Metacommunity dynamics and the detection of species associations in co‐occurrence analyses: Why patch disturbance matters

Abstract

Many statistical methods attempt to detect species associations—and so infer interspecific interactions—from species co‐occurrence patterns. Habitat heterogeneity and out‐of‐equilibrium colonization histories are well recognized as potentially causing species associations, even when interactions are absent. The potential for patch disturbance, a classical component of metacommunity dynamics, to also drive spurious species associations has however been overlooked. Using a new general metacommunity model, we derive mathematical predictions regarding how patch disturbance would affect the patterns of species associations detected in ‘null’ co‐occurrence matrices. We also conduct numerical simulations to test our predictions and to compare the performance of several widespread statistical methods, including direct tests of pairwise independence, matrix permutation approaches and joint species distribution modelling. We show how classical metacommunity dynamics can produce statistical associations, both positive and negative, even when species do not interact, when there is no habitat heterogeneity, and at equilibrium. This occurs as soon as there is some rate of patch disturbance (i.e. simultaneous extinction of several species in a patch) and/or a finite life span of patches, a common feature of a broad range of plant, animal or microbial systems. Patch disturbance can compromise species co‐occurrence analyses and cause the artefactual detection of species associations if not taken into account. Including patch age (i.e. the time since the last patch disturbance event) as a covariate in a joint species distribution model can resolve the artefact. However, this requires additional data that often are not available in practice. We argue that the consequences of patch disturbance should not be underestimated when analysing species distribution patterns in metacommunity‐like systems. Read the free Plain Language Summary for this article on the Journal blog.

Codistribution as an indicator of whole metacommunity response to environmental change

“…When JSDMs were initially proposed, the residual associations between species were identified as representing hypotheses for interactions between species. However, recent theoretical (Dormann et al 2018, Zurell et al 2018, Blanchet et al 2020, Poggiato et al 2021, Calcagno et al 2022) and empirical (Barner et al 2018, Freilich et al 2018, Brazeau and Schamp 2019, Thurman et al 2019) research has emphasized the poor correspondence with direct species interactions and the breadth of other factors that could determine the observed correlations in species responses. In particular, co‐occurrences of species can be attributable not to direct species interactions, but rather to additional unmeasured environmental variables that are likely to obscure any underlying signal of species interactions (Blanchet et al 2020).…”

Codistribution as an indicator of whole metacommunity response to environmental change

“…2018; Zurell et al . 2018; Blanchet et al 2020; Poggiato et al 2021; Calcagno et al . 2022) and empirical (Barner et al 2018; Freilich et al 2018; Brazeau & Schamp 2019; Thurman et al 2019) research has emphasized the poor correspondence with direct species interactions and the breadth of other factors that could determine the observed correlations in species responses.…”

“…When JSDMs were initially proposed, the residual associations between species were identified as representing hypotheses for interactions between species. However, recent theoretical (Dormann et al 2018;Zurell et al 2018;Blanchet et al 2020;Poggiato et al 2021;Calcagno et al 2022) and empirical (Barner et al 2018;Freilich et al 2018;Brazeau & Schamp 2019;Thurman et al 2019) research has emphasized the poor . CC-BY-NC 4.0 International license available under a (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.…”

“…When JSDMs were initially proposed, the residual associations between species were identified as representing hypotheses for interactions between species. However, recent theoretical (Dormann et al 2018;Zurell et al 2018;Blanchet et al 2020;Poggiato et al 2021;Calcagno et al 2022) and empirical (Barner et al 2018;Freilich et al 2018;Brazeau & Schamp 2019;Thurman et al 2019) research has emphasized the poor correspondence with direct species interactions and the breadth of other factors that could determine the observed correlations in species responses. In particular, co-occurrences of species can be attributable not to direct species interactions, but rather to additional unmeasured environmental variables that are likely to obscure any underlying signal of species interactions (Blanchet et al 2020).…”