1
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Bogdanowicz D, Giaro K. Generalization of Phylogenetic Matching Metrics with Experimental Tests of Practical Advantages. J Comput Biol 2023; 30:261-276. [PMID: 36576792 DOI: 10.1089/cmb.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The ability to quantify a dissimilarity of different phylogenetic trees is required in various types of phylogenetic studies, for example, such metrics are used to assess the quality of phylogeny construction methods and to define optimization criteria in supertree building algorithms. In this article, starting from the already described concept of matching metrics, we define three new metrics for rooted phylogenetic trees. One of them, Matching Pair Jaccard (MPJ) distance, is still purely topological, but we now utilize the Jaccard index set dissimilarity measure in its construction. This modification substantially changes the structural features of the metric space. In particular, we investigate the properties of the previously known Matching Cluster Jaccard (MCJ) and the new MPJ metrics, such as the asymptotic behavior of their expected distance between two random trees, the space diameter, and the change of a distance after a single leaf relocation. The other two metrics, Matching Cluster Weight-aware (MCW) and Matching Cluster Jaccard Weight-aware (MCJW) distances, are the first propositions of generalization of matching metrics designed for rooted phylogenies with branch lengths. The experimental tests of the practical utility of the phylogenetic metrics show the superiority of MCJ, MPJ over the previous best tree comparison method. To define the MCW and MCJW metrics, we introduce a general method for constructing matching metrics for weighted rooted phylogenetic trees.
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Affiliation(s)
- Damian Bogdanowicz
- Department of Algorithms and System Modeling, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland
| | - Krzysztof Giaro
- Department of Algorithms and System Modeling, Faculty of Electronics, Telecommunications and Informatics, Gdansk University of Technology, Gdansk, Poland
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2
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Tahiri N, Fichet B, Makarenkov V. Building alternative consensus trees and supertrees using k-means and Robinson and Foulds distance. Bioinformatics 2022; 38:3367-3376. [PMID: 35579343 DOI: 10.1093/bioinformatics/btac326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 04/28/2022] [Accepted: 05/10/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Each gene has its own evolutionary history which can substantially differ from evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer or recombination events. Thus, the evolutionary history of each gene should be represented by its own phylogenetic tree which may display different evolutionary patterns from the species tree that accounts for the main patterns of vertical descent. However, the output of traditional consensus tree or supertree inference methods is a unique consensus tree or supertree. RESULTS We present a new efficient method for inferring multiple alternative consensus trees and supertrees to best represent the most important evolutionary patterns of a given set of gene phylogenies. We show how an adapted version of the popular k-means clustering algorithm, based on some remarkable properties of the Robinson and Foulds distance, can be used to partition a given set of trees into one (for homogeneous data) or multiple (for heterogeneous data) cluster(s) of trees. Moreover, we adapt the popular Caliński-Harabasz, Silhouette, Ball and Hall, and Gap cluster validity indices to tree clustering with k-means. Special attention is given to the relevant but very challenging problem of inferring alternative supertrees. The use of the Euclidean property of the objective function of the method makes it faster than the existing tree clustering techniques, and thus better suited for analyzing large evolutionary datasets. AVAILABILITY AND IMPLEMENTATION Our KMeansSuperTreeClustering program along with its C ++ source code is available at: https://github.com/TahiriNadia/KMeansSuperTreeClustering. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nadia Tahiri
- Département d'informatique, Université du Québec à Montréal, Montreal, QC, Canada.,Département d'informatique, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Bernard Fichet
- Aix-Marseille Université, Faculté de Médecine, 27 Bd. Jean Moulin, F-13385 Marseille, France
| | - Vladimir Makarenkov
- Département d'informatique, Université du Québec à Montréal, Montreal, QC, Canada
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3
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Bansal MS. Deciphering Microbial Gene Family Evolution Using Duplication-Transfer-Loss Reconciliation and RANGER-DTL. Methods Mol Biol 2022; 2569:233-252. [PMID: 36083451 DOI: 10.1007/978-1-0716-2691-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Phylogenetic reconciliation has emerged as a principled, highly effective technique for investigating the origin, spread, and evolutionary history of microbial gene families. Proper application of phylogenetic reconciliation requires a clear understanding of potential pitfalls and sources of error, and knowledge of the most effective reconciliation-based tools and protocols to use to maximize accuracy. In this book chapter, we provide a brief overview of Duplication-Transfer-Loss (DTL) reconciliation, the standard reconciliation model used to study microbial gene families and provide a step-by-step computational protocol to maximize the accuracy of DTL reconciliation and minimize false-positive evolutionary inferences.
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Affiliation(s)
- Mukul S Bansal
- Department of Computer Science & Engineering, University of Connecticut, Storrs, CT, USA.
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4
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Collienne L, Gavryushkin A. Computing nearest neighbour interchange distances between ranked phylogenetic trees. J Math Biol 2021; 82:8. [PMID: 33492606 PMCID: PMC7835203 DOI: 10.1007/s00285-021-01567-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/20/2020] [Accepted: 01/07/2021] [Indexed: 11/26/2022]
Abstract
Many popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is [Formula: see text]-hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to [Formula: see text]-hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).
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Affiliation(s)
- Lena Collienne
- Department of Computer Science, University of Otago, Dunedin, New Zealand
| | - Alex Gavryushkin
- Department of Computer Science, University of Otago, Dunedin, New Zealand
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5
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Waite DW, Chuvochina M, Pelikan C, Parks DH, Yilmaz P, Wagner M, Loy A, Naganuma T, Nakai R, Whitman WB, Hahn MW, Kuever J, Hugenholtz P. Proposal to reclassify the proteobacterial classes Deltaproteobacteria and Oligoflexia, and the phylum Thermodesulfobacteria into four phyla reflecting major functional capabilities. Int J Syst Evol Microbiol 2020; 70:5972-6016. [DOI: 10.1099/ijsem.0.004213] [Citation(s) in RCA: 696] [Impact Index Per Article: 174.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The class
Deltaproteobacteria
comprises an ecologically and metabolically diverse group of bacteria best known for dissimilatory sulphate reduction and predatory behaviour. Although this lineage is the fourth described class of the phylum
Proteobacteria
, it rarely affiliates with other proteobacterial classes and is frequently not recovered as a monophyletic unit in phylogenetic analyses. Indeed, one branch of the class
Deltaproteobacteria
encompassing Bdellovibrio-like predators was recently reclassified into a separate proteobacterial class, the
Oligoflexia
. Here we systematically explore the phylogeny of taxa currently assigned to these classes using 120 conserved single-copy marker genes as well as rRNA genes. The overwhelming majority of markers reject the inclusion of the classes
Deltaproteobacteria
and
Oligoflexia
in the phylum
Proteobacteria
. Instead, the great majority of currently recognized members of the class
Deltaproteobacteria
are better classified into four novel phylum-level lineages. We propose the names Desulfobacterota phyl. nov. and Myxococcota phyl. nov. for two of these phyla, based on the oldest validly published names in each lineage, and retain the placeholder name SAR324 for the third phylum pending formal description of type material. Members of the class
Oligoflexia
represent a separate phylum for which we propose the name Bdellovibrionota phyl. nov. based on priority in the literature and general recognition of the genus Bdellovibrio. Desulfobacterota phyl. nov. includes the taxa previously classified in the phylum
Thermodesulfobacteria
, and these reclassifications imply that the ability of sulphate reduction was vertically inherited in the
Thermodesulfobacteria
rather than laterally acquired as previously inferred. Our analysis also indicates the independent acquisition of predatory behaviour in the phyla Myxococcota and Bdellovibrionota, which is consistent with their distinct modes of action. This work represents a stable reclassification of one of the most taxonomically challenging areas of the bacterial tree and provides a robust framework for future ecological and systematic studies.
