DOI: 10.5061/dryad.hhmgqnktp
title: Taphonomic megabiases constrain phylogenetic information in the squamate fossil record

description: Fossil data is subject to inherent biological, geological, and
 anthropogenic filters that can distort our interpretations of ancient life
 and environments. The inevitable presence of incomplete fossils thus
 requires a holistic assessment of how to navigate the downstream effects
 of bias on our ability to accurately reconstruct aspects of biology in
 deep time. In particular, we must assess how biases affect our capacity to
 infer evolutionary relationships, which are essential to analyses of
 diversification, paleobiogeography, and biostratigraphy in Earth history.
 In this study, we use an established completeness metric to quantify the
 effects of taphonomic filters on the amount of phylogenetic information
 available in the fossil record of 795 extinct squamate (e.g., lizards,
 snakes, amphisbaenians, and mosasaurs) species spanning 242 million years
 of geologic time. This study found no meaningful relationship between
 spatiotemporal sampling intensity and fossil record completeness. Instead,
 major differences in squamate fossil record completeness stem from a
 combination of anatomy/body-size and affinities of different squamate
 groups to specific lithologies and depositional environments. These
 results reveal that naturally occurring processes create structural
 megabiases that filter anatomical and phylogenetic data in the squamate
 fossil record, while anthropogenic processes play a secondary role.
description: # Taphonomic megabiases constrain phylogenetic information in the squamate
 fossil record Dataset DOI:
 [10.5061/dryad.hhmgqnktp](10.5061/dryad.hhmgqnktp) ## Description of the
 data and file structure Datasets, statistical analyses, and R Code used in
 this study * File **Supplemental Information**: PDF file containing
 supplementary methods, discussion, figures, and tables used for this
 study. * Files that begin with the title "**Data_S1..."**
  include detailed occurrence data for all squamate taxa examined in this
 study, including links to online versions of references where applicable,
 as well as datasets used for assessing the Character Completeness Metric
 (CCM2), and the corresponding scores for each squamate species. * The
 first sheet is entitled
 "**Data_S1a_Squamate_Fossil_record.csv**". It contains all
 occurrence data for the 795 squamate species sampled in this study. The
 sheet contains 27 columns that include taxonomic information (Column A-D);
 Specimen information (E-G), Age (H-J); Geologic information (K-N);
 Locality Information (O-S); Completeness score (T); and
 citations/references (U-AA). * The second sheet is entitled
 "**Data_S1b_CCM2_Character_List.csv**" which includes all the
 characters in our combined dataset we used to assess the completeness of
 each squamate taxon. Each character is organized by region of the
 skeleton. * The third sheet is titled
 "**Data_S1c_Taxon_scoring.csv**" and includes breakdowns of the
 number of characters scored for each of the 795 squamate taxa and final
 percentages. * The fourth sheet is titled
 "**Data_S1d_Squamate_collections_PBDB.csv**" which includes data
 from the Paleobiology Database (PBDB) on every published squamate
 collection in the database for comparison to our CCM2 data.  * The fifth
 sheet is titled "**Data_S1e_Squamate_Formations_PBDB.csv**",
 which includes all squamate-bearing geologic formations on the PBDB. *
 File **Data_S2_Statistical_Tests.xlsx**: Excel file containing results of
 all statistical tests in this study, formatted for ease of reading.  *
 There are 10 sheets within this .xlsx file: * The first sheet is entitled
 "Simple Linear Regression", which compares geologic stage-level
 values among the four time series variables: Median CCM2 per stage,
 Squamate-bearing formations per stage, squamate collections per stage,
 squamate species per stage. These tests were carried out in R and compiled
 in Microsoft Excel. * The second sheet is entitled "GLS
 (log-transformed", which includes results for the Generalized
 Least-Squares regression tests performed on log-transformed values for the
 same time-series variables as above: Median CCM2 per stage,
 Squamate-bearing formations per stage, squamate collections per stage,
 squamate species per stage. These tests were carried out in R and compiled
 in Microsoft Excel. * The third sheet is entitled "Anatomical Gap
 Taxon Tests" and includes results from the non-parametric statistical
 comparisons (Mann-Whitney U-Test [comparison of median CCM2 scores];
 Kolmogorov-Smirnov Test [comparison of distribution shapes]) between the
 four main anatomical groups of squamates: lizards, snakes, amphisbaenians,
 and mosasaurs. These tests were carried out in R and compiled in Microsoft
 Excel. * The fourth sheet is entitled "Anatomical Gap Taxon Tests
 (LC)" which carries out the same non-parametric statistical tests as
 above, but using corrected CCM2 scores for limb-reduced or limbless taxa
 (e.g., snakes and amphisbaenians). The LC stands for
 "Limbless-Corrected", and is used for all statistical tests.
