DOI: 10.5061/dryad.fttdz093x
title: Data from: Partitioning beta diversity at two spatial resolutions reveals biotic homogenisation with habitat degradation

description: 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. 
description: 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.
description: # Data from: Partitioning beta diversity at two spatial resolutions
 reveals biotic homogenisation with habitat degradation
 [https://doi.org/10.5061/dryad.fttdz093x](https://doi.org/10.5061/dryad.fttdz093x) ## Description of the data and file structure This data is assemblages data for bryophytes on deadwood, lichens on all substrates, and polypores and select cortioid fungi on deadwood surveyed in 2022-2023 in 120 20m circle plots in Sweden. The plots are distributed evenly between young forests (clearcut 20-30 years ago), retention patches in these young forests, and more mature forests set-aside for conservation. This data is associated with [https://doi.org/10.1111/ddi.70080](https://doi.org/10.1111/ddi.70080) ### Files and variables There are three CSV data filed in this dataset, each relating to one of the three taxa surveyed (bryophytes, lichens, and polypores). Data come from three types of forest management type: Retention patches (groups of trees left unharvested during clearcutting), young forests (forests clearcut 20-30 years ago), and setasides (larger areas of forest left unharvested, partly for biodiversity conservation purposes). The retention patches are always set in a young forest. Data also comes from two regions in Sweden: Hälsingland, which is coastal and more northerly, and Värmland, which is more inland and to the south. **lichenDataSweden.csv** Data on lichens growing on living and dead trees in forests in Värmland and Hälsingland, Sweden. Collected in 2021 and 2022 *Columns:* * Country: country the data came from (Sweden) * Region: whether the data are from Halsingland or Varmland, two different regions in Sweden * PlotID: individual ID of each plot. A unique id for each plot in the study. Most plots follow the code where the first letter says if the plot is in Finland (F), Hälsingland (T for triplet - not H because some old code use H already), and Värmland (V for triplet)the number designates which site cluster, and the final letter designates the forest type (R = retention, C= control, O = clearcut). There are also sites beginning with N or H, and these are old names from a previous study in Hälsingland. * ForestType: Type of forest the plot is located in (Retention, young forest (sometimes called old clearcut), or set-aside). * area.ha: the size of the surveyed plot  * SubstrateID: A unique ID for each substrate in a plot. First characters refer to the plot ID the substrate was found in, and the S or L refers to which team (S = fungi, L = lichen) surveyed the substrate first * TaxaType: Type of taxa * Species: clean species name * Taxon.id: taxon ID for each species from Dyntaxa ([https://artfakta.se/metadata/dyntaxa](https://artfakta.se/metadata/dyntaxa))  * Comments: any relevant comments by surveyors * Red.list.status : current (2023) red list status in Sweden * Year: The year the data were collected in the field **SwedenBryophyteData.csv** *Columns:* * Country: country the data came from (Sweden) * Region: whether the data are from Halsingland or Varmland, two different regions in Sweden * PlotID: individual ID of each plot. * ForestType: Type of forest the plot is located in (Retention, young forest (sometimes called old clearcut), or set-aside). * area.ha: the size of the surveyed plot  * SubstrateID: individual id of each substrate item * TaxaType: Type of taxa * Species: clean species name * Taxon.id: taxon ID for each species from Dyntaxa ([https://artfakta.se/metadata/dyntaxa](https://artfakta.se/metadata/dyntaxa))  * Comments: any relevant comments by surveyors * Red.list.status : current (2023) red list status in Sweden * Year: The year the data were collected in the field * LogAsSubstrate: A rough estimate of whether dead logs are listed as a substrate this species grows on  **woodFungiSweden.csv** Data on wood fungi species presence on dead wood in Sweden. Data were collected in 2021 by a variety of contractors. Original data contained info on substrates too, but these have been cleaned into another csv file. *Columns* * Country - the country the data comes from. Finland or Sweden. * Region - The region of the country each plot is located in. Hälsingland and Värmland in Sweden were collected by different people, whereas the Finnish data was collected as a unit. * PlotID - a unique id for each plot in the study. Most plots follow the code where the first letter says if the plot is in Finland (F), Hälsingland (T for triplett - not H because some old code uses H already), and Värmland (V for triplet) the number designates which site cluster, and the final letter designates the forest type (H = retention, K = control, U = clearcut). There are also sites beginning with N or H, and these are old names from a previous study in Hälsingland. * ForestType - category of forest management the plot has undergone in the last few decades * area.ha: the size of the surveyed plot  * SubstrateID - a unique ID for each substrate in a plot. First characters refer to the plot ID the substrate was found in, and the S or L refers to which team (S = fungi, L = lichen) surveyed the substrate first * TaxaType - what type of taxa data it is. Polypore or cortoid for this data * Species - Scientific name of wood fungi species * Taxon.ID - A unique ID from Dyntaxa for each species that doesn't change with new phylogenetic data * Year - the year that the species were surveyed