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Affiliation(s)
- David W Waite
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Maria Chuvochina
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Claus Pelikan
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Donovan H Parks
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | | | - Michael Wagner
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | - Alexander Loy
- University of Vienna, Centre for Microbiology and Environmental Systems Science, Division of Microbial Ecology, Vienna, Austria
| | | | - Ryosuke Nakai
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Hokkaido, Japan
| | - William B Whitman
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, Mondsee, Austria
| | - Jan Kuever
- Department of Microbiology, Bremen Institute for Materials Testing, Bremen, Germany
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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6
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Bansal MS. Linear-time algorithms for phylogenetic tree completion under Robinson-Foulds distance. Algorithms Mol Biol 2020; 15:6. [PMID: 32313549 PMCID: PMC7155338 DOI: 10.1186/s13015-020-00166-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 04/04/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We consider two fundamental computational problems that arise when comparing phylogenetic trees, rooted or unrooted, with non-identical leaf sets. The first problem arises when comparing two trees where the leaf set of one tree is a proper subset of the other. The second problem arises when the two trees to be compared have only partially overlapping leaf sets. The traditional approach to handling these problems is to first restrict the two trees to their common leaf set. An alternative approach that has shown promise is to first complete the trees by adding missing leaves, so that the resulting trees have identical leaf sets. This requires the computation of an optimal completion that minimizes the distance between the two resulting trees over all possible completions. RESULTS We provide optimal linear-time algorithms for both completion problems under the widely-used Robinson-Foulds (RF) distance measure. Our algorithm for the first problem improves the time complexity of the current fastest algorithm from quadratic (in the size of the two trees) to linear. No algorithms have yet been proposed for the more general second problem where both trees have missing leaves. We advance the study of this general problem by proposing a useful restricted version of the general problem and providing optimal linear-time algorithms for the restricted version. Our experimental results on biological data sets suggest that completion-based RF distances can be very different compared to traditional RF distances.
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7
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Goluch T, Bogdanowicz D, Giaro K. Visual TreeCmp
: Comprehensive Comparison of Phylogenetic Trees on the Web. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13358] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Tomasz Goluch
- Department of Algorithms and System Modeling Faculty of Electronics, Telecommunications and Informatics Gdańsk University of Technology Gdańsk Poland
| | - Damian Bogdanowicz
- Department of Algorithms and System Modeling Faculty of Electronics, Telecommunications and Informatics Gdańsk University of Technology Gdańsk Poland
| | - Krzysztof Giaro
- Department of Algorithms and System Modeling Faculty of Electronics, Telecommunications and Informatics Gdańsk University of Technology Gdańsk Poland
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8
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Fang Y, Liu C, Lin J, Li X, Alavian KN, Yang Y, Niu Y. PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. BMC Evol Biol 2019; 19:219. [PMID: 31791235 PMCID: PMC6889546 DOI: 10.1186/s12862-019-1541-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/13/2019] [Indexed: 02/05/2023] Open
Abstract
Background Phylogenetic species trees are widely used in inferring evolutionary relationships. Existing software and algorithms mainly focus on phylogenetic inference. However, less attention has been paid to intermediate steps, such as processing extremely large sequences and preparing configure files to connect multiple software. When the species number is large, the intermediate steps become a bottleneck that may seriously affect the efficiency of tree building. Results Here, we present an easy-to-use pipeline named PhySpeTree to facilitate the reconstruction of species trees across bacterial, archaeal, and eukaryotic organisms. Users need only to input the abbreviations of species names; PhySpeTree prepares complex configure files for different software, then automatically downloads genomic data, cleans sequences, and builds trees. PhySpeTree allows users to perform critical steps such as sequence alignment and tree construction by adjusting advanced options. PhySpeTree provides two parallel pipelines based on concatenated highly conserved proteins and small subunit ribosomal RNA sequences, respectively. Accessory modules, such as those for inserting new species, generating visualization configurations, and combining trees, are distributed along with PhySpeTree. Conclusions Together with accessory modules, PhySpeTree significantly simplifies tree reconstruction. PhySpeTree is implemented in Python running on modern operating systems (Linux, macOS, and Windows). The source code is freely available with detailed documentation (https://github.com/yangfangs/physpetools).
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Affiliation(s)
- Yang Fang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Chengcheng Liu
- State Key Laboratory of Oral Diseases & National Clinical Research Center for Oral Diseases &Department of Periodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiangyi Lin
- Wu YuZhang Honors College of Sichuan University, Chengdu, People's Republic of China
| | - Xufeng Li
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China
| | - Kambiz N Alavian
- Department of Medicine, Division of Brain Sciences, Imperial College London, London, UK.,Department of Internal Medicine, Endocrinology, Yale University, New Haven, USA
| | - Yi Yang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China.
| | - Yulong Niu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, People's Republic of China.
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9
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Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proc Natl Acad Sci U S A 2019; 116:19585-19592. [PMID: 31506349 DOI: 10.1073/pnas.1912006116] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Giant and large eukaryotic double-stranded DNA viruses from the Nucleo-Cytoplasmic Large DNA Virus (NCLDV) assemblage represent a remarkably diverse and potentially ancient component of the eukaryotic virome. However, their origin(s), evolution, and potential roles in the emergence of modern eukaryotes remain subjects of intense debate. Here we present robust phylogenetic trees of NCLDVs, based on the 8 most conserved proteins responsible for virion morphogenesis and informational processes. Our results uncover the evolutionary relationships between different NCLDV families and support the existence of 2 superclades of NCLDVs, each encompassing several families. We present evidence strongly suggesting that the NCLDV core genes, which are involved in both informational processes and virion formation, were acquired vertically from a common ancestor. Among them, the largest subunits of the DNA-dependent RNA polymerase were transferred between 2 clades of NCLDVs and proto-eukaryotes, giving rise to 2 of the 3 eukaryotic DNA-dependent RNA polymerases. Our results strongly suggest that these transfers and the diversification of NCLDVs predated the emergence of modern eukaryotes, emphasizing the major role of viruses in the evolution of cellular domains.
