Code for: A metapopulation model of social group dynamics and disease applied to Yellowstone wolves

Abstract The population structure of social species has important
consequences for both their demography and transmission of their
pathogens. We develop a new form of metapopulation model that tracks two
key components of a species’ social system: average group size and number
of groups within a population. While the model is general, we parameterize
it to mimic the dynamics of the Yellowstone wolf population and two
associated pathogens: sarcoptic mange and canine distemper. In the initial
absence of disease, we show that group size is mainly determined by the
birth, death rates, and the rates at which groups fission to form new
groups. The total number of groups is determined by rates of fission and
fusion, as well as upon environmental resources and rates of intergroup
aggression. Incorporating pathogens into the models reduces the size of
the host population, predominantly by reducing the number of social
groups. Average group size responds in more subtle ways: infected groups
decrease in size, but uninfected groups may increase when disease reduces
the number of groups and thereby reduces intraspecific aggression. Our
modeling approach allows for easy calculation of prevalence at multiple
scales (within group, across groups, and population level), illustrating
that aggregate population-level prevalence can be misleading for
group-living species. The model structure is general, can be applied to
other social species, and allows for a dynamic assessment of how pathogens
can affect social structure and vice versa.   Significance How do
social and infectious disease dynamics interact in group-living mammals? A
significant cost to group living is increased transmission of pathogens.
When a pathogen invades a group, members will be more vulnerable to
mortality, Allee effects, and ultimately group extinction. The presence of
a pathogen reduces the size of the population by reducing the number of
social groups, allowing uninfected groups to grow larger from a reduction
in inter-group aggression. Concomitantly, Allee effects are exacerbated in
infected groups; this reduces the probability of pathogen persistence as
infected groups die out more rapidly. Social structuring changes
prevalence across scales and influences pathogen invasion and persistence.
The models described here provide a new framework for understanding the
dynamics of these interactions.   About Here is the R code
associated with the paper Brandell et al.
2021. A metapopulation model of social group dynamics
and disease applied to Yellowstone wolves. Proceedings of the National
Academy of Sciences. We provide code for the basic metapopulation models
(central_allee.R) and the disease models: susceptible-infected-susceptible
(SIS_model.R) and susceptible-infected-recovered (SIR_model.R).
We have also included the parameters used (parameters.R) and the wolf
count data used in Figure 1 of the main text (wolf_counts.csv).