scholarly journals A quantitative framework for investigating the reliability of network construction

2018 ◽  
Author(s):  
Alyssa R. Cirtwill ◽  
Anna Eklöf ◽  
Tomas Roslin ◽  
Kate Wootton ◽  
Dominique Gravel
Keyword(s):  
Interspecific Interactions ◽  
Ecological Communities ◽  
Informative Priors ◽  
Network Construction ◽  
Pairwise Interactions ◽  
Species Abundances ◽  
Network Properties ◽  
Finite Sampling ◽  
Network Studies ◽  
Analytical Tools

ABSTRACTDescriptions of ecological networks typically assume that the same interspecific interactions occur each time a community is observed. This contrasts with the known stochasticity of ecological communities: community composition, species abundances, and link structure all vary in space and time. Moreover, finite sampling generates variation in the set of interactions actually observed. Here we develop the conceptual and analytical tools needed to capture uncertainty in the estimation of pairwise interactions. To define the problem, we identify the different contributions to the uncertainty of an interaction and its implications for the estimation of network properties. We then outline a framework to quantify the uncertainty around each interaction. We illustrate this framework using the most extensively sampled network to date. We found significant uncertainty in estimates for the probability of most pairwise interactions which we could, however, limit with informative priors. Through these efforts, we demonstrate the utility of our approach and the importance of acknowledging the uncertainty inherent in network studies. Most importantly, we stress that networks are best thought of as systems constructed from random variables, the stochastic nature of which must be acknowledged for an accurate representation. Doing so will fundamentally change networks analyses and yield greater realism.

scholarly journals Theoretical guidelines for editing ecological communities

2020 ◽  
Author(s):  
Vu Nguyen ◽  
Dervis Can Vural
Keyword(s):  
Community Resilience ◽  
Optimization Process ◽  
Community Control ◽  
Ecological Communities ◽  
Interspecies Interactions ◽  
Cost Parameter ◽  
Pairwise Interactions ◽  
Species Abundances

Having control over species abundances and community resilience is of great interest for experimental, agricultural, industrial and conservational purposes. Here, we theoretically explore the possibility of manipulating ecological communities by modifying pairwise interactions. Specifically, we establish which interaction values should be modified, and by how much, in order to alter the composition or resilience of a community towards a favorable direction. While doing so, we also take into account the experimental difficulties in making such modifications by including in our optimization process, a cost parameter, which penalizes large modifications. In addition to prescribing what changes should be made to interspecies interactions given some modification cost, our approach also serves to establish the limits of community control, i.e. how well can one approach an ecological goal at best, even when not constrained by cost.

Species richness and redundancy promote persistence of exploited mutualisms in yeast

Science ◽  
2020 ◽  
Vol 370 (6514) ◽  
pp. 346-350 ◽  
Author(s):  
Mayra C. Vidal ◽  
Sheng Pei Wang ◽  
David M. Rivers ◽  
David M. Althoff ◽  
Kari A. Segraves
Keyword(s):  
Species Richness ◽  
Interspecific Interactions ◽  
Functional Redundancy ◽  
Ecological Communities ◽  
Negative Effects ◽  
Community Members ◽  
Pairwise Interactions ◽  
Essential Question ◽  
Diverse Communities ◽  
High Species Richness

Mutualisms, or reciprocally beneficial interspecific interactions, constitute the foundation of many ecological communities and agricultural systems. Mutualisms come in different forms, from pairwise interactions to extremely diverse communities, and they are continually challenged with exploitation by nonmutualistic community members (exploiters). Thus, understanding how mutualisms persist remains an essential question in ecology. Theory suggests that high species richness and functional redundancy could promote mutualism persistence in complex mutualistic communities. Using a yeast system (Saccharomyces cerevisiae), we experimentally show that communities with the greatest mutualist richness and functional redundancy are nearly two times more likely to survive exploitation than are simple communities. Persistence increased because diverse communities were better able to mitigate the negative effects of competition with exploiters. Thus, large mutualistic networks may be inherently buffered from exploitation.

Climate-associated trends and variability in ichthyoplankton phenology from the longest continuous larval fish time series on the east coast of the United States

2020 ◽  
Vol 650 ◽  
pp. 269-287
Author(s):  
WC Thaxton ◽  
JC Taylor ◽  
RG Asch
Keyword(s):  
United States ◽  
Environmental Variability ◽  
Larval Fish ◽  
Interspecific Interactions ◽  
River Estuary ◽  
Atlantic Multidecadal Oscillation ◽  
The United States ◽  
Larval Survival ◽  
Ecological Communities ◽  
Northerly Wind

