Red-listed species under threat: Unexpectedly high deadwood thresholds for their presence in managed boreal forests
Data files
May 15, 2026 version files 4.76 MB
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README.md
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Thresholds_bryophytes_data.csv
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Thresholds_dead_trees_data.csv
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Thresholds_fungi_data.csv
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Thresholds_lichens_data.csv
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Thresholds_living_trees_data.csv
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Abstract
Red-listed species form an important basis for conservation action, yet their exact habitat requirements often remain elusive due to their rarity and cryptic nature. Their occurrence is therefore often assessed indirectly, and we explore whether common indirect measures of forest biodiversity can also indicate the presence of red-listed species and allow for detection of environmental threshold values. To this end, we conducted a fieldwork campaign covering 120 plots along a gradient of structural availability and forest management intensity in Sweden. In these plots, we inventoried epixylic fungi and bryophytes, epixylic and epiphytic lichens, and tree-related attributes. Using logistic regression, we investigated whether taxon-specific structural thresholds (relating to deadwood, broadleaved trees, and large trees) could be ascertained for an increasing number of red-listed species. We found that deadwood volume, which strongly correlated with deadwood diversity, indicated a significantly increased probability of presence of red-listed epixylic fungi and bryophytes. The threshold values, for a 50 % probability of presence, for one red-listed species ranged from 36 to 63 m3/ha of total deadwood for fungi and 31 to 58 m3/ha of lying deadwood for bryophytes. For lichens, we were unable to find significant predictors of their presence. With this study, we show that deadwood volume can be used as an informative indicator for the presence of red-listed species of bryophytes and fungi but not lichens. Deadwood amount has previously been found to be a valuable single-variable-indicator, and our results further strengthen this notion. However, within the context of our study area and design, threshold values substantially exceeded previous suggestions for critical volumes of deadwood, emphasizing the context-dependent nature of threshold dynamics. Our findings nevertheless corroborate previous studies, highlighting the conservation issues posed by current low levels of deadwood provision in managed forests and underscoring the importance of protecting areas with high deadwood quantities
This readme file was generated on 20 April 2026 by Alwin A. Hardenbol
GENERAL INFORMATION
Author/Principal Investigator Information
Name: Alwin A. Hardenbol
ORCID: 0000-0002-0615-505X
Institution: Natural Resources Institute Finland (Luke)
Email: alwin.hardenbol@luke.fi
Date of data collection: 2021-2023
Geographic location of data collection: Hälsingland and Värmland, Sweden
Information about funding sources that supported the collection of the data: This study was financially supported by Stora Enso AB and the Wallenberg Initiatives in Forest Research (WIFORCE) funded by the Knut and Alice Wallenberg Foundation
SHARING/ACCESS INFORMATION
Licenses/restrictions placed on the data: None
Links to publications that cite or use the data: Published in conjunction with these data in Journal of Applied Ecology (same title)
Recommended citation for this dataset: See Dryad webpage
DATA & FILE OVERVIEW
File List:
- Thresholds_bryophytes_data.csv --- Species survey data of bryophytes
- Thresholds_fungi_data.csv --- Species survey data of fungi
- Thresholds_lichens_data.csv --- Species survey data of lichens
- Thresholds_dead_trees_data.csv --- Tree inventory data of dead trees (includes some living tree data too, but not to be used for living tree calculations)
- Thresholds_living_trees_data.csv --- Tree inventory data of living trees (includes some data on stumps, but not to be used for dead tree calculations)
Relationship between files, if important: Files on the different taxa were each used in conjunction with the living and dead tree data but not with each other.
METHODOLOGICAL INFORMATION
Instrument- or software-specific information needed to interpret the data:
R (version 4.2.1 was used but later versions will work fine for these analyses). The necessary R packages are clearly documented in the published article.
People involved with sample collection, processing, analysis and/or submission:
Alwin A. Hardenbol, Faith A.M. Jones, Jörgen Sjögren, Albin Larsson Ekström, Anne-Maarit Hekkala, Mari Jönsson, Matti Koivula, and Joachim Strengbom
DATA-SPECIFIC INFORMATION FOR: Thresholds_bryophytes_data.csv
Number of variables: 8
Number of cases/rows: 5180
VARIABLES
- Region: The region where the data were from; either Hälsingland or Värmland.
