Partitioning beta diversity at two spatial resolutions reveals biotic homogenisation with habitat degradation

This data pertains to lichen, fungi, and bryophyte species composition from 120 forest sites across Sweden.  The data is from a detailed species inventory by species experts in 2021 and 2021 in two regions in Sweden: Hälsingland and Värmland. For each taxa we have assemblage data from 20m radius plots in three different forest management types: Young forests (clearcut 20-30 years ago), Retention Patches (small patches of forest left unharvested during the young forest's harvesting phase 20-30 years ago), and Set-asides (larger patches of forest left unharvested partly for biodiversity conservation. These three forest management types reflect three different levels of habitat degradation: high degradation (young forest), medium degradation (retention patches), and low degradation (set-asides). Using this data, we used beta diversity partitioning to assess how community composition varied between habitat degradation level. We examined how pairwise total beta diversity, nestedness, and turnover varied when comparing assemblages from sites of either the same or different habitat degradation levels. In addition, we examined the relationship between total beta diversity, nestedness and turnover when assemblages pooled at the habitat degradation level were compared. We detected a small increase in pairwise lichen total beta diversity (Cliffs delta 0.40) and nestedness (Cliffs delta 0.19), but not in any other pairwise comparisons. In contrast, for all taxa, comparisons between assemblages pooled at the habitat degradation level showed higher values of nestedness and lower values of turnover than the corresponding pairwise comparisons, suggesting biotic homogenisation in highly degraded sites. This data has potential for exploring how communities are assembled across different types of land management and between taxa. 

Methods
We undertook an extensive survey of 120 sites within Sweden, distributed evenly between the three different habitat degradation levels (low degradation: mature set-aside forests, medium degradation: retention patches, and high degradation: young forests, clearcut in ca 30 years ago, Rudolphi et al. 2014). At each site, we inventoried the presence of species from all three taxonomic groups in circular plots with a 20-m diameter. When retention patches were smaller than this, we surveyed the entire area of the retention plot, here defined as the area covered by the canopy layer of the dominant tree species.

Lichens were surveyed up to 2 m in height on all standing dead trees within the plot. A subset of living trees was also surveyed: three small (diameter at breast height of between 5 and 15 cm) trees and seven large (diameter at breast height of at least 15 cm) for each dominant tree species (either Norway spruce or Scotch pine). If insufficient trees from one size class were available, we surveyed more from the other size class to maintain a constant subsample of 10 living trees per plot. Most lichens were visually identified to species in the field, but some unclear specimens were further assessed in the laboratory.

For the fungi survey, three small (diameter at breast height of between 5 and 15 cm) lying items of deadwood and three small standing trees per dominant tree species were surveyed in each plot. Then, all dead wood with either a diameter at breast height of at least 15 cm, for standing trees, or for lying deadwood, a maximum diameter of 15 cm and a minimum length of 1.3 m, for all tree species including deciduous trees, was inventoried. Standing trees were surveyed up to a height of 3 m. Species identification of fungi was based on the appearance of fruiting bodies.

Bryophytes were surveyed on all deadwood with a minimum diameter greater than 15 cm and an additional five smaller deadwood items per dominant tree species. Highly decayed wood (Decay stage 5, Renvall 1995) was considered part of the organic topsoil layer and not surveyed.