DOI: 10.5061/dryad.1vhhmgr44
title: Larval brooding correlated with high early origination rates in cheilostome Bryozoa

description: Life-history traits such as dispersal affect population attributes like
 gene flow, which can have consequences for speciation and extinction rates
 over macroevolutionary timescales. Here we use the Cheilostomatida, a
 monophyletic order of marine bryozoans, to test whether a life-history
 trait, larval brooding, affected the origination and extinction rates of
 genera throughout their fossil record. Cheilostome lineages that brood
 their larvae have shorter larval dispersal distances than non-brooding
 lineages, which has led to the hypothesis that the evolution of larval
 brooding decreased gene flow, increased origination, and drove their
 Cretaceous diversification. Brooding cheilostomes are far more diverse
 than non-brooding cheilostomes today, but it remains to be shown that
 brooding lineages have a higher origination rate than non-brooders. We fit
 time-varying Pradel Seniority capture-mark-recapture models to look at the
 effect of brooding on origination and extinction rates during the
 Cretaceous cheilostome diversification, the Cretaceous-Paleogene mass
 extinction and recovery, and through the Cenozoic. Our results support the
 hypothesis that brooding affects origination rate, but only in the
 Cenomanian to Campanian. Extinction rates do not differ between brooding
 and non-brooding genera, and there is no regime shift specific to the
 Cretaceous-Paleogene mass extinction. Our work illustrates the importance
 of using fossil occurrences and time-varying models, which can detect
 interval-specific diversification differentials.
description: This dataset is derived from the fossil occurrence data compiled
 by Lidgard et al. 2021 (DOI: 10.1098/rspb.2021.1632 with additional fossil occurrences from Håkansson et al. 2024 (DOI: 10.18261/9788215072081-2024). This combined dataset is processed in our RStudio code by synonymizing taxa using taxonomy from WoRMS and removing occurrences not constrained to a single geologic stage. Then, the dataset is transformed into an RMark data frame for our Pradel models and our POPAN model.
description: # Larval brooding correlated with high early origination rates in
 cheilostome Bryozoa
 [https://doi.org/10.5061/dryad.1vhhmgr44](https://doi.org/10.5061/dryad.1vhhmgr44) ## Description of the data and file structure | Supplementary File | Description | | :--------------------------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | alldata.csv | A spreadsheet view of the occurrence dataset created by the R script, including our brooding classification | | brood\_data.csv | Novel compiled dataset of brooding traits for 621 Cheilostome genera from 270 references, used to identify inferred brooders for the sensitivity analysis | | CheiloDiv\_master\_SLMSF.Rmd | R script for all analyses | | labels\_categorical.csv | input file needed for R script figures | | labels\_categorical.posthoc.csv | input file needed for R script figures | | labels\_foote.csv | input file needed for R script figures | | labels.csv | input file needed for R script figures | | Lidgard\_wormsmatch.csv | input file matching genera to families using WORMS (cited in the main text) | | mark\_out\_post.data | RMark output for post-hoc model (Supplementary Figure 3) | | mark\_out\_sensitivity1.data | Same as mark\_out1.data but with data from sensitivity analysis | | mark\_out\_sensitivity2.data | Same as mark\_out2.data but with data from sensitivity analysis | | mark\_out1.data | RMark output for stage-level time-varying CMR models (Supplementary Figure 2) | | mark\_out2.data | RMark output for time-binned CMR models (main text analysis and figures) | | mark\_out3.data | Rmark output for CMR model comparison of origination-brooding interaction versus diversity-dependence | | mark\_popan.data | RMark output for POPAN model (Figure 2) | | SupplementaryFigure1.pdf | Supplementary Figure 1 of Foote's per-capita rate results | | SupplementaryFigure2.pdf | Supplementary Figure 2 of stage-level time-varying CMR results | | SupplementaryFigure3.pdf | Supplementary Figure 3 of post-hoc model | | Supplemental\_text.docx | Supplemental text file | | timescale\_2023.csv | input file needed for R script | | timescale\_plot\_categorical.csv | input file needed for R script figures | | timescale\_plot\_categorical.posthoc.csv | input file needed for R script figures | | timescale\_plot\_foote.csv | input file needed for R script figures | | timescale\_plot.csv | input file needed for R script figures | | WA\_Maast\_occurrences.csv | Occurrence data from Håkansson, E., Gordon, D. P. & Taylor, P. D. 2024: Bryozoa from the Maastrichtian Korojon Formation, Western Australia. Fossils and Strata. 