We obtained the large-scale, extensive data on colonization-extinction
dynamics by surveying spruce deadwood and fruit bodies of the focal
polypore fungi in 174 forest patches across southern and central Finland
once in 2003-2005 (Nordén et al. 2013) and then resurveying them in
2014. These two surveys revealed the colonisation and extinction events
that had taken place between the first and the second survey and
constituted the data to estimate (parameters for) rate of change in
occupancy in the colonization-extinction models. Data from the first
survey formed the basis for the occupancy models.
A forest patch is a contiguous and homogeneous forest area that is
surrounded by other land types or forests of different age or tree
species (Fig. 1). The survey plot was of the size 20 m x 100 m and
subdivided into survey cells of 20 m x 20 m. All patches were dominated
by Norway spruce (Picea abies ) and covered a range of forest
types: clear-cuts with retention trees (53 patches, 16 of which had a
plot, 16 x 5 cells), woodland key habitats (56 patches, 56 plots, 56 x 5
cells); and managed forests (65 patches, 65 plots, 65 x 5 cells). In
each forest patch, in both surveys (2003-2005 and 2014), we surveyed the
two fungal species (Phellinus ferrugineofuscus and P.
viticola ) and deadwood both in each cell and in the remaining patch
area. See Appendix S1 for a detailed description of the data collection
and the focal species.
MODELLING OCCUPANCY AND COLONISATION-EXTINCTION
For each species, we fitted hierarchical Bayesian state-space models to
the presence-absence data of the species at three spatial modelling
scales (cell, plot and patch) and two deadwood resource resolutions
(diameter ≥5 cm or ≥15 cm). We included covariates collected for
different spatial modelling scales that we hypothesised would explain
the occupancies and colonization-extinction dynamics of the focal
species (Appendix S1). For the comparison with the
colonisation-extinction models, we also fitted occupancy models to data
from the first survey.
A detailed description of the occupancy and colonisation-extinction
models at the cell level is provided in Appendix S1. The number of
colonisations and extinctions recorded allowed including the effects of
covariates on colonisation probability of mature patches. For the
extinction probability and the colonisation probability of clear-cut
patches, only intercepts (i.e. the rate parameters) were estimated.
The covariates to retain in the final fitted models were determined with
forwards stepwise model selection. This model selection was based on
overlap of 95% credible intervals with 0, reduction in deviance and
biological knowledge on the species, as suggested by Gelman and Hill
(2007). The models were fit using OpenBUGS (Lunn et al. 2009) in R
through the library R2OpenBUGS (Sturtz et al. 2005). The data and
computer code used for models, simulations, and statistical analyses are
archived in the Swedish National Data Service,
https://snd.gu.se/en.
PROJECTING POLYPORE OCCUPANCIES THE COMING CENTURY
To answer our study questions, we utilized available projections of
forest conditions on National Forest Inventory (NFI) plots in adjacent
boreal Sweden between 2010 and 2110, the nationwide Forestry Scenario
Analysis by the Swedish Forest Agency (Claesson et al. 2015, Eriksson et
al. 2015; Appendix S1). Next we projected the occupancy dynamics of the
species for the same time period. For each polypore species, the final
fitted occupancy model was utilised to initialise the occupancy states
in the first time step, here 2010. We used 10-year time steps to
simulate the subsequent colonisation and extinction dynamics on the NFI
plots until 2110 using the final fitted colonisation-extinction model
with its estimated parameter values. For investigating the effect of
making projections based on occupancy models, the final fitted occupancy
model was instead used for each time step.
All projections were made based on drawing 1000 values from the joint
posterior distribution of the parameters from the fitted models. All NFI
plots with no dead spruce or those with ages 26-63 were given an
occupancy probability of zero, because of the typical absence of spruce
deadwood suitable for the species in forests of this age range (Mair et
al. 2017).