Species‐pair associations, null models, and tests of mechanisms structuring ecological communities

Can fish species co-occurrence patterns be predicted by their trait dissimilarities?

Trait-based analyses have been successful in determining and predicting species association outcomes in diverse communities. Most studies have limited the scope of this approach to the biotic responses of a small number of species or geographical regions. We focused on determining whether three biologically relevant traits (body size, temperature preference and trophic level) influence the patterns of co-occurrence between multiple species. We used fish species presence/absence from 9204 lakes in Ontario, Canada, to obtain effect sizes of 2001 species-pair co-occurrence values, using a null model approach. Euclidean distances between each species-pair were calculated for each of the three traits selected. Multiple regression models and randomization tests were used to determine the direction and significance of the relationship of each trait with the observed co-occurrence values. The results show that species temperature preference was significantly related to co-occurrence patterns, indicating the effect of environmental filtering. Trophic level was significantly related to co-occurrence values for both linear and quadratic terms, suggesting that segregation between species is driven by large differences in this trait (predation effects). Unexpectedly, body size was not significantly related to the observed co-occurrence patterns. We provide a new approach to test relationships between species assemblages and trait conditions.

Organization of the macroinvertebrate community in a tropical annual agroecosystem into modules

The structure of macroinvertebrate communities in agroecosystems has been assumed to be modular and organized around key herbivore pests. We characterized the macroinvertebrate community in the annual organic brassica agroecosystem in tropical central Brazil to determine if the community was a random assemblage of independent populations or was organized into repeatable multi-species components. We sampled 36 macroinvertebrate taxa associated with six organic brassica farms at biweekly intervals during the dry season during two years in the Distrito Federal, Brazil. We used an unconstrained ordination based on latent variable modeling (boral) with negative binomial population counts to analyze community composition independent of variation in sample abundance. We evaluated observed community structure by comparing it with randomized alternatives. We found that the community was not a random assemblage and consistently organized itself into two modules based around the major herbivores; one with lepidoptera and whiteflies and their associated natural enemies which was gradually replaced during the season by one with brassica aphids, aphid parasitoids and coccinellids. This analysis suggests that the historical and present-day focus on pest herbivores and their associated species in agroecosystems may be justified based on community structure.

Positive associations matter: Microbial relationships drive tick microbiome composition

Untangling how factors such as environment, host, associations among bacterial species and dispersal predict microbial composition is a fundamental challenge. In this study, we use complementary machine-learning approaches to quantify the relative role of these factors in shaping microbiome variation of the blacklegged tick Ixodes scapularis. I. scapularis is the most important vector for Borrelia burgdorferi (the causative agent for Lyme disease) in the U.S. as well as a range of other important zoonotic pathogens. Yet the relative role of the interactions between pathogens and symbionts compared to other ecological forces is unknown. We found that positive associations between microbes where the occurrence of one microbe increases the probability of observing another, including between both pathogens and symbionts, was by far the most important factor shaping the tick microbiome. Microclimate and host factors played an important role for a subset of the tick microbiome including Borrelia (Borreliella) and Ralstonia, but for the majority of microbes, environmental and host variables were poor predictors at a regional scale. This study provides new hypotheses on how pathogens and symbionts might interact within tick species, as well as valuable predictions for how some taxa may respond to changing climate.

Soil fungal diversity and assembly along a xeric stress gradient in the central Namib Desert

The Namib Desert of south-western Africa is one of the oldest deserts in the world and possesses unique geographical, biological and climatic features. While research through the last decade has generated a comprehensive survey of the prokaryotic communities in Namib Desert soils, little is yet known about the diversity and function of edaphic fungal communities, and even less of their responses to aridity. In this study, we have characterized soil fungal community diversity across the longitudinal xeric gradient across the Namib desert (for convenience, divided into the western fog zone, the central low-rainfall zone and the eastern high-rainfall zone), using internal transcribed sequence (ITS) metabarcoding. Ascomycota, Basidiomycota and Chytridiomycota consistently dominated the Namib Desert edaphic fungal communities and a core mycobiome composed of only 15 taxa, dominated by members of the class Dothideomycetes (Ascomycota), was identified. However, fungal community structures were significantly different in the fog, low-rainfall and high-rainfall zones. Furthermore, Namib Desert gravel plain fungal community assembly was driven by both deterministic and stochastic processes; the latter dominating in the all three xeric zones. We also present data that suggest that the inland limit of fog penetration represents an ecological barrier to fungal dispersal across the Namib Desert.

