scholarly journals A Metric on the Space of Partly Reduced Phylogenetic Networks

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Juan Wang
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Polynomial Time ◽  
Phylogenetic Trees ◽  
Special Kind ◽  
Population Level ◽  
Phylogenetic Networks

Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of evolutionary events acting at the population level, such as recombination between genes, hybridization between lineages, and horizontal gene transfer. The researchers have designed several measures for computing the dissimilarity between two phylogenetic networks, and each measure has been proven to be a metric on a special kind of phylogenetic networks. However, none of the existing measures is a metric on the space of partly reduced phylogenetic networks. In this paper, we provide a metric,de-distance, on the space of partly reduced phylogenetic networks, which is polynomial-time computable.

scholarly journals UNIQUENESS, INTRACTABILITY AND EXACT ALGORITHMS: REFLECTIONS ON LEVEL-K PHYLOGENETIC NETWORKS

2009 ◽  
Vol 07 (04) ◽  
pp. 597-623 ◽  
Author(s):  
LEO VAN IERSEL ◽  
STEVEN KELK ◽  
MATTHIAS MNICH
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Exact Algorithm ◽  
Exact Algorithms ◽  
Phylogenetic Networks ◽  
Np Hard ◽  
Level 1

Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network determines how non-treelike the evolution can be, with level-0 networks being trees. We study the problem of constructing level-k phylogenetic networks from triplets, i.e. phylogenetic trees for three leaves (taxa). We give, for each k, a level-k network that is uniquely defined by its triplets. We demonstrate the applicability of this result by using it to prove that (1) for all k ≥ 1 it is NP-hard to construct a level-k network consistent with all input triplets, and (2) for all k ≥ 0 it is NP-hard to construct a level-k network consistent with a maximum number of input triplets, even when the input is dense. As a response to this intractability, we give an exact algorithm for constructing level-1 networks consistent with a maximum number of input triplets.

scholarly journals Tree-Based Unrooted Phylogenetic Networks

2017 ◽  
Vol 80 (2) ◽  
pp. 404-416 ◽  
Author(s):  
A. Francis ◽  
K. T. Huber ◽  
V. Moulton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Phylogenetic Network ◽  
Simple Graph ◽  
Phylogenetic Networks ◽  
Underlying Graph ◽  
Finite Set ◽  
Computational Properties

Abstract Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An unrooted phylogenetic network on a non-empty, finite set X of taxa, or network, is a connected, simple graph in which every vertex has degree 1 or 3 and whose leaf set is X. It is called a phylogenetic tree if the underlying graph is a tree. In this paper we consider properties of tree-based networks, that is, networks that can be constructed by adding edges into a phylogenetic tree. We show that although they have some properties in common with their rooted analogues which have recently drawn much attention in the literature, they have some striking differences in terms of both their structural and computational properties. We expect that our results could eventually have applications to, for example, detecting horizontal gene transfer or hybridization which are important factors in the evolution of many organisms.

scholarly journals Indirect identification of horizontal gene transfer

2021 ◽  
Vol 83 (1) ◽  
Author(s):  
David Schaller ◽  
Manuel Lafond ◽  
Peter F. Stadler ◽  
Nicolas Wieseke ◽  
Marc Hellmuth
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Polynomial Time ◽  
Divergence Time ◽  
Recognition Algorithm ◽  
Vertex Coloring ◽  
Implicit Methods ◽  
Colored Graphs ◽  
Wide Range ◽  
Complete Multipartite

