DOI: 10.5061/dryad.3ffbg79rj
title: Data from: Trait-fitness associations via fecundity and competition in a two-million-year-long fossil record

description: The evolution of phenotypic traits is usually studied on generational
 times or across species on million-year timescales. We bridge this
 conceptual gap by using high density sampling of a species lineage,
 Microporella agonistes (Bryozoa, Cheilostomatida), over 2 million years of
 its evolutionary history, to ask if trait-fitness associations are
 consistent with evolutionary trait models often applied to phenotypic time
 series. We use average fecundity and competitive outcome as two different
 fitness components, where competitive outcome is a proxy for partial
 survival. Examining three quantitative traits in multivariate analyses, we
 present evidence that some traits experienced substantial selective
 pressures, in part controlled by past environments. A complex interplay of
 resource competition with an altering set of competitors and past
 temperatures, has contributed to the changing patterns of phenotypes
 within the focal species. A comparison with congeneric species living in
 the same regional community suggests that size traits are more temporally
 variable and less constrained than shape traits. Our analyses also show
 that while controls on phenotypes are complex and varied in time,
 ecological and evolutionary processes that unfold on shorter time scales
 are not inconsistent with macroevolutionary patterns observed on longer
 timescales.
description: Fossil and contemporary bryozoan colonies were collected over
 several fossil field expeditions to the Whanganui Basin of North Island
 New Zealand and dredges in Cook Strait and Taranaki Bight. The bryozoans
 were encrusting on hard substrates, mainly bivalve shells. Images of
 bryozoans were taken with Scanning Electron Microscopy and data of
 colonies and images extracted using a combination of deep-learning
 (DEEPBRYO) and manual measurements/collection. All the
 scanning electron microscope images associated with the work are supplied
 here and image names are associated with detailed metadata.
  
description: # Data from: Trait-fitness associations via fecundity and competition in a
 two-million-year-long fossil record
 [https://doi.org/10.5061/dryad.3ffbg79rj](https://doi.org/10.5061/dryad.3ffbg79rj) This dataset and associated R script and images are associated with the peer-reviewed publication "Trait-fitness associations via fecundity and competition in a two-million-year-long fossil record" at The American Naturalist. ## Description of the data and file structure All the bryozoan data, including the metadata data associated with the image files, are supplied in the excel file Microporella_SELECT_final_datasets_30.06.2023.xlsx. The sheets and column names are described below. The paleo delta O18 values used are from Lisiecki and Raymo 2005, and supplied in O18.txt. The column names are described below. The recent O18 values span 1988-2016 for the southern hemisphere latitude encompassing New Zealand (25-90°S) from NASA data repository ([https://data.giss.nasa.gov/) and are supplied in data.giss.nasa.gov.txt.](https://data.giss.nasa.gov/)The column names are described below. The images are deposited at [https://zenodo.org/records/10795305 (embargoed until April 2026)](https://zenodo.org/records/10795305) #### Detailed data description **Detailed description of data Microporella_SELECT_final_datasets_30.06.2023.xlsx from Trait-fitness associations via fecundity and competition in a two-million-year-long fossil record, sheet by sheet:** **Sheet name: SEMs_Metadata** Column name: **Image_ID**:unique ID for image with initials of person who imagined the colony and a number.         