ArticleBMC bioinformatics2014
A unifying model of genome evolution under parsimony.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Generalizations of the genomic rank distance to indels.Bioinformatics (Oxford, England) · 2023Article
- A Sequence Distance Graph framework for genome assembly and analysis.F1000Research · 2019Article
- Earth BioGenome Project: Sequencing life for the future of life.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Representing and decomposing genomic structural variants as balanced integer flows on sequence graphs.BMC bioinformatics · 2016Article
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4 authors.
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Abstract
backgroundParsimony and maximum likelihood methods of phylogenetic tree estimation and parsimony methods for genome rearrangements are central to the study of genome evolution yet to date they have largely been pursued in isolation.
resultsWe present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double cut and join (DCJ) rearrangements in the presence of duplications. The problem of constructing parsimonious history graphs thus subsumes related maximum parsimony problems in the fields of phylogenetic reconstruction and genome rearrangement. We show that tractable functions can be used to define upper and lower bounds on the minimum number of substitutions and DCJ rearrangements needed to explain any history graph. These bounds become tight for a special type of unambiguous history graph called an ancestral variation graph (AVG), which constrains in its combinatorial structure the number of operations required. We finally demonstrate that for a given history graph G, a finite set of AVGs describe all parsimonious interpretations of G, and this set can be explored with a few sampling moves.
conclusionThis theoretical study describes a model in which the inference of genome rearrangements and phylogeny can be unified under parsimony.
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