scholarly journals Inferring species interactions from co-occurrence data with Markov networks

2015 ◽  
Author(s):  
David J. Harris
Keyword(s):  
Indirect Effects ◽  
Species Interactions ◽  
Markov Random Fields ◽  
Linear Models ◽  
Abiotic Factors ◽  
Species Interaction ◽  
Pairwise Interaction ◽  
Interaction Matrix ◽  
Markov Networks ◽  
Occurrence Data

Inferring species interactions from co-occurrence data is one of the most controversial tasks in community ecology. One difficulty is that a single pairwise interaction can ripple through an ecological network and produce surprising indirect consequences. For example, the negative correlation between two competing species can be reversed in the presence of a third species that is capable of outcompeting both of them. Here, I apply models from statistical physics, called Markov networks or Markov random fields, that can predict the direct and indirect consequences of any possible species interaction matrix. Interactions in these models can also be estimated from observed co-occurrence rates via maximum likelihood, controlling for indirect effects. Using simulated landscapes with known pairwise interaction strengths, I evaluated Markov networks and six existing approaches. The Markov networks consistently outperformed other methods, correctly isolating direct interactions between species pairs even when indirect interactions or abiotic factors largely overpowered them. Two computationally efficient approximations, based on controlling for indirect effects with linear or generalized linear models, also performed well. Indirect effects reliably caused a common null modeling approach to produce incorrect inferences, however.

scholarly journals Phylogenetic and metabolic diversity have contrasting effects on the ecological functioning of bacterial communities

2021 ◽  
Vol 97 (3) ◽  
Author(s):  
Constantinos Xenophontos ◽  
Martin Taubert ◽  
W Stanley Harpole ◽  
Kirsten Küsel
Keyword(s):  
Bacterial Communities ◽  
Species Interactions ◽  
Phylogenetic Diversity ◽  
Molecular Mechanisms ◽  
Linear Models ◽  
Theory Development ◽  
Metabolic Diversity ◽  
Community Functioning ◽  
Metabolic Functions ◽  
Independent Effects

ABSTRACT Quantifying the relative contributions of microbial species to ecosystem functioning is challenging, because of the distinct mechanisms associated with microbial phylogenetic and metabolic diversity. We constructed bacterial communities with different diversity traits and employed exoenzyme activities (EEAs) and carbon acquisition potential (CAP) from substrates as proxies of bacterial functioning to test the independent effects of these two aspects of biodiversity. We expected that metabolic diversity, but not phylogenetic diversity would be associated with greater ecological function. Phylogenetically relatedness should intensify species interactions and coexistence, therefore amplifying the influence of metabolic diversity. We examined the effects of each diversity treatment using linear models, while controlling for the other, and found that phylogenetic diversity strongly influenced community functioning, positively and negatively. Metabolic diversity, however, exhibited negative or non-significant relationships with community functioning. When controlling for different substrates, EEAs increased along with phylogenetic diversity but decreased with metabolic diversity. The strength of diversity effects was related to substrate chemistry and the molecular mechanisms associated with each substrate's degradation. EEAs of phylogenetically similar groups were strongly affected by within-genus interactions. These results highlight the unique flexibility of microbial metabolic functions that must be considered in further ecological theory development.

scholarly journals Facilitation costs and benefits function simultaneously on stress gradients for animals

2018 ◽  
Vol 285 (1885) ◽  
pp. 20180983 ◽  
Author(s):  
Olivier Dangles ◽  
Mario Herrera ◽  
Carlos Carpio ◽  
Christopher J. Lortie
Keyword(s):  
Conceptual Framework ◽  
Environmental Conditions ◽  
Species Interactions ◽  
Stress Gradient ◽  
Species Interaction ◽  
Positive Interactions ◽  
Costs And Benefits ◽  
Strong Basis ◽  
Stress Gradients ◽  
High Resource

Understanding the variation in species interactions along environmental stress gradients is crucial for making robust ecological predictions about community responses to changing environmental conditions. The facilitation–competition framework has provided a strong basis for predictions (e.g. the stress-gradient hypothesis, SGH), yet the mechanisms behind patterns in animal interactions on stress gradients are poorly explored in particular for mobile animals. Here, we proposed a conceptual framework modelling changes in facilitation costs and benefits along stress gradients and experimentally tested this framework by measuring fitness outcomes of benefactor–beneficiary interactions across resource quality levels. Three arthropod consumer models from a broad array of environmental conditions were used including aquatic detritivores, potato moths and rainforest carrion beetles. We detected a shift to more positive interactions at increasing levels of stress thereby supporting the application of the SGH to mobile animals. While most benefactors paid no significant cost of facilitation, an increase in potato moth beneficiary's growth at high resource stress triggered costs for benefactors. This study is the first to experimentally show that both costs and benefits function simultaneously on stress gradients for animals. The proposed conceptual framework could guide future studies examining species interaction outcomes for both animals and plants in an increasingly stressed world.

