DOI: 10.5061/dryad.wwpzgmsm9
title: Data from: Evolution of fungal phenotypic disparity

description: 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.
description: See linked manuscript. 
description: Follow ReadMe files for explanation. 
description: # Data from: Evolution of fungal phenotypic disparity
 [https://doi.org/10.5061/dryad.wwpzgmsm9](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. ### ## Code/software R version 4+ ## Access information Other publicly accessible locations of the data: * NA Data was derived from the following sources: * AFTOL, Literature