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Vegan: Community Ecology Package
Abstract
The vegan package provides tools for descriptive community ecology. It has most basic functions of diversity analysis, community ordination and dissimilarity analysis. Most of its multivariate tools can be used for other data types as well.
The functions in the vegan package contain tools for diversity analysis, ordination methods and tools for the analysis of dissimilarities. Together with the labdsv package, the vegan package provides most standard tools of descriptive community analysis. Package ade4 provides an alternative comprehensive package, and several other packages complement vegan and provide tools for deeper analysis in specific fields. Package https://CRAN.R-project.org/package=BiodiversityR provides a Graphical User Interface (GUI) for a large subset of vegan functionality.
The vegan package is developed at GitHub (https://github.com/vegandevs/vegan/). GitHub provides up-to-date information and forums for bug reports. Most important changes in vegan documents can be read with news(package="vegan") and vignettes can be browsed with browseVignettes("vegan"). The vignettes include a vegan FAQ, discussion on design decisions, short introduction to ordination and discussion on diversity methods. A tutorial of the package at http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf provides a more thorough introduction to the package. To see the preferable citation of the package, type citation("vegan").
... To avoid bias caused by different sequencing depth, samples were resampled to the minimum 27 061 sequences per sample, and then 'Hellinger' transformed to calculate fungal alpha diversity indices (species richness, Shannon and InvSimpson). The alpha diversity indices were calculated using the function 'diversity' in R package 'vegan' (Oksanen et al., 2013). To analyze the effects of N and water addition and their interactions on soil properties, fungal abundance and alpha diversity indices, two-way analysis of variance (ANOVA) was performed, followed by Duncan's multiple range test. ...
... The significant difference was accepted at P < 0.05. To assess the impacts of N, water addition and their interactions on fungal community composition, two-way permutational multivariate analysis of variance (PERMA-NOVA) (Anderson, 2010) were performed with the "Bray-Curtis dissimilarity" using the function 'adonis2' in R package 'vegan' (Oksanen et al., 2013) with 9999 permutations. To analyze the relationship between soil parameters (available phosphorus (AP), pH, soil organic matter (SOM), total carbon (TC), total N (TN), soil moisture, NH 4 + -N, NO 3 --N, available N (AN), C/N ratio, N/P ratio) and fungal abundance, alpha diversity indices or the richness of each functional group, we performed Pearson correlation analysis. ...
... Mantel test was conducted to analyze the disparity of soil factors and the dissimilarity of fungal community composition. The disparity of soil factors was evaluated by 'Euclidean distance' and the dissimilarity of fungal community composition was determined by 'Bray-Curtis distance', both were implemented by 'vegdist' function in R package 'vegan' (Oksanen et al., 2013). To identify the contribution of each soil parameters, we conducted variation partition analysis using 'varpart' function in R package 'vegan' (Oksanen et al., 2013). ...
Nitrogen (N) deposition and intensified rainfall can strongly affect soil microbial community, but compared with available studies on bacteria, those on soil fungi are quite limited. Here we carried out a field experiment in a mixed deciduous forest of China to study the influences of increased N deposition and rainfall on soil fungi by using quantitative PCR and high-throughput sequencing method. The results demonstrated that (1) N addition significantly increased fungal abundance and alpha diversity (richness, Shannon index and Invsimpson index), changed fungal community composition at OTU level, and marginally increased the relative abundance of Ascomycota and Zygomycota, while water addition showed no remarkable effects on fungal abundance, biodiversity and community composition. (2) N addition significantly increased the richness of saprotrophic fungi and pathogenic fungi, and the relative abundance of saprotrophic fungi, but water addition only slightly increased the abundance of pathogenic fungi. (3) Fungal composition dissimilarity closely correlated with the disparity of soil parameters as a whole. Soil NH4+-N exhibited strong positive correlation with the richness of pathogenic fungi and mycorrhizal fungi, while both soil moisture and NH4+-N tightly correlated with soil fungal abundance and alpha diversity indices. We concluded that in this N-limited but non-water-limited forest ecosystem, N deposition posed stronger effects on soil fungi than increased rainfall, partially mediated by changes in soil properties.
... The 95% confidence intervals of observed richness were calculated directly in Mothur with 5000 iterations (randomization). Richness, diversity indices and Bray-Curtis dissimilarity matrix were calculated from the rarefied OTU table using the vegan package in R (Oksanen et al., 2011). Richness and diversity indices were compared among sample types using the non-parametric Kruskal-Wallis test followed by a post hoc Dunn's test in R with a correction of p-value using the Holm's method (significance threshold p < 0.05) (Dunn, 1961) to determine which groups were different. ...
