Data from: Shell constraints on evolutionary body size-limb size allometry can explain morphological conservatism in the turtle body plan
Data files
Nov 11, 2024 version files 3.61 MB
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Code_data_Dryad.zip
3.60 MB
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README.md
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Abstract
Turtles are a small clade of vertebrates despite having existed since the Late Triassic. Turtles have a conservative body plan relative to other amniotes, characterized by the presence of a shell and quadrupedality. This morphology is even retained in strong ecological specialists, such as sea turtles, which are secondarily adapted to marine locomotion by strong allometric scaling in their hands. It is possible that the body plan of turtles is strongly influenced by the presence of the shell, acting as a constraint to achieving greater diversity of body forms. Here, we explore the evolutionary allometric relationships of fore- and hindlimb stylopodia (i.e., humerus and femur) with one another as well as their relationship with shell size (carapace length) to assess evidence of constraint. All turtles, including Triassic shelled stem turtles, have near-isometric relationships that do not vary strongly between clades, and evolve at slow evolutionary rates. This indeed indicates that body proportions of turtles are constrained to a narrow range of possibilities. Minor allometric deviations are seen in highly aquatic sea turtles and softshell turtles, which modified their shells by bone losses. Our allometric regressions allow accurate body size estimations for fossils. Several independent sea turtle lineages converged on maximum sizes of 2.2 m of shell length, which may be a biological maximum for the group.
This zipped folder includes:
- raw data of measurements available in
csv
format - phylogenetic tree files used in PGLS regressions
R
scripts used to perform analyses and produce figures in the publication- all supplementary files (tables, text and figures) related to the publication
Description of R
scripts:
script_size.R
reads the raw data and filters the data to only include the adult specimens in our sample (see Main Text for explanation), and prunes the turtle phylogenetic tree to match the taxa in each subset used for downstream analysespgls_runs.R
executes PGLS analyses on the global and clade-specific subsets of our data and runs the predictions for fossil specimens with unknown straight carapace lengthsresiduals.R
extracts both global and clade-specific residual values from PGLS regressions that will be used at a later point for visual purposes (see e.g., Figures 1-3 in the Main Text)slope_differences.R
compare the purely allometric slopes of PGLS and OLS regressions of our global datasets. This is a modified code based on Paiva et al. (2023)body_mass_pgls.R
reads the extant turtle data of body mass and carapace length measurements from Regis and Meik (2017) and performs a PGLS regression of BM ~ SCL to obtain sigma2 values for turtles based on a cubic body mass index (body mass), comparable to other studies. This script also is used to estimate the BM for all specimens in our dataset for which we have empirical SCL measurementscomparisons_sigma.R
reads the raw data from additional amniote allometric datasets (see ‘Datasets’ folder) and phylogenetic trees related to these datasets and executes PGLS regressions of body size vs. humerus/femur size and femur vs. humerus size as a means to compare the sigma2 values of these allometric relationships with the values of turtle allometriesscript_plot_final.R
contains the code to reproduce the figures shown in the Main Text and also in Supplementary File S2. These figures were exported inpdf
format and later edited (i.e., inclusion of silhouettes, removal of unnecessary blank space etc) in Adobe Illustrator
Description of tree files (see Main Text for more details):
- bird_tree_timetree.nwk: phylogenetic tree of extant bird species retrieved from http://timetree.org
- CampioneEvans_tree_timetree.nwk: phylogenetic tree of extant amniote species retrieved from http://timetree.org
- crocs_tree_timetree.nwk: phylogenetic tree of extant crocodylians retrieved from http://timetree.org
- Dinosaur trees cal3 Benson 2017.tre: phylogenetic trees of non-avian dinosaurs scaled in time retrieved from Benson et al. (2018; https://doi.org/10.1111/pala.12329)
- Panciroli_trees.nex: phylogenetic trees of extant mammals scaled in time retrieved from Panciroli et al. (2024; https://www.nature.com/articles/s41586-024-07733-1)
- Pereira.tre: phylogenetic tree of extant turtles retrieved from Pereira et al. (2017; https://doi.org/10.1016/j.ympev.2017.05.008)
- Sterli_MCCT.tre: phylogenetic tree dated using Bayesian tip-dating combining extant and extinct turtle taxa retrieved from Farina et al. (2023; https://doi.org/10.1002/ece3.10201)
In the raw data supplementary files, NAs
correspond to non-applicable data. For example, in SupplementaryFileS1 , NAs
are included in the columns of fossil taxa for parameters that cannot be applied to these specimens (e.g., maximum carapace size of female/male in the species).
