Space of Gene/Species Trees Reconciliations and Parsimonious Models

Doyon, Jean-Philippe; Chauve, Cédric; Hamel, Sylvie

doi:10.1089/cmb.2009.0095

Cited by 42 publications

(71 citation statements)

References 18 publications

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“…While there exists previous work on exploring and summarizing the reconciliation space, they consider only duplications and losses (Arvestad et al 2004;Doyon et al 2008Doyon et al , 2009Doyon et al , 2012 or additionally horizontal gene transfer (Scornavacca et al 2013), or, if ILS is addressed, they model only a subset of the evolutionary histories that are possible in our model (Vernot et al 2007). That is, this work presents the first approach for fully exploring the reconciliation space while accounting for duplications, losses, and ILS.…”

Section: Discussionmentioning

confidence: 99%

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

et al. 2013

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Accurate gene tree-species tree reconciliation is fundamental to inferring the evolutionary history of a gene family. However, although it has long been appreciated that population-related effects such as incomplete lineage sorting (ILS) can dramatically affect the gene tree, many of the most popular reconciliation methods consider discordance only due to gene duplication and loss (and sometimes horizontal gene transfer). Methods that do model ILS are either highly parameterized or consider a restricted set of histories, thus limiting their applicability and accuracy. To address these challenges, we present a novel algorithm DLCpar for inferring a most parsimonious (MP) history of a gene family in the presence of duplications, losses, and ILS. Our algorithm relies on a new reconciliation structure, the labeled coalescent tree (LCT), that simultaneously describes coalescent and duplication-loss history. We show that the LCT representation enables an exhaustive and efficient search over the space of reconciliations, and, for most gene families, the least common ancestor (LCA) mapping is an optimal solution for the species mapping between the gene tree and species tree in an MP LCT. Applying our algorithm to a variety of clades, including flies, fungi, and primates, as well as to simulated phylogenies, we achieve high accuracy, comparable to sophisticated probabilistic reconciliation methods, at reduced run time and with far fewer parameters. These properties enable inferences of the complex evolution of gene families across a broad range of species and large data sets.

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Section: Discussionmentioning

confidence: 99%

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

et al. 2013

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“…The MPR represents the mapping between each gene-tree vertex to either a species tree vertex (speciation) or to a species tree edge (gene duplication) in a parsimonious way (minimizing the number of duplications). The MPR is preferred to other reconciliations, because in most cases the MPR represents the true reconciliation between gene tree and the species tree [36, 37]. …”

Section: Methodsmentioning

confidence: 99%

S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinoma

et al. 2016

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S18 family of mitochondrial ribosomal proteins (MRPS18, S18) consists of three members, S18-1 to −3. Earlier, we found that overexpression of S18-2 protein resulted in immortalization and eventual transformation of primary rat fibroblasts. The S18-1 and −3 have not exhibited such abilities. To understand the differences in protein properties, the evolutionary history of S18 family was analyzed. The S18-3, followed by S18-1 and S18-2 emerged as a result of ancient gene duplication in the root of eukaryotic species tree, followed by two metazoan-specific gene duplications. However, the most conserved metazoan S18 homolog is the S18-1; it shares the most sequence similarity with S18 proteins of bacteria and of other eukaryotic clades. Evolutionarily conserved residues of S18 proteins were analyzed in various cancers. S18-2 is mutated at a higher rate, compared with S18-1 and −3 proteins. Moreover, the evolutionarily conserved residue, Gly132 of S18-2, shows genetic polymorphism in colon adenocarcinomas that was confirmed by direct DNA sequencing.Concluding, S18 family represents the yet unexplored important mitochondrial ribosomal proteins.

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“…In the present context, we are thus motivated to define larger classes of reconciliations, including M (T, S), but also sub-optimal solutions (with respect to the number of duplications) [38,54,55,89]. This allows to explore a larger space of reconciliations and alternative evolutionary scenarios for gene families.…”

Section: Optimization Criteriamentioning

confidence: 99%

Analysis of Gene Order Evolution Beyond Single-Copy Genes

El-Mabrouk

Sankoff

2012

Methods in Molecular Biology

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The purpose of this chapter is to provide a comprehensive review of the field of genome rearrangement, i.e., comparative genomics based on representation of genomes as ordered sequences of signed genes. We specifically focus on the "hard part" of genome rearrangement, how to handle duplicated genes. The main questions are: how have present-day genomes evolved from a common ancestor? What are the most realistic evolutionary scenarios explaining the observed gene orders? What was the content and structure of ancestral genomes? We aim to provide a concise but complete overview of the field, starting with the practical problem of finding an appropriate representation of a genome as a sequence of ordered genes or blocks, namely the problems of orthology, paralogy and synteny block identification. We then consider three levels of gene organization: the gene family level (evolution by duplication, loss and speciation), the cluster level (evolution by tandem duplications) and the genome level (all types of rearrangement events, including whole genome duplication).

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Space of Gene/Species Trees Reconciliations and Parsimonious Models

Cited by 42 publications

References 18 publications

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees

S18 family of mitochondrial ribosomal proteins: evolutionary history and Gly132 polymorphism in colon carcinoma

Analysis of Gene Order Evolution Beyond Single-Copy Genes

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