DOI: 10.5061/dryad.69p8cz9cc
title: Co‑occurrence structure of late Ediacaran communities and influence of emerging ecosystem engineers

description: Understanding the roles of habitat filtering, dispersal limitations, and
 biotic interactions in shaping the organization of animal communities is a
 central research goal in ecology. Attempts to extend these approaches into
 deep time have the potential to illuminate the role of these processes
 over key intervals in evolutionary history. The Ediacaran marks one such
 interval, recording the first macroscopic benthic communities and a
 step-wise intensification in animal ecosystem engineering. Here, we use
 taxonomic co‑occurrence analysis to evaluate how community structure
 shifted through the late Ediacaran and the role of different community
 assembly processes in driving these changes. We find that community
 structure shifted significantly throughout the Ediacaran, with the most
 dramatic shift occurring at the White Sea‑Nama boundary (~550 Ma)
 characterized by a split between older, more enigmatic taxonomic groups
 (the ‘Ediacara-type’ fauna) and more recognizable (‘Cambrian-type’)
 metazoans. While ecosystem engineering via bioturbation is implicated in
 this shift, dispersal limitations also played a role in separating biota
 types. We hypothesize that bioturbation acted as a local habitat filter in
 the late Ediacaran, selecting against genera adapted to microbial mat
 ecosystems. Ecosystem engineering regime shifts in the Ediacaran may thus
 have had a large impact on the development of subsequent metazoan
 communities.
description: Data collection began with a download from the Paleobiology
 Database (July 2021) of all macrofossil occurrences dated to the Ediacaran
 period (635-538ma). We searched the primary literature for additional
 fossil collections and incorporated these data into the initial occurrence
 data set. This final data set encompassed 1540 fossil specimens from 173
 references. Collected data included genus, species, reported collection
 identification, stratigraphic unit, formation, member, lithological
 descriptions, modern latitude and longitude of collection, ichnogenera
 present, algae present, estimated water depth (shallow/deep at coarsest
 resolution), assemblage zone, and reference information for each fossil
 specimen. Assemblage zone assignments (the finest temporal units available
 to the Ediacaran period at present) were manually reviewed for each
 formation and member from a review of the chronostratigraphic literature,
 using radiometric dates, stratigraphic sequence, biostratigraphic
 correlations to assign each fossil occurrence to the Avalon, White Sea, or
 Nama.  Genus and species assignments were also manually
 reviewed for each collection and updated to the latest consensus reported
 in the primary literature. Generalized biota type was assigned based on
 morphological and ecological characteristics (eg. feeding mode, body plan)
 as defined by the primary literature for each genus or member of the same
 morphogroup. Supporting references are included with Pseudofossils, algae,
 and microfossils were removed from the data set analyses. While the PDBD
 includes estimated paleo latitude and longitude, these were recalculated
 using the software GPlates and Wright et al. (2013) continental
 reconstruction models after vetting and correcting (where necessary)
 reported latitude and longitude for existing data. Paleo lat/long were
 estimated for all data at the midpoint of each assemblage zone each
 collection was identified to. Fossil occurrence data was assembled into
 paleocommunities by lumping collections within an estimated 5km radius (at
 the time of original deposition) of the same formation and member.
 Paleocommunity lumping was performed in R and these operations have been
 included in the R scripts included with this supplemental.
description: # Co‑occurrence structure of late Ediacaran communities and influence of
 emerging ecosystem engineers
 [https://doi.org/10.5061/dryad.69p8cz9cc](https://doi.org/10.5061/dryad.69p8cz9cc) ## Description of the data and file structure The data was collected to test 1) how community structure changed across the Ediacaran period through the lens of taxonomic pairwise co-occurrence and 2) whether environmental factors, dispersal limitations, and ecosystem engineering by other taxa (e.g., burrowing worm fauna) significantly influenced co-occurrence. The data includes occurrence information for global Ediacaran macrofossils (e.g., genus, species, stratigraphic information, associated environmental factors) as well as information on local environmental conditions (presence of algae, estimated water depth, paleo latitude/longitude). The data also includes, in two supplemental files, a table of genus traits and a list of bioturbating ichnogenera. All analyses and community data preparation were performed in R. ### Files and variables #### File: Craffey\_et\_al\_2024\_Supp\_-\_Data\_\_\_Code.zip **Description:** Contains all r code, data, and the required folder structure necessary to run our analyses. #### File: Bioturbation\_List.csv **Description:** List of ichnofauna with bioturbation behavior, used for running some variants of the analysis. ##### Variables * genus: Ichnogenus * time_bins: Interval reported (Ediacaran or Cambrian) * EE.Behavior: Assessed ecosystem engineering behavior (bioturbation or bioirrigation) #### File: Craffey\_et\_al\_2024\_Occurrence\_Data.csv **Description:** Occurrence dataset of Ediacaran genera. ##### Variables * collection_no: Collection number * genus: Genus * lng: Collection longitude (modern) * lat: Collection latitude (modern) * environ: Environment as defined by water depth (shallow/deep). * formation: Formation of collection * stratgroup: Stratigraphic group of collection. NA represents collections for which this stratigraphic unit is not applicable. * member: Member of collection. NA represents collections for which this stratigraphic unit is not reported or applicable. * localbed: Bed of collection. NA represents collections for which this stratigraphic unit is not reported. * lithology1: Lithology of collection. NA represents collections for which this information is not reported. * lithology2: Additional reported lithology of collection. NA represents collections for which this information is not reported or applicable. * lithadj1: Adjectives used to describe lithology1. NA represents collections for which this information is not reported or applicable. * Lith.Type: Adjectives used to describe lithology2. NA represents collections for which this information is not reported or applicable. * zone: Assemblage zone of collection * reference: Original primary literature reporting the collection * reference_no: PBDB reference number of collection (where applicable) * abund_value: A value specifying the abundance of each collection. This has been reduced to 1 (presence-absence) and is used for one data prep step in the primary code. * max: Maximum age of collection in ma * min: Minimum age of collection in ma * paleolng: Estimated paleolongitude of collection * paleolat: Estimated paleolatitude of collection * type: Type of fossil reported (ex. body fossil, pseudofossil) * Cat1: Biota type assigned to the genus. NA represents taxa that cannot be assigned to either type from available literature. * Cat2: Finer-level taxonomic group reported for genus. NA represents taxa that cannot be assigned to a group from available literature. * Feeding: Feeding mode reported for the genus. NA represents taxa that cannot be assigned to a feeding type from available literature. * T.bin: Binary variable for whether bioturbation was reported as present or absent for collection * algae: Binary variable for whether algae was reported as present or absent for collection * eng: Binary variable for whether algae or bioturbation were reported for the collection * delta: Binary variable for whether a deltaic preservation environment was reported for the collection ## Code/software We used R (version 4.3.3) and R studio (version 2023.12.1) to perform our analyses. Within R, we used the packages ggplot2, reshape2, cooccur, fossil, rgdal, raster, tidyverse, dplyr, vegan, lmPerm, car, and data.table. An accessory R script with additional functions for data preparation and analyses (ex. calculation of co-occurrence strength, subsetting routine) is also included with the main R script and is automatically loaded by.3 that script. Paleolatitude and longitude were calculated in Gplates version 2.4.0. and Wright et al. (2013)'s continental reconstruction models. ## Access information Other publicly accessible locations of the data: * None other presently Data was derived from the following sources: * The Paleobiology Database (PBDB) and additional primary literature, cited with each fossil occurrence.