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Zhang R, Drummond A. Improving the performance of Bayesian phylogenetic inference under relaxed clock models. BMC Evol Biol 2020; 20:54. [PMID: 32410614 PMCID: PMC7222466 DOI: 10.1186/s12862-020-01609-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/01/2020] [Indexed: 11/27/2022] Open
Abstract
Background Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms. Results This paper develops a new algorithm to improve the efficiency of Bayesian phylogenetic inference for models that include a per-branch rate parameter. In a Markov chain Monte Carlo algorithm, the presented proposal kernel changes evolutionary rates and divergence times at the same time, under the constraint that the implied genetic distances remain constant. Specifically, the proposal operates on the divergence time of an internal node and the three adjacent branch rates. For the root of a phylogenetic tree, there are three strategies discussed, named Simple Distance, Small Pulley and Big Pulley. Note that Big Pulley is able to change the tree topology, which enables the operator to sample all the possible rooted trees consistent with the implied unrooted tree. To validate its effectiveness, a series of experiments have been performed by implementing the proposed operator in the BEAST2 software. Conclusions The results demonstrate that the proposed operator is able to improve the performance by giving better estimates for a given chain length and by using less running time for a given level of accuracy. Measured by effective samples per hour, use of the proposed operator results in overall mixing more efficient than the current operators in BEAST2. Especially for large data sets, the improvement is up to half an order of magnitude.
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Affiliation(s)
- Rong Zhang
- School of Computer Science, University of Auckland, Auckland, New Zealand.
| | - Alexei Drummond
- School of Computer Science, University of Auckland, Auckland, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
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2
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Anderson PSL, Rivera MD, Suarez AV. "Simple" Biomechanical Model for Ants Reveals How Correlated Evolution among Body Segments Minimizes Variation in Center of Mass as Heads Get Larger. Integr Comp Biol 2020; 60:1193-1207. [PMID: 32386301 DOI: 10.1093/icb/icaa027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The field of comparative biomechanics strives to understand the diversity of the biological world through the lens of physics. To accomplish this, researchers apply a variety of modeling approaches to explore the evolution of form and function ranging from basic lever models to intricate computer simulations. While advances in technology have allowed for increasing model complexity, insight can still be gained through the use of low-parameter "simple" models. All models, regardless of complexity, are simplifications of reality and must make assumptions; "simple" models just make more assumptions than complex ones. However, "simple" models have several advantages. They allow individual parameters to be isolated and tested systematically, can be made applicable to a wide range of organisms and make good starting points for comparative studies, allowing for complexity to be added as needed. To illustrate these ideas, we perform a case study on body form and center of mass stability in ants. Ants show a wide diversity of body forms, particularly in terms of the relative size of the head, petiole(s), and gaster (the latter two make-up the segments of the abdomen not fused to thorax in hymenopterans). We use a "simple" model to explore whether balance issues pertaining to the center of mass influence patterns of segment expansion across major ant clades. Results from phylogenetic comparative methods imply that the location of the center of mass in an ant's body is under stabilizing selection, constraining the center of mass to the middle segment (thorax) over the legs. This is potentially maintained by correlated rates of evolution between the head and gaster on either end. While these patterns arise from a model that makes several assumptions/simplifications relating to shape and materials, they still offer intriguing insights into the body plan of ants across ∼68% of their diversity. The results from our case study illustrate how "simple," low-parameter models both highlight fundamental biomechanical trends and aid in crystalizing specific questions and hypotheses for more complex models to address.