- PlotID: The individual ID of of each plot that we assigned.
- ForestType: The "forest type" each plot was located in (old clearcuts, retention patches, or set-asides).
- SubstrateID: The individual ID of each substrate item that we assigned on which the species was found.
- Species: The scientific name of the species in 2025.
- Taxon.id: The Swedish taxon ID for each species in 2025 (see https://artfakta.se/)
- Red.list.status: The red list status of the species in Sweden based on the 2023 red list.
- Year: Year in which the row of data was collected.
Missing data codes: NA
DATA-SPECIFIC INFORMATION FOR: Thresholds_fungi_data.csv
Number of variables: 8
Number of cases/rows: 686
VARIABLES
- Region: The region where the data were from; either Hälsingland or Värmland.
- PlotID: The individual ID of of each plot that we assigned.
- ForestType: The "forest type" each plot was located in (old clearcuts, retention patches, or set-asides).
- SubstrateID: The individual ID of each substrate item that we assigned on which the species was found.
- Species: The scientific name of the species in 2025.
- Taxon.id: The Swedish taxon ID for each species in 2025 (see https://artfakta.se/)
- Red.list.status: The red list status of the species in Sweden based on the 2023 red list.
- Year: Year in which the row of data was collected.
Missing data codes: NA
DATA-SPECIFIC INFORMATION FOR: Thresholds_lichens_data.csv
Number of variables: 8
Number of cases/rows: 48137
VARIABLES
- Region: The region where the data were from; either Hälsingland or Värmland.
- PlotID: The individual ID of of each plot that we assigned.
- ForestType: The "forest type" each plot was located in (old clearcuts, retention patches, or set-asides).
- SubstrateID: The individual ID of each substrate item that we assigned on which the species was found.
- Species: The scientific name of the species in 2025.
- Taxon.id: The Swedish taxon ID for each species in 2025 (see https://artfakta.se/)
- Red.list.status: The red list status of the species in Sweden based on the 2023 red list.
- Year: Year in which the row of data was collected.
Missing data codes: NA
DATA-SPECIFIC INFORMATION FOR: Thresholds_dead_trees_data.csv
Number of variables: 21
Number of cases/rows: 3588
VARIABLES
- Region: The region where the data were from; either Hälsingland or Värmland.
- PlotID: The individual ID of of each plot that we assigned.
- ForestType: The "forest type" each plot was located in (old clearcuts, retention patches, or set-asides).
- SubstrateID: The individual ID of each substrate item that we assigned.
- dateLichenSurvey: Date the substrate was assessed by the lichen surveyors. NA if it was not assessed by them.
- dateFungiSurvey: Date the substrate was assessed by the fungi surveyors. NA if it was not assessed by them.
- Condition: The condition of the substrate; either Dead or Living
- deadWoodType: The type of deadwood. NA = living tree or missing data (five instances). 1 = Standing deadwood. 2 = snag. 3 = fallen whole tree. 4 = fallen part of a tree.
- MeanDiameter: Mean diameter of the piece of wood. Measured in cm. Sometimes collected, or sometimes min and max diameters were collected.
- MinDiameter: Minimum diameter of the piece of wood. Measured in cm.
- MaxDiameter: Maximum diameter of the piece of wood. Measured in cm.
- Length: Length of the piece of wood if it is lying on the ground. Measured in m.
- Dbh: Diameter at breast height of standing trees. Measured in cm.
- Height: Height of standing trees (often estimated in the field by eye rather than measured). Measured in m.
- estimatedHeight: Estimated height using whole tree dbh calulations. Measured in m.
- TreeSpecies: Tree species of the substrate.