scholarly journals Water Birds as Indicators of Ecological Conditions in a Ramsar Wetland (Sebkhet Bazer, East of Algeria)

2021 ◽  
Author(s):  
Sabrina Djerboua ◽  
Sofia Djerdali ◽  
José Guerrero-Casado ◽  
Abdelkrim Si Bachir ◽  
Ali Guendouz
Keyword(s):  
Water Body ◽  
Linear Models ◽  
Abiotic Factors ◽  
Bird Community ◽  
Ecological Indicator ◽  
Bird Abundance ◽  
Seasonal Differences ◽  
Water Bird ◽  
Physico Chemical ◽  
Water Birds

Background: Wetlands are the highly complex ecosystems due to various interactions between the components, where, the most iconic of ecological changes are the water birds. The current study was aimed to examine the interactions between the water birds diversity, abundance and the abiotic factors in Sebkhet Bazer. Methods: The investigation was conducted between March 2013 and December 2014 in Sebkhet Bazer (Sétif, Algeria, 36°05'N and 5°45'E), by monitoring water birds abundance (grouped into 4: Anatidae, Rallidae, Phoenicopteridae and Shorebirds) and measuring the physico-chemical water parameters (depth, temperature, pH, salinity and vegetation cover). All statistical analysis was performed using the InfoStat software (2017), it was carried out in two steps, by testing of fixed linear models; first of the seasonal differences in water body variables and second of the seasonal differences in bird abundance for the 4 water bird groups. Result: The results showed that the physico-chemical parameters of water varied considerably from season to season. The four groups of birds reached their lowest abundance in summer, with Rallidae and Phonicopteridae being more abundant in spring, Anatidae in winter and Shorebirds in autumn, suggesting that this variation is attributed to changes in water body characteristics between the four seasons. Therefore, the abundance of the different water bird group could be used as an ecological indicator of this wetland’s characteristics. If these features are altered by climate change, the water bird community would be also affected.

scholarly journals Dynamic population stage structure due to juvenile–adult asymmetry stabilizes complex ecological communities

2021 ◽  
Vol 118 (21) ◽  
pp. e2023709118
Author(s):  
André M. de Roos
Keyword(s):  
Self Regulation ◽  
Interaction Network ◽  
Population Level ◽  
Stage Structure ◽  
Current Theory ◽  
Species Interaction ◽  
Interaction Matrix ◽  
Foraging Efficiency ◽  
Ecological Communities ◽  
The Stability

Natural ecological communities are diverse, complex, and often surprisingly stable, but the mechanisms underlying their stability remain a theoretical enigma. Interactions such as competition and predation presumably structure communities, yet theory predicts that complex communities are stable only when species growth rates are mostly limited by intraspecific self-regulation rather than by interactions with resources, competitors, and predators. Current theory, however, considers only the network topology of population-level interactions between species and ignores within-population differences, such as between juvenile and adult individuals. Here, using model simulations and analysis, I show that including commonly observed differences in vulnerability to predation and foraging efficiency between juvenile and adult individuals results in up to 10 times larger, more complex communities than observed in simulations without population stage structure. These diverse communities are stable or fluctuate with limited amplitude, although in the model only a single basal species is self-regulated, and the population-level interaction network is highly connected. Analysis of the species interaction matrix predicts the simulated communities to be unstable but for the interaction with the population-structure subsystem, which completely cancels out these instabilities through dynamic changes in population stage structure. Common differences between juveniles and adults and fluctuations in their relative abundance may hence have a decisive influence on the stability of complex natural communities and their vulnerability when environmental conditions change. To explain community persistence, it may not be sufficient to consider only the network of interactions between the constituting species.

scholarly journals Endangered species’ trait responses to environmental variability in agricultural settings