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Affiliation(s)
- Philip S L Anderson
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana-Champaign, IL, USA.,Beckman Institute for Science and Technology, University of Illinois, Urbana-Champaign, IL, USA
| | - Michael D Rivera
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Andrew V Suarez
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana-Champaign, IL, USA.,Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana-Champaign, IL, USA.,Beckman Institute for Science and Technology, University of Illinois, Urbana-Champaign, IL, USA.,Department of Entomology, University of Illinois, Urbana-Champaign, IL, USA
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3
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Khan MA, Mahmudi O, Ullah I, Arvestad L, Lagergren J. Probabilistic inference of lateral gene transfer events. BMC Bioinformatics 2016; 17:431. [PMID: 28185583 PMCID: PMC5123345 DOI: 10.1186/s12859-016-1268-2] [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] [Indexed: 12/20/2022] Open
Abstract
Background Lateral gene transfer (LGT) is an evolutionary process that has an important role in biology. It challenges the traditional binary tree-like evolution of species and is attracting increasing attention of the molecular biologists due to its involvement in antibiotic resistance. A number of attempts have been made to model LGT in the presence of gene duplication and loss, but reliably placing LGT events in the species tree has remained a challenge. Results In this paper, we propose probabilistic methods that samples reconciliations of the gene tree with a dated species tree and computes maximum a posteriori probabilities. The MCMC-based method uses the probabilistic model DLTRS, that integrates LGT, gene duplication, gene loss, and sequence evolution under a relaxed molecular clock for substitution rates. We can estimate posterior distributions on gene trees and, in contrast to previous work, the actual placement of potential LGT, which can be used to, e.g., identify “highways” of LGT. Conclusions Based on a simulation study, we conclude that the method is able to infer the true LGT events on gene tree and reconcile it to the correct edges on the species tree in most cases. Applied to two biological datasets, containing gene families from Cyanobacteria and Molicutes, we find potential LGTs highways that corroborate other studies as well as previously undetected examples. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1268-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mehmood Alam Khan
- KTH Royal Institute of Technology, School of Computer Science and Communication, Box 1031, Solna, 171 21, Sweden.,Science for Life Laboratory, Box 1031, Solna, 171 21, Sweden
| | - Owais Mahmudi
- KTH Royal Institute of Technology, School of Computer Science and Communication, Box 1031, Solna, 171 21, Sweden.,Science for Life Laboratory, Box 1031, Solna, 171 21, Sweden
| | - Ikram Ullah
- KTH Royal Institute of Technology, School of Computer Science and Communication, Box 1031, Solna, 171 21, Sweden.,Science for Life Laboratory, Box 1031, Solna, 171 21, Sweden
| | - Lars Arvestad
- Science for Life Laboratory, Box 1031, Solna, 171 21, Sweden.,Stockholm University, Dept. of Numerical Analysis and Computer Science, Box 1031, Solna, 171 21, Sweden.,Swedish e-Science Research Centre, Solna, Sweden
| | - Jens Lagergren
- KTH Royal Institute of Technology, School of Computer Science and Communication, Box 1031, Solna, 171 21, Sweden. .,Science for Life Laboratory, Box 1031, Solna, 171 21, Sweden.
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4
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Volkova VV, KuKanich B, Riviere JE. Exploring Post-Treatment Reversion of Antimicrobial Resistance in Enteric Bacteria of Food Animals as a Resistance Mitigation Strategy. Foodborne Pathog Dis 2016; 13:610-617. [DOI: 10.1089/fpd.2016.2152] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- Victoriya V. Volkova
- Department of Diagnostic Medicine/Pathobiology, Institute of Computational Comparative Medicine, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Butch KuKanich
- Department of Anatomy and Physiology, Institute of Computational Comparative Medicine, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
| | - Jim E. Riviere
- Department of Anatomy and Physiology, Institute of Computational Comparative Medicine, College of Veterinary Medicine, Kansas State University, Manhattan, Kansas
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5
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Inferring gene duplications, transfers and losses can be done in a discrete framework. J Math Biol 2015; 72:1811-44. [PMID: 26337177 DOI: 10.1007/s00285-015-0930-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 05/20/2015] [Indexed: 10/23/2022]
Abstract
In the field of phylogenetics, the evolutionary history of a set of organisms is commonly depicted by a species tree-whose internal nodes represent speciation events-while the evolutionary history of a gene family is depicted by a gene tree-whose internal nodes can also represent macro-evolutionary events such as gene duplications and transfers. As speciation events are only part of the events shaping a gene history, the topology of a gene tree can show incongruences with that of the corresponding species tree. These incongruences can be used to infer the macro-evolutionary events undergone by the gene family. This is done by embedding the gene tree inside the species tree and hence providing a reconciliation of those trees. In the past decade, several parsimony-based methods have been developed to infer such reconciliations, accounting for gene duplications ([Formula: see text]), transfers ([Formula: see text]) and losses ([Formula: see text]). The main contribution of this paper is to formally prove an important assumption implicitly made by previous works on these reconciliations, namely that solving the (maximum) parsimony [Formula: see text] reconciliation problem in the discrete framework is equivalent to finding a most parsimonious [Formula: see text] scenario in the continuous framework. In the process, we also prove several intermediate results that are useful on their own and constitute a theoretical toolbox that will likely facilitate future theoretical contributions in the field.
