DOI: 10.5061/dryad.sj3tx96gr
title: Changes in metazoan functional diversity during the Cambrian Sinsk Event

description: A dataset of Cambrian skeletal metazoans, detailing their species richness
 and functional traits across a number of time bins. We examined functional
 diversity changes across a mass extinction event. Enclosed R scripts are
 fully annotated to facilitate the reproduction of all analyses and
 figures. 
description: Functional diversity analyses were performed in the R environment
 (Version 2.2.2) using the package mFD (multifaceted Functional Diversity)
 (Magneville et al., 2022; R Core Team, 2022; see Supplementary Materials).
 Trait-based distances between taxonomic groups were calculated using the
 Gower distance metric, since this can accommodate both continuous and
 categorical variables (de Bello et al., 2021).
 Principal Coordinates Analysis (PCoA) was used to calculate
 Euclidean distances between taxonomic groups based on the pairwise Gower
 distances calculated from the functional traits of all taxonomic groups
 across the study interval. A convex hull was then constructed for each
 assemblage, and functional richness and functional dispersion were
 calculated. Functional richness quantifies the proportional occupation of
 all possible functional space, while functional dispersion is the centroid
 between taxonomic groups in functional space, calculated from a species
 richness weighting. Functional beta-diversity between assemblages was also
 calculated to evaluate the degree of functional nestedness and turnover
 between assemblages. These functional diversity metrics were then compared
 with taxonomic diversity, which is a count of the number of taxonomic
 groups in each time bin.
description: # Changes in metazoan functional diversity during the Cambrian Sinsk Event
 Dataset DOI: [10.5061/dryad.sj3tx96gr](10.5061/dryad.sj3tx96gr) ##
 Description of the data and file structure We have submitted all data
 files used for analysis and generation of figures for the paper
 'Changes in metazoan functional diversity across the Cambrian
 Radiation and the first Phanerozoic mass extinction: the Cambrian Sinsk
 Event' (Murphy et al. 2025). Data include species richness across
 time bins (species_richness.csv), species richness compared to functional
 richness (functional___species_richness.csv), rates of origination &
 extinction (origination_extinction.csv), proportionate species richness
 across taxonomic groups (stack_area_ungrouped.csv), functional traits of
 taxonomic groups (trait_data.csv), tags of data trait types
 (trait_categories.csv), and a matrix of species across time bins
 (trait_matrix.csv). These are accompanied by two fully annotated R scripts
 to reproduce the analyses and figure generation using the above datasets:
 * Sinsk_metazoan_functional_diversity_-_additional_code_for_figures.R *
 Sinsk_metazoan_functional_diversity_-_main_analyses.R # Descriptions ##
 Species_richness.csv * 'time start': Year of start of time bin *
 'interval': Duration of time bin * 'interval length':
 Number of years in time bin (Myr) * 'group': Taxa grouped by
 attachment and motility traits * 'no_spp': Number of species in
 each group ## Functional_species_richness.csv * The first three columns
 are the same as above * 'Time bin': Code of time bin *
 'Total groups': Number of taxonomic groups * 'Total
 spp': Number of species * 'Spp prop': Species as a
 proportion of total * 'FRic': Functional richness indices *
 'Origination': New taxonomic groups in time bin *
 'Extinction': Taxonomic groups going extinct in the time bin ##
 Origination_extinction.csv * 'bin_start', 'bin_end',
 'bin_mid', start, end, and mid-point of time bins (in MA,
 millions of years ago) * 'Origination', 'Extinction',
 'Total_groups', 'Total_spp' as described above *
 'Rate_ori' & 'Rate_ext': Rates of origination and
 extinction, as the number of groups originating or going extinct as a
 proportion of the total number of groups ## Stack_area_ungrouped *
 'time_start', 'interval', 'interval_length':
 as described above * 'Taxon': Scientific name of taxonomic group
 * 'no_spp': Number of species in taxonomic group *
 'bin_total': Total species present in time bin *
 'prop': Species in group as proportion of total *
 'perc': Species in group as percentage of total ##
 Trait_data.csv * 'Taxon': As above * Remaining columns are
 functional trait categories for each taxon, with trait name in top row and
 modalities for each trait in subsequent row. Traits and trait modalities
 are explained in full in Table S1 of the associated paper. \** Note that
 two traits have missing values, which are blank - these are n/a values for
 which no trait data is available in the published literature. These are
 left blank as any infilling will result in the mFD package treating them
 as new trait categories, whilst left blank, they are treated properly as
 n/a's. ## Trait_categories.csv * 'trait_name': Name of
 functional trait * 'trait_type': Type of data used for trait
 (all are factors) \** Note that this file is necessary for the mFD
 analysis to function, and basically tells mFD what type of data to expect
 for each trait (this is independent of assigning data type in R) ##
 Trait_matrix.csv * 'Bin': Time interval of time bin (MYr) *
 Subsequent column headers are names of taxonomic groups, and rows denote
 number of species in each taxonomic group in each time bin ##
 Code/software Analyses require R and the R package mFD. The workflow is
 elaborated in the annotated R scripts provided, which are sufficient to
 perform all analyses and generate all figures in the paper from which this
 dataset is derived. ## Access information Other publicly accessible
 locations of the data: * N/A Data was derived from the following sources
 (and references therein): * Zhuravlev, A.Y. and Wood, R.A. (2018). The two
 phases of the Cambrian explosion. Scientific Reports 8, 16656. *
 Zhuravlev, A.Y. and Wood, R.A. (2020). Dynamic and synchronous changes in
 metazoan body size during the Cambrian Explosion. Scientific Reports 10,
 6784.