As the effects of climate change become more pronounced, variation in the direction and magnitude of shifts in species occurrence in space and time may disrupt interspecific interactions in ecological communities. In this study, we examined how the fall and winter ichthyoplankton community in the Newport River Estuary located inshore of Pamlico Sound in the southeastern United States has responded to environmental variability over the last 27 yr. We relate the timing of estuarine ingress of 10 larval fish species to changes in sea surface temperature (SST), the Atlantic Multidecadal Oscillation, the North Atlantic Oscillation, wind strength and phenology, and tidal height. We also examined whether any species exhibited trends in ingress phenology over the last 3 decades. Species varied in the magnitude of their responses to all of the environmental variables studied, but most shared a common direction of change. SST and northerly wind strength had the largest impact on estuarine ingress phenology, with most species ingressing earlier during warm years and delaying ingress during years with strong northerly winds. As SST warms in the coming decades, the average date of ingress of some species (Atlantic croaker Micropogonias undulatus, summer flounder Paralichthys dentatus, pinfish Lagodon rhomboides) is projected to advance on the order of weeks to months, assuming temperatures do not exceed a threshold at which species can no longer respond through changes in phenology. These shifts in ingress could affect larval survival and growth since environmental conditions in the estuarine and pelagic nursery habitats of fishes also vary seasonally.

Complex environments alter competitive dynamics in fungi

2021 ◽  
Author(s):  
Justin Chan ◽  
Stephen Bonser ◽  
Michael M. Kasumovic ◽  
Jeff Powell ◽  
William Kirkham Cornwell
Keyword(s):  
Interspecific Interactions ◽  
Fungal Species ◽  
Wood Block ◽  
Complex Environments ◽  
Biotic Factor ◽  
Pairwise Interactions ◽  
Agar Media ◽  
Contextual Environment ◽  
Natural Settings ◽  
Natural Communities

Competition is a key biotic factor that often structures natural communities. Many attempts to disentangle how competition shapes natural communities have relied on experiments on simplified systems or through simple mathematical models. But these simplified approaches are limited in their ability to represent the complexity seen in more natural settings. Here, we considered the competitive pairwise dynamics between four saprotrophic fungal species. We tested whether the contextual environment changed these dynamics, repeating competitive experiments in a simple agar media and a more ecologically realistic wood block setting. We found that the competitive outcomes on agar media differed from those within the wood blocks. While superior competitors were identified across all pairwise interactions on agar, within the wood blocks, two of six interactions resulted in deadlock, where neither competitor could breach territory of the other, and one interaction resulted in a reversed competitive outcome. These results suggest that the complexity within natural substrates can alter the strength of interspecific interactions and may contribute to coexistence and the resulting high diversity of fungi often observed within wood.

scholarly journals The ecological consequences of temperament in spiders

2012 ◽  
Vol 58 (4) ◽  
pp. 589-596 ◽  
Author(s):  
Jonathan N. Pruitt ◽  
Susan E. Riechert
Keyword(s):  
Interspecific Interactions ◽  
Model Systems ◽  
Behavioral Syndromes ◽  
Ecological Communities ◽  
Ecological Consequences ◽  
Behavioral Trait ◽  
Trade Offs ◽  
Evolutionary Studies ◽  
Front Running ◽  
Trait Correlations

Abstract Ecological and evolutionary studies on spiders have been featured prominently throughout the contemporary behavioral syndromes movement. Here we review the behavioral syndromes literature devoted to spiders, and identify some ways in which behavioral syndromes can impact the function of spiders in ecological communities. We further highlight three general themes within the behavioral syndromes literature for which spiders have served as front running model systems: (1) how trait correlations beget performance trade-offs, (2) the influence that behavioral trait variants have on interspecific interactions and (3) mechanisms that aid in maintaining behavioral variation withinand among-populations. Research on behavioral syndromes continues to grow at an impressive rate, and we feel the success of behavioral syndromes studies in spiders bodes well for their continued prominence.

scholarly journals On the temporally flexible structure of plant-pollinator interaction networks

2020 ◽  
Author(s):  
Paul J. CaraDonna ◽  
Nickolas M. Waser
Keyword(s):  
Temporal Variation ◽  
Network Structure ◽  
Species Interactions ◽  
Interspecific Interactions ◽  
Activity Period ◽  
Individual Species ◽  
Ecological Communities ◽  
Short Term ◽  
Temporal Flexibility ◽  
Plant Pollinator

AbstractEcological communities consist of species that are joined in complex networks of interspecific interaction. The interactions that networks depict often form and dissolve rapidly, but this temporal variation is not well integrated into our understanding of the causes and consequences of network structure. If interspecific interactions exhibit temporal flexibility across time periods over which organisms co-occur, then the emergent structure of the corresponding network may also be temporally flexible, something that a temporally-static perspective would miss. Here, we use an empirical system to examine short-term flexibility in network structure (connectance, nestedness, and specialization), and in individual species interactions that contribute to that structure. We investigated weekly plant-pollinator networks in a subalpine ecosystem across three summer growing seasons. To link the interactions of individual species to properties of their networks, we examined weekly temporal variation in species’ contributions to network structure. As a test of the potential robustness of networks to perturbation, we also simulated the random loss of species from weekly networks. We then compared the properties of weekly networks to the properties of cumulative networks that aggregate field observations over each full season. A week-to-week view reveals considerable flexibility in the interactions of individual species and their contributions to network structure. For example, species that would be considered relatively generalized across their entire activity period may be much more specialized at certain times, and at no point as generalized as the cumulative network may suggest. Furthermore, a week-to-week view reveals corresponding temporal flexibility in network structure and potential robustness throughout each summer growing season. We conclude that short-term flexibility in species interactions leads to short-term variation in network properties, and that a season-long, cumulative perspective may miss important aspects of the way in which species interact, with implications for understanding their ecology, evolution, and conservation.

