TraitAM, a global spore trait database for arbuscular mycorrhizal fungi

Contact: Dr. V. Bala Chaudhary, bala.chaudhary@dartmouth.edu

Filenames: All files have names of the form "DataRecord_(number)(contents)(date updated, DDMonYYYY)," for example, "DataRecord_1_CalculatedTraitMetrics_18Jun2024.csv" is a data record #1, contains "calculated trait metrics," and was last updated on June 18th, 2024.

TraitAM contains data on the spore traits of all Arbuscular Mycorrhizal (AM) fungi with available species descriptions through 2023. Data were collected by manually reading species descriptions and extracting relevant information from 2019 to 2024. For full description, methods, and metadata see publication:

Chaudhary, V. B., Gonzalez, J. B., Nokes, L. F., Cooper, P. O., Katula, A. M., Mares, E. C., Limbu, S. P., Robinson, J. N., Aguilar-Trigueros, C. A. (2024). TraitAM, a global spore trait and phylogeny database for arbuscular mycorrhizal fungi. Manuscript submitted for publication.

Files:

DataRecord_1_CalculatedTraitMetrics_18Jun2024.csv: Table containing the calculated trait metrics for all taxa in the database, including spore volume, shape, color, wall investment, and ornamentation height.

DataRecord_2_TraitAMraw_18Jun2024.csv: Table containing the raw data used to calculate the trait metrics in DataRecord_1. Cells containing "NA" reflect data that was not present in the species descriptions.

DataRecord_3_TraitMetricsCode_18Jun2024.R: R script containing the annotated code used to calculate the trait metrics in DataRecord_1 from the raw data in DataRecord_2.

DataRecord_4_SpeciesDescriptions_18Jun2024.csv: Table containing a list of all species in the TraitAM database and the bibliographic information for the paper containing the species description we used to collect data on the species for DataRecord_2.

DataRecord_5_SpeciesListWithAccnNum_Oct2023.csv: Table containing a list of species used in the creation of the Arbuscular Mycorrhizal fungal phylogeny, with the GenBank accession numbers for the sequences used in the creation of the phylogenetic tree.

DataRecord_6_LSUseqsLROR-FLR2_28Oct2023.fasta: LSU sequences used in phylogenetic analysis, trimmed to LROR-FLR2 (n=231).

DataRecord_7_FinalTree_Oct2023.tre: Phylogenetic tree generated from DataRecord_6.

DataRecord_8_PhyloanalysisCode_28Oct2023.txt: Code used in phylogenetic analysis for Maximum Likelihood and Bayesian Inference approaches used to generate DataRecord_7.

Metadata for DataRecord_1:

species = species binomial nomenclature, followed by “_morpha” for acaulosporoid morphs and “_morphg” for glomoid morphs, if applicable

order = Taxonomic order of the species

family = Taxonomic family of the species

genus = Genus

vol_mean = Spore volume (μm3)

shape_mean = Spore shape, aspect ratio of spore length (μm) / spore width (μm)

color_most = Color mode (see metadata for DataRecord_2)

investment_mean = Spore wall investment, ratio of wall volume / total spore volume

orn_height_mean = Mean ornamentation height (μm) (see metadata for DataRecord_2)

Metadata for DataRecord_2:

species = Species binomial nomenclature

order = Taxonomic order of the species

family = Taxonomic family of the species

genus = Genus

color_low = “Minimum” color: To standardize the color data across the database, we assigned the following ordinal scale for common color along a pigmentation gradient ranging from 0 (hyaline, no pigmentation) to 6 (fully melanized, dark). The intermediate values include 1, white to cream or pink, 2, yellow, 3, green, 4, orange to red, and 5, brown. For each species we include three color data points: minimum, mode, and maximum. If a spore with “yellow to yellow orange” it would have color minimum 2, color mode 2, and color maximum 4.