Column name: **Date** : Date imaged (in day.month.year format) Column name: **Formation_name**: Name of the formation or population (can be matched to other spreadsheets) Column name: **Age**: Verbal tag for the age of the formation or population Column name:**SAMPLE_ID**: unique sample ID from the WABO expeditions headed by Liow L. H. and/or Voje K. L. from 2014 to 2020. Column name:**Shell_ID**: shell ids (numbered uniquely within each SAMPLE_ID) Column name: **Colony_ID**: colony ids (numbers with each shell_ID) such that SAMPLE_ID, Shell_ID and Colony_ID can be combined as a unique tag for a colony. Column name:**Genus**: Genus name of the colony in that row Column name:**Species**: species name of the colony in that row  **Sheet name: Formation_Age in Ma_L&R2005** Column name:**ID:** corresponding to the tags in figures in the main text of the ms these data are associated with. Column name:**Formation_name**: Name of the formation or population (can be matched to other spreadsheets) Column name: **Isotope_Stage_Start**: Start of Oxygen Isotope stages for that formation from Naish et al. (2005), Pillans et al. (2005) and Rust (2008). Column name: **Isotope_Stage_End**: End of Oxygen Isotope stages (OIS) for that formation from Naish et al. (2005), Pillans et al. (2005) and Rust (2008). Column name:**Start_age**: Age in Millions of years of start of the OIS from Lisiecki, L. E., and M. E. Raymo. 2005. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20:PA1003. Column name: **End_age**: Age in Millions of years of end of the OIS from Lisiecki, L. E., and M. E. Raymo. 2005. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20:PA1003. **Sheet name: Interactions_Microporella_only** Overgrowth interaction data where at least one partner (colony) is identified as a *Microporella* sp. Column name: **Formation_name**: Name of the formation or population (can be matched to other spreadsheets)                  Column name:**Interaction_section_ID**: unique identifier of the overgrowth interaction between two colonies in all samples/shells studied Column name:**Date:** date the overgrowth interaction was scored             Column name:**Person:** initials of person who determined the overgrowth interaction (EDM = Emanuela Di Martino; MR = Mali Ramsfjell)                  Column name:**Shell_ID:** shell ids (numbered uniquely within each SAMPLE_ID) Column name:**Area (cm2):** area of shell if measured (area enclosed in the perimeter drawn using ImageJ) Column name: **INT_or_EXT:** internal surface or external surface of shell if noted Column name: **SAMPLE_ID**: unique sample ID from the WABO expeditions headed by Liow L. H. and Voje K. L. from 2014 to 2020. Column name: **Local_no:** identifier of the overgrowth interaction between two colonies on one surface (INT or EXT) of the shell Column name: **Colony_1_no**: uniquely numbered colony on a given shell that is desginated “1” in order to score the overgrowth interaction        Column name: **Colony_1_Order**: Can take the states Cheilostomata or Cyclostomata (Orders of Bryozoa) for colony designated “1” in the overgrowth interaction Column name: **Colony_1_Genus** : genus name of the colony designated “1” in the overgrowth interaction Column name: **Colony_1_Species**: species name of the colony designated “1” in the overgrowth interaction          Column name: **Colony_2_no**: uniquely numbered colony on a given shell that is desginated “2” in order to score the overgrowth interaction        Column name: **Colony_2_Order**: Can take the states Cheilostomata or Cyclostomata (Orders of Bryozoa) for colony designated “2” in the overgrowth interaction    Column name: **Colony_2_Genus**: genus name of the colony designated “2” in the overgrowth interaction Column name: **Colony_2_Species**: species name of the colony designated “2” in the overgrowth interaction                             Column name: **Col1_2_int**: overgrowth interaction of colony 1 with respect to colony 2. W = 1 wins 2 (1 overgrows 2); L = 1 loses to 2 (1 is overgrown by 2); SO = stand off; F = fouling; R = reciprocal overgrowth  Column name: **Zooid_col1_size**: autozooid size of colony 1 with respect to colony 2. L = colony 1 autozooid size is detactably larger than those of colony 2; S = colony 1 autozooid size is detactably smaller than those of colony 2:   equal= autozooid sizes are not detactably different:  NA =not applicable Column name: **Certainty**: how certain the observer is of the type of overgrowth interaction they scored. C= certain; U = uncertain            Column name:**Direction**: how colony 1 is approaching colony 2. Frontal = colony 1 and 2 are both approaching with their distal (growing) edges: Rear = The growing edge of Colony 1 approaches the non-growing edge of Colony 2; Flank = Colony 1 is approaching colony 2 from the side, rather than in the direction of growth.       