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.

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.

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).