... functions, was applied to investigate the contribution of site and sample type contribution in the samples' clustering. These functions are implemented in the vegan and pairwiseAdonis R packages, respectively, Oksanen et al. (2011), Martinez Arbizu (2017. Pairwise comparisons were performed using the R package limma, with moderated t-tests on log-transformed OTU relative abundance and corrected for multiple hypothesis testing (Smyth, 2005;Bulgarelli et al., 2012) to identify the differentially abundant OTUs in each of the three sample types. ...
Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition and putative functional capacity, evaluating its differentiation among the gut content and the gut tissue in comparison with the external sediment. Additionally, we aimed to define a core gut microbiota between A. agassizii populations to identify potential keystone bacterial taxa. Our results show that the diversity and the composition of the microbiota, at both genetic and predicted functional levels, were mostly driven by the sample type, and to a lesser extent by the population location. Specific bacterial taxa, belonging mostly to Planctomycetacia and Spirochaetia, were differently enriched in the gut content and the gut tissue, respectively. Predictive functional profiles revealed higher abundance of specific pathways, as the sulfur cycle in the gut content and the amino acid metabolism, in the gut tissue. Further, the definition of a core microbiota allowed to obtain evidence of specific localization of bacterial taxa and the identification of potential keystone taxa assigned to the Desulfobacula and Spirochaeta genera as potentially host selected. The ecological relevance of these keystone taxa in the host metabolism is discussed.
... Multivariate analyses were performed with the R package 'vegan' (Oksanen et al., 2017) and R Package 'mvabund' . ...
... In order to explore the relationships between different restoration strategies and benthic community structure, we compared the benthic community structure of the restored locations before and after implementation of the revegetation actions (2018 vs. 2019) and the reference ones, using a non-metric multidimensional scaling (nMDS) ordination (Kruskal, 1964). The nMDS was performed with the R package "vegan" (Oksanen et al., 2017) on a Bray-Curtis dissimilarity matrix (Bray and Curtis, 1957) calculated from log transformed data of bare rock, erect algae, and turf algae cover. All statistical analysis and plots were run with the software R 3.3.3 ...
This thesis addressed marine vegetation changes in the shallow rocky shores of the Montgrí Illes Medes and Baix Ter Natural Park integrating the macroalgal and sea urchin dynamics in front of natural and human-related impacts, and the role and effectiveness of Marine Protected Areas and restoration actions as conservation tools at lower trophic levels.
Besides, since most of this thesis is based on long-term monitoring data, a valuable baseline of the algal community’s structure and functioning was provided here which could be vital to predict and detect ecological changes that could jeopardize the preservation of marine forests.
... Alpha and beta diversity were visualized with the phyloseq package (McMurdie and Holmes, 2013). To quantify the contribution of spatial distance, soil properties, and floristic composition on the total variation of the AMF OTU abundances, variation partitioning (Borcard et al., 1992) was performed using the vegan R package (Oksanen et al., 2012). Regarding the spatial matrix, a set of spatial predictors from the geographical coordinates was computed by principal coordinates of neighbour matrices (PCNM). ...
Arbuscular mycorrhizal fungi (AMF) play central roles in terrestrial ecosystems by interacting with both above and belowground communities as well as by influencing edaphic properties. The AMF communities associated with the roots of the fern Botrychium lunaria (Ophioglossaceae) were sampled in four transects at 2400 m a.s.l. in the Swiss Alps and analyzed using metabarcoding. Members of five Glomeromycota genera were identified across the 71 samples. Our analyses revealed the existence of a core microbiome composed of four abundant Glomus operational taxonomic units (OTUs), as well as a low OTU turnover between samples. The AMF communities were not spatially structured, which contrasts with most studies on AMF associated with angiosperms. pH, microbial connectivity and humus cover significantly shaped AMF beta diversity but only explained a minor fraction of variation in beta diversity. AMF OTUs associations were found to be significant by both cohesion and co‐occurrence analyses, suggesting a role for fungus–fungus interactions in AMF community assembly. In particular, OTU co‐occurrences were more frequent between different genera than among the same genus, rising the hypothesis of functional complementarity among the AMF associated to B. lunaria. Altogether, our results provide new insights into the ecology of fern symbionts in alpine grasslands.
... (R Development Core Team, 2014), on the OTU abundance/sites table (Table S1), and the environmental parameters (Table S3 & Table S4), the latter normalized by the K-nearest neighbours. Unless otherwise specified, community analyses were performed with the package vegan (Oksanen et al., 2013). Alpha diversity: To evaluate if more sampling and sequencing effort would have revealed more OTU richness, we carried out an analysis based on OTUs accumulation curves, function specaccum, method rarefaction and 1,000 random permutations; species richness was extrapolated using the function specpool. ...
