Data from: A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group

Evolutionary transitions to marine habitats occurred frequently among Mesozoic reptiles. Only one such clade survives to the present: sea turtles (Chelonioidea). Other marine turtles originated during the Mesozoic, but uncertain affinities of key fossils have obscured the number of transitions to marine life, and the timing of the origin of marine adaptation in chelonioids. Phylogenetic studies support either a highly‐inclusive chelonioid total‐group including fossil marine clades from the Jurassic and Cretaceous (e.g. protostegids, thalassochelydians, sandownids) or a less inclusive chelonioid total‐group excluding those clades. Under this paradigm, these clades belong outside Cryptodira, and represent at least one additional evolutionary transition to marine life in turtles. We present a new phylogenetic hypothesis informed by high resolution computed tomographic data of living and fossil taxa. Besides a well‐supported Chelonioidea, which includes protostegids, we recover a previously unknown clade of stem‐group turtles, Angolachelonia, which includes the Late Jurassic thalassochelydians, and the Cretaceous–Palaeogene sandownids. Accounting for the Triassic Odontochelys, our results indicate three independent evolutionary transitions to marine life in non‐pleurodiran turtles (plus an additional two‐three in pleurodires). Among all independent origins of marine habits, a pelagic ecology only evolved once, among chelonioids. All turtle groups that independently invaded marine habitats in the Jurassic–Cretaceous (chelonioids, angolachelonians, bothremydid pleurodires) survived the Cretaceous–Palaeogene mass extinction event. This highlights extensive survival of marine turtles compared to other marine reptiles. Furthermore, deeply‐nested clades such as chelonioids are found by the middle Early Cretaceous, suggesting a rapid diversification of crown‐group turtles during the Early Cretaceous.Tempelton's Tests filesThis zipped folder contains all files used for the Templeton's test. This folder is organised in subfolders, whereas "1 - Pasimony Analysis Input files" contains the character-taxon matrix (in PAUP format), the molecular backbone constraint, and constraint files for all 20 alternative hypotheses tested. "2 - Parsimony Analysis Results" contains consensus tree files and MPT tree files for all analyses. "3- Symmetric Distance Analysis Input files" contains nexus files used to compute symmetric distances. "4 - Symmetric Distance Analysis Results" contains the symmetric distance matrices for all constraints as text-files. "5 - Tree selection for Templeton" contains the R code used to select tree-pairs for Templeton's tests. "6 - Templeton's Test Input files" contains nexus files in which selected trees to be compared are included. Files are provided for each constraint for maximum and minimum symmetric distance tree pairs. "7 - Templeton's Test Results" are PAUP log-files that include the test results.Similarity Matrix filesThe zipped folder contains two documents, the R code used to calculate the similarity matrix and produce the heatmaps, and the character-taxon matrix ("Similarity_matrix.txt") that was used for computing similarity values. The "Similarity_matrix.txt" file differs from our original character-taxon matrix in that polymorphisms were exchanged with "?", and the taxa we re-arranged to mirror our tree topology of the unordered analysis.Appendix S1. Character_list_with_figuresAppendix S1 includes our character list, explanations of character modifications, optimizations for each character, character illustrations, and an extended discussion of c characters related to the cartid arterial system.Appendix S2. Character_optimisationAppendix S2 includes a figure of the MPT used for character optimization, and the character optimizations for each node of the tree.Appendix S3. Constraint_trees_and_reduced_analysisAppendix S3 includes supplemenatry figures showing the consensus topology of our analysis in which 'marine' characters have been deleted from the dataset, consensus topologies for the 'least specialised taxa analyses', and consensus topologies for all Templeton's test contraint analyses.Appendix S4. Evers & Benson 2018_matrixAppendix S4 is our character-taxon matrix in .txt format, readable in TNT and including TNT code for constraining the tree topology of extant taxa