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6
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Abstract
Motivation: Traditionally, gene phylogenies have been reconstructed solely on the basis of molecular sequences; this, however, often does not provide enough information to distinguish between statistically equivalent relationships. To address this problem, several recent methods have incorporated information on the species phylogeny in gene tree reconstruction, leading to dramatic improvements in accuracy. Although probabilistic methods are able to estimate all model parameters but are computationally expensive, parsimony methods—generally computationally more efficient—require a prior estimate of parameters and of the statistical support. Results: Here, we present the Tree Estimation using Reconciliation (TERA) algorithm, a parsimony based, species tree aware method for gene tree reconstruction based on a scoring scheme combining duplication, transfer and loss costs with an estimate of the sequence likelihood. TERA explores all reconciled gene trees that can be amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate that TERA achieves the same accuracy as the corresponding probabilistic method while being faster, and outperforms other parsimony-based methods in both accuracy and speed. Running TERA on a set of 1099 homologous gene families from complete cyanobacterial genomes, we find that incorporating knowledge of the species tree results in a two thirds reduction in the number of apparent transfer events. Availability and implementation: The algorithm is implemented in our program TERA, which is freely available from http://mbb.univ-montp2.fr/MBB/download_sources/16__TERA. Contact:celine.scornavacca@univ-montp2.fr, ssolo@angel.elte.hu Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Celine Scornavacca
- ISEM, UM2-CNRS-IRD, Place Eugène Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galéra, 34095 Montpellier, France and ELTE-MTA 'Lendület' Biophysics Research Group 1117 Bp., Pázmány P. stny. 1A., Budapest, Hungary ISEM, UM2-CNRS-IRD, Place Eugène Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galéra, 34095 Montpellier, France and ELTE-MTA 'Lendület' Biophysics Research Group 1117 Bp., Pázmány P. stny. 1A., Budapest, Hungary
| | - Edwin Jacox
- ISEM, UM2-CNRS-IRD, Place Eugène Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galéra, 34095 Montpellier, France and ELTE-MTA 'Lendület' Biophysics Research Group 1117 Bp., Pázmány P. stny. 1A., Budapest, Hungary
| | - Gergely J Szöllősi
- ISEM, UM2-CNRS-IRD, Place Eugène Bataillon 34095 Montpellier, France, Institut de Biologie Computationnelle (IBC), 95 rue de la Galéra, 34095 Montpellier, France and ELTE-MTA 'Lendület' Biophysics Research Group 1117 Bp., Pázmány P. stny. 1A., Budapest, Hungary
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7
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Abstract
This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.
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Affiliation(s)
- Gergely J Szöllősi
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Eric Tannier
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Vincent Daubin
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Bastien Boussau
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France;
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8
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Fontanez KM, Cavanaugh CM. Evidence for horizontal transmission from multilocus phylogeny of deep-sea mussel (Mytilidae) symbionts. Environ Microbiol 2014; 16:3608-21. [DOI: 10.1111/1462-2920.12379] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 12/22/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Kristina M. Fontanez
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
| | - Colleen M. Cavanaugh
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge MA 02138 USA
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9
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Sjostrand J, Tofigh A, Daubin V, Arvestad L, Sennblad B, Lagergren J. A Bayesian Method for Analyzing Lateral Gene Transfer. Syst Biol 2014; 63:409-20. [DOI: 10.1093/sysbio/syu007] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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10
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Sand A, Steel M. The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees. J Theor Biol 2013; 335:295-8. [PMID: 23859822 DOI: 10.1016/j.jtbi.2013.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/21/2013] [Accepted: 07/04/2013] [Indexed: 10/26/2022]
Abstract
Evolutionary events such as incomplete lineage sorting and lateral gene transfers constitute major problems for inferring species trees from gene trees, as they can sometimes lead to gene trees which conflict with the underlying species tree. One particularly simple and efficient way to infer species trees from gene trees under such conditions is to combine three-taxon analyses for several genes using a majority vote approach. For incomplete lineage sorting this method is known to be statistically consistent; however, for lateral gene transfers it was recently shown that a zone of inconsistency exists for a specific four-taxon tree topology, and it was posed as an open question whether inconsistencies could exist for other four-taxon tree topologies? In this letter we analyze all remaining four-taxon topologies and show that no other inconsistencies exist.
