Data from: Evolution of fungal phenotypic disparity
Data files
Aug 11, 2022 version files 518.96 KB
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data.zip
500.87 KB
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PCA_versus_NMDS.zip
14.39 KB
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README
3.70 KB
Oct 07, 2024 version files 519.31 KB
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data.zip
500.87 KB
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PCA_versus_NMDS.zip
14.39 KB
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README.md
4.05 KB
Abstract
Organismal grade multicellularity has been achieved only in animals, plants, and fungi. All three kingdoms manifest phenotypically disparate body plans, but their evolution has only been considered in detail for animals. Here we seek to test the general relevance of hypotheses on the evolution of animal body plans by characterising the evolution of fungal phenotypic variety (disparity). The distribution of living fungal form is defined by four distinct morphotypes: flagellated, zygomycetous, sac-bearing, and club-bearing. The discontinuity between morphotypes is a consequence of the extinction of phylogenetic intermediates, indicating that a complete record of fungal disparity would present a much more homogeneous distribution of form. Fungal phenotypic variety gradually expands through time for the most part but sharply increases with the emergence of multicellular body plans. Simulations show these temporal trends to be decidedly non-random, and at least partially shaped by hierarchical contingency. Fungal phenotypic distance is decoupled from changes in gene number, genome size, and taxonomic diversity. Only differences in organismal complexity, the number of traits that constitute an organism, at the cellular and multicellular levels present a meaningful relationship with fungal disparity. Both animals and fungi exhibit a gradual increase in disparity through time, resulting in distributions of form made discontinuous by the extinction of phylogenetic intermediates. These congruences hint at a common mode of multicellular body plan evolution.
https://doi.org/10.5061/dryad.wwpzgmsm9
Description of the data and file structure
Data from: Evolution of fungal phenotypic disparity
Thomas J. Smith & Philip C. J. Donoghue (2022), Nature Ecology & Evolution, DOI: 10.1038/s41559-022-01844-6.
Files and variables
File: PCA_versus_NMDS.zip
Description: Contains results of Spearman's Rank Correlation Tests between principal coordinate and non-metric multidimensional scaling for
different numbers of principal coordinate axes. Results provided for analyses conduct on ordinations of complete dataset,
subcellular dataset, and supracellular dataset.SR = sum of rages, AEDC = average Euclidean distance from centroid, SV = sum of variances,
ANNED = average nearest neighbour Euclidean distance, AMSTED = average minimum spanning tree Euclidean distance,
p = p value, coeff = Spearman's rank correlation coefficient.
File: data.zip
Description: Contains phenotypic discrete character, complexity, genome length, gene number, and diversity data. Also
includes ordination outputs and phylogeny used in analyses.
1a. complexity_data
Contains complexity data for each taxon derived from complete dataset, subcellular partition, and supracellular partition in CSV format.
1b. nexus
Contains phenotypic discrete character data in nexus format. Nexus files for complete, subcellular, and supracellular partition are provided.
0 = absent, 1 = present. For character descriptions, see Phenotypic_data_all_metadata.xlsx.
1c. NMDS_output
Contains non-metric multidimensional scaling (NMDS) scores for each sampled taxon along two NMDS axes (columns 1 and 2) in CSV format.
Scores derived from complete dataset, subcellular partition, and supracellular partition are provided.
1d. PCA_output
Contains principal coordinate scores (PCA) for each sampled taxon along each axis in CSV format. Each column represents a PCA axis.
Relative eigenvalues accounted for by each axis diminishes from 1 to 2, 2 to 3, and so on.
Scores derived from complete dataset, subcellular partition, and supracellular partition are provided.
1e. phenotypic_data_recoded_complexity
Contains phenotypic discrete character data in CSV format where each row represents a taxon and each column a character.
0 = absent, 1+ = present. All inapplicable character scores ("-") were recoded to absent ("0") prior to complexity score calculation.
CSV files for complete, subcellular, and supracellular partition are provided.
1f. phenotypic_data_recoded_ordination
Contains phenotypic discrete character data in CSV format where each row represents a taxon and each column a character.
0 = absent, 1+ = present. All inapplicable character scores ("-") were recoded to absent ("0") prior to distance matrix calculation,
and all other character scores were increased by 1 (i.e. inapplicable character scores were treated as a distinct character state).
CSV files for complete, subcellular, and supracellular partition are provided.
1g. secondary_data
Contains fungal taxonomic diversity (CSV) and genetic data (CSV/XLSX). Fungal diversity data takes the form of species richness values
for each taxon, with original source noted (COL = Catalogue of Life). Genetic data takes the form of an XLSX file, where each tab contains
the number of genes and genome length for each constituent taxon of the sampled taxa on Mycocosm, and a CSV file, where these values have been averaged for each sampled taxon.
1h. Naranjo_Ortiz_calibrated.tre
Tree file contained time-calibrated phylogenetic tree.
1i. Phenotypic_data_all_metadata.xlsx
XLSX file containing discrete phenotypic character data with character descriptions, hierarchical contingencies and sources.
0 = absent, 1 = present.
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Code/software
R version 4+
Access information
Other publicly accessible locations of the data:
- NA
Data was derived from the following sources:
- AFTOL, Literature
See linked manuscript.
Follow ReadMe files for explanation.