METADATA FOR Data for Deciduous forest restoration alters but does not restore functional and phylogenetic diversity of saproxylic beetles https://doi.org/10.5878/f467-k877 Containing: functional_pcoa_axes.csv, functional_traits.csv, sample_environmental_data.csv, species_abundance_matrix.csv, taxonomic_hierarchy.csv, diversity_metrics.csv, community_weighted_means.csv DESCRIPTION The data files contains the processed data used to analyse the taxonomic, functional and phylogenetic diversity of saproxylic beetles sampled in 67 flight-interception traps in 2021. The traps were distributed among non-restored, restored and target deciduous forest stands in Sweden. The workbook includes 316 beetle species. Missing trait classifications are coded as "unknown". Sampling information of beetles and environmental variables can be found in: Larsson Ekström A, Hjältén J, Löfroth T (2024) A decadal study reveals that restoration guided by an umbrella species does not reach target levels. Journal of Applied Ecology 61:513–525. https://doi.org/10.1111/1365-2664.14586 Calculation of diversity metrics (R): Richness and Shannon diversity was calculated with the vegan package - Oksanen J, Blanchet FG, Kindt R, Legendre P, Minchin P, O’Hara R, Simpson G, Solymos P, Stevens M, Wagner H (2017) vegan: community ecology package. R package Functional diversity metrics (FRic, FEve, FDiv) including Community weighted means of trait values were calculated with the FD package - Laliberté E, Legendre P, Shipley B (2014) FD: measuring functional diversity from multiple traits, and other tools for functional ecology. R package version 1.0-12 Phylogenetic diversity metrics (PSR,PSE,PSV) were calculated with the picante package - Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO (2010) Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464. https://doi.org/10.1093/bioinformatics/btq166 Phylogenetic dissimilarity with Kling MM (2025) Phylospatial: an R package for spatial phylogenetic analysis with quantitative community data. Methods in Ecology and Evolution 16:1075–1083. https://doi.org/10.1111/2041-210X.70056 Beetle functional traits were compiled based on literature and expert oppinions: Dahlberg A, Stokland JN (2004) Vedlevande arters krav på substrat. Skogsstyrelsen Rapport 7:1–74 Ehnström B, Axelsson R (2002) Insektsgnag i bark och ved. ArtDatabanken, SLU, Uppsala, Sweden Hagge J, Abrego N, Bässler C, Bouget C, Brin A, Brustel H, Christensen M, Gossner MM, Heilmann-Clausen J, Horák J, Gruppe A, Isacsson G, Köhler F, Lachat T, Larrieu L, Schlaghamersky J, Thorn S, Zapponi L, Müller J (2019) Congruent patterns of functional diversity in saproxylic beetles and fungi across European beech forests. Journal of Biogeography 46:1054–1065. https://doi.org/10.1111/jbi.13556 Hansen AK, Justesen MJ, Kepfer-Rojas S, Byriel DB, Pedersen J, Solodovnikov A (2018) Ecogeographic patterns in a mainland–island system in northern Europe as inferred from the rove beetles (Coleoptera: Staphylinidae) on Læsø island. European Journal of Entomology 115:256–263. https://doi.org/10.14411/eje.2018.025 Koch K (1992) Die Käfer Mitteleuropas: Ökologie. Goecke & Evers, Krefeld, Germany Seibold S, Brandl R, Buse J, Hothorn T, Schmidl J, Thorn S, Müller J (2015) Association of extinction risk of saproxylic beetles with ecological degradation of forests in Europe. Conservation Biology 29:382–390. https://doi.org/10.1111/cobi.12427 Swedish Species Information Centre (2024) Artfakta. Swedish University of Agricultural Sciences, Uppsala, Sweden. https://artfakta.se/ (accessed 19 June 2023) UK Beetles (2022) UK Beetles. https://www.ukbeetles.co.uk/ (accessed 19 June 2023) TREATMENT AND SAMPLE CODES C = non-restored stand R = restored stand W = target stand trapid identifies an individual trap. The first letter identifies the stand type, the number identifies the stand, and the final letter (A, B or C) identifies one of three traps within the stand. Plotid identifies the forest stand. File: species_abundance_matrix.csv, 68 rows, 317 columns Species-by-trap community matrix used throughout the analyses. - Rows represent individual traps. - trapid: Unique trap identifier. - All remaining columns represent beetle species. - Values are the total number of individuals of each species collected in each trap between June and October 2021. - A value of 0 indicates that the species was not recorded in that trap. File: functional_traits.csv, 317 rows, 9 columns Functional traits for the 316 beetle species included in the analyses. - Species: Scientific species name according to Swedish Dyntaxa nomenclature. - Tree: Tree-species association. Con = associated with coniferous trees Dec = associated with deciduous trees Both = tree-species generalist unknown = no reliable classification available - Size: Mean adult body length in millimetres, based on literature. - succ: Association with deadwood successional or decay stage. early = damaged trees or early decay stages middle = intermediate decay stages