- Volume: Volume of the substrate in cubic m. If we had mean diameter and length we used a formula for a cylinder. If we had min and max diameter and length we used a formula
- for a truncated cone. If we had dbh (for whole trees), the volumes were calculated using allometric equations. Volume for deadwood type 2 was calculated using ratios of the measured/estimated height. For further information, see Appendix S3 in the Supporting Information of the published article.
- For deadwood volume per hectare (m3/ha), volume can be aggregated to the plot level by summing all substrates classified as dead (Condition = "Dead") within each plot. This total volume is then divided by plot area (in hectares). However, because plot area was recorded separately by the lichen and fungi teams, small discrepancies may occur. To ensure consistency, plot area should be harmonised by using the minimum of PlotAreaHectaresLichen and PlotAreaHectaresFungi for each plot (see below). If plot area is missing, a default value of 0.1256637 ha (standard plot size) is to be used.
- MeasuredBy: Who collected the data. Either just the fungi team, just the lichen team, or both teams collected data on the same substrate.
- PlotAreaHectaresLichen: The area of the plot in Ha of the lichen team.
- PlotAreaHectaresFungi: The area of the plot in Ha of the fungi team.
- decayStage: Decay stage of dead trees based on Siitonen et al. 2000 ranging from 1 to 5.
Missing data codes: NA
DATA-SPECIFIC INFORMATION FOR: Thresholds_living_trees_data.csv
Number of variables: 13
Number of cases/rows: 3979
VARIABLES
- Region: The region where the data were from; either Hälsingland or Värmland.
- PlotID: The individual ID of of each plot that we assigned.
- ForestType: The "forest type" each plot was located in (old clearcuts, retention patches, or set-asides).
- SubstrateID: The individual ID of each substrate item that we assigned.
- Condition: The condition of the substrate; either Living or Stump (the latter was not used in our analyses, however).
- TreeSpecies: Tree species of the substrate.
- LT-quality: Living tree quality.
- DT-quality: Dead tree quality.
- Diameter: Diameter at breast height (1.3 m) for living trees. Top diameter for stumps. Measured in cm.
- Length: Length/height of stumps. Measured in cm.
- decayStage: Decay stage of dead trees based on Siitonen et al. 2000 ranging from 1 to 5.
- estimatedHeight: Estimated height using whole tree dbh calulations. Measured in m.
- Volume: Volume of the substrate in cubic m. The volumes were calculated using allometric equations with dbh and estimated height. For stumps, it also assumed whole trees.
Missing data codes: NA
Data were collected from 120 forest plots in managed boreal forests in Fennoscandia between 2021 and 2023. Plots were selected to represent three forest types while maintaining comparable site conditions. All stands were conifer-dominated (≥ 70 % conifers), with similar non-conifer composition, and located on mesic to moist soils; very wet, dry, or steep sites were excluded. Plots were generally circular with a radius of 20 m (0.125 ha), although smaller retention patches were inventoried in their entirety.
Species inventories targeted four groups of sessile organisms: epixylic fungi, epixylic bryophytes, epixylic lichens, and epiphytic lichens. Surveys were conducted by expert field personnel using standardised protocols. Epixylic fungi were recorded on both standing and lying deadwood, including all large deadwood items (≥ 15 cm diameter) and a subsample of smaller diameter classes. Epixylic bryophytes were surveyed on lying deadwood only, while lichens were surveyed on both dead (epixylic) and living (epiphytic) trees up to 2 m height. Living trees were subsampled to include both small and large individuals per species. Lichen species were classified as epixylic or epiphytic depending on the condition (dead or living) of the substrate on which they were observed.
Tree and deadwood inventories were conducted alongside the species surveys. For dead trees, species identity, decay stage, orientation (standing or lying), intactness, and size were recorded. Measurements differed depending on tree condition but included diameter at breast height for standing trees and diameter and/or length for lying logs. Only deadwood with a minimum base diameter ≥10 cm was included. Living trees were inventoried in circular subplots (7 m radius), recording species identity and diameter at breast height.
From these data, plot-level variables were derived, including volumes of total and lying deadwood (m3/ha), as well as structural attributes of living trees. Species data were summarised as the number of unique nationally red-listed species per plot for each taxonomic group.