Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

  title={Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)},
  author={Ylenia Chiari and Vincent Cahais and Nicolas Galtier and Fr{\'e}d{\'e}ric Delsuc},
  journal={BMC Biology},
  pages={65 - 65}
BackgroundThe morphological peculiarities of turtles have, for a long time, impeded their accurate placement in the phylogeny of amniotes. Molecular data used to address this major evolutionary question have so far been limited to a handful of markers and/or taxa. These studies have supported conflicting topologies, positioning turtles as either the sister group to all other reptiles, to lepidosaurs (tuatara, lizards and snakes), to archosaurs (birds and crocodiles), or to crocodilians. Genome… 
A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia
A novel statistical method is developed and tested that identifies sites that have a high probability of containing biased signal for a specific phylogenetic relationship, and support emerged for a sister relationship between turtles and either crocodilians or archosaurs, as well as for a caecilian-salamander sister relationship within Lissamphibia.
Toward consilience in reptile phylogeny: miRNAs support an archosaur, not lepidosaur, affinity for turtles
This work recovers strong support for turtles sharing a more recent common ancestor with archosaurs, and tests the hypothesis with an expanded miRNA presence/absence dataset, and employs more rigorous criteria for miRNA annotation.
Using Genes as Characters and a Parsimony Analysis to Explore the Phylogenetic Position of Turtles
The phylogenetic position of turtles within the vertebrate tree of life remains controversial and the incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles.
Inferring the shallow phylogeny of true salamanders (Salamandra) by multiple phylogenomic approaches.
Evolutionary history of selected squamates: insights from nuclear genes and species tree with implications for biogeography and taxonomy
The phylogenetic position of most remaining genera was unresolved, corroborating the hypothesis of a hard polytomy in the Lacertini phylogeny due to a fast radiation, and it is shown that the supermatrix approach may provide high support for incorrect nodes that are not supported either by original sequence data or by new data from this study.
Mitochondrial phylogenomics, the origin of swallowtail butterflies, and the impact of the number of clocks in Bayesian molecular dating
A mitogenomic, time‐calibrated phylogeny for all swallowtail genera is presented, confirming that Baroniinae is sister to Parnassiinae + Papilioninae, both recovered as monophyletic and laying the foundations for classification at tribe and genus level.
A phylogenomic framework and timescale for comparative studies of tunicates
This study represents the most comprehensive phylogenomic dataset for the main tunicate lineages, offering a reference phylogenetic framework and first tentative timescale for tunicates, allowing a direct comparison with vertebrate model species in comparative genomics and evolutionary developmental biology studies.
The New Mode of Thought of Vertebrates’ Evolution
This molecular analysis coupled with analysis of phylogenetic trees constructed on a basis of manual alignment allows us to hypothesize that primitive chordates being the nearest relatives of simplest vertebrates represent the real base of the vertebrate phylogenetic tree.
The origin of turtles: a paleontological perspective.
  • W. Joyce
  • Environmental Science
    Journal of experimental zoology. Part B, Molecular and developmental evolution
  • 2015
The recently revived paleontological hypothesis that the Middle Permian Eunotosaurus africanus is an intermediate stem turtle is now robustly supported by numerous characters that were previously thought to be unique to turtles and that are now shown to have originated over the course of tens of millions of years unrelated to the origin of the turtle shell.
Are 100 enough? Inferring acanthomorph teleost phylogeny using Anchored Hybrid Enrichment
It may be that both stochastic and systematic error resulting from model misspecification play a role in the poor resolution at the base of the Ovalentaria tree as a Bayesian approach was able to resolve some of the deeper nodes, where the other methods failed.


Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins.
Cloned and sequenced two nuclear genes encoding the catalytic subunit of DNA polymerase alpha and glycinamide ribonucleotide synthetase-aminoimidazole ribon DNA synthetases from amniotes and an amphibian showed that turtles are the sister group to a monophyletic cluster of archosaurs.
The evolutionary position of turtles revised
Abstract. Consensus on the evolutionary position of turtles within the amniote phylogeny has eluded evolutionary biologists for more than a century. This phylogenetic problem has remained unsolved
MicroRNAs support a turtle + lizard clade
A novel molecular dataset, the presence versus absence of specific microRNAs, is applied to the problem of the phylogenetic position of turtles and the root of the reptilian tree, and it is found that this dataset unambiguously supports a turtle + lepidosaur group.
Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles.
It is likely that turtles originated from a Permian-Triassic archosauromorph ancestor with two pairs of temporal fenestrae behind the skull orbit that were subsequently lost and the traditional classification of turtles in the Anapsida may need to be reconsidered.
Complete mitochondrial genome suggests diapsid affinities of turtles.
  • R. Zardoya, A. Meyer
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1998
The results challenge the classic view of turtles as the only survivors of primary anapsid reptiles and imply that turtles might have secondarily lost their skull fenestration.
Molecular evidence for a clade of turtles.
  • H. Mannen, S. Li
  • Biology, Environmental Science
    Molecular phylogenetics and evolution
  • 1999
In the phylogenetic analyses, the turtle was found to be closely related to the alligator and the turtle had diverged after the divergence of squamates and birds, suggesting that turtles are the latest of divergent reptiles.
Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.
Interordinal relationships of birds and other reptiles based on whole mitochondrial genomes.
Support is found for a sister relationship between turtles and a bird/crocodilian clade, and for rejecting both the Haemothermia hypothesis and the placement of turtles as basal within the phylogenetic tree for amniote animals.
Investigating stagnation in morphological phylogenetics using consensus data.
Data pertaining to the relationships of turtles is used to illustrate the use of a consensus approach for investigating conflict in morphological phylogenetics and to identify and investigate agreements and disagreements between recent osteological data sets employed in the debate over diapsid and anapsid hypotheses.