Co‑occurrence structure of late Ediacaran communities and influence of emerging ecosystem engineers
Data files
Nov 26, 2024 version files 238.01 KB
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Craffey_et_al_-_Proc_B_-_2024_Data_and_Code.zip
232.99 KB
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README.md
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Abstract
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.
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.
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.