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…
12 Citations
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation
- BiologyGenome biology and evolution
- 2016
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
- BiologyFront. Genet.
- 2017
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
- BiologyWABI
- 2016
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
- BiologyRECOMB-CG
- 2018
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
- BiologybioRxiv
- 2021
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
- BiologyCiE
- 2016
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
- BiologyBioinform.
- 2020
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
- BiologyAlgorithms for Molecular Biology
- 2017
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
- Computer ScienceAlgorithms for Molecular Biology
- 2019
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
- Economics
- 2016
Experimental evolution provides independent and challenging benchmarks for comparative genomics Priscila Biller, Eric Tannier, Guillaume Beslon, Carole Knibbe.
References
SHOWING 1-10 OF 23 REFERENCES
Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation
- BiologyGenome biology and evolution
- 2016
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
- BiologyISMB
- 2008
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
- BiologyFront. Genet.
- 2017
The results imply that implicit appearance of transpositions in DCJ scenarios may be unavoidable or even abundant for some pairs of genomes.
Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution
- BiologyProceedings of the National Academy of Sciences of the United States of America
- 2003
The genome rearrangement analysis of the human and mouse genomes implies the existence of a large number of very short “hidden” synteny blocks that were invisible in the comparative mapping data and ignored in the random breakage model, suggesting a model of chromosome evolution that postulates that mammalian genomes are mosaics of fragile regions with high propensity for rearrangements and solid regions with low propensity for reorganisation.
Comparative genomics reveals birth and death of fragile regions in mammalian evolution
- BiologyGenome Biology
- 2010
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
- BiologyRECOMB-CG
- 2009
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
- BiologyBMC Bioinformatics
- 2011
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
- BiologyIWBBIO
- 2015
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
- BiologyBioinform.
- 2005
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.
- BiologyProceedings of the National Academy of Sciences of the United States of America
- 1984
Evidence is presented suggesting that chromosomal rearrangements that determine the lengths of these segments are randomly distributed within the genome.