 These tests were carried out in R and compiled in Microsoft Excel. * The
 fifth sheet is entitled "Clade Taxon Tests (LC)", and includes
 non-parametric statistical comparisons of completeness score distribution
 of all major squamate clades. These tests include the Mann-Whitney U-Test
 [comparison of median CCM2 scores] and Kolmogorov-Smirnov Test [comparison
 of distribution shapes]. These tests were carried out in R and compiled in
 Microsoft Excel. * The sixth sheet is entitled "Landmass Tests",
 and includes non-parametric statistical comparisons of completeness score
 distributions across sampled landmasses. These tests include the
 Mann-Whitney U-Test [comparison of median CCM2 scores] and
 Kolmogorov-Smirnov Test [comparison of distribution shapes]. These tests
 were carried out in R and compiled in Microsoft Excel. * The seventh sheet
 is entitled "Landmass Tests (LC)" and includes non-parametric
 statistical comparisons of limbless-corrected completeness score
 distributions across sampled landmasses. These tests include the
 Mann-Whitney U-Test [comparison of median CCM2 scores] and
 Kolmogorov-Smirnov Test [comparison of distribution shapes]. These tests
 were carried out in R and compiled in Microsoft Excel. * The eighth sheet
 is entitled "Depositional Setting Tests" and includes
 non-parametric statistical comparisons of completeness score distributions
 across sampled depositional settings containing squamate fossils. These
 tests include the Mann-Whitney U-Test [comparison of median CCM2 scores]
 and Kolmogorov-Smirnov Test [comparison of distribution shapes]. These
 tests were carried out in R and compiled in Microsoft Excel. * The ninth
 sheet is entitled "Depositional Setting Tests (LC)" and includes
 non-parametric statistical comparisons of limbless-corrected completeness
 score distributions across sampled depositional settings containing
 squamate fossils. These tests include the Mann-Whitney U-Test [comparison
 of median CCM2 scores] and Kolmogorov-Smirnov Test [comparison of
 distribution shapes]. These tests were carried out in R and compiled in
 Microsoft Excel. * The tenth and final sheet is entitled" Lithology
 Tests (LC)" and includes non-parametric statistical comparisons of
 limbless-corrected completeness score distributions across sampled
 lithologies preserving squamate fossils. These tests include the
 Mann-Whitney U-Test [comparison of median CCM2 scores] and
 Kolmogorov-Smirnov Test [comparison of distribution shapes]. These tests
 were carried out in R and compiled in Microsoft Excel. *
 File **Data_S3_R_Code_examples.R**: R file including generalized code used
 to carry out graphical displays and statistical analyses in this study.
 The following files, derived from **Data_S1_Squamate_fossil_record.xlsx**,
 can be used to run the example analyses: *
 Data_S3a_timescale_age_ranges.txt. This is a file containing abbreviated
 geologic stage names and their corresponding age ranges to upload in the
 geoscale functions in Data_S3_R_Code_examples.R for replicating the time
 series plots in this study.  * Data_S3b_Squamate_Species_Thru_Time.txt.
 This is a text file containing the number of sampled squamate species for
 each geologic stage in Data S3a. This can be uploaded in
 Data_S3_R_Code_examples.R for replicating the time series plots in this
 study.  * Data_S3c_Lizards_CCM2.csv. This file is a single-column CSV file
 that includes the Character Completeness Metric 2 (CCM2) scorings for all
 sampled lizard taxa. This can be uploaded in Data_S3_R_Code_examples.R for
 replicating the violin plots in this study.  *
 Data_S3d_Species_Specimens_CCM2.csv. This file is a multicolumn CSV file
 that includes all time series data in this study.  This can be uploaded in
 Data_S3_R_Code_examples.R for replicating the Generalized Least Squares
 (GLS) regression analyses in this study.  * Data_S3e_All_Lithologies.csv.
 This file is a multicolumn CSV file that includes the CCM2 scores of all
 squamates preserved in specific rock lithologies around the globe.  This
 can be uploaded in Data_S3_R_Code_examples.R for replicating the
 non-parametric statistical tests we used in this study. 
 **Supplemental_Information.pdf**: It contains additional figures,
 statistical test tables, datasets, and extensive references on fossil
 squamates, providing detailed evidence and analyses of how preservation
 biases affect our understanding of lizard and snake evolutionary history.
 ## Code/software All analyses can be carried out in the latest version of
 R. Citation: R Core Team (2021). R: A language and environment for
 statistical computing. R Foundation for Statistical Computing, Vienna,
 Austria. URL [https://www.R-project.org/](https://www.R-project.org/).