Column name: **Multilaminar_Col1**: states if Colony 1 has multilaminar growth (can be Y = yes or N = no)   Column name: **Multilaminar_Col2**: states if Colony 2 has multilaminar growth (can be Y = yes or N = no)    Missing data code: NA **Sheet name: Counts** All data (from the column Ascopore onwards) are from DEEPBRYO (see Di Martino, E., B. Berning, D. P. Gordon, P. Kuklinski, L. H. Liow, M. H. Ramsfjell, H. L. Ribeiro, et al. 2023. DeepBryo: A web app for AI-assisted morphometric characterization of cheilostome bryozoans. Limnology and Oceanography: Methods 21:542–551) Column name: **Image_ID**: unique ID for image with initials of person who imagined the colony and a number. (EDM = Emanuela Di Martino; MHR = Mali Hamre Ramsfjell) Column name: **Ascopores**: Total counts of ascopores on that image Column name: **Zooids_total**: Total counts of zooids on that image Column name: **Avicularia**: Total counts of avicularia on that image Column name: **Orifices**: Total counts of orifices on that image Column name: **Ovicells**: Total counts of ovicells on that image Column name:**Colony_Area**: total area occupied by the colony fragment on that image in mm2 Column name: **Ovicells_Area**: total area occupied by the ovicells on that image in mm2 **Sheet name: Measurements** All data (from the column Category onwards) are from DEEPBRYO (see Di Martino, E., B. Berning, D. P. Gordon, P. Kuklinski, L. H. Liow, M. H. Ramsfjell, H. L. Ribeiro, et al. 2023. DeepBryo: A web app for AI-assisted morphometric characterization of cheilostome bryozoans. Limnology and Oceanography: Methods 21:542–551) Column name:**Image_ID**:unique ID for image with initials of person who imagined the colony and a number Column name:**Category**: the identified structure from DEEPBRYO (Di Martino et al. 2023)  Column name:**Hierarchy**: A unique tag of the structure (where the first part of the number is the image_ID and the second a unique number for that structure in that image) Column name: **Area**: surface area of the named structure (Category) in mm2 Column name:**Length**: maximum length of the named structure (Category) in mm Column name:**Width**: maximum width of the named structure (Category) in mm  **Sheet name: FOSSIL SAMPLE METADATA** Column name:**Lithostratigraphic unit/Population**: Name of the formation or population (can be matched to other spreadsheets)  Column name:**Sample ID**: unique sample ID from the WABO expeditions headed by Liow L. H. and Voje K. L. from 2014 to 2020 Column name:**Lat.**: Latitude of collection of that sample Column name:**Long.** : Longitude of collection of that sample  Column name:**Coll. Year**: Calender year in which the sample was collected **Sheet name: RECENT SAMPLES METADATA** Column name:**Population**: short description of expeditions or survey by NIWA or U Otago Column name: **Sample ID**: unique sample ID expeditions or survey by NIWA or U Otago Column name:**Lat.**:Latitude of collection of that sample Column name:**Long.** : Longitude of collection of that sample  Column name:**Coll. Year**: Calendar year in which the sample was collected Column name:**max depth**: maximum depth (meters)      **Detailed description of O18.txt**: This text file has three columns, namely Time, d18O and Error, from Lisiecki and Raymo 2005. Column name:**Time**: time in units of kilo years ago (kyr) Column name:**d18O**: averaged delta O18 values (unitless ratio) given in Lisiecki and Raymo 2005 for the given time interval (Time) Column name:**Error:** stand error for delta O18 values given in Lisiecki and Raymo 2005 for the given time interval (Time) **Detailed description of  data.giss.nasa.gov.txt[:](https://data.giss.nasa.gov/)** The recent O18 values span 1988-2016 for the southern hemisphere latitude, encompassing New Zealand (25-90°S) from NASA data repository ([https://data.giss.nasa.gov/) ](https://data.giss.nasa.gov/) Column name:**Longitude:** longitude at which the observation given in row was measured (this column was not used in our analyses, only for delimiting the spatial data) Column name:**Latitude:** latitude at which the observation given in row was measured (this column was not used in our analyses, only for delimiting the spatial data) Column name:**Depth:** water depth (meters) at which the observation given in row was measured (this column was not used in our analyses) Column name:**pTemperature:** temperature measured in Celcius (this column was not used in our analyses) Column name:**Salinity:** salinity in parts per thousand (this column was not used in our analyses) Column name:**dO18:** delta O18 (unitless ratio) equivalent to those in Raymo and Lisiecki 2005 Column name:**dD:** (this column was not used in our analyses) Column name:**Year:** calendar year when observation given in row was measured (these were assigned as "0 million years ago" in our analyses) Column name:**Month:** month during which the observation given in row was measured (this column was not used in our analyses) Column name:**Reference:** references from which the data in the row were drawn, see NASA for details. ### Code/Software **Prep.R** reads the data file and prepares the data for analyses. The data are read in and linked with formation ages, and there are functions for making averages of colonies and formations. (associated with Table S1 in the SI of the published article) **exploreTS.R** uses the R packages paleoTS and EvoTS for modeling of trait means and model selection for Microporella agonistes. (associated with Fig. 2 in the main text, Fig. S2. Fig. S3, Table S2 in the SI of the published article) **TraitFitness.R** fits binomial glm to Microporella agonistes data (associated with Fig. S4, Table S3, S4, Fig. 3, Fig. S5 in the SI of the published article) including Fig. 2alt (not presented) **subsampled.R** draws random samples from the Microporella agonistes data to do sensitivity analyses on how much sampling of the populations potentially affect the trait-fitness results. (associated with Fig. S6 in the SI of the published article) **WinLose.R** explores win-lose data for Microporella agonistes then fits binomial glm like in TraitFitness.R (associated with Fig. 4, Fig. 5 in the main text Table S5, Fig. S7, Fig. S8, Table S6 in the SI of the published article) **O18.R** explores paleotemperature association (associated with Fig. 6 of the main text, Table S7, Fig. S9, Table S8 in the SI of the published article). Also runs for the other two species (speculum, intermedia and discors) Associated with Fig. S12 and S13 in the SI of the published article. **Fig.S10.R** fits binomial glm to other Microporella species lumped. Associated with Fig. S10 in the SI of the published article **Fig.S10.R** fits binomial glm to other Microporella species lumped. Associated with Fig. S10 in the SI of the published article **Fig.S10.R** fits binomial glm to other Microporella species lumped. Associated with Fig. S10 in the SI of the published article **Fig.S11A & Fig.S11BC** fit binomial glm to other Microporella species. Associated with Fig. S11 in the SI of the published article **References cited** Lisiecki, L. E., and M. E. Raymo. 2005. A Pliocene-Pleistocene stack of 57 globally distributed benthic δ18O records. Paleoceanography 20:PA1003 Naish, T. R., B. Field, H. Zhu, A. Melhuish, R. J. Carter, S. T. Abbott, S. Edwards, et al. 2005. Integrated outcrop, drill core, borehole and seismic stratigraphic architecture of a cyclothemic, shallow-marine depositional system, Wanganui Basin, New Zealand. Journal of the Royal Society of New Zealand 35:91–122. Pillans, B. J., B. Alloway, T. R. Naish, J. A. Westgate, S. T. Abbott, and A. R. Palmer. 2005. Silicic tephras in Pleistocene shallow‐marine sediments of Wanganui Basin, New Zealand. Journal of the Royal Society of New Zealand 35:43–90. Rust, S. 2008. *Plio-Pleistocene bryozoan faunas of the Wanganui Basin, New Zealand*. PhD Thesis, University of Auckland, New Zealand.