DOI: 10.5061/dryad.9ghx3ffj5
title: Early origins of divergent patterns of morphological evolution on the mammal and reptile stem-lineages

description: The origin of amniotes 320 million years ago signalled independence from
 water in vertebrates and was closely followed by divergences within the
 mammal and reptile stem lineages (Synapsida and Reptilia). Early members
 of both groups had highly similar morphologies, being superficially
 ‘lizard-like’ forms with many plesiomorphies. However, the extent to which
 they might have exhibited divergent patterns of evolutionary change, with
 potential to explain the large biological differences between their living
 members, is unresolved. We use a new, comprehensive phylogenetic dataset
 to quantify variation in rates and constraints of morphological evolution
 among Carboniferous–early Permian amniotes. We find evidence for an early
 burst of evolutionary rates, resulting in the early origins of
 morphologically distinctive subgroups that mostly persisted through the
 Cisuralian. Rates declined substantially through time, especially in
 reptiles. Early reptile evolution was also more constrained compared to
 early synapsids, exploring a more limited character state space.
 Postcranial innovation in particular was important in early synapsids,
 potentially related to their early origins of large body size. In
 contrast, early reptiles predominantly varied the temporal region,
 suggesting disparity in skull and jaw kinematics, and foreshadowing the
 variability of cranial biomechanics seen in reptiles today. Our results
 demonstrate that synapsids and reptiles underwent an early divergence of
 macroevolutionary patterns. This laid the foundation for subsequent
 evolutionary events and may be critical in understanding the substantial
 differences between mammals and reptiles today. Potential explanations
 include an early divergence of developmental processes or of ecological
 factors, warranting cross-disciplinary investigation.
description: # Early origins of divergent patterns of morphological evolution on the
 mammal and reptile stem-lineages
 This README file was
 generated on 09/02/2024 by Neil Brocklehurst. GENERAL INFORMATION 1\.
 Title of Dataset: Early origins of divergent patterns of morphological
 evolution on the mammal and reptile stem-lineages. 2\. Corresponding
 Author Information ``` Corresponding author Name: Neil Brocklehurst
 Institution: University of Cambridge Address: Cambridge, UK Email:
 neilbrockpalaeo@gmail.com Co authors David Ford, Roger Benson ``` 3\.
 Recommended citation for this dataset: Leimberger, K. G., Hadley, A. S.,
 Frey, S. J. K., & Betts, M. G. (2023). Data from: Tropical
 plant–hummingbird interactions withstand short-term experimental removal
 of a common flowering plant. Dryad Digital Repository.
 DATA & FILE OVERVIEW
 1\. File List: Fig_S2.tif Fig_S3.tif Fig_S4.tif Fig_S5.tif Fig_S6.tif
 Supplementary_Data_1.docx Supplementary_Data_2.nex
 Supplementary_Data_3.nex Supplementary_Data_4.tre Supplementary_Data_5.tre
 Supplementary_Data_6.tre Supplementa...y_Data_7.R Supplementa...y_Data_8.R
 Supplementary_Data_9.nex Supplementary_Data_10.nex
 Supplementary_Data_11.nex Supplementary_Data_12.nex
 Supplementary_Data_13.nex Supplementary_Data_14.tre
 Supplementary_Data_15.tre Supplementary_Data_16.tre
 Supplementary_Data_17.tre Supplementary_Data_18.tre
 Supplementary_Data_19.csv Supplementary_Data_20.xlsx
 Supplementary_Data_21.xlsx
 \#########################################################################
 SUPPLEMENTARY FIGURES Fig_S1.tf: Supplementary Figure 1- The phylogeny
 obtained through Fossilised Birth Death analysis of Supplementary Data 2,
 showing 95% confidence intervals on the node age posterior Fig_S2.tif:
 Supplementary Figure 2 - The phylogeny obtained through Fossilised Birth
 Death analysis of Supplementary Data 2, showing posterior probability
 (support) for each node Fig_S3.tif: Supplementary Figure 3 - The disparity
 (pairwise morphological dissimilarity) of reptiles and synapsids based on
 different anatomical regions: A) Skull; B) Antorbital skull; C)
 postorbital skull; D) postcranium Fig_S4.tif: Supplementary Figure 4 - The
 disparity (pairwise morphological dissimilarity) of reptiles and synapsids
 based on different anatomical regions: A) Skull; B) Antorbital skull; C)
 postorbital skull; D) postcranium Fig_S5.tif: Supplementary Figure 5 -
 Comparison of patristic distances and morphological dissimilarity in
 synapsids (red) and reptiles (blue) within different anatomical regions.