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10
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Chan YB, Robin C. Reconciliation of a gene network and species tree. J Theor Biol 2019; 472:54-66. [DOI: 10.1016/j.jtbi.2019.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 03/29/2019] [Accepted: 04/02/2019] [Indexed: 12/26/2022]
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11
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Stival F, Michieletto S, Cognolato M, Pagello E, Müller H, Atzori M. A quantitative taxonomy of human hand grasps. J Neuroeng Rehabil 2019; 16:28. [PMID: 30770759 PMCID: PMC6377750 DOI: 10.1186/s12984-019-0488-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/21/2019] [Indexed: 11/17/2022] Open
Abstract
Background A proper modeling of human grasping and of hand movements is fundamental for robotics, prosthetics, physiology and rehabilitation. The taxonomies of hand grasps that have been proposed in scientific literature so far are based on qualitative analyses of the movements and thus they are usually not quantitatively justified. Methods This paper presents to the best of our knowledge the first quantitative taxonomy of hand grasps based on biomedical data measurements. The taxonomy is based on electromyography and kinematic data recorded from 40 healthy subjects performing 20 unique hand grasps. For each subject, a set of hierarchical trees are computed for several signal features. Afterwards, the trees are combined, first into modality-specific (i.e. muscular and kinematic) taxonomies of hand grasps and then into a general quantitative taxonomy of hand movements. The modality-specific taxonomies provide similar results despite describing different parameters of hand movements, one being muscular and the other kinematic. Results The general taxonomy merges the kinematic and muscular description into a comprehensive hierarchical structure. The obtained results clarify what has been proposed in the literature so far and they partially confirm the qualitative parameters used to create previous taxonomies of hand grasps. According to the results, hand movements can be divided into five movement categories defined based on the overall grasp shape, finger positioning and muscular activation. Part of the results appears qualitatively in accordance with previous results describing kinematic hand grasping synergies. Conclusions The taxonomy of hand grasps proposed in this paper clarifies with quantitative measurements what has been proposed in the field on a qualitative basis, thus having a potential impact on several scientific fields.
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Affiliation(s)
- Francesca Stival
- Intelligent Autonomous Systems Lab (IAS-Lab), Department of Information Engineering (DEI), University of Padova, Padova, Italy.,Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO), Sierre, Switzerland
| | - Stefano Michieletto
- Intelligent Autonomous Systems Lab (IAS-Lab), Department of Information Engineering (DEI), University of Padova, Padova, Italy.
| | - Matteo Cognolato
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO), Sierre, Switzerland.,Rehabilitation Engineering Laboratory, Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Enrico Pagello
- Intelligent Autonomous Systems Lab (IAS-Lab), Department of Information Engineering (DEI), University of Padova, Padova, Italy.,Now retired from academy, and with EXiMotion Srl, Via Prima Strada, 35, Padova, Italy
| | - Henning Müller
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO), Sierre, Switzerland.,University of Geneva, Geneva, Switzerland
| | - Manfredo Atzori
- Information Systems Institute, University of Applied Sciences Western Switzerland (HES-SO), Sierre, Switzerland
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12
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Fleischauer M, Böcker S. BCD Beam Search: considering suboptimal partial solutions in Bad Clade Deletion supertrees. PeerJ 2018; 6:e4987. [PMID: 29900080 PMCID: PMC5995099 DOI: 10.7717/peerj.4987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 05/26/2018] [Indexed: 11/20/2022] Open
Abstract
Supertree methods enable the reconstruction of large phylogenies. The supertree problem can be formalized in different ways in order to cope with contradictory information in the input. Some supertree methods are based on encoding the input trees in a matrix; other methods try to find minimum cuts in some graph. Recently, we introduced Bad Clade Deletion (BCD) supertrees which combines the graph-based computation of minimum cuts with optimizing a global objective function on the matrix representation of the input trees. The BCD supertree method has guaranteed polynomial running time and is very swift in practice. The quality of reconstructed supertrees was superior to matrix representation with parsimony (MRP) and usually on par with SuperFine for simulated data; but particularly for biological data, quality of BCD supertrees could not keep up with SuperFine supertrees. Here, we present a beam search extension for the BCD algorithm that keeps alive a constant number of partial solutions in each top-down iteration phase. The guaranteed worst-case running time of the new algorithm is still polynomial in the size of the input. We present an exact and a randomized subroutine to generate suboptimal partial solutions. Both beam search approaches consistently improve supertree quality on all evaluated datasets when keeping 25 suboptimal solutions alive. Supertree quality of the BCD Beam Search algorithm is on par with MRP and SuperFine even for biological data. This is the best performance of a polynomial-time supertree algorithm reported so far.
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Affiliation(s)
| | - Sebastian Böcker
- Chair for Bioinformatics, Friedrich-Schiller-University, Jena, Germany
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13
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Pavan ME, Pavan EE, Glaeser SP, Etchebehere C, Kämpfer P, Pettinari MJ, López NI. Proposal for a new classification of a deep branching bacterial phylogenetic lineage: transfer of Coprothermobacter proteolyticus and Coprothermobacter platensis to Coprothermobacteraceae fam. nov., within Coprothermobacterales ord. nov., Coprothermobacteria classis nov. and Coprothermobacterota phyl. nov. and emended description of the family Thermodesulfobiaceae. Int J Syst Evol Microbiol 2018; 68:1627-1632. [PMID: 29595416 DOI: 10.1099/ijsem.0.002720] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The genus Coprothermobacter (initially named Thermobacteroides) is currently placed within the phylum Firmicutes. Early 16S rRNA gene based phylogenetic studies pointed out the great differences between Coprothermobacter and other members of the Firmicutes, revealing that it constitutes a new deep branching lineage. Over the years, several studies based on 16S rRNA gene and whole genome sequences have indicated that Coprothermobacter is very distant phylogenetically to all other bacteria, supporting its placement in a distinct deeply rooted novel phylum. In view of this, we propose its allocation to the new family Coprothermobacteraceae within the novel order Coprothermobacterales, the new class Coprothermobacteria, and the new phylum Coprothermobacterota, and an emended description of the family Thermodesulfobiaceae.
