Data from: Fecundity in fossil Bryozoa: Accounting for colony fragmentation and the spatial division of reproductive labor
Data files
Oct 16, 2025 version files 119.32 MB
-
alldata_submission.RData
117.43 MB
-
ColonyMapFiles.zip
1.78 MB
-
RCode_submission.Rmd
98.55 KB
-
README.md
8.22 KB
-
SpeciesID_ZooidMeasurements.xlsx
10.62 KB
Abstract
Our ability to measure evolution by natural selection in the fossil record is limited by the near impossibility of estimating the fecundity and thus relative fitness of most fossil organisms. Neocheilostome bryozoans are an important exception, because they have calcified larval brood chambers known as ovicells that provide an approximate estimate of the colony’s sexual fecundity. This clade has a rich fossil record dating back ~100 million years, providing potential opportunities to observe changes in relative fitness and natural selection through many past intervals of environmental change. However, neocheilostome fossil specimens are often highly fragmented, and fragments are not necessarily randomized subsets of a colony. To make use of the majority of the neocheilostome fossil record, we need to test the effect colony organization has on our methods of inferring colony fecundity from fragmented specimens.
In this study, we measure colony fecundity in a population of Recent neocheilostome bryozoan specimens of the species Parasmittina eccentrica Winston & Jackson, 2021, and quantify the nonrandom spatial arrangement of ovicells due to colony organization. We then simulate fragmenting these specimens and test the statistical robustness of standard methods one might use to reconstruct fecundity from fossil specimens. We find that ovicells are clustered and concentrated at mid-distances from the ancestrula (the oldest part of the colony). As a result, estimates of a colony’s fecundity from a single fragment have higher variance than would be expected if ovicells were randomly distributed. When estimating average population fecundity, observed variance among fossil fragments is a better estimator of sample variance than methods that assume spatial independence (such as a binomial distribution), especially for fragment sizes of 8 mm or less. While there is much to be learned about neocheilostome ovicell arrangement across taxa and environments, we can robustly estimate fecundity from small fossil fragments even in extinct neocheilostome species.
Dataset DOI: 10.5061/dryad.r2280gbrj
Description of the data and file structure
In this study, we map the location of ovicells (larval brood chambers) across 27 bryozoan colonies in the species Parasmittina eccentrica. The dataset includes the 27 colony maps and the code for quantifying the arrangement of ovicells across a colony. The original specimens are from the Smithsonian National Museum of Natural History (USNM PAL Collection # 787). The specimen images are available upon request from the corresponding author.
Files and variables
File: alldata_submission.RData
Description: This.RData file will load everything necessary to run the R script (except packages) into your R Environment, so you can recreate all results and figures. There is no need to use the raw colony map files (ColonyMapFiles.zip) if you use this.RData file.
Variables
1) Colony_distboot: Simulated versions of the colonies with randomized ovicell locations
X: row number
Colony: Colony ID
Density_distclass: average density of ovicells a given distance from the ancestrula
distance: A range of distances from the ancestrula in mm (e.g. "6-8" means 6 to 8 mm from the ancestrula)
2) data: Observed data from the real colonies
X: row number
File: Colony mapping file the data come from
Colony: Colony ID
Pointtype: "A" for ancestrula, "NOV" for zooid without ovicell, and "OVI" for zooid with ovicell
x: x coordinate in mm (measured from the lower left corner of the image)
y: y coordinate in mm (measured from the lower left corner of the image)
Parent: Parent of the Colony (if Parent is the same as Colony, then the Colony is said Parent)
x_a: x coordinate in mm measured from the ancestrula
y_a: y coordinate in mm measured from the ancestrula
r: radius, i.e. the straight-line distance from the ancestrula to the point
theta: angle in radians from the ancestrula to the point
Zooids: total zooids in the colony
NonOv: number of zooids without ovicells in the colony
Ovicells: number of zooids with ovicells in the colony
Density: number of ovicells divided by number of zooids in the colony
distance: A range of distances from the ancestrula in mm (e.g. "6-8" means 6 to 8 mm from the ancestrula)
Zooids_distclass: number of zooids in the given distance bracket from the ancestrula
NonOv_distclass: number of zooids without ovicells in the given distance bracket from the ancestrula
Ovicells_distclass: number of zooids with ovicells in the given distance bracket from the ancestrula
Density_distclass: number of ovicells divided by number of zooids in the colony in the given distance bracket
3) Ov_data: for every zooid with an ovicell, what proportion within a certain radius also have ovicells?