2020 ◽  
Vol 72 (1) ◽  
pp. 13-21
Author(s):  
Tijana Nikolic ◽  
Maja Arok ◽  
Dimitrije Radisic ◽  
Marko Mirc ◽  
Lea Velaja ◽  
...  
Keyword(s):  
Endangered Species ◽  
Vegetation Index ◽  
Normalized Difference Vegetation Index ◽  
Agricultural Landscape ◽  
Linear Models ◽  
Environmental Variability ◽  
Abiotic Factors ◽  
Patch Occupancy ◽  
System Productivity ◽  
Demographic Traits

Understanding the spatial and temporal effects of variable environmental conditions on demographic characteristics is important in order to stop the decline of endangered-species populations. To capture interactions between a species and its environment, in this work the demographic traits of the European ground squirrel (EGS), Spermophilus citellus, were modeled as a function of agricultural landscape structure. The habitat suitability index was determined for 20 localities within the study area based on habitat use, management and type. After mapping the habitat patch occupancy in the field, crop cover maps, the average normalized difference vegetation index (NDVI) and automated water extraction index (AWEI) were obtained from satellite images covering the period 2013-2015. This data was used to develop population-level generalized linear models (GLMs) and individual-level conditional mixed-effects models (GLMMs) in R package Ime4, focusing on the key demographic traits of the EGS. The land composition and patch carrying capacity (PCC) are the key determinants of the endangered EGS population size, while system productivity is the main factor influencing individuals? body condition after monitoring for variations across sampling years and age classes. The proposed landscape structural models show that human activities and abiotic factors shape the demographic rates of the EGS. Thus, to conserve threatened species, an appropriate focus on the spatial adaptation strategies should be employed.

Answers.

2020 ◽  
pp. 179-214
Author(s):  
Paul A. Rees
Keyword(s):  
Community Ecology ◽  
Population Ecology ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Multiple Choice ◽  
Ecological Genetics ◽  
Major Topic ◽  
Production Ecology ◽  
Material Cycles ◽  
Ecological Methods

Abstract A multiple choice question has a stem (the 'question'), a key (the 'answer') and a number of distracters (wrong answers intended to distract the student from the key). This part of the book contains the key to each question along with a brief explanation of why this is correct and, in some cases, what the distracters mean. The questions are grouped into 10 major topic areas: (1) The history and foundations of ecology, (2) Abiotic factors and environmental monitoring, (3) Taxonomy and biodiversity, (4) Energy flow and production ecology, (5) Nutrient and material cycles, (6) Ecophysiology, (7) Population ecology, (8) Community ecology and species interactions, (9) Ecological genetics and evolution, (10) Ecological methods and statistics.

scholarly journals Aridity weakens population-level effects of multiple species interactions on Hibiscus meyeri

2017 ◽  
Vol 115 (3) ◽  
pp. 543-548 ◽  
Author(s):  
Allison M. Louthan ◽  
Robert M. Pringle ◽  
Jacob R. Goheen ◽  
Todd M. Palmer ◽  
William F. Morris ◽  
...  
Keyword(s):  
Population Growth ◽  
Species Interactions ◽  
Abiotic Factors ◽  
Population Level ◽  
Distinct Species ◽  
High Elevation ◽  
Relative Strength ◽  
Herbaceous Plant ◽  
Species Abundances ◽  
Multiple Species

Predicting how species’ abundances and ranges will shift in response to climate change requires a mechanistic understanding of how multiple factors interact to limit population growth. Both abiotic stress and species interactions can limit populations and potentially set range boundaries, but we have a poor understanding of when and where each is most critical. A commonly cited hypothesis, first proposed by Darwin, posits that abiotic factors (e.g., temperature, precipitation) are stronger determinants of range boundaries in apparently abiotically stressful areas (“stress” indicates abiotic factors that reduce population growth), including desert, polar, or high-elevation environments, whereas species interactions (e.g., herbivory, competition) play a stronger role in apparently less stressful environments. We tested a core tenet of this hypothesis—that population growth rate is more strongly affected by species interactions in less stressful areas—using experimental manipulations of species interactions affecting a common herbaceous plant, Hibiscus meyeri (Malvaceae), across an aridity gradient in a semiarid African savanna. Population growth was more strongly affected by four distinct species interactions (competition with herbaceous and shrubby neighbors, herbivory, and pollination) in less stressful mesic areas than in more stressful arid sites. However, contrary to common assumptions, this effect did not arise because of greater density or diversity of interacting species in less stressful areas, but rather because aridity reduced sensitivity of population growth to these interactions. Our work supports classic predictions about the relative strength of factors regulating population growth across stress gradients, but suggests that this pattern results from a previously unappreciated mechanism that may apply to many species worldwide.

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