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Affiliation(s)
- María Elisa Pavan
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Esteban E Pavan
- Biomedical Technologies Laboratory, Department of Electronics, Information and Bioengineering, Politecnico di Milano, Milan, Italy
| | - Stefanie P Glaeser
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - Claudia Etchebehere
- Microbial Ecology Laboratory, Department of Biochemistry and Microbial Genetics, Biological Research Institute "Clemente Estable", Montevideo, Uruguay
| | - Peter Kämpfer
- Institut für Angewandte Mikrobiologie, Universität Giessen, Giessen, Germany
| | - María Julia Pettinari
- Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nancy I López
- IQUIBICEN-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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14
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Avni E, Yona Z, Cohen R, Snir S. The Performance of Two Supertree Schemes Compared Using Synthetic and Real Data Quartet Input. J Mol Evol 2018; 86:150-165. [PMID: 29460038 DOI: 10.1007/s00239-018-9833-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 02/05/2018] [Indexed: 11/26/2022]
Abstract
Despite impressive advancements in technological and theoretical tools, construction of phylogenetic (evolutionary) trees is still a challenging task. The availability of enormous quantities of molecular data has made large-scale phylogenetic reconstruction involving thousands of species, a more viable goal. For this goal, separate trees over different, overlapping subsets of species, representing histories of various markers of these species, are collected. These trees, typically with conflicting signals, are subsequently combined into a single tree over the full set, an operation denoted as supertree construction. The amalgamation of such trees into a single tree lies at the heart of many tasks in phylogenetics, yet remains a daunting endeavor, especially in light of conflicting signals. In this work, we study the performance of matrix representation with parsimony (MRP), the most widely used supertree method to date, when confronted with quartet trees. Quartet trees are the most basic informational unit when amalgamation of unrooted trees is attempted, and they remain relevant in more general settings even though standard supertree methods are not necessarily confined to quartets. This study involves both real and simulated data, and the effects of several parameters on the results are evaluated, revealing a number of anomalies associated with MRP. We show that these anomalies are surmountable when using a recently introduced supertree method, weighted quartet MaxCut (wQMC).
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Affiliation(s)
- Eliran Avni
- Department of Evolutionary Biology, University of Haifa, 31905, Haifa, Israel
| | - Zahi Yona
- Department of Computer Scienece, University of Haifa, 31905, Haifa, Israel
| | - Reuven Cohen
- School of Engineering, Kinneret College, 15132, Tzemach, Israel
| | - Sagi Snir
- Department of Evolutionary Biology, University of Haifa, 31905, Haifa, Israel.
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15
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Whidden C, Matsen F. Calculating the Unrooted Subtree Prune-and-Regraft Distance. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 16:898-911. [PMID: 29994585 DOI: 10.1109/tcbb.2018.2802911] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo phylogenetic inference. Although the rooted version of SPR distance can be computed relatively efficiently between rooted trees using fixed-parameter-tractable maximum agreement forest (MAF) algorithms, no MAF formulation is known for the unrooted case. Correspondingly, previous algorithms are unable to compute unrooted SPR distances larger than 7.
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16
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Antonelli A, Hettling H, Condamine FL, Vos K, Nilsson RH, Sanderson MJ, Sauquet H, Scharn R, Silvestro D, Töpel M, Bacon CD, Oxelman B, Vos RA. Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa. Syst Biol 2018; 66:152-166. [PMID: 27616324 PMCID: PMC5410925 DOI: 10.1093/sysbio/syw066] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 07/19/2016] [Indexed: 01/06/2023] Open
Abstract
Rapidly growing biological data—including molecular sequences and fossils—hold an unprecedented potential to reveal how evolutionary processes generate and maintain biodiversity. However, researchers often have to develop their own idiosyncratic workflows to integrate and analyze these data for reconstructing time-calibrated phylogenies. In addition, divergence times estimated under different methods and assumptions, and based on data of various quality and reliability, should not be combined without proper correction. Here we introduce a modular framework termed SUPERSMART (Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa), and provide a proof of concept for dealing with the moving targets of evolutionary and biogeographical research. This framework assembles comprehensive data sets of molecular and fossil data for any taxa and infers dated phylogenies using robust species tree methods, also allowing for the inclusion of genomic data produced through next-generation sequencing techniques. We exemplify the application of our method by presenting phylogenetic and dating analyses for the mammal order Primates and for the plant family Arecaceae (palms). We believe that this framework will provide a valuable tool for a wide range of hypothesis-driven research questions in systematics, biogeography, and evolution. SUPERSMART will also accelerate the inference of a “Dated Tree of Life” where all node ages are directly comparable.
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Affiliation(s)
- Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,Gothenburg Botanical Garden, Carl Skottsbergs Gata 22A, SE-41319 Göteborg, Sweden
| | - Hannes Hettling
- Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands
| | - Fabien L Condamine
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,CNRS, UMR 5554 Institut des Sciences de l'Evolution (Université de Montpellier), Place Eugéne Bataillon, 34095 Montpellier, France
| | - Karin Vos
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - R Henrik Nilsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Michael J Sanderson
- Department of Ecology and Evolutionary Biology, University of Arizona, 1041 E. Lowell, Tucson, AZ 85721, USA
| | - Hervé Sauquet
- Université Paris-Sud, Laboratoire Écologie, Systématique, Évolution, CNRS UMR 8079, 91405 Orsay, France
| | - Ruud Scharn
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden.,Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland
| | - Mats Töpel
- Swedish Bioinformatics Infrastructure for Life Sciences, Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, SE-405 30, Göteborg, Sweden.,Department of Marine Sciences, University of Gothenburg, Box 460, SE-405 30 Göteborg, Sweden
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, SE-405 30 Göteborg, Sweden
| | - Rutger A Vos
- Naturalis Biodiversity Center, Darwinweg 4, 2333 CR Leiden, The Netherlands
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17
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Matsen FA, Billey SC, Kas A, Konvalinka M. Tanglegrams: A Reduction Tool for Mathematical Phylogenetics. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:343-349. [PMID: 28113515 DOI: 10.1109/tcbb.2016.2613040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Many discrete mathematics problems in phylogenetics are defined in terms of the relative labeling of pairs of leaf-labeled trees. These relative labelings are naturally formalized as tanglegrams, which have previously been an object of study in coevolutionary analysis. Although there has been considerable work on planar drawings of tanglegrams, they have not been fully explored as combinatorial objects until recently. In this paper, we describe how many discrete mathematical questions on trees "factor" through a problem on tanglegrams, and how understanding that factoring can simplify analysis. Depending on the problem, it may be useful to consider a unordered version of tanglegrams, and/or their unrooted counterparts. For all of these definitions, we show how the isomorphism types of tanglegrams can be understood in terms of double cosets of the symmetric group, and we investigate their automorphisms. Understanding tanglegrams better will isolate the distinct problems on leaf-labeled pairs of trees and reveal natural symmetries of spaces associated with such problems.
