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

@article{Crawford2012MoreT1,
  title={More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs},
  author={Nicholas G. Crawford and B. Faircloth and J. McCormack and R. T. Brumfield and K. Winker and T. Glenn},
  journal={Biology Letters},
  year={2012},
  volume={8},
  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… Expand
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Background: Ultraconserved elements (UCEs) have been successfully used in phylogenomics for a variety of taxa, but their power in phylogenetic inference has yet to be extensively compared with thatExpand
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References

SHOWING 1-10 OF 34 REFERENCES
Complete mitochondrial genome suggests diapsid affinities of turtles.
  • R. Zardoya, A. Meyer
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1998
TLDR
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. Expand
Sister group relationship of turtles to the bird-crocodilian clade revealed by nuclear DNA-coded proteins.
TLDR
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. Expand
Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.
TLDR
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. Expand
From Reptilian Phylogenomics to Reptilian Genomes: Analyses of c-Jun and DJ-1 Proto-Oncogenes
TLDR
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. Expand
Complete mitochondrial DNA sequences of the green turtle and blue-tailed mole skink: statistical evidence for archosaurian affinity of turtles.
TLDR
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. Expand
Phylogenetic position of turtles among amniotes: evidence from mitochondrial and nuclear genes.
TLDR
The analysis strongly suggests that turtles are closely related to archosaurs, and supports both Tree-2: (((birds, crocodilians), turtles), squamates) and Tree-3: ((birds, (crocodilians, turtles)), squamate). Expand
Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.
TLDR
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. Expand
MicroRNAs support a turtle + lizard clade
TLDR
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. Expand
Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.
TLDR
P phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes support monophyly of Archosauria, and a sister relationship between turtles and archosaurs. Expand
Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome
TLDR
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. Expand
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