late = late succession or highly decayed deadwood generalist = no specific successional-stage association unknown = no reliable classification available - P: Predatory feeding guild. - Fu: Fungivorous feeding guild. - W: Wood-boring feeding guild. - C: Cambivorous feeding guild. - D: Detritivorous feeding guild. Feeding guilds are binary: 1 indicates membership and 0 indicates non-membership. Species may belong to multiple feeding guilds. File: taxonomic_hierarchy.csv, 317 rows, 8 columns Taxonomic hierarchy used as a proxy for beetle phylogeny. The hierarchy was obtained from the Swedish Dyntaxa system. All branches were assigned equal length when constructing the phylogenetic tree. - Ordning: Order. - Underordning: Suborder. - Överfamilj: Superfamily. - Familj: Family. - Underfamilj: Subfamily. - Tribus: Tribe. - Släkte: Genus. - Species: Species. The Swedish column names were retained from the original taxonomic database. File: sample_environmental_data.csv, 68 rows, 7 columns Sample identifiers and stand-level environmental variables used in the linear mixed-effects models. - trapid: Unique trap identifier. - Treatment: Stand type (C, R or W). - Plotid: Stand identifier used as the random effect in the models. - dw: Deadwood volume (m3 ha-1). - ba: Basal area of living trees (m2 ha-1). - dwshannon: Shannon diversity of deadwood, based on combinations of tree species, diameter class, decay class and deadwood type. - ltshannon: Shannon diversity of living trees, based on tree species and diameter class. Environmental variables were measured at stand level and are therefore repeated for the traps within each stand. File: diversity_metrics.csv, 68 rows, 12 columns Trap-level taxonomic, functional and phylogenetic diversity metrics used in the statistical analyses. - trapid: Unique trap identifier. - Treatment: Stand type (C, R or W). - Plotid: Stand identifier. - richness: Number of beetle species recorded in the trap. - shannon: Shannon diversity calculated from species abundances. - evenness: Taxonomic evenness, calculated as Shannon diversity divided by the natural logarithm of species richness. - FRic: Functional richness; the amount of functional trait space occupied by the community. - FEve: Functional evenness; the evenness of species-abundance distribution within functional trait space. - FDiv: Functional divergence; the degree to which abundance is concentrated towards the edges or centre of functional trait space. - PSR: Phylogenetic species richness, combining species richness and phylogenetic relatedness. - PSE: Phylogenetic species evenness. - PSV: Phylogenetic species variability, representing phylogenetic relatedness independently of species richness. All diversity metrics were calculated separately for each trap. File: community_weighted_means.csv, 68 rows, 26 columns Community-weighted means of functional traits for each trap. Continuous-trait CWMs represent abundance-weighted mean values. For categorical traits, each category was represented as a binary variable, and its CWM therefore represents the relative abundance of individuals belonging to that category. - Treatment: Stand type (C, R or W). - trapid: Unique trap identifier. - Tree_Both: Relative abundance of tree-species generalists. - Tree_Con: Relative abundance of conifer-associated species. - Tree_Dec: Relative abundance of deciduous-associated species. - Tree_unknown: Relative abundance of species without a reliable tree association classification. - Size: Abundance-weighted mean adult body length in millimetres. - succ_early: Relative abundance associated with early deadwood succession or decay. - succ_middle: Relative abundance associated with intermediate deadwood succession or decay. - succ_late: Relative abundance associated with late deadwood succession or decay. - succ_generalist: Relative abundance of successional-stage generalists. - succ_unknown: Relative abundance without a reliable successional-stage classification. - P_1, Fu_1, W_1, C_1 and D_1: Relative abundance belonging to the respective feeding guild. - Columns ending in _0: Relative abundance not belonging to the corresponding feeding guild. - Plot: Numeric stand identifier. - Trap: Trap replicate (A, B or C). - Plotid: Stand identifier. - Year: Sampling year (2021). Because species may belong to multiple feeding guilds, feeding-guild proportions are not mutually exclusive and should not be summed across guilds. File: functional_pcoa_axes.csv 317 rows, 6 columns Species coordinates on the five principal coordinate analysis axes used to construct the functional trait space. - Species: Scientific species name. - Axis.1-Axis.5: Species scores on the first five PCoA axes. The PCoA was based on a Gower distance matrix calculated from body size, feeding guild, tree-species association and deadwood successional-stage association. A Cailliez correction was applied. These five axes were used to calculate functional richness, evenness and divergence and to analyse functional composition.