X: placeholder text, each row is data for one ovicell in the colony
V1: Colony ID
V2 - V19: density of ovicells within a radius of this ovicell, each column is a new radius in mm, from 0-2, 2-4, 4-6, 6-8, 8-10, 10-12, 12-14, 14-16, 16-18, 18-20, 20-22, 22-24, 24-26, 26-28, 28-30, 30-32, 32-34, 34-36
4) Ov_databoot: randomized simulations of Ov_data, where the ** is a placeholder for a given colony e.g. there is Ov_databoot_Pa55 and there is Ov_databoot_Pa55M11). In each, the variables are:
X: row number
Colony: Colony ID
distance_Ovi: distance from the ovicell in mm
Density: the simulated average density of ovicells in that distance bracket
5) SEMsim_data: simulated fragments of a real colony
Colony: Colony ID
SubColonyArea: The area in squared mm of the colony fragment
SampleSize: The number of Zooids in the colony fragment, always 1 or greater
Sim_Density: the density of ovicells on the simulated fragment
colony_xmin: the lower x limit of the colony image in mm from the ancestrula
colony_xmax: the upper x limit of the colony image in mm from the ancestrula
colony_ymin: the lower y limit of the colony image in mm from the ancestrula
colony ymax: the upper y limit of the colony image in mm from the ancestrula
frag_x: the x coordinate of the center of the fragment
frag_y: the y coordinate of the center of the fragment
frag_r: the radial distance from the ancestrula to the center of the fragment
sim_number: the iterative number of the simulation
(All other data files starting with SEMsim_data_ have been merged into SEMsim_data)
6) sim_boot: Randomized version of SEMsim_data. All the variables are the same.
(All other data files starting with sim_boot_ have been merged into sim_boot)
File: RCode_submission.Rmd
Description: This R Markdown file includes all the code necessary to recreate the entire manuscript, including loading packages, importing the raw data, quantifying ovicell arrangement, and running the simulations. You may run this by loading the files in ColonyMapFiles.zip, or you can load in alldata_submission.RData.
File: SpeciesID_ZooidMeasurements.xlsx
Description: The specimens used in this study are from a museum collection, and we updated their species identification from Parasmittina areolata to Parasmittina eccentrica. This file includes some zooid measurements to support this taxonomic claim, which is just a minor note in the paper.
Variables
- Colony: The official specimen ID in USNM PAL #787 (the Smithsonian National Museum of Natural History collection)
- Measurement: The quantity measured in micrometers
- Value: The part of the zooid we were measuring (orifice length, zooid width, etc.)
File: ColonyMapFiles.zip
Description: This file contains 121 .mrk.json files, which are colony maps containing the coordinates of ovicellate and non-ovicellate zooids on the 27 bryozoan colonies. These are imported by the R Markdown file. The colony maps were created in 3D Slicer.
Zenodo Supplement: SuppFig1.tiff
Description: Supplementary Figure 1 for the affiliated manuscript. Caption: Light microscope images to support reclassification of study specimens from Parasmittina areolata Canu & Bassler, 1927 to P. eccentrica Winston & Jackson, 2021 (Winston & Jackson, 2021; Farias et al., 2024). Mean Zooid Length = 532 μm, Mean Zooid Width = 395 μm, Mean Primary Orifice Length = 114 μm, Mean Primary Orifice Width = 119 μm. A) Peripheral zooids have 2–3 oral spines (colony Pa67M157). B) Most zooids have two large elongate avicularia (colony Pa62M115). C) A minority of zooids have large spatulate avicularia (colony Pa69M113). D) Many zooids also have small avicularia triangular to elliptical in shape, which unlike the other two avicularia types do not seem to share a common location or orientation on zooids (colony Pa69M117). Avicularia types also appear clustered, which is worthy of further research.
Zenodo Supplement: SuppFig2.tiff
Description: Supplementary Figure 2 for the affiliated manuscript. Caption: The estimates and 95% confidence intervals of average population fecundity for a random sample of colony fragments for each of the 3 methods (methods described in Table 1). The “true” ovicell density of each colony is indicated with a vertical black line. There are 500 iterations per method per colony, 13,500 total iterations per method. For brevity, this figure only depicts the estimates for the 2–4 mm size class.
Zenodo Supplement: SuppFig3.tiff
Description: Supplementary Figure 3 for the affiliated manuscript. Caption: There is a significant but weak positive correlation between ovicell density and the number of zooids in a colony (R2 = 0.22, p = 0.009). Each point represents one of the 27 colonies. The line is a linear regression, but the 95% confidence interval is too small to see (SE = 3e-5).
Code/software
The. Rmd and .RData files can be used to entirely recreate this study. We used RStudio Version 2024.12.0+467 and R Version 4.4.2. The following R packages are necessary (which are all cited in the main article): Morpho, geomorph, tidyverse, ggpubr, ggforce, ggtext, ggplot2, doParallel, foreach, and scales.