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Mallo D, Posada D. Multilocus inference of species trees and DNA barcoding. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0335. [PMID: 27481787 PMCID: PMC4971187 DOI: 10.1098/rstb.2015.0335] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2016] [Indexed: 11/30/2022] Open
Abstract
The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent. This article is part of the themed issue ‘From DNA barcodes to biomes’.
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Affiliation(s)
- Diego Mallo
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo 36310, Spain
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20
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Abstract
Supertree methods merge a set of overlapping phylogenetic trees into a supertree containing all taxa of the input trees. The challenge in supertree reconstruction is the way of dealing with conflicting information in the input trees. Many different algorithms for different objective functions have been suggested to resolve these conflicts. In particular, there exist methods based on encoding the source trees in a matrix, where the supertree is constructed applying a local search heuristic to optimize the respective objective function. We present a novel heuristic supertree algorithm called Bad Clade Deletion (BCD) supertrees. It uses minimum cuts to delete a locally minimal number of columns from such a matrix representation so that it is compatible. This is the complement problem to Matrix Representation with Compatibility (Maximum Split Fit). Our algorithm has guaranteed polynomial worst-case running time and performs swiftly in practice. Different from local search heuristics, it guarantees to return the directed perfect phylogeny for the input matrix, corresponding to the parent tree of the input trees, if one exists. Comparing supertrees to model trees for simulated data, BCD shows a better accuracy (F1 score) than the state-of-the-art algorithms SuperFine (up to 3%) and Matrix Representation with Parsimony (up to 7%); at the same time, BCD is up to 7 times faster than SuperFine, and up to 600 times faster than Matrix Representation with Parsimony. Finally, using the BCD supertree as a starting tree for a combined Maximum Likelihood analysis using RAxML, we reach significantly improved accuracy (1% higher F1 score) and running time (1.7-fold speedup).
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Affiliation(s)
- Markus Fleischauer
- Chair for Bioinformatics, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
| | - Sebastian Böcker
- Chair for Bioinformatics, Institute for Computer Science, Friedrich-Schiller-University Jena, Jena, Germany
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21
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van Iersel L, Kelk S, Stamoulis G, Stougie L, Boes O. On Unrooted and Root-Uncertain Variants of Several Well-Known Phylogenetic Network Problems. ALGORITHMICA 2017; 80:2993-3022. [PMID: 30956378 PMCID: PMC6428403 DOI: 10.1007/s00453-017-0366-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 08/11/2017] [Indexed: 05/04/2023]
Abstract
The hybridization number problem requires us to embed a set of binary rooted phylogenetic trees into a binary rooted phylogenetic network such that the number of nodes with indegree two is minimized. However, from a biological point of view accurately inferring the root location in a phylogenetic tree is notoriously difficult and poor root placement can artificially inflate the hybridization number. To this end we study a number of relaxed variants of this problem. We start by showing that the fundamental problem of determining whether an unrooted phylogenetic network displays (i.e. embeds) an unrooted phylogenetic tree, is NP-hard. On the positive side we show that this problem is FPT in reticulation number. In the rooted case the corresponding FPT result is trivial, but here we require more subtle argumentation. Next we show that the hybridization number problem for unrooted networks (when given two unrooted trees) is equivalent to the problem of computing the tree bisection and reconnect distance of the two unrooted trees. In the third part of the paper we consider the "root uncertain" variant of hybridization number. Here we are free to choose the root location in each of a set of unrooted input trees such that the hybridization number of the resulting rooted trees is minimized. On the negative side we show that this problem is APX-hard. On the positive side, we show that the problem is FPT in the hybridization number, via kernelization, for any number of input trees.
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Affiliation(s)
- Leo van Iersel
- Delft Institute of Applied Mathematics, Delft University of Technology, Delft, The Netherlands
| | - Steven Kelk
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
| | - Georgios Stamoulis
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
| | - Leen Stougie
- CWI, INRIA-Erable and Department of Econometrics and Operations Research, Vrije Universiteit, Amsterdam, The Netherlands
| | - Olivier Boes
- Department of Data Science and Knowledge Engineering (DKE), Maastricht University, Maastricht, The Netherlands
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22
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Bogdanowicz D, Giaro K. Comparing Phylogenetic Trees by Matching Nodes Using the Transfer Distance Between Partitions. J Comput Biol 2017; 24:422-435. [PMID: 28177699 PMCID: PMC5421509 DOI: 10.1089/cmb.2016.0204] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Ability to quantify dissimilarity of different phylogenetic trees describing the relationship between the same group of taxa is required in various types of phylogenetic studies. For example, such metrics are used to assess the quality of phylogeny construction methods, to define optimization criteria in supertree building algorithms, or to find horizontal gene transfer (HGT) events. Among the set of metrics described so far in the literature, the most commonly used seems to be the Robinson-Foulds distance. In this article, we define a new metric for rooted trees-the Matching Pair (MP) distance. The MP metric uses the concept of the minimum-weight perfect matching in a complete bipartite graph constructed from partitions of all pairs of leaves of the compared phylogenetic trees. We analyze the properties of the MP metric and present computational experiments showing its potential applicability in tasks related to finding the HGT events.
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Affiliation(s)
- Damian Bogdanowicz
- Department of Algorithms and System Modeling, Gdansk University of Technology , Gdansk, Poland
| | - Krzysztof Giaro
- Department of Algorithms and System Modeling, Gdansk University of Technology , Gdansk, Poland
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23
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Dupont PY, Cox MP. Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi. G3 (BETHESDA, MD.) 2017; 7:1301-1314. [PMID: 28235827 PMCID: PMC5386878 DOI: 10.1534/g3.116.038448] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 02/17/2017] [Indexed: 12/26/2022]
Abstract
Lateral gene transfer (LGT, also known as horizontal gene transfer), an atypical mechanism of transferring genes between species, has almost become the default explanation for genes that display an unexpected composition or phylogeny. Numerous methods of detecting LGT events all rely on two fundamental strategies: primary structure composition or gene tree/species tree comparisons. Discouragingly, the results of these different approaches rarely coincide. With the wealth of genome data now available, detection of laterally transferred genes is increasingly being attempted in large uncurated eukaryotic datasets. However, detection methods depend greatly on the quality of the underlying genomic data, which are typically complex for eukaryotes. Furthermore, given the automated nature of genomic data collection, it is typically impractical to manually verify all protein or gene models, orthology predictions, and multiple sequence alignments, requiring researchers to accept a substantial margin of error in their datasets. Using a test case comprising plant-associated genomes across the fungal kingdom, this study reveals that composition- and phylogeny-based methods have little statistical power to detect laterally transferred genes. In particular, phylogenetic methods reveal extreme levels of topological variation in fungal gene trees, the vast majority of which show departures from the canonical species tree. Therefore, it is inherently challenging to detect LGT events in typical eukaryotic genomes. This finding is in striking contrast to the large number of claims for laterally transferred genes in eukaryotic species that routinely appear in the literature, and questions how many of these proposed examples are statistically well supported.
