DOI: 10.5061/dryad.vmcvdnd2g
title: Data from: Shell constraints on evolutionary body size-limb size allometry can explain morphological conservatism in the turtle body plan

description: 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.
description: ## 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 analyses *
 `pgls_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 lengths * `residuals.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](https://doi.org/10.1016/j.jsames.2022.103970)) *
 `body_mass_pgls.R` reads the extant turtle data of body mass and carapace
 length measurements from Regis and Meik
 ([2017](https://peerj.com/articles/2914/)) 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 measurements * `comparisons_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 allometries * `script_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 in `pdf` 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](http://timetree.org) *
 *CampioneEvans_tree_timetree.nwk:* phylogenetic tree of extant amniote
 species retrieved from [http://timetree.org](http://timetree.org) *
 *crocs_tree_timetree.nwk:* phylogenetic tree of extant crocodylians
 retrieved from [http://timetree.org](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](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](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](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](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](https://link.springer.com/article/10.1186/1741-7007-10-60)), Field et al. (2013; [https://doi.org/10.1371/journal.pone.0082000](https://doi.org/10.1371/journal.pone.0082000)), Benson et al. (2018; [https://doi.org/10.1111/pala.12329](https://doi.org/10.1111/pala.12329)), Iijima et al. (2018; [https://doi.org/10.1098/rsos.171774](https://doi.org/10.1098/rsos.171774)), Panciroli et al. (2024; [https://www.nature.com/articles/s41586-024-07733-1](https://www.nature.com/articles/s41586-024-07733-1)), Regis and Meik (2017; [https://peerj.com/articles/2914/](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)