SylvX: a viewer for phylogenetic tree reconciliations

Chevenet, François; Doyon, Jean-Philippe; Scornavacca, Céline; Jacox, Edwin; Jousselin, Emmanuelle; Berry, Vincent

doi:10.1093/bioinformatics/btv625

Cited by 22 publications

(14 citation statements)

References 12 publications

(10 reference statements)

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“…To investigate which branches the transfer events most likely involved, we used the software ecceTERA version 1.2.4 [33] (Supplementary Information). The software SylvX version 1.3 [34] was used for visualizing reconciliations computed by ecceTERA.…”

Section: Reconciliation Analysismentioning

confidence: 99%

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

et al. 2018

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The description of comammox Nitrospira spp., performing complete ammonia-to-nitrate oxidation, and their co-occurrence with canonical β-proteobacterial ammonia oxidizing bacteria (β-AOB) in the environment, calls into question the metabolic potential of comammox Nitrospira and the evolutionary history of their ammonia oxidation pathway. We report four new comammox Nitrospira genomes, constituting two novel species, and the first comparative genomic analysis on comammox Nitrospira. Unlike canonical Nitrospira, comammox Nitrospira genomes lack genes for assimilatory nitrite reduction, suggesting that they have lost the potential to use external nitrite nitrogen sources. By contrast, compared to canonical Nitrospira, comammox Nitrospira harbor a higher diversity of urea transporters and copper homeostasis genes and lack cyanate hydratase genes. Additionally, the two comammox clades differ in their ammonium uptake systems. Contrary to β-AOB, comammox Nitrospira genomes have single copies of the two central ammonia oxidation pathway operons. Similar to ammonia oxidizing archaea and some oligotrophic AOB strains, they lack genes involved in nitric oxide reduction. Furthermore, comammox Nitrospira genomes encode genes that might allow efficient growth at low oxygen concentrations. Regarding the evolutionary history of comammox Nitrospira, our analyses indicate that several genes belonging to the ammonia oxidation pathway could have been laterally transferred from β-AOB to comammox Nitrospira. We postulate that the absence of comammox genes in other sublineage II Nitrospira genomes is the result of subsequent loss.

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Section: Reconciliation Analysismentioning

confidence: 99%

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

et al. 2018

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“…Third, the algorithm given in Section 6 that computes a dated scenario equivalent to a given sliced scenario (hence a reconciliation), provides a practical solution to draw a reconciliation as an embedding of the gene tree within the species tree. Indeed, for such a drawing, each event (node of the gene tree) should be assigned to a precise date, and not just to a time interval on a branch [6].…”

Section: Resultsmentioning

confidence: 99%

Inferring gene duplications, transfers and losses can be done in a discrete framework

et al. 2015

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In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications ([Formula: see text]), transfers ([Formula: see text]) and losses ([Formula: see text]). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony [Formula: see text] reconciliation problem in the discrete framework is equivalent to finding a most parsimonious [Formula: see text] scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field.

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“…9(b)). SylvX [7] is a more complex reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking sub-reconciliations).…”

Section: B Co-phylogenetic Trees Visualization Toolsmentioning

confidence: 99%

Visualizing co-phylogenetic reconciliations

Calamoneri

Donato

Mariottini

et al. 2020

Theoretical Computer Science

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We introduce a hybrid metaphor for the visualization of the reconciliations of co-phylogenetic trees, that are mappings among the nodes of two trees. The typical application is the visualization of the co-evolution of hosts and parasites in biology. Our strategy combines a space-filling and a node-link approach. Differently from traditional methods, it guarantees an unambiguous and 'downward' representation whenever the reconciliation is time-consistent (i.e., meaningful). We address the problem of the minimization of the number of crossings in the representation, by giving a characterization of planar instances and by establishing the complexity of the problem. Finally, we propose heuristics for computing representations with few crossings.

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SylvX: a viewer for phylogenetic tree reconciliations

Abstract: SylvX is an open source, cross-platform, standalone editor available for Windows and Unix-like systems including OSX. It is publicly available at www.sylvx.org.

Cited by 22 publications

References 12 publications

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

Comparative genomics sheds light on niche differentiation and the evolutionary history of comammox Nitrospira

Inferring gene duplications, transfers and losses can be done in a discrete framework

Visualizing co-phylogenetic reconciliations

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