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Affiliation(s)
- Pierre-Yves Dupont
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
| | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand
- the Bio-Protection Research Centre, Massey University, Palmerston North 4442, New Zealand
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24
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Chan CX, Beiko RG, Ragan MA. Scaling Up the Phylogenetic Detection of Lateral Gene Transfer Events. Methods Mol Biol 2017; 1525:421-432. [PMID: 27896730 DOI: 10.1007/978-1-4939-6622-6_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Lateral genetic transfer (LGT) is the process by which genetic material moves between organisms (and viruses) in the biosphere. Among the many approaches developed for the inference of LGT events from DNA sequence data, methods based on the comparison of phylogenetic trees remain the gold standard for many types of problem. Identifying LGT events from sequenced genomes typically involves a series of steps in which homologous sequences are identified and aligned, phylogenetic trees are inferred, and their topologies are compared to identify unexpected or conflicting relationships. These types of approach have been used to elucidate the nature and extent of LGT and its physiological and ecological consequences throughout the Tree of Life. Advances in DNA sequencing technology have led to enormous increases in the number of sequenced genomes, including ultra-deep sampling of specific taxonomic groups and single cell-based sequencing of unculturable "microbial dark matter." Environmental shotgun sequencing enables the study of LGT among organisms that share the same habitat.This abundance of genomic data offers new opportunities for scientific discovery, but poses two key problems. As ever more genomes are generated, the assembly and annotation of each individual genome receives less scrutiny; and with so many genomes available it is tempting to include them all in a single analysis, but thousands of genomes and millions of genes can overwhelm key algorithms in the analysis pipeline. Identifying LGT events of interest therefore depends on choosing the right dataset, and on algorithms that appropriately balance speed and accuracy given the size and composition of the chosen set of genomes.
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Affiliation(s)
- Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert G Beiko
- Faculty of Computer Science, Dalhousie University, Halifax, NS, B3H 4R2, Canada
| | - Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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25
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Abstract
The history of particular genes and that of the species that carry them can be different for a variety of reasons. In particular, gene trees and species trees can differ due to well-known evolutionary processes such as gene duplication and loss, lateral gene transfer, or incomplete lineage sorting. Species tree reconstruction methods have been developed to take this incongruence into account; these can be divided grossly into supertree and supermatrix approaches. Here we introduce a new Bayesian hierarchical model that we have recently developed and implemented in the program guenomu. The new model considers multiple sources of gene tree/species tree disagreement. Guenomu takes as input posterior distributions of unrooted gene tree topologies for multiple gene families, in order to estimate the posterior distribution of rooted species tree topologies.
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Affiliation(s)
- Leonardo de Oliveira Martins
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain.
- Department of Materials, Imperial College London, London, UK.
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
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26
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Fleischauer M, Böcker S. Collecting reliable clades using the Greedy Strict Consensus Merger. PeerJ 2016; 4:e2172. [PMID: 27375971 PMCID: PMC4928488 DOI: 10.7717/peerj.2172] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 06/03/2016] [Indexed: 12/02/2022] Open
Abstract
Supertree methods combine a set of phylogenetic trees into a single supertree. Similar to supermatrix methods, these methods provide a way to reconstruct larger parts of the Tree of Life, potentially evading the computational complexity of phylogenetic inference methods such as maximum likelihood. The supertree problem can be formalized in different ways, to cope with contradictory information in the input. Many supertree methods have been developed. Some of them solve NP-hard optimization problems like the well-known Matrix Representation with Parsimony, while others have polynomial worst-case running time but work in a greedy fashion (FlipCut). Both can profit from a set of clades that are already known to be part of the supertree. The Superfine approach shows how the Greedy Strict Consensus Merger (GSCM) can be used as preprocessing to find these clades. We introduce different scoring functions for the GSCM, a randomization, as well as a combination thereof to improve the GSCM to find more clades. This helps, in turn, to improve the resolution of the GSCM supertree. We find this modifications to increase the number of true positive clades by 18% compared to the currently used Overlap scoring.
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Affiliation(s)
- Markus Fleischauer
- Lehrstuhl für Bioinformatik, Friedrich-Schiller Universität , Jena , Thüringen , Germany
| | - Sebastian Böcker
- Lehrstuhl für Bioinformatik, Friedrich-Schiller Universität , Jena , Thüringen , Germany
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27
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De Oliveira Martins L, Mallo D, Posada D. A Bayesian Supertree Model for Genome-Wide Species Tree Reconstruction. Syst Biol 2016; 65:397-416. [PMID: 25281847 PMCID: PMC4851173 DOI: 10.1093/sysbio/syu082] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Accepted: 09/30/2014] [Indexed: 11/16/2022] Open
Abstract
Current phylogenomic data sets highlight the need for species tree methods able to deal with several sources of gene tree/species tree incongruence. At the same time, we need to make most use of all available data. Most species tree methods deal with single processes of phylogenetic discordance, namely, gene duplication and loss, incomplete lineage sorting (ILS) or horizontal gene transfer. In this manuscript, we address the problem of species tree inference from multilocus, genome-wide data sets regardless of the presence of gene duplication and loss and ILS therefore without the need to identify orthologs or to use a single individual per species. We do this by extending the idea of Maximum Likelihood (ML) supertrees to a hierarchical Bayesian model where several sources of gene tree/species tree disagreement can be accounted for in a modular manner. We implemented this model in a computer program called guenomu whose inputs are posterior distributions of unrooted gene tree topologies for multiple gene families, and whose output is the posterior distribution of rooted species tree topologies. We conducted extensive simulations to evaluate the performance of our approach in comparison with other species tree approaches able to deal with more than one leaf from the same species. Our method ranked best under simulated data sets, in spite of ignoring branch lengths, and performed well on empirical data, as well as being fast enough to analyze relatively large data sets. Our Bayesian supertree method was also very successful in obtaining better estimates of gene trees, by reducing the uncertainty in their distributions. In addition, our results show that under complex simulation scenarios, gene tree parsimony is also a competitive approach once we consider its speed, in contrast to more sophisticated models.
