More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs

  title={More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs},
  author={Nicholas G. Crawford and Brant C. Faircloth and John E McCormack and Robb Thomas Brumfield and Kevin Winker and Travis C. Glenn},
  journal={Biology Letters},
  pages={783 - 786}
We present the first genomic-scale analysis addressing the phylogenetic position of turtles, using over 1000 loci from representatives of all major reptile lineages including tuatara. Previously, studies of morphological traits positioned turtles either at the base of the reptile tree or with lizards, snakes and tuatara (lepidosaurs), whereas molecular analyses typically allied turtles with crocodiles and birds (archosaurs). A recent analysis of shared microRNA families found that turtles are… 

Figures and Tables from this paper

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.
A Genomic Perspective on the Evolutionary Diversification of Turtles
It is suggested that, in addition to incomplete lineage sorting, an overall lack of gene informativeness stemming from a slow rate of evolution can confound inferred patterns in turtle phylogenomics, particularly at more recent divergences.
Phylogenomics of Horned Lizards (Genus: Phrynosoma) Using Targeted Sequence Capture Data
Targeted sequence capture data from 540 ultraconserved elements and 44 protein-coding genes are used to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma and provides a robust new framework for conducting comparative analyses.
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.
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.
Title Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history : A case study of formicine ants Permalink
A comparison of divergence ages from both Sanger and UCE data demonstrates the effectiveness of UCEs for dating analyses, and is useful to the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.
Phylogenomic methods outperform traditional multi-locus approaches in resolving deep evolutionary history: a case study of formicine ants
This comparative study highlights both the promise and limitations of UCEs for insect phylogenomics, and will prove useful to the growing number of evolutionary biologists considering the transition from Sanger to next-generation sequencing approaches.
High Phylogenetic Utility of an Ultraconserved Element Probe Set Designed for Arachnida
This probe set will open the door to phylogenomic and population genomic studies across the arachnid tree of life, enabling systematics, species delimitation, species discovery, and conservation of these diverse arthropods.
Phylogenomics of a rapid radiation: is chromosomal evolution linked to increased diversification in north american spiny lizards (Genus Sceloporus)?
This study provides new evidence for a putative link between chromosomal evolution and the rapid divergence and radiation of Sceloporus across North America.


Complete mitochondrial genome suggests diapsid affinities of turtles.
  • R. ZardoyaA. 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.
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.
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.
This study outlines a phylogenomic approach using a novel class of phylogenetic markers derived from ultraconserved elements and flanking DNA, and shows that this class of marker is useful for recovering deep-level phylogeny in placental mammals.
From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes
CDNA sequences for the c-Jun(JUN) and DJ-1(PARK7) proto-oncogenes from 3 reptiles are reported, it is shown that both genes are expressed in the alligator, and they are integrated into analyses of their homologs from other organisms.
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.
Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.
This work takes advantage of the multiple genome alignment resources from the University of California-San Cruz Genome Browser and presents a simple and straightforward bioinformatic approach to automatically screen for candidate nuclear protein-coding locus (NPCL) markers.
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome
A megabase-scale phylogenomic analysis of the Reptilia suggests a diverse array of interspersed and SSRs in the common ancestor of amniotes and a genomic conservatism and gradual loss of retroelements in reptiles that culminated in the minimalist chicken genome.
The mitochondrial genomes of the iguana (Iguana iguana) and the caiman (Caiman crocodylus): implications for amniote phylogeny
The complete mitochondrial genomes of two reptiles, the common iguana and the caiman, were sequenced in order to investigate phylogenetic questions of tetrapod evolution and corroborated the view that turtles are at the base of the bird–crocodile branch.