AbstractSeveral implicit methods to infer horizontal gene transfer (HGT) focus on pairs of genes that have diverged only after the divergence of the two species in which the genes reside. This situation defines the edge set of a graph, the later-divergence-time (LDT) graph, whose vertices correspond to genes colored by their species. We investigate these graphs in the setting of relaxed scenarios, i.e., evolutionary scenarios that encompass all commonly used variants of duplication-transfer-loss scenarios in the literature. We characterize LDT graphs as a subclass of properly vertex-colored cographs, and provide a polynomial-time recognition algorithm as well as an algorithm to construct a relaxed scenario that explains a given LDT. An edge in an LDT graph implies that the two corresponding genes are separated by at least one HGT event. The converse is not true, however. We show that the complete xenology relation is described by an rs-Fitch graph, i.e., a complete multipartite graph satisfying constraints on the vertex coloring. This class of vertex-colored graphs is also recognizable in polynomial time. We finally address the question “how much information about all HGT events is contained in LDT graphs” with the help of simulations of evolutionary scenarios with a wide range of duplication, loss, and HGT events. In particular, we show that a simple greedy graph editing scheme can be used to efficiently detect HGT events that are implicitly contained in LDT graphs.

scholarly journals Reconstructing the Phylogeny of Corynebacteriales while Accounting for Horizontal Gene Transfer

2020 ◽  
Vol 12 (4) ◽  
pp. 381-395
Author(s):  
Nilson Da Rocha Coimbra ◽  
Aristoteles Goes-Neto ◽  
Vasco Azevedo ◽  
Aïda Ouangraoua
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Bacterial Species ◽  
Gene Tree ◽  
Gene Families ◽  
Common Mechanism ◽  
Species Trees ◽  
Bacterial Phylogeny ◽  
Homologous Genes

Abstract Horizontal gene transfer is a common mechanism in Bacteria that has contributed to the genomic content of existing organisms. Traditional methods for estimating bacterial phylogeny, however, assume only vertical inheritance in the evolution of homologous genes, which may result in errors in the estimated phylogenies. We present a new method for estimating bacterial phylogeny that accounts for the presence of genes acquired by horizontal gene transfer between genomes. The method identifies and corrects putative transferred genes in gene families, before applying a gene tree-based summary method to estimate bacterial species trees. The method was applied to estimate the phylogeny of the order Corynebacteriales, which is the largest clade in the phylum Actinobacteria. We report a collection of 14 phylogenetic trees on 360 Corynebacteriales genomes. All estimated trees display each genus as a monophyletic clade. The trees also display several relationships proposed by past studies, as well as new relevant relationships between and within the main genera of Corynebacteriales: Corynebacterium, Mycobacterium, Nocardia, Rhodococcus, and Gordonia. An implementation of the method in Python is available on GitHub at https://github.com/UdeS-CoBIUS/EXECT (last accessed April 2, 2020).

Genetic relatedness of Streptococcus dysgalactiae isolates causing recurrent bacteraemia

2021 ◽  
Author(s):  
Erik Senneby ◽  
Björn Hallström ◽  
Magnus Rasmussen
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Sequence Similarity ◽  
Streptococcus Dysgalactiae ◽  
High Sequence Similarity ◽  
Content Type ◽  
Link Type ◽  
Clonal Origin

Introduction. Streptococcus dysgalactiae subspecies equisimilis (SDSE) is becoming increasingly recognized as an important human pathogen. Recurrent bacteremia with SDSE has been described previously. Aim. The aims of the study were to establish the genetic relatedness of SDSE isolates with emm-type stG643 that had caused recurrent bacteraemia in three patients and to search for signs of horizontal gene transfer of the emm gene in a collection of SDSE stG643 genomes. Hypothesis. Recurring SDSE bacteremia is caused by the same clone in one patient. Methodology. Whole genome sequencing of 22 clinical SDSE stG643 isolates was performed, including three paired blood culture isolates and sixteen isolates from various sites. All assemblies were aligned to a reference assembly and SNPs were extracted. A total of 53 SDSE genomes were downloaded from GenBank. Two phylogenetic trees, including all 75 SDSE isolates, were created. One tree was based on the emm gene only and one tree was based on all variable positions in the genomes. Results. The genomes from the three pairs of SDSE isolates showed high sequence similarity (1–17 SNPs difference between the pairs), whereas the median SNP difference between the 22 isolates in our collection was 1694 (range 1–11257). The paired isolates were retrieved with 7–53 months between episodes. The 22 SDSE isolates from our collection formed a cluster in the phylogenetic tree based on the emm gene, while they were more scattered in the tree based on all variable positions. Conclusions. Our results show that the paired isolates were of the same clonal origin, which in turn supports carriage between bacteraemia episodes. The phylogenetic analysis indicates that horizontal gene transfer of the emm-gene between some of the SDSE isolates has occurred.

