Data from: A deep dive into the fossil record of diving beetles (Coleoptera: Dytiscidae): Bayesian inferences reveal their origin and pulsed diversification at the genus level
Data files
Jun 13, 2026 version files 31.32 MB
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File_S1.zip
6.43 MB
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File_S2.zip
24.88 MB
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README.md
3.30 KB
Abstract
Predaceous diving beetles (Dytiscidae) are among the best-known and most extensively studied beetle clades. Yet, their fossil record remains surprisingly sparse and uneven, failing to reflect their broad extant diversity. Consequently, the study of their evolutionary history, leveraging the fossil record, particularly their diversification dynamics, has often been limited. To overcome this issue, we used the Bayesian Brownian Bridge model, which is particularly suited for clades with incomplete fossil records. Although primarily designed to estimate clade origination times, the model can also be applied to infer origination and extinction dynamics while accounting for biases due to uneven sampling. Using this model and a curated dataset of fossil occurrences covering 41 genera and 155 species of Dytiscidae, we estimated the timing of the family’s origination and of each genus represented in its fossil record. Our results show an origin of Dytiscidae either during the Late Triassic (~220 million years ago), or during the Early Jurassic (~190 million years ago). Although these estimates are consistent with most recent time-calibrated phylogenies, they provide additional clues for an ancient origin of the family. Following their origin, Dytiscidae diversified across the different geological epochs, likely in response to tectonic shifts and climate oscillations.
Corresponding author:
Name: Ferreira Jules
Institutions: Institut Botànic de Barcelona (CSIC-CMCNB), 08038 Barcelona, Spain
Facultat de Ciències de la Terra, Universitat de Barcelona, 08028 Barcelona, Spain
Email: jules.ferreira27@gmail.com
Abbreviations and Conventions:
Ma: Million years ago
rootBBB: A software tool used to perform analyses of clade origination
PyRate: A Bayesian software framework used to estimate origination, extinction, and diversification dynamics through time from fossil occurrence data.
PyRate BDCS: A PyRate flavor based on the Birth–Death model with Constrained Shifts (BDCS), used to estimate diversification rates while allowing for changes in speciation and extinction rates across different time intervals.
- File_S1.zip: Files used to run rootBBB analyses and the resulting outputs.
Description
The File S1 contains two subfiles named "230_Ma_max_age" and "300_Ma_max_age". These subfiles compile the results from the rootBBB analyses, one with the maximum age of 230 Ma and one with the maximum age of 300 Ma.
In each of these subfiles, two more subfiles correspond to results at the family level (named "Family"; for the analyses performed at the family level for Dytiscidae) and at the genus level (named "Genera"; for the analyses performed on each genus of Dytiscidae in the fossil record).
Additionally, in the File S1, the diversity table ("Div_table.txt") as well as the fossil table (Fossil_table.txt) used as input in the rootBBB program are provided along with the prompts used ("Prompts.txt").
- File_S2.zip: Files used for analysis with PyRate 3, along with the resulting outputs.
Description
The File S2 contains a file named "BDCS1", with the log files obtained from the PyRate BDCS analysis using the genus-level occurrences from the fossil record of Dytiscidae, with 10 replicates to account for age uncertainty in fossils.
The dataset used to run the analysis ("DYT_foss.txt"), as well as the formatted PyRate file for direct use ("DYT_foss_PyRate.py") and the prompts ("Prompts.txt"), are present.
Finally, there is also the LTT file used to generate the lineage-through time plot ("Dytiscidae_genera_LTT.txt") from the PyRate data.
File S3. R scripts used to generate figures based on rootBBB results and to generate the lineage-through-time plot for Dytiscidae genera.
Description
This file contains all the R scripts used to generate the figures from the manuscript, including:
- The script to generate the lineage-through time plot ("Plot_Fig_LTT_PyRate.R")
- The scripts to visualize the origination rates at the genus-level under the 230 Ma and 300 Ma maximum root age (respectively "Plot_Fig_origination_rates_230_Ma.R" and "Plot_Fig_origination_rates_300_Ma.R")
- The scripts to generate the plots with the origination and extinction time for all genera, along with their 95% HPD, either for 230 Ma as a maximum age or 300 Ma (respectively "Plot_Fig_origination_time_230_Ma.R" and "Plot_Fig_origination_time_300_Ma.R")