scholarly journals Simultaneous equations modelling of communities with interacting species networks

2021 ◽  
Author(s):  
Miguel Porto ◽  
Pedro Beja
Keyword(s):  
Virtual Communities ◽  
Biotic Interactions ◽  
Interaction Network ◽  
Environmental Predictors ◽  
Interacting Species ◽  
Network Topologies ◽  
Multiple Species ◽  
Occurrence Patterns ◽  
Parsimony Criterion

AbstractTo understand community assembly, ecologists have long sought to extract the signal of biotic interactions from species co-occurrence patterns. These efforts face multiple difficulties such as confounding environmental effects, confounding indirect interactions between multiple species and asymmetry of interactions. To address these problems, we propose Simultaneous Community Equations Modelling (SCEM) as a framework to explicitly account for asymmetric interaction networks in community models. SCEM uses a system of equations to model the occurrence of each species as a function of measured and unmeasured (latent) environmental predictors, and the occurrence of potentially all the other species in the community. Biotic interactions most supported by the data are identified using heuristic optimization of a parsimony criterion, implemented as a Genetic Algorithm. Extensive simulations show that SCEM can recover interaction network topologies in virtual communities. We present a software to implement SCEM and illustrate its application with a case study.

THE IMPORTANCE OF BIOTIC INTERACTIONS IN SHAPING EDIACARAN BENTHIC COMMUNITIES: A COMPARATIVE CASE STUDY OF THE GAOJIASHAN AND MISTAKEN POINT BIOTAS

2016 ◽  
Author(s):  
Gretchen R. O'Neil ◽  
◽  
James D. Schiffbauer ◽  
James D. Schiffbauer ◽  
John Warren Huntley ◽  
...  
Keyword(s):  
Benthic Communities ◽  
Biotic Interactions ◽  
Comparative Case Study

Applications of random graphs

2017 ◽  
Author(s):  
A.C.C. Coolen ◽  
A. Annibale ◽  
E.S. Roberts
Keyword(s):  
Social Networks ◽  
Random Graphs ◽  
Interaction Network ◽  
Power Grids ◽  
Protein Protein Interaction ◽  
Topological Features ◽  
First Case ◽  
The Stability ◽  
Protein Protein Interaction Network

This chapter reviews graph generation techniques in the context of applications. The first case study is power grids, where proposed strategies to prevent blackouts have been tested on tailored random graphs. The second case study is in social networks. Applications of random graphs to social networks are extremely wide ranging – the particular aspect looked at here is modelling the spread of disease on a social network – and how a particular construction based on projecting from a bipartite graph successfully captures some of the clustering observed in real social networks. The third case study is on null models of food webs, discussing the specific constraints relevant to this application, and the topological features which may contribute to the stability of an ecosystem. The final case study is taken from molecular biology, discussing the importance of unbiased graph sampling when considering if motifs are over-represented in a protein–protein interaction network.

scholarly journals Combining connectivity and species distribution modeling to define conservation and restoration priorities for multiple species: A case study in the eastern Amazon

2021 ◽  
Vol 257 ◽  
pp. 109148
Author(s):  
Leonardo de Sousa Miranda ◽  
Marcelo Awade ◽  
Rodolfo Jaffé ◽  
Wilian França Costa ◽  
Leonardo Carreira Trevelin ◽  
...  
Keyword(s):  
Species Distribution ◽  
Species Distribution Modeling ◽  
Distribution Modeling ◽  
Multiple Species

scholarly journals Parallel changes in gut microbiome composition and function in parallel local adaptation and speciation

2019 ◽  
Author(s):  
Diana J. Rennison ◽  
Seth M. Rudman ◽  
Dolph Schluter
Keyword(s):  
Microbial Communities ◽  
Local Adaptation ◽  
Biotic Interactions ◽  
Ecological Speciation ◽  
Microbiome Composition ◽  
Interacting Species ◽  
Microbe Interactions ◽  
Host Microbe Interactions ◽  
And Function ◽  
Host Evolution

AbstractThe processes of local adaptation and ecological speciation are often strongly shaped by biotic interactions such as competition and predation. One of the strongest lines of evidence that biotic interactions drive evolution comes from repeated divergence of lineages in association with repeated changes in the community of interacting species. Yet, relatively little is known about the repeatability of changes in gut microbial communities and their role in adaptation and divergence of host populations in nature. Here we utilize three cases of rapid, parallel adaptation and speciation in freshwater threespine stickleback to test for parallel changes in associated gut microbiomes. We find that features of the gut microbial communities have shifted repeatedly in the same direction in association with parallel divergence and speciation of stickleback hosts. These results suggest that changes to gut microbiomes can occur rapidly and predictably in conjunction with host evolution, and that host-microbe interactions might play an important role in host adaptation and diversification.

scholarly journals The geographic scaling of biotic interactions

2013 ◽  
Author(s):  
Miguel B Araújo ◽  
Alejandro Rozenfeld
Keyword(s):  
Biotic Interactions ◽  
Species Distributions ◽  
Scale Dependence ◽  
Positive Interactions ◽  
Ample Evidence ◽  
Species Ranges ◽  
Central Tenet ◽  
Resource Interactions ◽  
Occurrence Patterns ◽  
Consumer Resource

A central tenet of ecology and biogeography is that the broad outlines of species ranges are determined by climate, whereas the effects of biotic interactions are manifested at local scales. While the first proposition is supported by ample evidence, the second is still a matter of controversy. To address this question, we develop a mathematical model that predicts the spatial overlap, i.e., co-occurrence, between pairs of species subject to all possible types of interactions. We then identify the scale in which predicted range overlaps are lost. We found that co-occurrence arising from positive interactions, such as mutualism (+/+) and commensalism (+/0), are manifested across scales of resolution. Negative interactions, such as competition (-/-) and amensalism (-/0), generate checkerboard-type co-occurrence patterns that are discernible at finer resolutions. Scale dependence in consumer-resource interactions (+/-) depends on the strength of positive dependencies between species. Our results challenge the widely held view that climate alone is sufficient to characterize species distributions at broad scales, but also demonstrate that the spatial signature of competition is unlikely to be discernible beyond local and regional scales.