scholarly journals Interaction capacity underpins community diversity

2020 ◽  
Author(s):  
Masayuki Ushio
Keyword(s):  
Interspecific Interactions ◽  
Experimental Studies ◽  
Interaction Strength ◽  
Single Species ◽  
Species Interaction ◽  
Community Diversity ◽  
Ecological Communities ◽  
Total Dna ◽  
Mathematical Equations ◽  
The Mean

AbstractHow patterns in community diversity emerge is a long-standing question in ecology. Theories and experimental studies suggested that community diversity and interspecific interactions are interdependent. However, evidence from multitaxonomic, high-diversity ecological communities is lacking because of practical challenges in characterizing speciose communities and their interactions. Here, I analyzed time-varying causal interaction networks that were reconstructed using 1197 species, DNA-based ecological time series taken from experimental rice plots and empirical dynamic modeling, and show that species interaction capacity, namely, the sum of interaction strength that a single species gives and receives, underpins community diversity. As community diversity increases, the number of interactions increases exponentially but the mean species interaction capacity of a community becomes saturated, weakening interaction among species. These patterns are explicitly modeled with simple mathematical equations, based on which I propose the “interaction capacity hypothesis”, namely, that species interaction capacity and network connectance are proximate drivers of community diversity. Furthermore, I show that total DNA concentrations and temperature influence species interaction capacity and connectance nonlinearly, explaining a large proportion of diversity patterns observed in various systems. The interaction capacity hypothesis enables mechanistic explanations of community diversity, and how species interaction capacity is determined is a key question in ecology.

scholarly journals A Holling Functional Response Model for Mapping QTLs Governing Interspecific Interactions

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao-Yu Zhang ◽  
Huiying Gong ◽  
Qing Fang ◽  
Xuli Zhu ◽  
Libo Jiang ◽  
...  
Keyword(s):  
Functional Response ◽  
Species Interactions ◽  
Community Dynamics ◽  
Interspecific Interactions ◽  
Microbial Interactions ◽  
Ecological Communities ◽  
Response Model ◽  
Ecological Interactions ◽  
Dynamic Complexity ◽  
Genome Level

Genes play an important role in community ecology and evolution, but how to identify the genes that affect community dynamics at the whole genome level is very challenging. Here, we develop a Holling type II functional response model for mapping quantitative trait loci (QTLs) that govern interspecific interactions. The model, integrated with generalized Lotka-Volterra differential dynamic equations, shows a better capacity to reveal the dynamic complexity of inter-species interactions than classic competition models. By applying the new model to a published mapping data from a competition experiment of two microbial species, we identify a set of previously uncharacterized QTLs that are specifically responsible for microbial cooperation and competition. The model can not only characterize how these QTLs affect microbial interactions, but also address how change in ecological interactions activates the genetic effects of the QTLs. This model provides a quantitative means of predicting the genetic architecture that shapes the dynamic behavior of ecological communities.

scholarly journals Null-model-based network comparison reveals core associations

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Lisa Röttjers ◽  
Doris Vandeputte ◽  
Jeroen Raes ◽  
Karoline Faust
Keyword(s):  
Time Series ◽  
Null Hypothesis ◽  
Null Model ◽  
Ecological Interactions ◽  
Network Construction ◽  
Network Comparison ◽  
Microbial Association ◽  
Multiple Networks ◽  
Microbial Network ◽  
Network Properties

AbstractMicrobial network construction and analysis is an important tool in microbial ecology. Such networks are often constructed from statistically inferred associations and may not represent ecological interactions. Hence, microbial association networks are error prone and do not necessarily reflect true community structure. We have developed anuran, a toolbox for investigation of noisy networks with null models. Such models allow researchers to generate data under the null hypothesis that all associations are random, supporting identification of nonrandom patterns in groups of association networks. This toolbox compares multiple networks to identify conserved subsets (core association networks, CANs) and other network properties that are shared across all networks. We apply anuran to a time series of fecal samples from 20 women to demonstrate the existence of CANs in a subset of the sampled individuals. Moreover, we use data from the Global Sponge Project to demonstrate that orders of sponges have a larger CAN than expected at random. In conclusion, this toolbox is a resource for investigators wanting to compare microbial networks across conditions, time series, gradients, or hosts.

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