Early origins of divergent patterns of morphological evolution on the mammal and reptile stem-lineages
Data files
Feb 09, 2024 version files 2.88 MB
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Fig_S1.tif
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Fig_S2.tif
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Fig_S3.tif
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Fig_S4.tif
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Fig_S5.tif
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Fig_S6.tif
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README.md
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Supplementary_Data_1.docx
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Supplementary_Data_10.nex
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Supplementary_Data_11.nex
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Supplementary_Data_12.nex
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Supplementary_Data_13.nex
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Supplementary_Data_14.tre
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Supplementary_Data_15.tre
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Supplementary_Data_16.tre
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Supplementary_Data_17.tre
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Supplementary_Data_18.tre
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Supplementary_Data_19.csv
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Supplementary_Data_2.nex
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Supplementary_Data_20.xlsx
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Supplementary_Data_21.xlsx
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Supplementary_Data_3.nex
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Supplementary_Data_4.tre
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Supplementary_Data_5.tre
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Supplementary_Data_6.tre
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Supplementary_Data_7.R
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Supplementary_Data_8.R
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Supplementary_Data_9.nex
Abstract
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.
README: Early origins of divergent patterns of morphological evolution on the mammal and reptile stem-lineages
https://doi.org/10.5061/dryad.9ghx3ffj5
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. https://doi.org/10.5061/dryad.jwstqjqbh
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
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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
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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); https://doi.org/10.5061/dryad.t4b8gthx8
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.
https://www.nature.com/articles/s41559-019-1047-3#data-availability
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 (https://paleobiodb.org/)
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