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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12 Citations
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12 Citations

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.
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.
Genome Rearrangements on Both Gene Order and Intergenic Regions
TLDR
A new genome rearrangement model called wDCJ is defined, a generalization of the well-known Double Cut and Join model that allows for modifying both the gene order and the intergene size distribution of a genome.
Estimation of the True Evolutionary Distance Under the INFER Model
TLDR
The rearrangement distance between two genomes is estimated as the minimal number of rearrangements needed to transform one genome into another, which is usually referred to as the parsimony assumption.
SynTracker: a synteny based tool for tracking microbial strains
TLDR
This strain-comparison tool is based on synteny comparisons between strains, or the comparison of the arrangement of sequence blocks in two homologous genomic regions in pairs of metagenomic assemblies or genomes, and can be used to study the population structure of specific microbial species between and within environments, to identify evolutionary trajectories in longitudinal datasets, and to further understanding of strain sharing networks.
Comparative Genomics on Artificial Life
TLDR
This work uses Aevol, an in silico experimental evolution platform, to produce benchmarks, and shows that most combinatorial or statistical estimators of the number of inversions fail on this dataset while they were behaving perfectly on ad-hoc simulations.
A unified ILP framework for core ancestral genome reconstruction problems
TLDR
Since the ILP formulations for the conserved versions have linear size, they provide a novel practical approach to ancestral genome reconstruction, which combines the advantages of homology- and rearrangements-based methods.
Algorithms for computing the double cut and join distance on both gene order and intergenic sizes
TLDR
A new genome rearrangement model called wDCJ is defined, a generalization of the well-known double cut and join operation that modifies both the gene order and the intergene size distribution of a genome, and theoretical and empirical bounds on the expected growth of the parameter at the center of FPT and ILP algorithms are provided.
A general framework for genome rearrangement with biological constraints
TLDR
A model for weighted DCJ is proposed, along with a family of optimization problems called $$\varphi$$φ-MCPS (Minimum Cost Parsimonious Scenario), that are based on labeled graphs that generalize the results of Bulteau, Fertin, and Tannier on the Sorting by wDCJs and indels in intergenes problem.
In silico experimental evolution provides independent and challenging benchmarks for comparative genomics
TLDR
Experimental evolution provides independent and challenging benchmarks for comparative genomics Priscila Biller, Eric Tannier, Guillaume Beslon, Carole Knibbe.
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References

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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.
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