DOI: 10.5061/dryad.jh9w0vtk5
title: Plankton and benthic foraminiferal dataset for the study of the Eocene-Oligocene transition

description: The Eocene–Oligocene transition (EOT) was the crucial turning point when
 Earth’s climate shifted to its current icehouse state. Understanding how
 the marine biosphere responded during this transition is not
 well-constrained, appearing as a simple extinction pulse in low temporal
 resolution global compendia. Here we designed a novel AI-inspired
 metaheuristics algorithm to construct a high-resolution global species
 richness history across the EOT for the rich foraminifera fossil record
 with an imputed ~29,000-year resolution. The revealed diversity dynamics
 are complex and differ for each foraminiferal group with distinct ecology.
 Planktonic and shallow-water larger benthic foraminifera show steady
 diversity levels in the early phases of the transition in the latest
 Eocene after a long-term reduction, while the deeper-water small benthic
 foraminifera radiate remarkably and decline over the same interval. In the
 earliest Oligocene, the planktonic and larger foraminifera suffered major
 species losses coincident with the first continental-scale ice sheet
 forming on Antarctica, while small benthic foraminifera diversity held
 steady, followed by an accelerating lowering as the early Oligocene
 proceeded. These findings reveal complicated and ecologically
 differentiated environment-life processes, indicating the importance of
 high-resolution temporal data for dissecting out ecological responses to
 major environmental changes.
description: Data used in this study were manually collected from
 peer-reviewed publications. Each data record includes clear metadata
 linking back to the original source in the OneStratigraphy database. Any
 errors were corrected (e.g., spelling mistakes in species names), and
 missing information was filled in (e.g., latitude and longitude data). We
 selected sections/sites containing foraminifera occurrences from the
 Eocene to the Oligocene. The raw dataset contained 13,138 local bioevents
 records (i.e., first and last appearance records) and ~60,000 occurrences
 of 2,988 taxonomic units from 163 published stratigraphic sections,
 encompassing both calcareous and agglutinated foraminifera. These
 sections, including drill cores and outcrops, are widely distributed in
 the present oceans and continents such as Europe, Africa, and Asia. The
 dataset was first cleaned by excluding open nomenclature, such as sp./spp.
 (622), aff. (63), question marks for species names (6). Nevertheless, the
 conferring species (cf.; 175) and the group species (ex gr.; 25) were
 preserved and assigned to the referenced species. Taxonomic assignments
 below the species level (i.e., subspecies and variety) were mostly
 integrated to the species level. All non-foraminifera fossils were
 removed. The dataset after cleaning was thoroughly examined and verified
 against other independent data sources, including taxonomic atlases,
 foraminiferal databases (Mikrotax and WoRMS), and related taxonomic
 references, and further verified and resolved by a group of foraminiferal
 taxonomic experts for correctness and consistency: Bridget Wade (PF), Laia
 Alegret (SBF), Qinghai Zhang (LBF and SBF), and Peiyue Fang (PF, LBF and
 SBF). In the present dataset, the drill core Hole 647A
 has been studied repeatedly, focusing on both SBF and PF for variable use,
 such as testing biotic response to EOT, studying high-latitude deep-water
 sedimentary sequence, and stratigraphic correlation. The three
 reports were integrated into one section by depth. The
 final dataset after data cleaning and verification included 9,032 local
 first and last occurrence records of 1,269 species in 161 published
 sections. The Constrained Optimization with an
 Evolutionary Algorithm (CONOP.EA) compositing method is used to integrate
 the local biostratigraphic data from all 161 sections/sites and to correct
 regional diachronism caused by migration, fossil preservation, and
 sampling biases.
