Species co-occurrence networks Can they reveal trophic and non-trophic interactions in ecological communities?

Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this...

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Vydané v:Ecology (Durham) Ročník 99; číslo 3; s. 690 - 699
Hlavní autori: Freilich, Mara A., Wieters, Evie, Broitman, Bernardo R., Marquet, Pablo A., Navarrete, Sergio A.
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States John Wiley and Sons, Inc 01.03.2018
Ecological Society of America
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ISSN:0012-9658, 1939-9170
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Abstract Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction-based ecological theory to interpret network variability and stability. Co-occurrence networks may be particularly valuable for analysis of community dynamics that blends interactions and environment, rather than pairwise interactions alone.
AbstractList Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction-based ecological theory to interpret network variability and stability. Co-occurrence networks may be particularly valuable for analysis of community dynamics that blends interactions and environment, rather than pairwise interactions alone.
Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction-based ecological theory to interpret network variability and stability. Co-occurrence networks may be particularly valuable for analysis of community dynamics that blends interactions and environment, rather than pairwise interactions alone.Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is difficult to obtain. Their use is particularly common, but not restricted to, microbial networks constructed from metagenomic analyses. In this study, we test the efficacy of this procedure by comparing an inferred network constructed using spatially intensive co-occurrence data from the rocky intertidal zone in central Chile to a well-resolved, empirically based, species interaction network from the same region. We evaluated the overlap in the information provided by each network and the extent to which there is a bias for co-occurrence data to better detect known trophic or non-trophic, positive or negative interactions. We found a poor correspondence between the co-occurrence network and the known species interactions with overall sensitivity (probability of true link detection) equal to 0.469, and specificity (true non-interaction) equal to 0.527. The ability to detect interactions varied with interaction type. Positive non-trophic interactions such as commensalism and facilitation were detected at the highest rates. These results demonstrate that co-occurrence networks do not represent classical ecological networks in which interactions are defined by direct observations or experimental manipulations. Co-occurrence networks provide information about the joint spatial effects of environmental conditions, recruitment, and, to some extent, biotic interactions, and among the latter, they tend to better detect niche-expanding positive non-trophic interactions. Detection of links (sensitivity or specificity) was not higher for well-known intertidal keystone species than for the rest of consumers in the community. Thus, as observed in previous empirical and theoretical studies, patterns of interactions in co-occurrence networks must be interpreted with caution, especially when extending interaction-based ecological theory to interpret network variability and stability. Co-occurrence networks may be particularly valuable for analysis of community dynamics that blends interactions and environment, rather than pairwise interactions alone.
Author Freilich, Mara A.
Broitman, Bernardo R.
Navarrete, Sergio A.
Marquet, Pablo A.
Wieters, Evie
Author_xml – sequence: 1
  givenname: Mara A.
  surname: Freilich
  fullname: Freilich, Mara A.
– sequence: 2
  givenname: Evie
  surname: Wieters
  fullname: Wieters, Evie
– sequence: 3
  givenname: Bernardo R.
  surname: Broitman
  fullname: Broitman, Bernardo R.
– sequence: 4
  givenname: Pablo A.
  surname: Marquet
  fullname: Marquet, Pablo A.
– sequence: 5
  givenname: Sergio A.
  surname: Navarrete
  fullname: Navarrete, Sergio A.
BackLink https://www.ncbi.nlm.nih.gov/pubmed/29336480$$D View this record in MEDLINE/PubMed
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Issue 3
Keywords co-occurrence
anthropogenic impacts
ecological networks
species interactions
food webs
keystone species
non-trophic interactions
intertidal
Language English
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2018 by the Ecological Society of America.
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Snippet Co-occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is...
Co‐occurrence methods are increasingly utilized in ecology to infer networks of species interactions where detailed knowledge based on empirical studies is...
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StartPage 690
SubjectTerms anthropogenic impacts
biocenosis
Biota
Chile
Commensalism
Communities
co‐occurrence
Ecological effects
ecological networks
Ecology
Empirical analysis
Environmental conditions
Environmental effects
environmental factors
Food Chain
food webs
intertidal
Intertidal zone
Keystone species
littoral zone
metagenomics
Microorganisms
Mixtures
Networks
non‐trophic interactions
probability
Sensitivity
species interactions
Stability analysis
Symbiosis
Trophic relationships
Subtitle Can they reveal trophic and non-trophic interactions in ecological communities?
Title Species co-occurrence networks
URI https://www.jstor.org/stable/26624185
https://onlinelibrary.wiley.com/doi/abs/10.1002%2Fecy.2142
https://www.ncbi.nlm.nih.gov/pubmed/29336480
https://www.proquest.com/docview/2009237893
https://www.proquest.com/docview/1989573265
https://www.proquest.com/docview/2053894234
Volume 99
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