Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.

@article{Shen2011MultipleGA,
  title={Multiple genome alignments facilitate development of NPCL markers: a case study of tetrapod phylogeny focusing on the position of turtles.},
  author={Xing-Xing Shen and Dan Liang and Jun-Zhi Wen and Peng Zhang},
  journal={Molecular biology and evolution},
  year={2011},
  volume={28 12},
  pages={
          3237-52
        }
}
In recent years, the increasing availability of genomic resources has provided an opportunity to develop phylogenetic markers for phylogenomics. Efficient methods to search for candidate markers from the huge number of genes within genomic data are particularly needed in the era of phylogenomics. Here, rather than using the traditional approach of comparing genomes of two distantly related taxa to develop conserved primers, we take advantage of the multiple genome alignment resources from the… 

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References

SHOWING 1-10 OF 83 REFERENCES
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
TLDR
A practical approach that systematically compares whole genome sequences to identify single-copy nuclear gene markers for inferring phylogeny is presented and is an improvement over traditional approaches because it uses genomic information and automates the process to identify large numbers of candidate makers.
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
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.
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.
A multilocus molecular phylogeny of the parrots (Psittaciformes): support for a Gondwanan origin during the cretaceous.
TLDR
The results support a Cretaceous origin of Psittaciformes in Gondwana after the separation of Africa and the India/Madagascar block with subsequent diversification through both vicariance and dispersal.
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.
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.
Mitogenomic perspectives on the origin and phylogeny of living amphibians.
TLDR
It is suggested that the temnospondyl-origin hypothesis for lissamphibians is more credible than other hypotheses, and under this timescale, the potential geographic origins of the main living amphibian groups are discussed.
Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.
...
...