Functional traits are increasingly used in ecology to link the structure of microbial communities to ecosystem processes. We investigated two important protistan lineages, Cercozoa and Endomyxa (Rhizaria) in soil using Illumina sequencing and analysed their diversity and functional traits along with their responses to environmental factors in grassland and forest across Germany. From 600 soil samples, we obtained 2,101 Operational Taxonomy Units representing ~18 million Illumina reads (region V4, 18S rRNA gene). All major taxonomic and functional groups were present, dominated by small bacterivorous flagellates (Glissomonadida). Endomyxan plant parasites were absent from forest. In grassland, they were promoted by more intensive land use management. Grassland and forest strikingly differed in community composition. Relative abundances of bacterivores and eukaryvores were contrastingly influenced by environmental factors, indicating bottom-up regulation by food resources. These patterns provide new insights into the functional organization of soil biota and indications for a more sustainable land-use management.
Highlights
Protistan plant parasites of worldwide importance (Phytomyxea) are absent from forest
Protistan plant parasites are enhanced by land use intensification in grassland
Opposite responses of protistan trophic guilds to environmental conditions in forest
Drastic differences in protistan community composition between grassland and forest
... The use of several simulated larger data matrixes as a central element of the procedure will assure a better appreciation of the MultSE -n relationship over a wider range of sample sizes. package (Oksanen et al. 2015). The probability of occurrence of each species is calculated between and within sites. ...
SSP (simulation based sampling protocol) is an R package that uses simulation of ecological data and dissimilarity based multivariate standard error (MultSE) as an estimator of precision to evaluate the adequacy of different sampling efforts for studies that will test hypothesis using permutational multivariate analysis of variance. The procedure consists in simulating several extensive data matrixes that mimic some of the relevant ecological features of the community of interest using a pilot data set. For each simulated data, several sampling efforts are repeatedly executed and MultSE calculated. The mean value, 0.025 and 0.975 quantiles of MultSE for each sampling effort across all simulated data are then estimated and standardized regarding the lowest sampling effort. The optimal sampling effort is identified as that in which the increase in sampling effort do not improve the precision beyond a threshold value (e.g. 2.5 %). The performance of SSP was validated using real data, and in all examples the simulated data mimicked well the real data, allowing to evaluate the relationship MultSE and n beyond the sampling size of the pilot studies. SSP can be used to estimate sample size in a wide range of situations, ranging from simple (e.g. single site) to more complex (e.g. several sites for different habitats) experimental designs. The latter constitutes an important advantage, since it offers new possibilities for complex sampling designs, as it has been advised for multi-scale studies in ecology.
... To determine our sample effectiveness of the bee community, we combined all bee captures across sites and explored regional species richness by fitting an accumulation curve and estimating asymptotic species richness. Using the vegan package (Oksanen et al. 2018) for (R Core Team 2020) we generated a species accumulation curve using the random method with 100 permutations to estimate the total number of unseen species in the study area. Total expected species richness was assessed using the Chao estimator because bee abundance data contains many singletons and it is a relatively unbiased estimator for species-rich assemblages (Fortel et al. 2014;Walther and Morand 1998). ...
Over a third of the world’s crops require insect pollination, and reliance on pollination services for food continues to rise as human populations increase. Furthermore, as interest in urban agriculture has grown, so has a need for studies of urban pollinator ecology and pollination. Analyzing pollinator assemblages along a rural-urban gradient provides powerful mechanistic insight into how urbanization impacts pollinators. Yet, studies examining pollinators along urban-rural gradients are limited and results vary. Since pollinators vary tremendously in life history characteristics and respond to urbanization differently, studies from different regions would improve our understanding of pollinator response to urbanization. This study documents different bee assemblages along a high-plains semi-arid urban-rural gradient in Denver, Colorado, USA. Percent impervious surface was used to define the extent of urbanization at 12 sites and local and landscape characteristics were estimated using field assessments and geospatial analysis. Wild bees were collected and the relationships between urbanization and bee communities were explored using linear modeling. Overall, bee abundance and diversity decreased with increasing urbanization, suggesting that urban areas negatively impact bee communities. However, all bee guilds responded positively to local floral richness and negatively to the degree of landscape urbanization, suggesting that different types of bees responded similarly to urbanization. These findings suggest that providing a greater diversity of floral resources is key to mitigating the negative impacts of urbanization on pollinator communities.
