DOI: 10.5061/dryad.2pb356h
title: Data from: A new phylogenetic hypothesis of turtles with implications for the timing and number of evolutionary transitions to marine lifestyles in the group

description: 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.
description: 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.