Urban park layers: Spatial variation in plant community structure

Horizontal structure of natural plant communities attracted the attention of researchers for a long time, while the problem of horizontal structure of urban park plantations was not studied sufficiently. Species richness of different tiers of park plantation in the large industrial city of Dnipro (Ukraine) was revealed in this study. Also features of variation in the structure of plant communities at different spatial levels were revealed, the influence of park plantation canopy on the understory and herbaceous layer of the park. There were 30 plant species in the tree layer of the park plantation. The most common species were Robinia pseudoacacia L., Acer platanoides L., A. negundo L., Gleditsia triacanthos L., Aesculus hippocastanum L., Populus carolinensis Moench. The variance-to-mean ratio revealed that 13 tree species were randomly distributed throughout the park, and 14 species were aggregated. The number of occurrences of a given tree species per site and variance-to-mean ratio were positively correlated. The numerous tree species showed a tendency of aggregated distribution within the park. Sixteen plant species were found in the understory. Among them, the most abundant species were Acer platanoides L., A. negundo L., A. pseudoplatanus L., Sambucus nigra L., Robinia pseudoacacia L. Eight species were found to be randomly distributed over the park area, and eight species showed an aggregate distribution. The number of species encountered in the understory and variance-to-mean ratio were positively correlated. In the herbaceous stand, 99 plant species were found, of which Chelidonium majus L., Viola odorata L., Impatiens parviflora DC., Parthenocissus quinquefolia (L.) Planch., Geum urbanum L. predominated. The variance-to-mean ratio of all species was significantly less than unity, indicating regular spatial distribution. The values of alpha- and gamma-diversity of the plant community in separate layers are very different. The highest gamma diversity was found for the herbaceous stand, while the diversity of the tree stand and understory was significantly lower. Alpha biodiversity of the tree stand and the understory did not practically differ. Beta diversity values between the layers are very close, and beta diversity is practically equal for tree stand and herbaceous layer. Thus, we can assume that the mechanisms of species turnover for the plant communities of different layers are determined by the common causes. The spatial broad-scale component was able to explain 8.2% of community variation, the medium-scale component was able to explain 4.2% of community variation, and the fine-scale component was able to explain 0.7% of community variation. The understory is the most sensitive to the environmental factors, the herbaceous stand is somewhat less sensitive, and the tree stand is the least sensitive to the environmental factors. The environmental factors in this study are represented by a set of variables. The spatial variation of the stand is predominantly influenced by the factors of trophicity and moisture of the edaphotope. These same factors also act on the herbaceous stand and understory, but along with them are included the environmental variables, which are determined by the architectonics of the crown space and thus the light regime, which is regulated by the tree stand. It is important to note that the variation of the communities of the different layers of the park plantation is subject to spatial patterns. The herbaceous and understory variation is more spatially structured than the tree stand variation. The spatial patterns can arise as a result of the influence of spatially structured environmental factors and as a result of factors of a neutral nature. The latter aspect of variation is best described by the pure spatial component of community variation.

A needle in the haystack? Applying species co-occurrence frameworks with fish assemblage data to identify species associations and sharpen ecological hypotheses