In SupplementaryFileS2 , empty cells are merely left blank for aesthetics purposes only. Column names are the same as those used in the Main Text (please refer to it for the abbreviations). The last tab (‘BM estimates for SCL specimens’) includes body mass predictions for all specimens with measured SCL values. These values are provided in grams (g).
In SupplementaryFileS4, column names correspond to:
- Taxon: taxon name
- Specimen: specimen number
- fit: predicted SCL for that specimen
- lwr95: lower 95% confidence interval of the prediction
- upr95: upper 95% confidence interval of the prediction
- fit_clade: predicted SCL for that specimen based on clade-specific regressions (see Main Text). Cells with no values indicate that the specimen was predicted using only the global regression coefficients
In the array of amniote datasets we used for our sigma2 comparisons, spreadsheets with either NAs
or empty (blank) cells simply indicate non-applicability or absence of data for the referred species/specimen. As we simply outsource these data from other studies, users should refer to the original paper for the original files and their respective descriptions.
In SupplementaryFileS1 , column names correspond to the following:
- Taxon: taxon name
- Specimen: specimen number
- Correct_taxonomy: the updated species name of the referred taxon
- Clade: major turtle clade to which the taxon belongs
- HL_mm: Humerus length in milimeters
- FL_mm: Femur length in milimeters
- SCL_mm: straight carapace length (SCL) in milimeters
- Max_SCL_F_mm: maximum SCL in milimeters of female individuals for that species
- Max_SCL_M_mm: maximum SCL in milimeters of male individuals for that species
- Ratio_F: the SCL of the referred specimen divided by the maximum SCL of females for that species
- Ratio_M: the SCL of the referred specimen divided by the maximum SCL of males for that species
- Terr_spec: binary variable (1/0) indicating if a species is (1) a terrestrial specialist or not (0)
- Aq_spec: binary variable (1/0) indicating if a species is (1) an aquatic specialist or not (0)
- Trion: binary variable (1/0) indicating if a species is (1) a trionychid turtle or not (0)
- Sex: sex of the referred specimen, when available
- To_use: logical argument to determine whether that specimen should be included in the analyses or not
- Reason_exclusion: the rationale for not considering a given specimen in downstream analyses
- Material: indicates if the specimen is from extant species or fossils
- Source: reference from which measurements were taken for the referred specimen
Within the datasets used, here is the description of all the variables included in the spreadsheets, although one may also check them themselves in the following references as they can provide even more accurate descriptions: Campione and Evans (2012; https://link.springer.com/article/10.1186/1741-7007-10-60), Field et al. (2013; https://doi.org/10.1371/journal.pone.0082000), Benson et al. (2018; https://doi.org/10.1111/pala.12329), Iijima et al. (2018; https://doi.org/10.1098/rsos.171774), Panciroli et al. (2024; https://www.nature.com/articles/s41586-024-07733-1), Regis and Meik (2017; https://peerj.com/articles/2914/).
In the file CampioneEvansData.csv
, column names correspond to:
- Higher Clade: clade to which species belong
- Family: family-level to which species belong
- Species: species name
- Common name: common name of that species
- SP#: specimen number
- Body Mass (g): body mass of specimen in grams
- Humerus Lengh: humerus length in milimeters
- Humerus Circumference: humerus circumference in milimeters
- Femur Length: femur length in milimeters
- Femur circumference: femur circumference in milimeters
In the file Field2013_birds.csv
, column names correspond to:
- Order: order-level to which species belong
- Genus: genus name
- species: species name
- Specimen: specimen number
- mass (g): mass in grams of the specimen
- femur_circumference, femur_diameter, femur_length, humerus_diameter, humerus_length, tarsus_circumference, tarsus_diameter, tarsus_length, tibia_length, humerus_circumference, coracoid HAF, coracoid shaft width, coracoid max length: correspond to femur circumference, femur diameter, femur length, humerus diameter, humerus length, tarsus circumference, tarsus diameter, tarsus length, tibia length, humerus circumference, maximum diameter of coracoid’s articulation facet, coracoid shaft width and coracoid max length, respectively, all measured in milimeters.