70, 1–155. [https://doi.org/10.18261/9788215072081-2024](https://doi.org/10.18261/9788215072081-2024) | | SupplementaryTable1\_SLMSF.pdf | Model comparison for linear regressions of per-capita extinction rates | | SupplementaryTable2\_SLMSF.pdf | Model comparison for linear regressions of per-capita origination rates | | SupplementaryTable3\_SLMSF.pdf | Model comparison for the CMR models from the sensitivity analysis | ### Files and variables #### File: Supplemental\_text.docx **Description:**  Supplemental text file #### File: brood\_data.csv **Description:**  Novel compiled dataset of brooding traits for 621 Cheilostome genera from 270 references, was used to identify inferred brooders for the sensitivity analysis ##### Variables * genus: genus names * Family: family names * brooding (genus-level): TRUE (brooding present) or FALSE (brooding absent). NA values correspond to taxa for which information was unavailable. * references: source for genus-level brooding status. NA values correspond to taxa for which information was unavailable. * Brooding (family-level): TRUE (brooding present) or FALSE (brooding absent). NA values correspond to taxa for which information was unavailable. #### File: labels\_categorical.csv **Description:**  input file needed for R script figures ##### Variables * tpx: text displayed in timescale * epochs: order of timescale labels in plot #### File: labels.csv **Description:**  input file needed for R script figures ##### Variables * tpx: text displayed in timescale * epochs: order of timescale labels in plot #### File: timescale\_plot\_categorical.csv **Description:**  input file needed for R script figures ##### Variables * stage.age: order of categories to plot #### File: labels\_foote.csv **Description:**  input file needed for R script figures ##### Variables * tpx: text displayed in timescale * epochs: order of timescale labels in plot #### File: timescale\_plot\_foote.csv **Description:**  input file needed for R script figures ##### Variables * stage.age: start and end ages of each geologic epoch used in plotting #### File: labels\_categorical.posthoc.csv **Description:**  input file needed for R script figures ##### Variables * tpx: text to display on labels * epochs: order of timescale labels in plot #### File: timescale\_2023.csv **Description:**  ##### Variables * stage_name: names of geologic stages * max_ma: lower boundary of each stage (Myr) * min_ma: upper boundary of each stage (Myr) * stage_num: chronological number of stages from 1 (oldest) to 30 (youngest) #### File: WA\_Maast\_occurrences.csv **Description:**  Occurrence data from Håkansson, E., Gordon, D. P. & Taylor, P. D. 2024: Bryozoa from the Maastrichtian Korojon Formation, Western Australia. Fossils and Strata. 70, 1–155. [https://doi.org/10.18261/9788215072081-2024](https://doi.org/10.18261/9788215072081-2024) ##### Variables * genus: genus names * stage: stage names * max_ma: lower boundary of each stage (Myr) * min_ma: upper boundary of each stage (Myr) * stage_num: chronological numbering of stages used in our analysis from 1 (oldest) to 30 (youngest) * brooding: brooding status: b (brooding) or nb (non-brooding) #### File: timescale\_plot\_categorical.posthoc.csv **Description:**  input file needed for R script figures ##### Variables * stage.age: order of categories to plot #### File: timescale\_plot.csv **Description:**  input file needed for R script figures ##### Variables * stage.age: start and end ages of each stage (Myr) #### File: mark\_out\_post.data **Description:**  RMark output for post-hoc model (Supplementary Figure 3) #### File: mark\_out\_sensitivity1.data **Description:**  Same as mark_out1.data but with data from sensitivity analysis #### File: mark\_out3.data **Description:**  Rmark output for CMR model comparison of origination-brooding interaction versus diversity-dependence #### File: mark\_out\_sensitivity2.data **Description:**  Same as mark_out2.data but with data from sensitivity analysis #### File: mark\_out2.data **Description:**  RMark output for time-binned CMR models (main text analysis and figures) #### File: mark\_popan.data **Description:**  RMark output for POPAN model (Figure 2) #### File: mark\_out1.data **Description:**  RMark output for stage-level time-varying CMR models (Supplementary Figure 2) #### File: alldata.csv **Description:**  A spreadsheet view of the occurrence dataset created by the R script, including our brooding classification ##### Variables * Occ_num: occurrence number in list (internal ID) * genus: genus of fossil * stage: stage of occurrence * max_ma: maximum age estimate of stage (Myr) * min_ma: minimum age estimate of stage (Myr) * stage_num: chronological numbering of stages used in our analysis from 1 (oldest) to 30 (youngest) * brooding: brooding status for each genus occurrence: b (brooding) or nb (non-brooding) #### File: Lidgard\_wormsmatch.csv **Description:**  input file matching genera to families using WORMS (cited in the main text) ##### Variables * ScientificName: genus name, phylum name * AphiaID: ID in WoRMS system * Match type: match type from WoRMS (exact or ambiguous) * Kingdom: taxonomic kingdom * Phylum: taxonomic phylum * class: taxonomic class * order: taxonomic order * family: taxonomic family * genus: taxonomic genus * Subgenus: taxonomic subgenus * Species: taxonomic species * Subspecies: taxonomic subspecies ## Code/software R (version 3.6.0), RStudio (version 2024.09.1+394), RMark (version 3.0.0) ## Access information Data was derived from the following sources: * Lidgard et al. 2021 (DOI: [https://doi.org/10.1098/rspb.2021.1632)](https://doi.org/10.1098/rspb.2021.1632) * Håkansson et al. 2024 (DOI: [https://doi.org/10.18261/9788215072081-2024-01)](https://doi.org/10.18261/9788215072081-2024-01) ## Change log **28 Feb 2025:** I added the text file for the supplement (Supplemental_text.docx)