An a posteriori measure of network modularity

Poisot, Timothée

doi:10.12688/f1000research.2-130.v3

Cited by 5 publications

(1 citation statement)

References 36 publications

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“…Bascompte et al 2003;Olesen et al 2007;Guimarães et al 2007;Thébault and Fontaine 2010;Mello et al 2011), there is still considerable debate with respect to antagonistic networks (e.g., on whether antagonistic networks are more compartmentalised than random expectation; e.g. Poisot 2013).…”

Section: Introductionmentioning

confidence: 99%

Defining invasiveness and invasibility in ecological networks

et al. 2016

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The success of a biological invasion is context dependent, and yet two key concepts-the invasiveness of species and the invasibility of recipient ecosystems-are often defined and considered separately. We propose a framework that can elucidate the complex relationship between invasibility and invasiveness. It is based on trait-mediated interactions between species and depicts the response of an ecological network to the intrusion of an alien species, drawing on the concept of community saturation. Here, invasiveness of an introduced species with a particular trait is measured by its per capita population growth rate when the initial propagule pressure of the introduced species is very low. The invasibility of the recipient habitat or ecosystem is dependent on the structure of the resident ecological network and is defined as the total width of an opportunity niche in the trait space susceptible to invasion. Invasibility is thus a measure of network instability. We also correlate invasibility with the asymptotic stability of resident ecological network, measured by the leading eigenvalue of the interaction matrix that depicts traitbased interaction intensity multiplied by encounter rate (a pairwise product of propagule pressure of all members in a community). We further examine the relationship between invasibility and network architecture, including network connectance, nestedness and modularity. We exemplify this framework with a trait-based assembly model under perturbations in ways to emulate fluctuating resources and random trait composition in ecological networks. The maximum invasiveness of a potential invader (greatest Electronic supplementary material The online version of this article

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Section: Introductionmentioning

confidence: 99%

Defining invasiveness and invasibility in ecological networks

et al. 2016

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Ongoing worldwide homogenization of human pathogens

Poisot

Nunn

Morand

2014

Preprint

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Fungi stabilize connectivity in the lung and skin microbial ecosystems

et al. 2018

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BackgroundNo microbe exists in isolation, and few live in environments with only members of their own kingdom or domain. As microbiome studies become increasingly more interested in the interactions between microbes than in cataloging which microbes are present, the variety of microbes in the community should be considered. However, the majority of ecological interaction networks for microbiomes built to date have included only bacteria. Joint association inference across multiple domains of life, e.g., fungal communities (the mycobiome) and bacterial communities, has remained largely elusive.ResultsHere, we present a novel extension of the SParse InversE Covariance estimation for Ecological ASsociation Inference (SPIEC-EASI) framework that allows statistical inference of cross-domain associations from targeted amplicon sequencing data. For human lung and skin micro- and mycobiomes, we show that cross-domain networks exhibit higher connectivity, increased network stability, and similar topological re-organization patterns compared to single-domain networks. We also validate in vitro a small number of cross-domain interactions predicted by the skin association network.ConclusionsFor the human lung and skin micro- and mycobiomes, our findings suggest that fungi play a stabilizing role in ecological network organization. Our study suggests that computational efforts to infer association networks that include all forms of microbial life, paired with large-scale culture-based association validation experiments, will help formulate concrete hypotheses about the underlying biological mechanisms of species interactions and, ultimately, help understand microbial communities as a whole.

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An a posteriori measure of network modularity

Cited by 5 publications

References 36 publications

Defining invasiveness and invasibility in ecological networks

Defining invasiveness and invasibility in ecological networks

Ongoing worldwide homogenization of human pathogens

Fungi stabilize connectivity in the lung and skin microbial ecosystems

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