description: # Plankton and benthic foraminiferal dataset for the study of the
 Eocene-Oligocene transition
 [https://doi.org/10.5061/dryad.jh9w0vtk5](https://doi.org/10.5061/dryad.jh9w0vtk5) We have submitted our raw data in both computable and readable formats, including a CSV file titled "EOT_forams_Readable.csv". Additionally, we have compiled a comprehensive package, "EOT_forams_CONOP_r1.zip", which encompasses the computable dataset ("EOT_forams_Computable.csv"), data transfer software ("SinoCor2CONOP.exe"), software for CONOP configuration and initialization ("CONMAN.exe" and "CONOPDataInitialization-V2.exe"), and the CONOP.EA packages ("CONOP.EA_executable" and "CONOP.EA_source code"), the benchmark results file ("EOT_forams_CONOP_r1\CONOP.EA_executable\data\CONOP benchmark result.xlsx"), and documentation (README.md and README.txt). This package is for analyzing foraminiferal data during the Eocene-Oligocene transition (EOT) using the CONstrained OPtimization with an evolutionary algorithm (CONOP.EA) computational approach. This collection enables researchers to achieve high-resolution insights into foraminiferal richness changes across this significant geologic period. To complement the dataset and software tools, a demonstration package is included within "EOT_forams_CONOP_r1.zip" (refer to the "CONOP.EA_executable" section), providing examples of computed analyses ("CONOP benchmark result.xlsx" and CONOP.EA files) to aid users in replicating the study's results. ## **Description of the data and file structure** ### EOT_forams_Computable.csv and EOT_forams_Readable.csv (dataset) The files "EOT_forams_Readable.csv" and "EOT_forams_Computable.csv" represent two versions of the same raw dataset, each formatted to meet specific requirements. "EOT_forams_Readable.csv" adheres to Dryad's guidelines, ensuring that there are no empty cells within the dataset ('N/A' and 'null' are used for formatting purposes). On the other hand, "EOT_forams_Computable.csv" is optimized for CONOP computation, with a specific format that accommodates empty cells. Despite these differences in handling empty cells, both files contain identical foraminiferal range data. The dataset is organized such that rows correspond to species names, while every pair of columns indicates the first and last appearance positions (base and top) of the species in each section. ### CONOP benchmark result.xlsx Sp_num: code referring to a species Event_type: first appearance or last appearance (0 or 1) Level_placed: position placed (ordering) of a bioevent in the CONOP-derived composite section Sample_point: Assembled sample level (ordering) from the CONOP-derived composite sequence Age_Ma: Calibrated age (Ma) for each sample point Species_Richness: Calculated foraminiferal species richness based on the unbinned method ## **Sharing/Access information** Data was derived from the following sources: * OneStratigraphy Database ([http://onestratigraphy.ddeworld.org/](http://onestratigraphy.ddeworld.org/)) ## **Code/Software** ### **SinoCor2CONOP.exe** This software is used for converting the SinoCor formatted file into a set of CONOP-ready files. Place the SinoCor file in the same directory as the utility to ensure smooth processing. Upon completion, a new folder named after the current operation time will be created, containing essential files such as ".sec" and ".dic" required for further analysis. ### **CONMAN and CONOPDataInitialization-V2** These programs can configure the CONOP files before initiating the main CONOP computation * In "CONMAN", follow the "EXPORT" menu instructions sequentially. * In "CONOPDataInitialization-V2", select the appropriate options to filter data before clicking the "process" button. ## CONOP.EA_source code and CONOP.EA_executable These packages include source code and demo files of "CONOP.EA". Please see "ReadMe.txt"/"ReadMe.md" inside the packages for instructions. ## Version changes 26-July-2025: Further validated taxonomic information by three foraminiferal experts: Prof. Bridget Wade (PF), Prof. Laia Alegret (SBF), and Prof. Qinghai Zhang (LBF and SBF). Updated fossil counts in both EOT_forams_Computable.csv and EOT_forams_Readable.csv, now totaling 1,269 species and 18 magnetochrons across 161 published sections. To enhance compatibility and usability, we've updated the software package, now named "EOT_forams_CONOP_r1.zip", in collaboration with Prof. Chao Qian and his students, Ke Xue, Yuchang Wu, and Rongxi Tan. This updated package contains two main folders: 1. "CONOP.EA_executable": Includes executable programs ready for immediate use. 2. "CONOP.EA_source code": Contains the source code for transparency and customization. Two execution modes are provided: * Optimization from initial input data. * Optimization from pre-existing high-quality solutions (benchmark data included). Default parameter settings have been configured to facilitate quick initialization and data loading. Users can easily adjust these settings in the "configs\config.yaml" file to enable more intensive analyses.