Data from: Life-history traits and phylogeny structure taxon-specific species-substrate relationships in deadwood
Data files
Aug 03, 2026 version files 29.32 MB
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myTreeeffar.csv
42.18 KB
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README.md
3.62 KB
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TrDataeffar.csv
21.42 KB
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UNITE_ITS_euk_out.txt
2.01 MB
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XDataeffar.csv
24.27 KB
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Yeffar.csv
212.81 KB
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zotus.fa
4.75 MB
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zotutab_global.txt
22.26 MB
Abstract
To understand the structuring of species assemblages, integrating life-history traits and evolutionary heritage in analyses is vital. This allows the establishment of a mechanistic link between species and their environment. Deadwood systems are vital for nutrient cycling and biodiversity support, governed by complex intra- and inter-specific fungal and insect species interactions. However, trait- and phylogeny-based approaches to studying species-host and species-to-species relationships in deadwood community assembly have received little attention. We link life-history traits and phylogeny to species-host and species-to-species relationships of saproxylic beetles and fungi in 256 Scots pine (Pinus sylvestris) deadwood substrates derived from a forest restoration experiment in central Sweden. We test how the composition of deadwood substrates shapes beetle and fungal assemblages through their ecological traits (body size, feeding guild, and primary lifestyle) and phylogenetic relatedness. We compare substrates that differ in posture (standing or lying) and origin (machine-created or burned). Trait composition differed among substrate types for both taxa, but only fungi revealed a phylogenetic relationship with substrate type. Lying substrates were characterized by smaller-bodied and fungivore beetles, while standing substrates supported larger beetle species. Lichenized fungi were more prevalent on machine-created than burned substrates. After accounting for substrate type, traits, and phylogenetic signal, we found one species-to-species association between beetles and numerous fungi-fungi associations. We found that deadwood posture and origin structured the trait- and phylogenetic composition of saproxylic beetles and fungi. Differences in trait composition and phylogeny, and lack of detected species-to-species associations, suggest that life history traits and phylogeny explain community assembly patterns in deadwood, with interspecific relationships playing a minimal role for beetles but a larger role for fungi at later stages of wood decay. Trait information for beetles can reveal meaningful species-host relationships, while fungal assemblages are phylogenetically structured and generally lack detailed trait information for whole species communities.
Dataset DOI: 10.5061/dryad.8cz8w9h6w
Description of the data and file structure
Contains data used for the HMSC models. Beetle data is collected from emergence traps and fungal data from wood DNA samples (see https://doi.org/10.1016/j.jenvman.2024.123416 for details).
The data is divided into four CSV files containing phylogeny, traits, substrate information, and the species matrix.
myTreeeffar.csv - contains phylogeny (taxonomy as proxy) for all species/zOTUs that are found on 3 or more substrates. Columns containing Class, Family, Genus, Order, Phylum, Species
TrDataeffar.csv - contains trait information for all species/zOTUs that are found on 3 or more substrates, including "beetlefungi" that is used to run beetles and fungi together, "Nutr" is feeding guild for beetles, e.g., predator, fungivore, etc., "primary_lifestyle" for fungi, "Size" is body size in mm for beetles, "Species" is species name
XDataeffar.csv contains substrate information for the deadwood samples, including type, size, etc. Column descriptions for XDataeffar.csv:
- ID = Unique ID for the substrate
- Stand = ID of the forest stand in which the substrate is in
- Substrate = The alignment/type of the substrate, log = lying deadwood, HS = high-stump, ~3 m height, snag = whole dead standing tree.
- Creation = Type of creation/origin of death, CR = machine-created by a harvester head and BR = died from prescribed burning.
- Type2 = Combination of Substrate and creation, for example HSCR is High-stump + machine-created.
- Trt = Stand-level treatment; numbers are related to the % of retained trees during felling: 3, 10, 30, and 50 % retained trees. B50 is 50% retention and prescribed burning; B100 is 100% retention and prescribed burning. NS = 100% retention and deadwood enrichment.
- Trapno = the Substrate + trap number within that stand
- Transect = Repetition of the stand-level treatment, 1, 2 or 3.
- d1 = Bottom diameter for logs and DBH for snags and high-stumps in cm
- d2 = top diameter for logs in cm
- h.l = height/length in meters
- decay = Decay stage following Siitonen & Saaristo (2000) (doi:10.1016/S0006-3207(99)00174-3)
- bark = Estimated % of bark cover
- Location = estimated shading/openness whether within retention patch, on edge of retention patch, open or in forest interior
- Tragosoma, M. sutor & Tomicus = Presence/absence of emergence holes of Tragosoma depsarium, Monochamus sutor or Tomicus minor.
- Align = Alignment whether Standing, Downed or Fallen
Yeffar.csv contains a species matrix with species as columns and samples (substrates) as rows for all species that are found on 3 or more substrates
UNITE_ITS_euk_out.txt contains probabilistic taxonomic assignment of ZOTUs using downloaded UNITE sequences as a reference database with the SINTAX algorithm
zotus.fa contains non-chimeric sequence variants (zero radius OTU = ZOTU). Contains all ZOTUs, some of which may not be present in the final data.
zotutab_global.txt contains the raw OTU table with ZOTUs as rows, samples as columns, and count of sequence reads in the cells.
Code/software
No specific software is needed to view the data. The data was analysed with the HMSC framework; see https://doi.org/10.1111/2041-210X.13345