Changes in metazoan functional diversity during the Cambrian Sinsk Event
Data files
Jul 09, 2025 version files 41.34 KB
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functional___species_richness.csv
782 B
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origination_extinction.csv
708 B
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README.md
4.32 KB
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Sinsk_metazoan_functional_diversity_-_additional_code_for_figures.R
7.76 KB
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Sinsk_metazoan_functional_diversity_-_main_analyses.R
11.11 KB
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species_richness.csv
1.87 KB
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stack_area_ungrouped.csv
11.72 KB
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trait_categories.csv
154 B
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trait_data.csv
1.96 KB
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trait_matrix.csv
956 B
Abstract
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.
Dataset DOI: 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. in press).
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 2 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.
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.