color_most = Color mode, see above

color_high = Color maximum, see above

orn_height_min = Minimum height of ornamentation, as given in species description. 0 if there is no ornamentation

orn_height_mean = Mean height of ornamentation, as given or as the average of the minimum and maximum given if not. 0 if there is no ornamentation

orn_height_max = Maximum height of ornamentation, as given. 0 if there is no maximum ornamentation

orn_diam_min = Minimum diameter of ornamentation, as given in species description. 0 if there is no ornamentation

orn_diam_mean = Mean diameter of ornamentation, as given or as the average of the minimum and maximum given if not. 0 if there is no ornamentation

orn_diam_max = Maximum diameter of ornamentation, as given. 0 if there is no maximum ornamentation

min_wall_thickness = Minimum wall thickness of the spores

mean_wall_thickness = Mean wall thickness of the spores

max_wall_thickness = Maximum wall thickness of the spores

dim1.min2 = Dimension 1 minimum 2 (lower minimum). Spore dimensions are given for each spore shape as ranges with up to four values describing the distribution of each dimension. The traitAM database includes eight dimension data points for each spore shape described: dimension lower minimum, dimension higher minimum, dimension lower maximum, and dimension higher maximum for two dimensions, length and width.

dim1.min = Dimension 1 minimum

dim1.max = Dimension 1 lower maximum

dim1.max2 = Dimension 1 upper maximum

dim2.min2 = Dimension 2 lower minimum

dim2.min = Dimension 2 upper minimum

dim2.max = Dimension 2 lower maximum

dim2.max2 = Dimension 2 upper maximum

Changelog: all changes to the TraitAM database and any files will be logged here with a timestamp and a description of changes.

Provenance

This section was added after capturing a versioned copy of TraitAM

for humans

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README.md	hash://sha256/de75afb0a7222a5591e3e39869befa2c0fb5d7a2e4ade47d49380e1ccb8b39fb

as generated via

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Indexing

Configuration to help Global Biotic Interactions (GloBI, https://globalbioticinteractions.org) index:

Chaudhary, Bala; Nokes, Liam; Gonzalez, Jennifer et al. (2025). TraitAM, a global spore trait database for arbuscular mycorrhizal fungi [Dataset]. Dryad. https://doi.org/10.5061/dryad.6hdr7sr8z

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TraitAM, a global spore trait database for arbuscular mycorrhizal fungi

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Name		Name	Last commit message	Last commit date
Latest commit History 5 Commits
.github/workflows		.github/workflows
data		data
.gitignore		.gitignore
DataRecord_1_CalculatedTraitMetrics_18Jun2024.csv		DataRecord_1_CalculatedTraitMetrics_18Jun2024.csv
DataRecord_2_TraitAMraw_18Jun2024.csv.csv		DataRecord_2_TraitAMraw_18Jun2024.csv.csv
DataRecord_3_TraitMetricsCode_18Jun2024.R		DataRecord_3_TraitMetricsCode_18Jun2024.R
DataRecord_4_SpeciesDescriptions_18Jun2024.csv		DataRecord_4_SpeciesDescriptions_18Jun2024.csv
DataRecord_5_SpeciesListWithAccnNum_Oct2023.csv		DataRecord_5_SpeciesListWithAccnNum_Oct2023.csv
DataRecord_5_SpeciesListWithAccnNum_Oct2023_edited20260724.csv		DataRecord_5_SpeciesListWithAccnNum_Oct2023_edited20260724.csv
DataRecord_6_LSUseqsLROR-FLR2_28Oct2023.fasta		DataRecord_6_LSUseqsLROR-FLR2_28Oct2023.fasta
DataRecord_7_FinalTree_Oct2023.tre		DataRecord_7_FinalTree_Oct2023.tre
DataRecord_8_PhyloanalysisCode_28Oct2023.txt		DataRecord_8_PhyloanalysisCode_28Oct2023.txt
README.md		README.md
globi.json		globi.json

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