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11
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Roch S, Snir S. Recovering the treelike trend of evolution despite extensive lateral genetic transfer: a probabilistic analysis. J Comput Biol 2013; 20:93-112. [PMID: 23383996 DOI: 10.1089/cmb.2012.0234] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lateral gene transfer (LGT) is a common mechanism of nonvertical evolution, during which genetic material is transferred between two more or less distantly related organisms. It is particularly common in bacteria where it contributes to adaptive evolution with important medical implications. In evolutionary studies, LGT has been shown to create widespread discordance between gene trees as genomes become mosaics of gene histories. In particular, the Tree of Life has been questioned as an appropriate representation of bacterial evolutionary history. Nevertheless a common hypothesis is that prokaryotic evolution is primarily treelike, but that the underlying trend is obscured by LGT. Extensive empirical work has sought to extract a common treelike signal from conflicting gene trees. Here we give a probabilistic perspective on the problem of recovering the treelike trend despite LGT. Under a model of randomly distributed LGT, we show that the species phylogeny can be reconstructed even in the presence of surprisingly many (almost linear number of) LGT events per gene tree. Our results, which are optimal up to logarithmic factors, are based on the analysis of a robust, computationally efficient reconstruction method and provides insight into the design of such methods. Finally, we show that our results have implications for the discovery of highways of gene sharing.
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Affiliation(s)
- Sebastien Roch
- Department of Mathematics and Bioinformatics Program, University of California at Los Angeles, Los Angeles, CA, USA.
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12
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Steel M, Linz S, Huson DH, Sanderson MJ. Identifying a species tree subject to random lateral gene transfer. J Theor Biol 2013; 322:81-93. [DOI: 10.1016/j.jtbi.2013.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 01/09/2013] [Accepted: 01/10/2013] [Indexed: 11/26/2022]
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13
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Bremner P, Liu Y, Samie M, Dragffy G, Pipe AG, Tempesti G, Timmis J, Tyrrell AM. SABRE: a bio-inspired fault-tolerant electronic architecture. BIOINSPIRATION & BIOMIMETICS 2013; 8:016003. [PMID: 23302298 DOI: 10.1088/1748-3182/8/1/016003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
As electronic devices become increasingly complex, ensuring their reliable, fault-free operation is becoming correspondingly more challenging. It can be observed that, in spite of their complexity, biological systems are highly reliable and fault tolerant. Hence, we are motivated to take inspiration for biological systems in the design of electronic ones. In SABRE (self-healing cellular architectures for biologically inspired highly reliable electronic systems), we have designed a bio-inspired fault-tolerant hierarchical architecture for this purpose. As in biology, the foundation for the whole system is cellular in nature, with each cell able to detect faults in its operation and trigger intra-cellular or extra-cellular repair as required. At the next level in the hierarchy, arrays of cells are configured and controlled as function units in a transport triggered architecture (TTA), which is able to perform partial-dynamic reconfiguration to rectify problems that cannot be solved at the cellular level. Each TTA is, in turn, part of a larger multi-processor system which employs coarser grain reconfiguration to tolerate faults that cause a processor to fail. In this paper, we describe the details of operation of each layer of the SABRE hierarchy, and how these layers interact to provide a high systemic level of fault tolerance.
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Affiliation(s)
- P Bremner
- Bristol Robotics Laboratory, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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14
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Affiliation(s)
- David P. Mindell
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA 94158, USA
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15
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Evolution of multicellularity coincided with increased diversification of cyanobacteria and the Great Oxidation Event. Proc Natl Acad Sci U S A 2013; 110:1791-6. [PMID: 23319632 DOI: 10.1073/pnas.1209927110] [Citation(s) in RCA: 180] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cyanobacteria are among the most diverse prokaryotic phyla, with morphotypes ranging from unicellular to multicellular filamentous forms, including those able to terminally (i.e., irreversibly) differentiate in form and function. It has been suggested that cyanobacteria raised oxygen levels in the atmosphere around 2.45-2.32 billion y ago during the Great Oxidation Event (GOE), hence dramatically changing life on the planet. However, little is known about the temporal evolution of cyanobacterial lineages, and possible interplay between the origin of multicellularity, diversification of cyanobacteria, and the rise of atmospheric oxygen. We estimated divergence times of extant cyanobacterial lineages under Bayesian relaxed clocks for a dataset of 16S rRNA sequences representing the entire known diversity of this phylum. We tested whether the evolution of multicellularity overlaps with the GOE, and whether multicellularity is associated with significant shifts in diversification rates in cyanobacteria. Our results indicate an origin of cyanobacteria before the rise of atmospheric oxygen. The evolution of multicellular forms coincides with the onset of the GOE and an increase in diversification rates. These results suggest that multicellularity could have played a key role in triggering cyanobacterial evolution around the GOE.