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Affiliation(s)
| | - Diego Mallo
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
| | - David Posada
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, 36310, Spain
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Dornas FP, Assis FL, Aherfi S, Arantes T, Abrahão JS, Colson P, La Scola B. A Brazilian Marseillevirus Is the Founding Member of a Lineage in Family Marseilleviridae. Viruses 2016; 8:76. [PMID: 26978387 PMCID: PMC4810266 DOI: 10.3390/v8030076] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 02/22/2016] [Accepted: 02/29/2016] [Indexed: 02/07/2023] Open
Abstract
In 2003, Acanthamoeba polyphaga mimivirus (APMV) was discovered as parasitizing Acanthamoeba. It was revealed to exhibit remarkable features, especially odd genomic characteristics, and founded viral family Mimiviridae. Subsequently, a second family of giant amoebal viruses was described, Marseilleviridae, whose prototype member is Marseillevirus, discovered in 2009. Currently, the genomes of seven different members of this family have been fully sequenced. Previous phylogenetic analysis suggested the existence of three Marseilleviridae lineages: A, B and C. Here, we describe a new member of this family, Brazilian Marseillevirus (BrMV), which was isolated from a Brazilian sample and whose genome was fully sequenced and analyzed. Surprisingly, data from phylogenetic analyses and comparative genomics, including mean amino acid identity between BrMV and other Marseilleviridae members and the analyses of the core genome and pan-genome of marseilleviruses, indicated that this virus can be assigned to a new Marseilleviridae lineage. Even if the BrMV genome is one of the smallest among Marseilleviridae members, it harbors the second largest gene content into this family. In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae.
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Affiliation(s)
- Fábio P Dornas
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
| | - Felipe L Assis
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
| | - Sarah Aherfi
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille 13385, France.
- Fondation Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Centre Hospitalo-Universitaire Timone, Fédération de Bactériologie-Hygiène-Virologie, 264 rue Saint-Pierre, Marseille 13385, France.
| | - Thalita Arantes
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
| | - Jônatas S Abrahão
- Laboratório de Vírus, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais 31270-901, Brazil.
| | - Philippe Colson
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille 13385, France.
- Fondation Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Centre Hospitalo-Universitaire Timone, Fédération de Bactériologie-Hygiène-Virologie, 264 rue Saint-Pierre, Marseille 13385, France.
| | - Bernard La Scola
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Aix-Marseille Univ., 27 boulevard Jean Moulin, Faculté de Médecine, Marseille 13385, France.
- Fondation Institut Hospitalo-Universitaire (IHU) Méditerranée Infection, Assistance Publique-Hôpitaux de Marseille, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Centre Hospitalo-Universitaire Timone, Fédération de Bactériologie-Hygiène-Virologie, 264 rue Saint-Pierre, Marseille 13385, France.
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29
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El Karkouri K, Pontarotti P, Raoult D, Fournier PE. Origin and Evolution of Rickettsial Plasmids. PLoS One 2016; 11:e0147492. [PMID: 26866478 PMCID: PMC4750851 DOI: 10.1371/journal.pone.0147492] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/05/2016] [Indexed: 11/21/2022] Open
Abstract
Background Rickettsia species are strictly intracellular bacteria that have undergone a reductive genomic evolution. Despite their allopatric lifestyle, almost half of the 26 currently validated Rickettsia species have plasmids. In order to study the origin, evolutionary history and putative roles of rickettsial plasmids, we investigated the evolutionary processes that have shaped 20 plasmids belonging to 11 species, using comparative genomics and phylogenetic analysis between rickettsial, microbial and non-microbial genomes. Results Plasmids were differentially present among Rickettsia species. The 11 species had 1 to 4 plasmid (s) with a size ranging from 12 kb to 83 kb. We reconstructed pRICO, the last common ancestor of the current rickettsial plasmids. pRICO was vertically inherited mainly from Rickettsia/Orientia chromosomes and diverged vertically into a single or multiple plasmid(s) in each species. These plasmids also underwent a reductive evolution by progressive gene loss, similar to that observed in rickettsial chromosomes, possibly leading to cryptic plasmids or complete plasmid loss. Moreover, rickettsial plasmids exhibited ORFans, recent gene duplications and evidence of horizontal gene transfer events with rickettsial and non-rickettsial genomes mainly from the α/γ-proteobacteria lineages. Genes related to maintenance and plasticity of plasmids, and to adaptation and resistance to stress mostly evolved under vertical and/or horizontal processes. Those involved in nucleotide/carbohydrate transport and metabolism were under the influence of vertical evolution only, whereas genes involved in cell wall/membrane/envelope biogenesis, cycle control, amino acid/lipid/coenzyme and secondary metabolites biosynthesis, transport and metabolism underwent mainly horizontal transfer events. Conclusion Rickettsial plasmids had a complex evolution, starting with a vertical inheritance followed by a reductive evolution associated with increased complexity via horizontal gene transfer as well as gene duplication and genesis. The plasmids are plastic and mosaic structures that may play biological roles similar to or distinct from their co-residing chromosomes in an obligate intracellular lifestyle.
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Affiliation(s)
- Khalid El Karkouri
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Pierre Pontarotti
- Aix Marseille Université, CNRS, Centrale Marseille, I2M UMR 7373, Equipe Evolution Biologique et Modélisation, Marseille, France
| | - Didier Raoult
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille cedex 5, France
| | - Pierre-Edouard Fournier
- Unité de Recherche en Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS7278, IRD198, INSERMU1095, Institut Hospitalo-Universitaire Méditerranée-Infection, Aix-Marseille Université, Faculté de Médecine, 27 boulevard Jean Moulin, 13385 Marseille cedex 5, France
- * E-mail:
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Goloboff PA, Szumik CA. Problems with supertrees based on the subtree prune-and-regraft distance, with comments on majority rule supertrees. Cladistics 2016; 32:82-89. [PMID: 34732022 DOI: 10.1111/cla.12111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2014] [Indexed: 11/26/2022] Open
Abstract
This paper examines a recent proposal to calculate supertrees by minimizing the sum of subtree prune-and-regraft distances to the input trees. The supertrees thus calculated may display groups present in a minority of the input trees but contradicted by the majority, or groups that are not supported by any input tree or combination of input trees. The proponents of the method themselves stated that these are serious problems of "matrix representation with parsimony", but they can in fact occur in their own method. The majority rule supertrees, being explicitly clade-based, cannot have these problems, and seem much more suited to retrieving common clades from a set of trees with different taxon sets. However, it is dubious that so-called majority rule supertrees can always be interpreted as displaying those clades present (or compatible with) with a majority of the trees. The majority rule consensus is always a median tree, in terms of the Robinson-Foulds distances (i.e. it minimizes the sum of Robinson-Foulds distances to the input trees). In contrast, majority rule supertrees may not be median-different, contradictory trees may minimize Robinson-Foulds distances, while their strict consensus does not. If being "majority" results from being median in Robinson-Foulds distances, this means that in the supertree setting a "majority" is ambiguously defined, sometimes achievable only by mutually contradictory trees.