Identification of Important Proteins in Protein Interaction Network Based on SVM

2014 ◽  
Vol 644-650 ◽  
pp. 5202-5206
Author(s):  
Yan Li Zha ◽  
Wan Cheng Luo
Keyword(s):  
Protein Interaction ◽  
Interaction Network ◽  
Biological Information ◽  
Yeast Protein ◽  
Essential Proteins ◽  
Svm Model ◽  
Network Topologies ◽  
Living Organisms ◽  
Yeast Protein Interaction ◽  
Relevant Experiment

Importance of proteins are different to perform functions of cells in living organisms according to the relevant experiment results, and more essential proteins is the most important kind of proteins. There are recently many computational approaches proposed to predict essential proteins in network level through network topologies combined with biological information of proteins. However it is still hard to identify them because of limitations of topological centralities and bioinformatic sources. And more it is the challenge is to perform better with less resources. Therefore in this paper, we first examine the correlation between common topological centralities and essential proteins and choose a few particular centralities, and then to build a SVM model, names as TC-SVM, for predicting the essential proteins. The new method has been applied to a yeast protein interaction networks, which are obtained from the BioGRID database. The ten folds experimental results show that the performance of predicting essential proteins by TC-SVM is excellent.

Biology and Management of Inland Striped Bass and Hybrid Striped Bass

2013 ◽  
Keyword(s):  
Striped Bass ◽  
Prey Availability ◽  
Biotic Interactions ◽  
Early Life History ◽  
Mountain Lake ◽  
First Year ◽  
Fish Prey ◽  
Abiotic And Biotic Factors

<em>Abstract</em>.—The stocking of fingerling striped bass <em>Morone saxatilis</em> in freshwater impoundments has led to the development of successful put-grow-take fisheries throughout the southern United States. However, first-year survival of stocked fingerlings is often low. To enhance stocking success of striped bass, a better understanding is needed on the impacts of different stocking strategies on early life-history dynamics. In this review paper, we first examined the existing literature on the role of abiotic and biotic factors on recruitment dynamics of stocked piscivores in inland freshwater systems. Second, we compiled the results of a progressive series of studies that were completed over a 25-year period in Smith Mountain Lake, Virginia, that focused on understanding the relationship between striped bass stocking success and biotic interactions, forage-fish prey availability and dynamics, and first-year recruitment. This case study demonstrated that differential intra-cohort growth and poor first-year winter survival are the primary factors limiting stocking success and that stocking fingerlings at a greater number of sites throughout the lake at lower densities improved recruitment to age 1. With this information, we provide stocking size, time, density, and location strategy recommendations that should yield increased survival and stocking success of striped bass in freshwater impoundments.

Methods for the Measurement and Visualization of Social Networks in Multi-User Virtual Worlds

2011 ◽  
pp. 530-541
Author(s):  
Devan Rosen
Keyword(s):  
Social Networks ◽  
Virtual Worlds ◽  
Virtual World ◽  
Virtual Communities ◽  
Communicative Interaction ◽  
Internet Relay Chat ◽  
Cornell University ◽  
Methodological Procedures

Virtual communities that allow many users to interact in a virtual world, often called multi-user virtual worlds (MUVWs), allow users to explore and navigate the virtual world as well as interact with other users. The communicative interaction within these virtual worlds is often text-based using Internet relay chat (IRC) and related systems. IRC has posed a difficulty for researchers looking to evaluate the interaction by analyzing and interpreting the communication since data is stored in the form of chatlogs. The current chapter explicates methodological procedures for the measurement and visualization of chat-based communicative interaction in MUVWs as social networks. A case study on an educational MUVW, the SciCentr programs sponsored by Cornell University, is used to elaborate methods and related findings.

Using Virtual Communities to Involve Users in E-Service Development

2011 ◽  
pp. 61-75
Author(s):  
Eva Söderström ◽  
Jesper Holgersson
Keyword(s):  
Virtual Communities ◽  
User Participation ◽  
Internet Technology ◽  
Service Development ◽  
End User ◽  
Major Player ◽  
Internet Presence ◽  
Major Trend ◽  
Travel Industry

Thriving in the Internet era requires both Internet presence and careful development of the e-services provided using this technology. However, one major problem is how to involve the end users of the e-service(s), something which is necessary if the e-services are to be useful and sustainable. This chapter presents a case study on the e-service development process using a major player in the travel industry as the case. The main focus is on how new technological advancements and phenomena, primarily virtual communities, can be used as a main source of end user requirements. Virtual communities are both of strategic and practical relevance and even cause a need to redefine the term “user participation.” E-services constitute a major trend for private as well as public organizations and should address Internet technology advancements when being developed.

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