scholarly journals QUARTETS AND UNROOTED PHYLOGENETIC NETWORKS

2012 ◽  
Vol 10 (04) ◽  
pp. 1250004 ◽  
Author(s):  
PHILIPPE GAMBETTE ◽  
VINCENT BERRY ◽  
CHRISTOPHE PAUL
Keyword(s):  
Phylogenetic Trees ◽  
Genetic Material ◽  
Special Kind ◽  
Equivalence Theorem ◽  
Phylogenetic Networks ◽  
Combinatorial Properties ◽  
Split Systems ◽  
Level 1 ◽  
Coexisting Species ◽  
Split Networks

Phylogenetic networks were introduced to describe evolution in the presence of exchanges of genetic material between coexisting species or individuals. Split networks in particular were introduced as a special kind of abstract network to visualize conflicts between phylogenetic trees which may correspond to such exchanges. More recently, methods were designed to reconstruct explicit phylogenetic networks (whose vertices can be interpreted as biological events) from triplet data. In this article, we link abstract and explicit networks through their combinatorial properties, by introducing the unrooted analog of level-k networks. In particular, we give an equivalence theorem between circular split systems and unrooted level-1 networks. We also show how to adapt to quartets some existing results on triplets, in order to reconstruct unrooted level-k phylogenetic networks. These results give an interesting perspective on the combinatorics of phylogenetic networks and also raise algorithmic and combinatorial questions.

scholarly journals Horizontal gene transfer: essentiality and evolvability in prokaryotes, and roles in evolutionary transitions

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1805 ◽  
Author(s):  
Eugene V. Koonin
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Point Mutations ◽  
Theoretical Models ◽  
Microbial Evolution ◽  
Gene Gain ◽  
Gene Trees ◽  
Ratchet Effect ◽  
Evolutionary Transitions

The wide spread of gene exchange and loss in the prokaryotic world has prompted the concept of ‘lateral genomics’ to the point of an outright denial of the relevance of phylogenetic trees for evolution. However, the pronounced coherence congruence of the topologies of numerous gene trees, particularly those for (nearly) universal genes, translates into the notion of a statistical tree of life (STOL), which reflects a central trend of vertical evolution. The STOL can be employed as a framework for reconstruction of the evolutionary processes in the prokaryotic world. Quantitatively, however, horizontal gene transfer (HGT) dominates microbial evolution, with the rate of gene gain and loss being comparable to the rate of point mutations and much greater than the duplication rate. Theoretical models of evolution suggest that HGT is essential for the survival of microbial populations that otherwise deteriorate due to the Muller’s ratchet effect. Apparently, at least some bacteria and archaea evolved dedicated vehicles for gene transfer that evolved from selfish elements such as plasmids and viruses. Recent phylogenomic analyses suggest that episodes of massive HGT were pivotal for the emergence of major groups of organisms such as multiple archaeal phyla as well as eukaryotes. Similar analyses appear to indicate that, in addition to donating hundreds of genes to the emerging eukaryotic lineage, mitochondrial endosymbiosis severely curtailed HGT. These results shed new light on the routes of evolutionary transitions, but caution is due given the inherent uncertainty of deep phylogenies.

scholarly journals On the Subnet Prune and Regraft Distance

10.37236/7860 ◽  
2019 ◽  
Vol 26 (2) ◽  
Author(s):  
Jonathan Klawitter ◽  
Simone Linz
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Tree ◽  
Phylogenetic Network ◽  
Directed Acyclic Graphs ◽  
Phylogenetic Networks ◽  
Evolutionary Relationships ◽  
Acyclic Graphs ◽  
Subtree Prune And Regraft

Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of phylogenetic networks, the popular tree rearrangement operation rooted subtree prune and regraft (rSPR) was recently generalised to phylogenetic networks. This new operation – called subnet prune and regraft (SNPR) – induces a metric on the space of all phylogenetic networks as well as on several widely-used network classes. In this paper, we investigate several problems that arise in the context of computing the SNPR-distance. For a phylogenetic tree $T$ and a phylogenetic network $N$, we show how this distance can be computed by considering the set of trees that are embedded in $N$ and then use this result to characterise the SNPR-distance between $T$ and $N$ in terms of agreement forests. Furthermore, we analyse properties of shortest SNPR-sequences between two phylogenetic networks $N$ and $N'$, and answer the question whether or not any of the classes of tree-child, reticulation-visible, or tree-based networks isometrically embeds into the class of all phylogenetic networks under SNPR.

scholarly journals Evolution of Aminoacyl-tRNA Synthetases—Analysis of Unique Domain Architectures and Phylogenetic Trees Reveals a Complex History of Horizontal Gene Transfer Events

1999 ◽  
Vol 9 (8) ◽  
pp. 689-710 ◽  
Author(s):  
Yuri I. Wolf ◽  
L. Aravind ◽  
Nick V. Grishin ◽  
Eugene V. Koonin
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Phylogenetic Trees ◽  
Domain Architecture ◽  
Specific Gene ◽  
Trna Synthetases ◽  
Aminoacyl Trna Synthetases ◽  
Eukaryotic Genes ◽  
Multiple Alignments

Phylogenetic analysis of aminoacyl-tRNA synthetases (aaRSs) of all 20 specificities from completely sequenced bacterial, archaeal, and eukaryotic genomes reveals a complex evolutionary picture. Detailed examination of the domain architecture of aaRSs using sequence profile searches delineated a network of partially conserved domains that is even more elaborate than previously suspected. Several unexpected evolutionary connections were identified, including the apparent origin of the β-subunit of bacterial GlyRS from the HD superfamily of hydrolases, a domain shared by bacterial AspRS and the B subunit of archaeal glutamyl-tRNA amidotransferases, and another previously undetected domain that is conserved in a subset of ThrRS, guanosine polyphosphate hydrolases and synthetases, and a family of GTPases. Comparison of domain architectures and multiple alignments resulted in the delineation of synapomorphies—shared derived characters, such as extra domains or inserts—for most of the aaRSs specificities. These synapomorphies partition sets of aaRSs with the same specificity into two or more distinct and apparently monophyletic groups. In conjunction with cluster analysis and a modification of the midpoint-rooting procedure, this partitioning was used to infer the likely root position in phylogenetic trees. The topologies of the resulting rooted trees for most of the aaRSs specificities are compatible with the evolutionary “standard model” whereby the earliest radiation event separated bacteria from the common ancestor of archaea and eukaryotes as opposed to the two other possible evolutionary scenarios for the three major divisions of life. For almost all aaRSs specificities, however, this simple scheme is confounded by displacement of some of the bacterial aaRSs by their eukaryotic or, less frequently, archaeal counterparts. Displacement of ancestral eukaryotic aaRS genes by bacterial ones, presumably of mitochondrial origin, was observed for three aaRSs. In contrast, there was no convincing evidence of displacement of archaeal aaRSs by bacterial ones. Displacement of aaRS genes by eukaryotic counterparts is most common among parasitic and symbiotic bacteria, particularly the spirochaetes, in which 10 of the 19 aaRSs seem to have been displaced by the respective eukaryotic genes and two by the archaeal counterpart. Unlike the primary radiation events between the three main divisions of life, that were readily traceable through the phylogenetic analysis of aaRSs, no consistent large-scale bacterial phylogeny could be established. In part, this may be due to additional gene displacement events among bacterial lineages. Argument is presented that, although lineage-specific gene loss might have contributed to the evolution of some of the aaRSs, this is not a viable alternative to horizontal gene transfer as the principal evolutionary phenomenon in this gene class.[Complete multiple alignments of all aaRSs from complete genomes as well as the alignments of conserved regions used for phylogenetic tree construction are available at ftp://ncbi.nlm.nih.gov/pub/koonin/aaRS]

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