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16
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de Vienne DM, Ollier S, Aguileta G. Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Mol Biol Evol 2012; 29:1587-98. [PMID: 22319162 DOI: 10.1093/molbev/msr317] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Full genome data sets are currently being explored on a regular basis to infer phylogenetic trees, but there are often discordances among the trees produced by different genes. An important goal in phylogenomics is to identify which individual gene and species produce the same phylogenetic tree and are thus likely to share the same evolutionary history. On the other hand, it is also essential to identify which genes and species produce discordant topologies and therefore evolve in a different way or represent noise in the data. The latter are outlier genes or species and they can provide a wealth of information on potentially interesting biological processes, such as incomplete lineage sorting, hybridization, and horizontal gene transfers. Here, we propose a new method to explore the genomic tree space and detect outlier genes and species based on multiple co-inertia analysis (MCOA), which efficiently captures and compares the similarities in the phylogenetic topologies produced by individual genes. Our method allows the rapid identification of outlier genes and species by extracting the similarities and discrepancies, in terms of the pairwise distances, between all the species in all the trees, simultaneously. This is achieved by using MCOA, which finds successive decomposition axes from individual ordinations (i.e., derived from distance matrices) that maximize a covariance function. The method is freely available as a set of R functions. The source code and tutorial can be found online at http://phylomcoa.cgenomics.org.
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Affiliation(s)
- Damien M de Vienne
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG) and UPF, Barcelona, Spain.
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17
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Abstract
Large-scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of life. Here, we discuss the approaches of increasing complexity aimed at extracting information on the pattern and process of gene family evolution from such datasets. In particular, we consider the models that invoke processes of gene birth (duplication and transfer) and death (loss) to explain the evolution of gene families. First, we review birth-and-death models of family size evolution and their implications in light of the universal features of family size distribution observed across different species and the three domains of life. Subsequently, we proceed to recent developments on models capable of more completely considering information in the sequences of homologous gene families through the probabilistic reconciliation of the phylogenetic histories of individual genes with the phylogenetic history of the genomes in which they have resided. To illustrate the methods and results presented, we use data from the HOGENOM database, demonstrating that the distribution of homologous gene family sizes in the genomes of the eukaryota, archaea, and bacteria exhibits remarkably similar shapes. We show that these distributions are best described by models of gene family size evolution, where for individual genes the death (loss) rate is larger than the birth (duplication and transfer) rate but new families are continually supplied to the genome by a process of origination. Finally, we use probabilistic reconciliation methods to take into consideration additional information from gene phylogenies, and find that, for prokaryotes, the majority of birth events are the result of transfer.
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Anderson CNK, Liu L, Pearl D, Edwards SV. Tangled trees: the challenge of inferring species trees from coalescent and noncoalescent genes. Methods Mol Biol 2012; 856:3-28. [PMID: 22399453 DOI: 10.1007/978-1-61779-585-5_1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Phylogenies based on different genes can produce conflicting phylogenies; methods that resolve such ambiguities are becoming more popular, and offer a number of advantages for phylogenetic analysis. We review so-called species tree methods and the biological forces that can undermine them by violating important aspects of the underlying models. Such forces include horizontal gene transfer, gene duplication, and natural selection. We review ways of detecting loci influenced by such forces and offer suggestions for identifying or accommodating them. The way forward involves identifying outlier loci, as is done in population genetic analysis of neutral and selected loci, and removing them from further analysis, or developing more complex species tree models that can accommodate such loci.
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Affiliation(s)
- Christian N K Anderson
- Department of Organismic and Evolutionary Biology & Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
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19
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Leigh JW, Lapointe FJ, Lopez P, Bapteste E. Evaluating phylogenetic congruence in the post-genomic era. Genome Biol Evol 2011; 3:571-87. [PMID: 21712432 PMCID: PMC3156567 DOI: 10.1093/gbe/evr050] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2011] [Indexed: 12/04/2022] Open
Abstract
Congruence is a broadly applied notion in evolutionary biology used to justify multigene phylogeny or phylogenomics, as well as in studies of coevolution, lateral gene transfer, and as evidence for common descent. Existing methods for identifying incongruence or heterogeneity using character data were designed for data sets that are both small and expected to be rarely incongruent. At the same time, methods that assess incongruence using comparison of trees test a null hypothesis of uncorrelated tree structures, which may be inappropriate for phylogenomic studies. As such, they are ill-suited for the growing number of available genome sequences, most of which are from prokaryotes and viruses, either for phylogenomic analysis or for studies of the evolutionary forces and events that have shaped these genomes. Specifically, many existing methods scale poorly with large numbers of genes, cannot accommodate high levels of incongruence, and do not adequately model patterns of missing taxa for different markers. We propose the development of novel incongruence assessment methods suitable for the analysis of the molecular evolution of the vast majority of life and support the investigation of homogeneity of evolutionary process in cases where markers do not share identical tree structures.
