DOI: 10.5061/dryad.hmgqnk9wn
title: Data from: Trait networks reveal turnover in Caribbean corals and changes in community resilience through the Cenozoic

description: This dataset comprises fossil occurrence records and life history trait
 data for reef-building scleractinian corals from the western equatorial
 Atlantic (including the Caribbean, Gulf of Mexico, and Bahamas) across
 multiple epochs of the Cenozoic Era. Coral occurrence data were downloaded
 from the Paleobiology Database (PBDB) on 01 October 2022, filtered to
 include collections from eight specific epochs and sub-epochs where data
 were available: Eocene, Oligocene, early and late Miocene, early and late
 Pliocene, and early and late Pleistocene. Only reef-building coral species
 were retained following taxonomic validation against WoRMS and removal of
 azooxanthellate and non-reef-building taxa. Species-level trait data,
 including growth form, colony form, maximum corallite diameter, and
 budding type, were compiled from NMITA, CoralTraits.org, published
 literature, and recent trait databases. Traits were categorized to assess
 functional diversity and coral life history strategies across ~54 million
 years. This curated dataset supports macroevolutionary and paleoecological
 analyses of coral community composition and functional change through
 time.
description: # Data from: Trait networks reveal turnover in Caribbean corals and
 changes in community resilience through the Cenozoic Dataset DOI:
 [10.5061/dryad.hmgqnk9wn](10.5061/dryad.hmgqnk9wn) ## Description of the
 data and file structure Cenozoic Coral Turnover Analysis This repository
 contains the raw data and supplementary material for the analyses and
 figures from our study: “Trait networks reveal turnover in Caribbean
 corals and changes in community resilience through the Cenozoic.”.
 Authors: C. G. Clay, A. Dunhill & M. Beger The R scripts and code
 required to reproduce the analysis and figure can be found here and in the
 Git hub repository:
 [[https://github.com/CharlotteGeorgina/CenozoicCoralTraitTurnover](https://github.com/CharlotteGeorgina/CenozoicCoralTraitTurnover)] Citation If you use this **code**, please cite the paper: ``` Clay et al. (in-review). Trait networks reveal turnover in Caribbean corals and changes in community resilience through the Cenozoic. Paleobiology ``` Acknowledgements This project was supported by the Leverhulme Trust. The analyses explore coral species and trait dynamics from the Eocene to the Pleistocene using bipartite networks, trait-trait co-occurrence networks, and dimensionality reduction techniques. ### Files and variables **Caribbean_SppbySubEpoch_Eocene_Pleisto_All_new.csv** - a collection by species matrix indicating which species were present or absent in each collection. Column A indicates the epoch or sub-epoch each collection came from, column B indicates the collection name and columns C: IM relate to species names. **Caribbean_Reefbuilding_Traits.csv** - Trait data for each of the reef building coral species. Column A:species names, Column B:genus name. Column C: Family name. Column D: whether the species is gobally extant or extinct. Column E: whether the species is extant or extinct in the Caribbean region. Column F: References for column D-E. Column G: whether the species is zooxanthellae or azooxanthellae. Column H: Reference for column G. Column I: the numerical integration level for each species. Column J: name for the integration level for each specues, Column K: maximum corallite diameter. Column L: Typical growth type. Column M: whether the species asexually reproduced through budding and if it did was that intracalicular or extracalicular. Column N: References for columns I-M. All missing data represented as NA. **Supplemental information:**  C.CLay_CeonozicTraitNetworks_Supplementary_Final.docx- The supplemental material for the paper includes the tables and figures with the respective legends.  **Code/software** Repository Structure The code is divided across six main scripts: 1. Bipartite_networks_Jaccard_analysis.R Constructs bipartite networks showing species presence across epochs/sub-epochs. Uses igraph for network projection and layout. Visualises species sharing via heatmaps. Calculates Jaccard dissimilarity between time bins to quantify species and trait turnover using the vegan package. Visualises species and trait dissimilarity as a line plot 2. Random_network.R Generates community weighted meand (CWM) for each collection within each epoch/sub-epoch Creates ten random samples of the data to account for differing numbers of collections between epochs/sub-epochs (e.g.,. 13 of the 23 Oligocene collections, as only 13 collections were available from the Eocene; early Miocene = 40, late Miocene = 38, late Pliocene = 36, early Pleistocene = 98). 3. Weighted_networks.R Constructs weighted edge networks representing all possible trait correlations. Calculates edge densities for comparison with filtered co-occurrence networks. 4. Trait_Trait_cooccurrenceNetworks.R Builds trait-trait co-occurrence networks for three key intervals of environmental change: ``` Eocene–Oligocene Early Miocene–Late Miocene Late Pliocene–Early Pleistocene ``` Based on community weighted means (CWM) calculated using the FD package. Significant Pearson correlations (p &lt; 0.05) used to build networks. Calculates node degree, edge density, and modularity with igraph. 5. PCA.R Uses Principal Component Analysis (PCA) to compare trait composition (CWM) across time. Highlights community shifts and trait divergence across sub-epochs. 6. PCoA_.R Uses Principal Coordinate Analysis (PCoA) and Gower dissimilarity to assess functional richness. Constructs convex hulls for visualizing trait space per time bin. Trait vectors overlaid to indicate drivers of functional divergence. Uses the mFD package for trait space quality assessment. Data & Dependencies ``` Data files are included in this repository. Required R packages: igraph, vegan, FD, mFD, ggplot2, and others as listed in individual scripts. ``` Visualisation Tools ``` Final visualisation of bipartite and trait-trait networks was enhanced using Inkscape (v1.2.2). Convex hulls and trait vectors in PCoA plots created using vegan.## Access information ``` Other publicly accessible locations of the data: * [https://github.com/CharlotteGeorgina/CenozoicCoralTraitTurnover](https://github.com/CharlotteGeorgina/CenozoicCoralTraitTurnover) Data was derived from the following sources: * The Paleobiology Database ([The Paleobiology Database),](https://paleobiodb.org/#/) which is made available under a CC0 International License. We gratefully acknowledge the contributions of PBDB authors and data providers. See [https://paleobiodb.org](https://paleobiodb.org) for source data and contributor information.