bao Zhang
Keyword(s):  
Species Richness ◽  
Environmental Gradients ◽  
Variation Partitioning ◽  
Elevational Gradient ◽  
Geometric Constraints ◽  
Mean Annual Precipitation ◽  
Mean Annual Temperature ◽  
The Family ◽  
Species Area ◽  
Upper Third

Knowledge about how species richness varies along spatial and environmental gradients is important for the conservation and use of biodiversity. The Ericaceae is a major component of alpine and subalpine vegetation globally. However, little is known about the spatial pattern of species richness and the factors that drive that richness in Ericaceae. We investigated variation in species richness of Ericaceae along an elevational gradient in Yunnan, China, and used a variation partitioning analysis based on redundancy analysis ordination to examine how those changes might be influenced by the mid-domain effect, the species-area relationship, and climatic variables. Species richness varied significantly with elevation, peaking in the upper third of the elevational gradient. Of the factors examined, climate explained a larger proportion of the variance in species richness along the elevational gradient than either land area or geometric constraints. Species richness showed a unimodal relationship with mean annual temperature and mean annual precipitation. The elevational pattern of species richness for Ericaceae was shaped by the combined effects of climate and competition. Our findings contribute to a better understanding of the potential effects of climate change on species richness for Ericaceae.

scholarly journals Geographical Gradients in Argentinean Terrestrial Mammal Species Richness and Their Environmental Correlates

2012 ◽  
Vol 2012 ◽  
pp. 1-13
Author(s):  
Ana L. Márquez ◽  
Raimundo Real ◽  
Marta S. Kin ◽  
José Carlos Guerrero ◽  
Betina Galván ◽  
...  
Keyword(s):  
Species Richness ◽  
Variation Partitioning ◽  
Spatial Form ◽  
Spatial Filters ◽  
Mammal Species ◽  
Terrestrial Mammal ◽  
Explanatory Variables ◽  
Longitudinal Gradients ◽  
Partial Correlations ◽  
Partitioning Procedure

We analysed the main geographical trends of terrestrial mammal species richness (SR) in Argentina, assessing how broad-scale environmental variation (defined by climatic and topographic variables) and the spatial form of the country (defined by spatial filters based on spatial eigenvector mapping (SEVM)) influence the kinds and the numbers of mammal species along these geographical trends. We also evaluated if there are pure geographical trends not accounted for by the environmental or spatial factors. The environmental variables and spatial filters that simultaneously correlated with the geographical variables and SR were considered potential causes of the geographic trends. We performed partial correlations between SR and the geographical variables, maintaining the selected explanatory variables statistically constant, to determine if SR was fully explained by them or if a significant residual geographic pattern remained. All groups and subgroups presented a latitudinal gradient not attributable to the spatial form of the country. Most of these trends were not explained by climate. We used a variation partitioning procedure to quantify the pure geographic trend (PGT) that remained unaccounted for. The PGT was larger for latitudinal than for longitudinal gradients. This suggests that historical or purely geographical causes may also be relevant drivers of these geographical gradients in mammal diversity.

scholarly journals Diversity and Geographic Distribution of Ligninolytic Fungi Associated With Castanopsis sieboldii Leaf Litter in Japan

2020 ◽  
Vol 11 ◽  
Author(s):  
Takashi Osono ◽  
Shunsuke Matsuoka ◽  
Dai Hirose
Keyword(s):  
Leaf Litter ◽  
Variation Partitioning ◽  
Climatic Conditions ◽  
Mean Annual Temperature ◽  
Priority Effect ◽  
Internal Transcribed Spacer Region ◽  
Biogeographic Patterns ◽  
Ligninolytic Fungi ◽  
Castanopsis Sieboldii ◽  
Study Sites

The diversity and geographic pattern of ligninolytic fungi were investigated within the distribution range of an evergreen tree, Castanopsis sieboldii (Fagaceae), in Japan. Fungal isolates obtained from 18 sites in subtropical and temperate regions in Japan were classified into 50 operational taxonomic units in Ascomycota and Basidiomycota according to the base sequence of the rDNA internal transcribed spacer region. Ordination by nonmetric multidimensional scaling showed the separation of fungal compositions between the study sites which was significantly related to the latitude, longitude, and mean annual temperature (MAT) of the study sites. We applied variation partitioning to separate the magnitude of the climatic, spatial, and leaf property factors and found the roles of MAT and spatial factors in structuring fungal assemblages, suggesting the importance of both niche processes and such non-niche processes as priority effect and dispersal limitation. The bleached area on leaf litter was greater at sites with higher MAT and precipitation located at lower latitudes and at sites where some major ligninolytic fungi occurred at greater relative frequencies, indicating that not only the climatic conditions but also the biogeographic patterns of distribution of ligninolytic fungi influence the decomposition of lignin in leaf litter.

Stochastic processes dominate marine free-living Vibrio community assembly in a subtropical gulf

2020 ◽  
Vol 96 (11) ◽  
Author(s):  
Nan Li ◽  
Ke Dong ◽  
Gonglingxia Jiang ◽  
Jinli Tang ◽  
Qiangsheng Xu ◽  
...  
Keyword(s):  
Stochastic Processes ◽  
Trophic State ◽  
Heterotrophic Bacteria ◽  
Variation Partitioning ◽  
Geographic Distance ◽  
Alpha Diversity ◽  
Mantel Test ◽  
Beibu Gulf ◽  
Assembly Features ◽  
Marine Environmental

ABSTRACT Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and assembly features of Vibrio, as well as their relationship with the environmental factors in the subtropical Beibu Gulf. We found that the alpha diversity of Vibrio increased in parallel with the trophic state they occupy. A Mantel test indicated that the trophic state was correlated to Vibrio beta diversity and the correlation gradually strengthened at higher trophic states. Variation partitioning analysis suggested that the geographic distance was an important factor impacting the variables of Vibrio communities in all the samples, but nutrients exerted more influence in the more highly eutrophic samples. Our results demonstrated that stochastic processes govern the turnover of marine Vibrio communities in the Beibu Gulf and that ecological drift was the most important process for assembly of the Vibrio communities.

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