Most of these columns were not used in our study.
In the file Benson2018Dataset.csv
, column names correspond to:
- Taxon: taxon name
- Name_in_tree: taxon name in the phylogenetic trees used
- Clade: clade to which taxon belongs
- Subclade: subclade to which taxon belongs
- Subclade2: subclade to which taxon belongs, classfied differently (see original paper)
- Max_age: maximum geological age when the taxon can be found
- Min_age: minimum geological age when the taxon can be found
- FL: femur length in milimeters
- FC: femur circumference in milimeters
- FML: femur meediolateral diameter in milimeters
- FAP: femur shaft anteroposterior diameter in milimeters
- TL_TLE: tibia length (or estimated) in milimeters
- TC: tibia circumference in milimeters
- HL: humerus length in milimeters
- HC: humerus circumference in milimeters
- HML: humerus mediolateral diameter in milimeters
- HAP: humerus anteroposterior diameter in milimeters
- RC: radius circumference
- RL_RLE: radius length (or estimated) in milimeters
- MtL:
- Source: source of the information
- Age/notes: notes on the specimen
- Juvenile: if it’s a juvenile or not
- Institution: institution where the specimen is housed
- Specimen: specimen used
Remaining columns (as well as most) were not used in our study. NAs
mean non-applicability or not available data for a given measurement.
In the Iijima2018_crocs.csv
file, column names correspond to:
- Taxon: taxon name
- Specimen: specimen number of the referred taxon
- Locality: original country of the specimen
- Humerus length: humerus length in milimeters
- Ulna length: ulna length in milimeters
- Metacarpal III length: third metacarpal length in milimeters
- Femur length: femur length in milimeters
- Tibia length: tibia length in milimeters
- Metatarsal III length: third metatarsal length in milimeters
-
Trunk length: trunk length in milimeters
Most columns were not used in our study. Empty cells indicate absent data for referred specimen.
In the Panciroli2024Dataset.csv
file, column names correspond to:
- Dataset: source of the data for the referred specimen
- Link to CT: URL to CT-data of the specimen on Morphosource
- Link to humerus: URL to humerus CT data on Morphosource
- Link to femur: URL to femur CT data on Morphosource
- Class: class-level of the referred specimen (e.g., Mammalia etc)
- Higher Clade: all cells left empty
- Family: family-level to which taxon belongs
- Species: species name
- Common Name: common name of the species
- SP#: specimen number
- BodyMass (g): body mass of the specimen in grams
- Body_mass_literature (g): body mass in grams of the species based on literature
- Humerus Length: humerus length in milimeters
- Humerus Circumference: humerus circumference in milimeters
- Femur Length: femur length in milimeters
- Femur Circumference: femur circumference in milimeters
- Dentary Length (mm): dentary length in milimeters
- Bi_Quad: classifies taxon into ‘bipedal’ or ‘quadrupedal’
- tree_names: taxon names in the phylogenetic trees used
In the Regis_Meik_2017_Data_S1_pruned.csv
file, column names correspond to:
- Genus: genus name
- Species: species name
- Correct_taxonomy: the updated species name of the referred specimen
- Mass_Male_g: body mass of males of that species (or specimen, if part of a population) in grams
- Mass_Female_g: body mass of females of that species (or specimen, if part of a population) in grams
- SCL_Male_mm: straight carapace length of males in milimeters of that species (or specimen, if part of a population)
- SCL_Female_mm: straight carapace length of females in milimeters of that species (or specimen, if part of a population)