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… Expand
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References

SHOWING 1-10 OF 84 REFERENCES
Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles.
TLDR
A general methodology for identifying candidate single-copy NPCL from genomic databases, targeted for higher-level phylogenetics of squamate reptiles, which has developed over 25 novel NPCL, which span a variety of desirable evolutionary rates for phylogenetic analyses. Expand
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. Expand
Higher-level salamander relationships and divergence dates inferred from complete mitochondrial genomes.
  • P. Zhang, D. Wake
  • Biology, Medicine
  • Molecular phylogenetics and evolution
  • 2009
TLDR
The results support the conventional morphological hypothesis that Sirenidae is the sister-group to all other salamanders and they statistically reject the hypothesis from nuclear genes that the suborder Cryptobranchoidea (Cryptobranchidae+Hynobiidae) branched earlier than the Sirenidae. Expand
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
Genome-scale approaches to resolving incongruence in molecular phylogenies
TLDR
The results suggest that data sets consisting of single or a small number of concatenated genes have a significant probability of supporting conflicting topologies, and have important implications for resolving branches of the tree of life. Expand
Combining phylogenomics and fossils in higher-level squamate reptile phylogeny: molecular data change the placement of fossil taxa.
TLDR
Significant promise is suggested for an integrated and comprehensive Tree of Life by combining molecular and morphological data for living and fossil taxa. Expand
The root of the mammalian tree inferred from whole mitochondrial genomes.
TLDR
It is reported that recoding nucleotides to RY-characters, and partitioning maximum-likelihood analyses among subsets of data reduces such biases, and improves the fit of models to the data, respectively. 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
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. 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
...
1
2
3
4
5
...