Morphometric analysis of the Late Cretaceous Placenticeras of Alabama, USA: Sexual dimorphism, allometry, and implications for taxonomy
Data files
Jan 04, 2024 version files 136.29 KB
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MOHR_et_al_Supplementary_Data.xlsx
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README.md
Abstract
A traditional typological approach to taxonomy often does not adequately account for intraspecific variation and can result in taxonomic oversplitting. For many groups, including ammonoids of the Placenticeras genus, intraspecific variation documented in recent studies (e.g., ontogenetic changes, sexual dimorphism, polymorphism) challenges the historic proliferation of species names. Here, we used a population approach to taxonomy and quantitatively evaluated morphometric variation in a sample of Late Cretaceous (Santonian -Campanian) Placenticeras from Alabama and adjacent counties.
We used linear mixed models (LMMs) to characterize how morphological variables scale with conch size across the sample, exploiting mixed longitudinal data to evaluate individual variation in growth and inform interpretations of multivariate analyses. Extended LMMs incorporating geological formation evaluated morphological changes through time. Principal component analysis and clustering analysis were then used to evaluate the number of distinct clusters that emerged in multivariate morphospace independent of previous taxon name assignments.
Discontinuous scaling relationships and distinct clusters in multivariate space suggest sexual dimorphism characterized by differences in adult size, and secondarily, shape. Previous Stantonoceras and Placenticeras assignments broadly overlap in our morphospace, failing to justify this historic distinction (as sexual dimorphs, or as genera or subgenera). Placenticeras conch morphology and ornament placement changed through time, suggesting a potential utility for coarse (stage-level) biostratigraphy. However, temporal changes were not associated with distinct clusters in morphospace and our data fail to support the plethora of reported species names. As few as one or two (successive) species may be present in our sample (representing 130 years of collection effort). In addition to highlighting the need for a significant taxonomic revision of the Placenticeras genus, this study demonstrates the utility of LMMs for distinguishing between different sources of morphological variation, improving interpretations of morphospace under a population approach to taxonomy, and maximizing the amount of ontogenetic information that can be obtained non-destructively.
README: Morphometric analysis of the Late Cretaceous Placenticeras of Alabama, USA: Sexual dimorphism, allometry, and implications for taxonomy
https://doi.org/10.5061/dryad.dfn2z358h
Supplemental Information accompanying the article:
"Morphometric analysis of the Late Cretaceous Placenticeras of Alabama, USA: sexual dimorphism, allometry, and implications for taxonomy"
Authors:
Rachel C. Mohr
Thomas S. Tobin
Emily M. Tompkins
Description of the data and file structure
"MOHR_et_al Supplement Text.pdf"
Includes:
Supplement Text
Supplementary Tables 1-8
Supplementary Figures 1-25
"MOHR_et_al Supplementary Data.xlsx"
Sheet 1: "Metadata": overview of contents, metadata about all variables
Sheet 2: "Specimen Information": basic information about Placenticeras specimens (accession numbers, previous taxonomic identifications, locality information, etc.)
Sheet 3: "Morphometric Data": morphometric data collected from n=112 Placenticeras specimens
Sheet 4: "main PCA (n=105)": data included in the main PCA and associated clustering results
Sheet 5: "main PCA - 'linear' version": data included in the Supplementary "linear" version of our main PCA, which includes only linear measurement variables
Sheet 6: "main PCA - 'shape' version": data included in the Supplementary "shape" version of our main PCA, which includes only Whorl Height and size-standardized or dimensionless variables
Sheet 7: "Ornament PCA (n=45)": data included in the secondary "Ornament PCA" and associated clustering results
Cells contain "NA" when the information is "not available" or "not applicable".
For morphometric measurement variable columns, a cell containing "NA" indicates that incomplete or poor preservation of the specimen prevented the measurement of the variable.
For the "ID_by" column on Sheet 2 (indicating the individual who assigned any prior taxonomic identification), "NA" is used when no prior taxonomic identification exists, and "unknown" is used when a taxonomic identification was present, but it is unknown who made the taxonomic identification.
For the "locality_code" column on Sheets 2 and 3 (indicating standard paleontological site numbers; further information about these site numbers are available at repositing institutions), "NA" is used in all cases where the locality was unknown, or if the locality was not assigned a site number by the repositing institution.
Empty cells in columns "VT_present", "LT_present", and "UT_present" (on Sheet 3: "Morphometric Data") indicate instances in which the presence/absence of VTs (ventral tubercles), LTs (lateral tubercles), or UTs (umbilical tubercles), respectively, could not be determined, typically due to poor preservation of the specimen. The associated R code scripts require these empty cells (rather than "NA" values) in order to load and format the data correctly.
"MOHR_et_al R code scripts" ZIP Folder
This folder includes 14 R code scripts used to analyze the data for the manuscript and produce the figures.
Also includes the "Plac_Morphometric_Data.csv" file, which is Sheet 3 from "MOHR_et_al Supplementary Data.xlsx", saved as a csv file. This csv file is the data used in the associated R scripts.
See "Code" section below for more detailed information about the R scripts.
Code
The 14 R scripts and their outputs are described below:
"load and format data.R"
This script must be run in its entirety before any other R scripts are run
Note that all analyses were performed in R version 4.0.4 (2021-02-15) -- "Lost Library Book"
"density histogram plots.R"
Produces Manuscript Figure 4
"LMM scatterplots.R"
Produces Manuscript Figures 6-8; Supplementary Figures 1, 22-24
Produces results included in Supplementary Tables 1, 3-5
"LMM random slope model.R"
Produces results included in Supplementary Table 2
"LMM summary figure.R"
Produces base of Manuscript Figure 5
"LMM temporal models.R"
Produces results included in Supplementary Tables 7 & 8
"LMM temporal model figure.R"
Produces Manuscript Figure 9
"power single-slope.R"
Produces data required for Supplementary Figures 9 & 10
"power threshold.R"
Produces data required for Supplementary Figures 9 & 10
"power plots.R"
Produces Supplementary Figures 9 & 10
"PCA datasets.R"
Produces datasets for PCAs
"PCA figures.R"
Produces parts of Manuscript Figures 10 & 11; Supplementary Figures 11, 13, 14, 17 & 18
Produces Manuscript Figures 12 & 13; Supplementary Figures 3-8, 12, 15, 16 & 19
"cluster figures.R"
Produces parts of Manuscript Figures 10 & 11; Supplementary Figures 11, 13, 14, 17 & 18
"dot plots.R"
Produces Supplementary Figure 25
Methods
Morphometric measurements were collected with digital calipers. See associated manuscript for details.