Species co‐occurrence analysis: pairwise versus matrix‐level approaches

Arita, Héctor T.

doi:10.1111/geb.12418

Cited by 23 publications

(28 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our examination of pairwise connections appear very useful for providing detailed insight into how communities may respond to agricultural transformation (Veech , Arita and Peres‐Neto ). Nearly all pairwise connections restructured (i.e.…”

Section: Discussionmentioning

confidence: 99%

“…D). Characterizing species by their potential to lose, gain or restructure co‐occurrence links provides a powerful opportunity to identify components of the community that are more at risk from anthropogenic change and could benefit most from targeted management (Arita and Peres‐Neto ). Furthermore, because changes to network connectance could be a result of factors such as lower site occupancy across the landscape (Tylianakis et al ), or particular functional trait associations (e.g.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Species co‐occurrence networks show reptile community reorganization under agricultural transformation

et al. 2017

View full text Add to dashboard Cite

Agricultural transformation represents one of the greatest threats to biodiversity, causing degradation and loss of habitat, leading to changes in the richness and composition of communities. These changes in richness and composition may, in turn, lead to altered species co-occurrence, but our knowledge of this remains limited. We used a novel co-occurrence network approach to examine the impact of agricultural transformation on reptile community structure within two large ( 172 000 km 2 ; 224 sites) agricultural regions in southeastern Australia. We contrasted assemblages from sites surrounded by intact and modified landscapes and tested four key hypotheses that agricultural transformation leads to (H1) declines in species richness, (H2) altered assemblages, (H3) declines in overall co-occurrence, and (H4) complex restructuring of pairwise associations. We found that modified landscapes differed in composition but not richness compared with intact sites. Modified landscapes were also characterized by differences in co-occurrence network structure; with species sharing fewer sites with each other (reduced co-occurrence connectance), fewer highly-connected species (truncation of the frequency distribution of co-occurrence degree) and increased modularity of co-occurrence networks. Critically, overall loss of co-occurrence was underpinned by complex changes to the number and distribution of pair-wise co-occurrence links, with 41-44% of species also gaining associations with other species. Change in co-occurrence was not correlated with changes in occupancy, nor by functional trait membership, allowing a novel classification of species susceptibility to agricultural transformation. Our study reveals the value of using co-occurrence analysis to uncover impacts of agricultural transformation that may be masked in conventional studies of species richness and community composition.

show abstract

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

Species co‐occurrence networks show reptile community reorganization under agricultural transformation

et al. 2017

View full text Add to dashboard Cite

show abstract

“…). Cooccur is based on a probabilistic model by Veech () to study species coexistence between every possible combination of emergent species pairs (Arita , Royan et al. ).…”

Section: Methodsmentioning

confidence: 99%

Linking changes in species–trait relationships and ecosystem function using a network analysis of traits

Siwicka

Thrush

Hewitt

2019

Ecological Applications

View full text Add to dashboard Cite

A major challenge in ecology and environmental management is linking changes in community composition to ecosystem functions. We developed the network analysis of traits (NAT) to show changes in community network structure based on the changes in the composition and connectivity between clusters of species that share traits that imply shifts in functional diversity. We tested the application of NAT on a 113 species found on an intertidal sandflat that was subject to experimental nitrogen addition (control [0 g N/m2], medium [150 g N/m2], and high [600 g N/m2]). This allowed us to directly link mechanistic changes in community composition and function with the trait‐space network patterns revealed by NAT. We demonstrate that under medium (150 g N/m2) N treatment, functional diversity remained consistent, whereas increasing disturbance to high (600 g N/m2) N treatment affected the species–trait network structure and caused merging of functional clusters implying a loss of functional trait diversity.

show abstract

“…In the current debate about the utility of pairwise vs. community‐wise approaches for understanding species interactions (Veech ; Soberón ; Arita ), our results suggest that pairwise co‐occurrence patterns are tightly linked to community scale patterns. Pairwise analyses, therefore, should incorporate information about the abundance distribution of the entire community when these data are available.…”

Section: Discussionmentioning

confidence: 99%

Non‐stationarity in the co‐occurrence patterns of species across environmental gradients

Bar‐Massada

Belmaker

2017

Journal of Ecology

View full text Add to dashboard Cite

Summary Quantifying the role of biotic interactions in driving community assembly often relies on analysing species co‐occurrence patterns, where segregated patterns are taken to indicate antagonistic interactions such as competition. It is unknown, however, if co‐occurrence patterns are stationary across environmental gradients, as it is possible that the strength of biotic interactions that drive these patterns also depends on the environment. In this study, we aim to understand how patterns of co‐occurrence change when species move from their environmental range centre towards their range periphery while isolating the potential signal of biotic interactions from confounding factors. We used two separate statistical approaches (null models and joint species distribution models) to quantify pairwise co‐occurrence patterns for tree species sampled in 9382 plots distributed across the conterminous US. We also analysed co‐occurrence patterns that emerged from a simple meta‐community model. We then assessed how patterns of species segregation and aggregation change in relation to habitat suitability while accounting for multiple factors known to confound co‐occurrence analyses. We found strong non‐stationarity in co‐occurrences, with patterns shifting from segregated at the environmental range centre towards aggregated at range margins for the majority of tree species. Patterns were in full agreement between model simulations and both empirical analyses. Model simulations suggest that this pattern is at least partly driven by variation in the relative abundances of non‐focal species even when no direct biological interactions are present. Synthesis. Patterns of tree species co‐occurrence vary across environmental gradients, with increased segregation when environmental conditions are optimal and increased aggregation when the environment is less suitable. This pattern may originate from a trade‐off between the abundance of the focal species pair, which decreases towards the environmental range margin, and the increasing abundance of non‐focal species to which the environment is more suitable. The strong dependence of co‐occurrence patterns on environmental conditions might limit the predictive ability of joint species distribution models, which couple species co‐occurrences and their environmental responses, because co‐occurrence patterns and environmental responses are confounded.

show abstract

Species co‐occurrence analysis: pairwise versus matrix‐level approaches

Cited by 23 publications

References 27 publications

Species co‐occurrence networks show reptile community reorganization under agricultural transformation

Species co‐occurrence networks show reptile community reorganization under agricultural transformation

Linking changes in species–trait relationships and ecosystem function using a network analysis of traits

Non‐stationarity in the co‐occurrence patterns of species across environmental gradients

Contact Info

Product

Resources

About