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Affiliation(s)
- Pablo A Goloboff
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Miguel Lillo 251, 4000, S.M. de Tucumán, Argentina
| | - Claudia A Szumik
- Unidad Ejecutora Lillo, Consejo Nacional de Investigaciones Científicas y Técnicas, Miguel Lillo 251, 4000, S.M. de Tucumán, Argentina
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Hall M, Woolhouse M, Rambaut A. Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set. PLoS Comput Biol 2015; 11:e1004613. [PMID: 26717515 PMCID: PMC4701012 DOI: 10.1371/journal.pcbi.1004613] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 10/17/2015] [Indexed: 12/14/2022] Open
Abstract
The use of genetic data to reconstruct the transmission tree of infectious disease epidemics and outbreaks has been the subject of an increasing number of studies, but previous approaches have usually either made assumptions that are not fully compatible with phylogenetic inference, or, where they have based inference on a phylogeny, have employed a procedure that requires this tree to be fixed. At the same time, the coalescent-based models of the pathogen population that are employed in the methods usually used for time-resolved phylogeny reconstruction are a considerable simplification of epidemic process, as they assume that pathogen lineages mix freely. Here, we contribute a new method that is simultaneously a phylogeny reconstruction method for isolates taken from an epidemic, and a procedure for transmission tree reconstruction. We observe that, if one or more samples is taken from each host in an epidemic or outbreak and these are used to build a phylogeny, a transmission tree is equivalent to a partition of the set of nodes of this phylogeny, such that each partition element is a set of nodes that is connected in the full tree and contains all the tips corresponding to samples taken from one and only one host. We then implement a Monte Carlo Markov Chain (MCMC) procedure for simultaneous sampling from the spaces of both trees, utilising a newly-designed set of phylogenetic tree proposals that also respect node partitions. We calculate the posterior probability of these partitioned trees based on a model that acknowledges the population structure of an epidemic by employing an individual-based disease transmission model and a coalescent process taking place within each host. We demonstrate our method, first using simulated data, and then with sequences taken from the H7N7 avian influenza outbreak that occurred in the Netherlands in 2003. We show that it is superior to established coalescent methods for reconstructing the topology and node heights of the phylogeny and performs well for transmission tree reconstruction when the phylogeny is well-resolved by the genetic data, but caution that this will often not be the case in practice and that existing genetic and epidemiological data should be used to configure such analyses whenever possible. This method is available for use by the research community as part of BEAST, one of the most widely-used packages for reconstruction of dated phylogenies. With sequence data becoming available in increasing high volumes and at decreasing costs, there has been substantial recent interest in the possibility of using pathogen genome sequences as a means to retrace the spread of disease amongst the infected hosts in an epidemic. While several such methods exist, many of them are not fully compatible with phylogenetic inference, which is the most commonly-used methodology for exploring the ancestry of the isolates represented by a set of sequences. Procedures using phylogenetics as a basis have either taken a single, fixed phylogenetic tree as input, or have been quite narrow in scope and not available in any current package for general use. For their part, standard phylogenetic methods usually assume a model of the pathogen population that is overly simplistic for the situation in an epidemic. Here, we bridge the gap by introducing a new, highly flexible method, implemented in the publicly-available BEAST package, which simultaneously reconstructs the transmission history of an epidemic and the phylogeny for samples taken from it. We apply the procedure to simulated data and to sequences from the 2003 H7N7 avian influenza outbreak in the Netherlands.
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Affiliation(s)
- Matthew Hall
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Mark Woolhouse
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, United Kingdom
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
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Abstract
Horizontal or Lateral Gene Transfer (HGT or LGT) is the transmission of portions of genomic DNA between organisms through a process decoupled from vertical inheritance. In the presence of HGT events, different fragments of the genome are the result of different evolutionary histories. This can therefore complicate the investigations of evolutionary relatedness of lineages and species. Also, as HGT can bring into genomes radically different genotypes from distant lineages, or even new genes bearing new functions, it is a major source of phenotypic innovation and a mechanism of niche adaptation. For example, of particular relevance to human health is the lateral transfer of antibiotic resistance and pathogenicity determinants, leading to the emergence of pathogenic lineages. Computational identification of HGT events relies upon the investigation of sequence composition or evolutionary history of genes. Sequence composition-based ("parametric") methods search for deviations from the genomic average, whereas evolutionary history-based ("phylogenetic") approaches identify genes whose evolutionary history significantly differs from that of the host species. The evaluation and benchmarking of HGT inference methods typically rely upon simulated genomes, for which the true history is known. On real data, different methods tend to infer different HGT events, and as a result it can be difficult to ascertain all but simple and clear-cut HGT events.
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Affiliation(s)
| | - Nives Škunca
- ETH Zurich, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Zurich, Switzerland
| | | | - Christophe Dessimoz
- University College London, London, United Kingdom
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Gagliano M, Braguglia C, Petruccioli M, Rossetti S. Ecology and biotechnological potential of the thermophilic fermentative Coprothermobacter spp. FEMS Microbiol Ecol 2015; 91:fiv018. [DOI: 10.1093/femsec/fiv018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2015] [Indexed: 12/29/2022] Open
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Whidden C, Matsen FA. Quantifying MCMC exploration of phylogenetic tree space. Syst Biol 2015; 64:472-91. [PMID: 25631175 PMCID: PMC4395846 DOI: 10.1093/sysbio/syv006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 01/20/2015] [Indexed: 11/30/2022] Open
Abstract
In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this article, we investigate this problem on phylogenetic tree topologies with a metric that is especially well suited to the task: the subtree prune-and-regraft (SPR) metric. This metric directly corresponds to the minimum number of MCMC rearrangements required to move between trees in common phylogenetic MCMC implementations. We develop a novel graph-based approach to analyze tree posteriors and find that the SPR metric is much more informative than simpler metrics that are unrelated to MCMC moves. In doing so, we show conclusively that topological peaks do occur in Bayesian phylogenetic posteriors from real data sets as sampled with standard MCMC approaches, investigate the efficiency of Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks, and show that conditional clade distribution (CCD) can have systematic problems when there are multiple peaks.
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Affiliation(s)
- Chris Whidden
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Frederick A Matsen
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Chaudhary R, Fernández-Baca D, Burleigh JG. MulRF: a software package for phylogenetic analysis using multi-copy gene trees. Bioinformatics 2014; 31:432-3. [DOI: 10.1093/bioinformatics/btu648] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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