Multilevel models for the distribution of hosts and symbionts
- Published
- Accepted
- Subject Areas
- Biodiversity, Ecology, Parasitology, Infectious Diseases, Statistics
- Keywords
- latent state, Bayesian hierarchical model, occupancy, mutualist, species interactions, parasite, abundance, symbiosis
- Copyright
- © 2015 Joseph et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. Multilevel models for the distribution of hosts and symbionts. PeerJ PrePrints 3:e1502v1 https://doi.org/10.7287/peerj.preprints.1502v1
Abstract
Symbiont occurrence is influenced by host occurrence and vice versa, which leads to correlations in host-symbiont distributions at multiple levels. Interactions between co-infecting symbionts within host individuals can cause correlations in the abundance of two symbiont species across individual hosts. Similarly, interactions between symbiont transmission and host population dynamics can drive correlations between symbiont and host abundance across habitat patches. If ignored, these interactions can confound estimated responses of hosts and symbionts to other factors. Here, we present a general hierarchical modeling framework for distributions of hosts and symbionts, estimating correlations in host-symbiont distributions at the among-site, within-site, among-species, and among-individual levels. We present an empirical example from a multi-host multi-parasite system involving amphibians and their micro- and macroparasites. Amphibian hosts and their parasites were correlated at multiple levels of organization. Macroparasites often co-infected individual hosts, but rarely co-infected with the amphibian chytrid fungus. Such correlations may result from interactions among parasites and hosts, joint responses to environmental factors, or sampling bias. Joint host-symbiont models account for environmental constraints and species interactions while partitioning variance and dependence in abundance at multiple levels. This framework can be adapted to a wide variety of study systems and sampling designs.
Author Comment
This is a preprint submission to PeerJ.
Supplemental Information
Code supplement
This supplement includes all code and data required to replicate our analysis. The analysis.R file will read in the data from the stan_d.rds file, compile the Stan model (mod.stan), then estimate the parameters and recreate the figures.