... Rarefaction curves (Fig. S1) were generated to estimate the degree of "coverage" of the bacterial community (Sanders 1968). The R packages vegan (Oksanen et al. 2016) and phyloseq (McMurdie and Holmes 2013) were used for bacterial community analysis. ...
Strategies to enhance process performance of anaerobic digestion remain of key importance to promote wider usage of this technology for integrated resource recovery from organic waste streams. Continuous inoculation of the microbial community in the digester via the feedstock could be such a cost-effective strategy. Here, anaerobic digestion of fresh waste activated sludge (WAS) was compared with sterilized WAS in response to two common process disturbances, i.e. organic overloading and increasing levels of salts, to determine the importance of feedstock inoculation. A pulse in the organic loading rate severely impacted process stability of the digesters fed sterile WAS, with a 92 ± 45% decrease in methane production, compared to a 42 ± 31% increase in the digesters fed fresh WAS, relative to methane production before the pulse. Increasing salt pulses did not show a clear difference in process stability between the digesters fed fresh and sterile WAS, and process recovery was obtained even at the highest salt pulse of 25 g Na+ L−1. Feedstock sterilization through thermal pretreatment strongly impacted the microbial community in the digesters. In conclusion, feedstock thermal pretreatment strongly impacted anaerobic digestion process stability, due to feedstock inoculation and compositional modification.
Discussion of the vertical stratification of organisms in tropical forests has traditionally focused on species distribution. Most studies have shown that, due to differences in abiotic conditions and resource distribution, species can be distributed along the vertical gradient according to their ecophysiological needs. However, the network structure between distinct vertical strata remains little‐explored. To fill this gap in knowledge, we used baits to sample ants in the canopy and understorey trees of a Mexican tropical rain forest to record the ant–tree co‐occurrences. We examined the ant–tree co‐occurrences in the canopy and understorey using complementary network metrics (i.e., specialization, interaction diversity, modularity, and nestedness). In addition, we evaluated co‐occurrence patterns between ant species on trees, using C‐score analysis. In general, we found no differences in the network structure, although the interaction diversity was greater in the understorey than in the canopy networks. We also observed that co‐occurrence networks of each vertical stratum featured four ant species in the central core of highly co‐occurring species, with three species unique to each stratum. Moreover, we found a similar trend toward ant species segregation in the both strata. These findings reveal a similar pattern of ant–ant co‐occurrences in both vertical strata, probably due to the presence of arboreal‐nesting ants in the understorey. Overall, we showed that despite the marked differences in species composition and environmental conditions between understorey and canopy strata, ant–tree co‐occurrences in these habitats could be governed by similar mechanisms, related to dominance and resource monopolization by ants.
Abstract in Spanish is available with online material.
We used fishery-independent gillnet and longline surveys to document the elasmobranch and large teleost assemblages in the Florida Big Bend seagrass system and examine how ichthyofaunal assemblages were related to environmental factors across the region. A total of 159 paired gillnet sets were conducted in June through August from 2009 to 2012. The Big Bend, an expansive system nearly 300 km in length with seagrass from nearshore up to 20 km offshore, is inhabited by at least 13 species of elasmobranch and 56 species of larger teleost fishes during the summer. Five species dominate, including three species of sharks, two carcharhinids (Atlantic sharpnose sharks, Rhizoprionodon terraenovae Richardson, and blacktip sharks, Carcharhinus limbatus Müeller and Henle) and one sphyrnid (bonnethead sharks, Sphyrna tiburo Linnaeus), and two species of ariid catfishes (hardhead catfish, Ariopsis felis Linnaeus, and gafftopsail catfish, Bagre marinus Mitchill). We used a tiered community analysis approach which included hierarchical cluster analysis, indicator species analysis, and non-metric multidimensional scaling with environmental fitting using a Bray-Curtis dissimilarity matrix. Abiotic variables correlated with community structure included salinity, water clarity, and depth. Summer ichthyofaunal assemblages were spatially variable with a distinct southern zone where salinity and water clarity are consistently high relative to the rest of the system, and we hypothesize the observed patterns in community structure are related to a gradient of river influence in the Big Bend.
The robustness of quantitative measures of compositional dissimilarity between sites was evaluated using extensive computer simulations of species’ abundance patterns over one and two dimensional configurations of sample sites in ecological space. Robustness was equated with the strength, over a range of models, of the linear and monotonic (rank-order) relationship between the compositional dissimilarities and the corresponding Euclidean distances between sites measured in the ecological space. The range of models reflected different assumptions about species’ response curve shape, sampling pattern of sites, noise level of the data, species’ interactions, trends in total site abundance, and beta diversity of gradients.
