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Reconciling multiple genes trees via segmental duplications and losses [PDF]
Algorithms for Molecular Biology, 2019 23 pages, 7 figures, WABI ...
Dondi, Riccardo +2 more
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Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers [PDF]
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2012 We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an
Zhi-Zhong, Chen +2 more
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INFERRING OPTIMAL SPECIES TREES UNDER GENE DUPLICATION AND LOSS [PDF]
Biocomputing 2013, 2012 Species tree estimation from multiple markers is complicated by the fact that gene trees can differ from each other (and from the true species tree) due to several biological processes, one of which is gene duplication and loss. Local search heuristics for two NP-hard optimization problems - minimize gene duplications (MGD) and minimize gene ...
M S, Bayzid, S, Mirarab, T, Warnow
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Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization [PDF]
Molecular Biology and Evolution, 2015 Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes.
Jean-Francois, Gout, Michael, Lynch
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Evolution of tuf genes: ancient duplication, differential loss and gene conversion [PDF]
FEBS Letters, 2001 The tuf gene of eubacteria, encoding the EF‐tu elongation factor, was duplicated early in the evolution of the taxon. Phylogenetic and genomic location analysis of 20 complete eubacterial genomes suggests that this ancient duplication has been differentially lost and maintained in eubacteria.
Lathe, Warren C, Bork, Peer
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Inference of Ancient Whole-Genome Duplications and the Evolution of Gene Duplication and Loss Rates [PDF]
Molecular Biology and Evolution, 2019 Abstract Gene tree–species tree reconciliation methods have been employed for studying ancient whole-genome duplication (WGD) events across the eukaryotic tree of life. Most approaches have relied on using maximum likelihood trees and the maximum parsimony reconciliation thereof to count duplication events on specific branches of ...
Zwaenepoel, Arthur, Van de Peer, Yves
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Gene Duplication and Loss in a MADS Box Gene Transcription Factor Circuit [PDF]
Molecular Biology and Evolution, 2011 Although many models have been proposed that could lead to the maintenance of gene duplicates, the ways in which interacting gene duplicates influence each other's evolution and function remain poorly understood. Here, we focus on duplication and loss of the B class MADS box transcription factor genes in the euasterids I and the ramifications of such ...
Hae-Lim, Lee, Vivian F, Irish
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Comparing Methods for Species Tree Estimation With Gene Duplication and Loss [PDF]
, 2021 AbstractSpecies tree inference from gene trees is an important part of biological research. One confounding factor in estimating species trees is gene duplication and loss which can lead to gene trees with multiple copies of the same gene. In recent years there have been several new methods developed to address this problem that have substantially ...
James Willson +2 more
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After the Duplication: Gene Loss and Adaptation in Saccharomyces Genomes [PDF]
Genetics, 2006 Abstract The ancient duplication of the Saccharomyces cerevisiae genome and subsequent massive loss of duplicated genes is apparent when it is compared to the genomes of related species that diverged before the duplication event. To learn more about the evolutionary effects of the duplication event, we compared the S.
Paul F, Cliften +3 more
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Intron gain and loss in segmentally duplicated genes in rice [PDF]
Genome Biology, 2006 Abstract Background Introns are under less selection pressure than exons, and consequently, intronic sequences have a higher rate of gain and loss than exons. In a number of plant species, a large portion of the genome has been segmentally duplicated, giving rise to a large set of duplicated genes.
Lin, Haining +4 more
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