scholarly journals Inferring species interactions from co-occurrence data with Markov networks

Ecology ◽  
2016 ◽  
Vol 97 (12) ◽  
pp. 3308-3314 ◽  
Author(s):  
David J. Harris
2015 ◽  
Author(s):  
David J. Harris

Inferring species interactions from co-occurrence data is one of the most controversial tasks in community ecology. One difficulty is that a single pairwise interaction can ripple through an ecological network and produce surprising indirect consequences. For example, the negative correlation between two competing species can be reversed in the presence of a third species that is capable of outcompeting both of them. Here, I apply models from statistical physics, called Markov networks or Markov random fields, that can predict the direct and indirect consequences of any possible species interaction matrix. Interactions in these models can also be estimated from observed co-occurrence rates via maximum likelihood, controlling for indirect effects. Using simulated landscapes with known pairwise interaction strengths, I evaluated Markov networks and six existing approaches. The Markov networks consistently outperformed other methods, correctly isolating direct interactions between species pairs even when indirect interactions or abiotic factors largely overpowered them. Two computationally efficient approximations, based on controlling for indirect effects with linear or generalized linear models, also performed well. Indirect effects reliably caused a common null modeling approach to produce incorrect inferences, however.


2020 ◽  
Vol 655 ◽  
pp. 139-155
Author(s):  
DC Yates ◽  
SI Lonhart ◽  
SL Hamilton

Marine reserves are often designed to increase density, biomass, size structure, and biodiversity by prohibiting extractive activities. However, the recovery of predators following the establishment of marine reserves and the consequent cessation of fishing may have indirect negative effects on prey populations by increasing prey mortality. We coupled field surveys with empirical predation assays (i.e. tethering experiments) inside and outside of 3 no-take marine reserves in kelp forests along the central California coast to quantify the strength of interactions between predatory fishes and their crustacean prey. Results indicated elevated densities and biomass of invertebrate predators inside marine reserves compared to nearby fished sites, but no significant differences in prey densities. The increased abundance of predators inside marine reserves translated to a significant increase in mortality of 2 species of decapod crustaceans, the dock shrimp Pandalus danae and the cryptic kelp crab Pugettia richii, in tethering experiments. Shrimp mortality rates were 4.6 times greater, while crab mortality rates were 7 times greater inside reserves. For both prey species, the time to 50% mortality was negatively associated with the density and biomass of invertebrate predators (i.e. higher mortality rates where predators were more abundant). Video analyses indicated that macro-invertivore fishes arrived 2 times faster to tethering arrays at sites inside marine reserves and began attacking tethered prey more rapidly. The results indicate that marine reserves can have direct and indirect effects on predators and their prey, respectively, and highlight the importance of considering species interactions in making management decisions.


Author(s):  
Michael K. Young ◽  
Daniel J. Isaak ◽  
Kevin S. McKelvey ◽  
Michael K. Schwartz ◽  
Kellie J. Carim ◽  
...  

Author(s):  
Mark Vellend

This chapter highlights the scale dependence of biodiversity change over time and its consequences for arguments about the instrumental value of biodiversity. While biodiversity is in decline on a global scale, the temporal trends on regional and local scales include cases of biodiversity increase, no change, and decline. Environmental change, anthropogenic or otherwise, causes both local extirpation and colonization of species, and thus turnover in species composition, but not necessarily declines in biodiversity. In some situations, such as plants at the regional scale, human-mediated colonizations have greatly outnumbered extinctions, thus causing a marked increase in species richness. Since the potential influence of biodiversity on ecosystem function and services is mediated to a large degree by local or neighborhood species interactions, these results challenge the generality of the argument that biodiversity loss is putting at risk the ecosystem service benefits people receive from nature.


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