 Each point represents a pairwise comparison of two taxa. The curves
 represent Loess-fitted regression curves. A) Skull; B) Antorbital skull;
 C) postorbital skull; D) postcranium Fig_S6.tif: Supplementary Figure 5 -
 - The disparity (pairwise morphological dissimilarity) of amniotes
 subdivided by size: A) Small; B) Medium; C) Large; D) Very Large
 \#########################################################################
 SUPPLEMENTARY DATA FILES Supplementary_Data_1.docx: Supplementary Data 1 -
 Modifications to the character list of Ford & Benson (2020); altered
 characters and added characters. The complete character list is used in
 the phylogenetic analysis and the analyses of disparity and constraint The
 original matrix of Ford & Benson 2020 is available at: Ford, D. P.
 & Benson, R. B. J. The Phylogeny of Early Amniotes and the Affinities
 of Parareptilia and Varanopidae (Dryad Digital Repository, 2019);
 Supplementary_Data_2.nex:
 Supplementary data 2 - The analysis file for a Fossilised Birth Death
 analysis of the character-taxon matrix described herin in MrBayes v3.2.6
 Supplementary_Data_3.nex: Supplementary data 3 - The analysis file for a
 Fossilised Birth Death analysis of the character-taxon matrix of
 Brocklehurst & Benson 2021 in MrBayes v3.2.6 The original character
 list and character taxon matrix of Brocklehurst & Benson 2020 is
 available at: Brocklehurst, N., & Benson, R. J. (2021). Multiple paths
 to morphological diversification during the origin of amniotes. Nature
 Ecology & Evolution, 5(9), 1243-1249.
 Supplementary_Data_4.tre: Supplementary data 4 - the maximum clade credibility tree produced by the Fossilised Birth Death analysis of Supplementary data 2, in nexus format Branch lengths correspond to time Supplementary_Data_5.tre: Supplementary data 6 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 2, in nexus format. Branch length correspond to morphological Change Supplementary_Data_6.tre: Supplementary data 6 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 3, in nexus format. Branch length correspond to morphological change Supplementary_Data_7.R: Supplementary Data 7- R code representing the new functions to carry out analyses of constraint over a phylogeny as described in this paper. Written in R v 3.6.1 Script should be run in R before Supplementary Data 8 Supplementary_Data_8.R: Supplementary Data 8 - R code representing the analyses of the datasets described in this paper. Written in R v 3.6.1 Script may be run out of the box, provided all supplementary data files are included in the working directory Supplementary_Data_9.nex: Supplementary data 9 - The analysis file for an undated analysis of the cranial character-taxon matrix described herin in MrBayes v3.2.6 Supplementary_Data_10.nex: Supplementary data 10 - The analysis file for an undated analysis of the postcranial character-taxon matrix described herin in MrBayes v3.2.6 Supplementary_Data_11.nex: Supplementary data 11 - The analysis file for an undated analysis of the antorbital cranial character-taxon matrix described herin in MrBayes v3.2.6 Supplementary_Data_12.nex: Supplementary data 12 - The analysis file for an undated analysis of the postorbital character-taxon matrix described herin in MrBayes v3.2.6 Supplementary_Data_13.nex: Supplementary data 13- The analysis file for an undated analysis of the dental character-taxon matrix described herin in MrBayes v3.2.6 Supplementary_Data_14.tre: Supplementary data 14 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 9, in nexus format. Branch length correspond to cranial morphological change Supplementary_Data_15.tre: Supplementary data 15 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 10, in nexus format. Branch length correspond to postcranial morphological change Supplementary_Data_16.tre: Supplementary data 16 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 11, in nexus format. Branch length correspond to pre-orbital morphological change Supplementary_Data_17.tre: Supplementary data 17 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 12, in nexus format. Branch length correspond to postorbital morphological change Supplementary_Data_18.tre: Supplementary data 18 - the maximum clade credibility tree produced by an undated analysis of Supplementary data 13, in nexus format. Branch length correspond to dental morphological change Supplementary_Data_19.csv: Supplementary Data 19 - Analysis file giving body size categories for each species. Two columns: Taxon (the species name as represented in the tree file) and Size category (a numerical value between 1 and 4 indicating size category, with unused taxa scored NA) Size category 1: small; 2: medium; 3: large; 4: very large Supplementary_Data_20.xlsx: Supplementary data 20 - Sources for first appearece dates used in the fossilised birth death analysis. Five columns: Taxon (the species name as represented in the tree file), Oldest occurence (the locality representing the oldest appearence in time of that taxon); Citation of occurence (the reference in which the occurence is recorded); Age of formation (the time interval of the formation represneting the oldest occurence); Citation of age (the reference giving the age of the occurence); Notes (any further details or justifications of ages) Sources marked PBDB were taken from the paleobiology database () Supplementary_Data_21.xlsx: Supplementary Data 20 - SOurces for the body size categories given in Supplementary Data 19. Three columns: Taxon (the species name as represented in the tree file) and Size category (a numerical value between 1 and 4 indicating size category, with unused taxa scored NA); Justification (sources and rationale for the assignment of the taxon to the body size category) Size category 1: small; 2: medium; 3: large; 4: very large