Estimation of the true evolutionary distance under the fragile breakage model

@article{Alexeev2015EstimationOT,
  title={Estimation of the true evolutionary distance under the fragile breakage model},
  author={Nikita Alexeev and Max A. Alekseyev},
  journal={BMC Genomics},
  year={2015},
  volume={18}
}
BackgroundThe ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be estimated as the rearrangement distance equal the minimal number of genome rearrangements required to transform one genome into the other. However, in reality the parsimony assumption may not always hold, emphasizing the need for estimation that does… 

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References

SHOWING 1-10 OF 23 REFERENCES

Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation

TLDR
A model of evolution by inversions where breakage probabilities vary across fragile regions and over time is proposed, and identifying coding genes with solid regions yields incoherent distance estimations, especially with the pseudouniform model, and to a lesser extent with the truly uniform model.

Estimating true evolutionary distances under the DCJ model

TLDR
A method to estimate the true evolutionary distance between two genomes under the ‘double-cut-and-join’ (DCJ) model of genome rearrangements, a model under which a single multichromosomal operation accounts for all genomic rearrangement events.

Implicit Transpositions in DCJ Scenarios

TLDR
The results imply that implicit appearance of transpositions in DCJ scenarios may be unavoidable or even abundant for some pairs of genomes.

Comparative genomics reveals birth and death of fragile regions in mammalian evolution

TLDR
It is demonstrated that fragile regions are subject to a birth and death process, implying that fragility has a limited evolutionary lifespan and suggests putative locations of the currently active fragile regions in the human genome.

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods II

TLDR
It is shown that the dataset does not seem to contain enough information to infer a reliable architecture, and a higher resolution dataset is constructed which gives a good reliability on a new ancestral configuration.

Yeast Ancestral Genome Reconstructions: The Possibilities of Computational Methods

TLDR
Adapting several methodological frameworks to the same yeast gene order data, the possibilities, differences and similarities of the available algorithms for ancestral genome reconstructions are discussed.

The rise and fall of breakpoint reuse depending on genome resolution

TLDR
The inferred breakpoint reuse rate depends on synteny block resolution in human-mouse genome comparisons, and at fine-scale resolution, the cycle structure for the transformation appears less random compared to that for coarse resolution.

A Computational Method for the Rate Estimation of Evolutionary Transpositions

TLDR
A computational method for estimating the rate of transpositions in evolutionary scenarios between genomes is applied to a set of mammalian genomes and it is estimated to be around 0.26.

Efficient sorting of genomic permutations by translocation, inversion and block interchange

TLDR
A universal double-cut-and-join operation that accounts for inversions, translocations, fissions and fusions, but also produces circular intermediates which can be reabsorbed, which converts one multi-linear chromosome genome to another in the minimum distance.

Lengths of chromosomal segments conserved since divergence of man and mouse.

  • J. NadeauB. Taylor
  • Biology
    Proceedings of the National Academy of Sciences of the United States of America
  • 1984
TLDR
Evidence is presented suggesting that chromosomal rearrangements that determine the lengths of these segments are randomly distributed within the genome.