Can Ecological Interactions be Inferred from Spatial Data?

Abstract

The characterisation and quantication of ecological interactions, and the construction
 of species distributions and their associated ecological niches, is of fundamental
 theoretical and practical importance. In this paper we give an overview of a Bayesian
 inference framework, developed over the last 10 years, which, using spatial data, offers
 a general formalism within which ecological interactions may be characterised and
 quantied. Interactions are identied through deviations of the spatial distribution
 of co-occurrences of spatial variables relative to a benchmark for the non-interacting
 system, and based on a statistical ensemble of spatial cells. The formalism allows for
 the integration of both biotic and abiotic factors of arbitrary resolution. We concentrate
 on the conceptual and mathematical underpinnings of the formalism, showing
 how, using the Naive Bayes approximation, it can be used to not only compare and
 contrast the relative contribution from each variable, but also to construct species
 distributions and niches based on arbitrary variable type. We show how the formalism
 can be used to quantify confounding and therefore help disentangle the complex
 causal chains that are present in ecosystems. We also show species distributions and
 their associated niches can be used to infer standard "micro" ecological interactions,
 such as predation and parasitism. We present several representative use cases that
 validate our framework, both in terms of being consistent with present knowledge of
 a set of known interactions, as well as making and validating predictions about new,
 previously unknown interactions in the case of zoonoses.

Using Data Mining and Network Analysis to Infer Arboviral Dynamics: The Case of Mosquito-Borne Flaviviruses Reported in Mexico

“…We will return, in the future, to a consideration of both mammalian and avian potential hosts so as to make a potential comparison of their relative importance in the transmission cycle of these MBFVs and, importantly, their potential role from a multi-pathogenic perspective. Additionally, our methodology is capable of disentangling causal chains so as to better understand the role of confounders [ 76 , 77 ]. This is particularly relevant in the case of mammals and birds as their co-occurrence with MBFVs may be intermediated by mutual interactions other than direct interactions with mosquitos.…”

Genome size mediates the effect of environmental filtering in determining plant β-diversity across temperate grasslands

“…Biotic interactions among species that share a common set of environmental tolerances, in whole or in part, can also be an important driver of variation in species composition (Cornell & Lawton 1992;Tilman 1994;Stephens et al 2020). We evaluated the direction and magnitude of these species' interactions, representative of facilitative and competitive interactions among species, via the residual species-to-species association matrices derived from the HMSC analysis (Fig.…”

Response to Stephens et al. (2019)

“…

Readers of the contributions to this debate will no doubt be daunted by the length and density of the presentation of the co-occurrences-imply-interactions methodology by Stephens et al (2020). That is, Stephens et al's (2020) presentation of the inspiration, concepts, and justification for the methodology is presented over too many pages, including considerable amounts of text that is lateral, peripheral, and/or extraneous to the main challenge of presenting, justifying, and defending a novel methodology in a debate.

…”

“…Clearly, Stephens et al (2020) are using a definition of "interaction" that is quite distinct from that which is in universal use in ecology. Rather than a definition that responds directly to the biological processes in question, such as one animal eating another (= predation), or an animal pollinating a plant, they have redefined "interaction" to refer simply to spatial co-occurrence.…”

“…Indeed, Stephens et al (2020) are aware of the challenges involved in the inferences that they are attempting to make. They stated:…”