The Kulczynski, Bray-Curtis and Relativized Manhattan measures were found to have not only a robust monotonic relationship with ecological distance, but also a robust linear (proportional) relationship until ecological distances became large. Less robust measures included Chord distance, Kendall’s coefficient, Chisquared distance, Manhattan distance, and Euclidean distance.
A new ordination method, hybrid multidimensional scaling (HMDS), is introduced that combines metric and nonmetric criteria, and so takes advantage of the particular properties of robust dissimilarity measures such as the Kulczynski measure.
Functional diversity is an important component of biodiversity, yet in comparison to taxonomic diversity, methods of quantifying functional diversity are less well developed. Here, we propose a means for quantifying functional diversity that may be particularly useful for determining how functional diversity is related to ecosystem functioning. This measure of functional diversity ''FD'' is defined as the total branch length of a functional dendrogram. Various characteristics of FD make it preferable to other measures of functional diversity, such as the number of functional groups in a community. Simulating species' trait values illustrates how the relative importance of richness and composition for FD depends on the effective dimensionality of the trait space in which species separate. Fewer dimensions increase the importance of community composition and functional redundancy. More dimensions increase the importance of species richness and decreases functional redundancy. Clumping of species in trait space increases the relative importance of community composition. Five natural communities show remarkably similar relationships between FD and species richness.
An update of the Angiosperm Phylogeny Group (APG) classification of the orders and families of angiosperms is presented. Several new orders are recognized: Boraginales, Dilleniales, Icacinales, Metteniusiales and Vahliales. This brings the total number of orders and families recognized in the APG system to 64 and 416, respectively. We propose two additional informal major clades, superrosids and superasterids, that each comprise the additional orders that are included in the larger clades dominated by the rosids and asterids. Families that made up potentially monofamilial orders, Dasypogonaceae and Sabiaceae, are instead referred to Arecales and Proteales, respectively. Two parasitic families formerly of uncertain positions are now placed: Cynomoriaceae in Saxifragales and Apodanthaceae in Cucurbitales. Although there is evidence that some families recognized in APG III are not monophyletic, we make no changes in Dioscoreales and Santalales relative to APG III and leave some genera in Lamiales unplaced (e.g. Peltanthera). These changes in familial circumscription and recognition have all resulted from new results published since APG III, except for some changes simply due to nomenclatural issues, which include substituting Asphodelaceae for Xanthorrhoeaceae (Asparagales) and Francoaceae for Melianthaceae (Geraniales); however, in Francoaceae we also include Bersamaceae, Ledocarpaceae, Rhynchothecaceae and Vivianiaceae. Other changes to family limits are not drastic or numerous and are mostly focused on some members of the lamiids, especially the former Icacinaceae that have long been problematic with several genera moved to the formerly monogeneric Metteniusaceae, but minor changes in circumscription include Aristolochiaceae (now including Lactoridaceae and Hydnoraceae; Aristolochiales), Maundiaceae (removed from Juncaginaceae; Alismatales), Restionaceae (now re-including Anarthriaceae and Centrolepidaceae; Poales), Buxaceae (now including Haptanthaceae; Buxales), Peraceae (split from Euphorbiaceae; Malpighiales), recognition of Petenaeaceae (Huerteales), Kewaceae, Limeaceae, Macarthuriaceae and Microteaceae (all Caryophyllales), Petiveriaceae split from Phytolaccaceae (Caryophyllales), changes to the generic composition of Ixonanthaceae and Irvingiaceae (with transfer of Allantospermum from the former to the latter; Malpighiales), transfer of Pakaraimaea (formerly Dipterocarpaceae) to Cistaceae (Malvales), transfer of Borthwickia, Forchhammeria, Stixis and Tirania (formerly all Capparaceae) to Resedaceae (Brassicales), Nyssaceae split from Cornaceae (Cornales), Pteleocarpa moved to Gelsemiaceae (Gentianales), changes to the generic composition of Gesneriaceae (Sanango moved from Loganiaceae) and Orobanchaceae (now including Lindenbergiaceae and Rehmanniaceae) and recognition of Mazaceae distinct from Phrymaceae (all Lamiales).
(1) Principal components analysis of incidence (presence and absence) data produces a horseshoe effect. A new method, called step-across, is described which removes this effect. (2) From a matrix of joint occurrences, distances are found directly for all positive values. Distances for zero joint occurrences are found from the shortest network distance. The complete distance matrix is then analysed by Gower's principal coordinates technique. (3) The method can be used on both the rows and columns of an incidence matrix. It is illustrated with artificial data and with data on euphausiids from the Indian Ocean.