Different species can associate or interact in many ways, and methods exist for inferring associations and underlying mechanisms from incidence data (e.g., co-occurrence frameworks). These methods have received criticism despite their recent resurgence in the literature. However, co-occurrence frameworks for identifying nonrandomly associated species pairs (e.g., aggregated or segregated pairs) have value as heuristic tools for sharpening hypotheses concerning fish ecology. This paper provides a case study examining species co-occurrence across 33 stream fish assemblages in southeastern Oklahoma, USA, which were sampled twice (1974 and 2014). This study sought to determine (a) which species were nonrandomly associated, (b) what processes might have driven these associations and (c) how consistent patterns were across time. Associations among most pairs of species (24 species, 276 unique pairs) were not significantly different from random (>80%). Among all significant, nonrandomly associated species pairs (54 unique pairs), 78% (42 pairs) were aggregated and 22% (12 pairs) segregated. Most of these (28 pairs, 52%) were hypothesized to be driven by nonbiotic mechanisms: habitat filtering (20 pairs, 37%), dispersal limitation (two pairs, 0.4%) or both (six pairs, 11%). The remaining 26 nonrandomly associated pairs (48%) had no detectable signal of spatial or environmental factors involved with the association, therefore the potential for biotic interaction was not refuted. Only five species pairs were consistently associated across both sampling periods: stonerollers Campostoma spp. and orangebelly darter Etheostoma radiosum; red shiner Cyprinella lutrensis and bullhead minnow Pimephales vigilax; bluegill sunfish Lepomis macrochirus and redear sunfish Lepomis microlophus; redfin shiner Lythrurus umbratilis and bluntnose minnow Pimephales notatus; and bigeye shiner Notropis boops and golden shiner Notemigonus crysoleucas. Frameworks for identifying nonrandomly associated species pairs can provide insight into broader mechanisms of species assembly and point to potentially interesting species interactions (out of many possible pairs). However, this approach is best applied as a tool for sharpening hypotheses to be investigated further. Rather than a weakness, the heuristic nature is the strength of such methods, and can help guide biologists toward better questions by employing relatively cheap diversity survey data, which are often already in hand, to reduce complex interaction networks down to their nonstochastic parts which warrant further investigation.

Disentangling the relative importance of spatio-temporal parameters and host specificity in shaping arbuscular mycorrhizal fungus communities in a temperate forest

Many woody and herbaceous plants in temperate forests cannot establish and survive in the absence of mycorrhizal associations. Most temperate forests are dominated by ectomycorrhizal woody plant species, which implies that the carrying capacity of the habitat for arbuscular mycorrhizal fungi (AMF) is relatively low and AMF could in some cases experience a limitation of propagules. Here we address how the AMF community composition varied in a small temperate forest site in Germany in relation to time, space, two plant host species, and also with regard to the degree to which plots were covered with AMF-associating woody species. The AMF communities in our study were non-random. We observed that space had a greater impact on fungal community composition than either time, mycorrhizal state of the close-by woody species, or the identity of the host plant. The identity of the host plant was the only parameter that modified AMF richness in the roots. The set of parameters which we addressed has rarely been studied together, and the resulting ranking could ease prioritizing some of them to be included in future surveys. AMF are crucial for the establishment of understory plants in temperate forests, making it desirable to further explore how they vary in time and space.

Abiotic factors influence species co-occurrence patterns of lake fishes

Abiotic factors are recognized for their strong influence on community structure. Habitat diversity is related to resource availability that influences species richness and abundance. In lakes, surface area and depth have been used as measures of the size and diversity of habitat, and have strong effects on the structure of entire communities. We tested whether abiotic variables, related to habitat size, influence co-occurrence patterns of species pairs of fishes by analysing groups of lakes within a specific area and depth categories in two regions in Ontario, Canada. We used null models to obtain co-occurrence patterns and standard effect sizes for each species pair within each area and depth category. We estimated standard effect sizes relative to lake area or depth and determined whether species co-occurrence patterns change systematically as these measures of habitat increase. We evaluated groups of species where factors such as predation and habitat filtering have been shown to structure those assemblages, and we tested whether area and depth alter the species associations and our interpretation of these relationships. We found significant differences between the observed and expected distributions of regression slopes relating co-occurrences to area and depth in both regions across all species, which indicated the strong influence of both variables on the overall co-occurrence patterns. We observed a significant negative trend of the co-occurrence patterns across lake area categories for the predator-prey species, indicating that the effect of predation was stronger in smaller lakes, but it was reduced in larger lakes, possibly due to increased habitat and resource availability. We show that pooling results as done in standard community null models can lead to Type II errors due to the 'cancellation' of opposing ecological signals. Our results demonstrate the effect of environmental variables on species co-occurrence patterns, but the divergent results obtained between geographical regions suggest that such patterns are context-dependent. This study emphasizes the importance of considering abiotic factors in null models of species co-occurrence to obtain reliable and detailed information about the association patterns between species.