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Affiliation(s)
- Jessica W Leigh
- Department of Mathematics and Statistics, University of Otago, Dunedin, New Zealand.
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20
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Matthews LJ, Tehrani JJ, Jordan FM, Collard M, Nunn CL. Testing for divergent transmission histories among cultural characters: a study using Bayesian phylogenetic methods and Iranian tribal textile data. PLoS One 2011; 6:e14810. [PMID: 21559083 PMCID: PMC3084691 DOI: 10.1371/journal.pone.0014810] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2010] [Accepted: 03/18/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Archaeologists and anthropologists have long recognized that different cultural complexes may have distinct descent histories, but they have lacked analytical techniques capable of easily identifying such incongruence. Here, we show how bayesian phylogenetic analysis can be used to identify incongruent cultural histories. We employ the approach to investigate Iranian tribal textile traditions. METHODS We used bayes factor comparisons in a phylogenetic framework to test two models of cultural evolution: the hierarchically integrated system hypothesis and the multiple coherent units hypothesis. In the hierarchically integrated system hypothesis, a core tradition of characters evolves through descent with modification and characters peripheral to the core are exchanged among contemporaneous populations. In the multiple coherent units hypothesis, a core tradition does not exist. Rather, there are several cultural units consisting of sets of characters that have different histories of descent. RESULTS For the Iranian textiles, the bayesian phylogenetic analyses supported the multiple coherent units hypothesis over the hierarchically integrated system hypothesis. Our analyses suggest that pile-weave designs represent a distinct cultural unit that has a different phylogenetic history compared to other textile characters. CONCLUSIONS The results from the Iranian textiles are consistent with the available ethnographic evidence, which suggests that the commercial rug market has influenced pile-rug designs but not the techniques or designs incorporated in the other textiles produced by the tribes. We anticipate that bayesian phylogenetic tests for inferring cultural units will be of great value for researchers interested in studying the evolution of cultural traits including language, behavior, and material culture.
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Affiliation(s)
- Luke J Matthews
- Department of Human Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America.
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Campbell V, Legendre P, Lapointe FJ. The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis. BMC Evol Biol 2011; 11:64. [PMID: 21388552 PMCID: PMC3065422 DOI: 10.1186/1471-2148-11-64] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 03/09/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices. It has been shown in previous studies to have a correct rate of type I error and good power when applied to dissimilarity matrices and to ultrametric distance matrices. Contrary to most other tests of incongruence used in phylogenetic analysis, the null hypothesis of the CADM test assumes complete incongruence of the phylogenetic trees instead of congruence. In this study, we performed computer simulations to assess the type I error rate and power of the test. It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated trees of varying sizes, and under different evolutionary conditions. RESULTS Our results showed that the test has an accurate type I error rate and good power. As expected, power increased with the number of objects (i.e., taxa), the number of partially or completely congruent matrices and the level of congruence among distance matrices. CONCLUSIONS Based on our results, we suggest that CADM is an excellent candidate to test for congruence and, when present, to estimate its level in phylogenomic studies where numerous genes are analysed simultaneously.
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Affiliation(s)
- Véronique Campbell
- Département de Sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - Pierre Legendre
- Département de Sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
| | - François-Joseph Lapointe
- Département de Sciences biologiques, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, Québec, H3C 3J7, Canada
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22
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Schirrmeister BE, Antonelli A, Bagheri HC. The origin of multicellularity in cyanobacteria. BMC Evol Biol 2011; 11:45. [PMID: 21320320 PMCID: PMC3271361 DOI: 10.1186/1471-2148-11-45] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Accepted: 02/14/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are one of the oldest and morphologically most diverse prokaryotic phyla on our planet. The early development of an oxygen-containing atmosphere approximately 2.45-2.22 billion years ago is attributed to the photosynthetic activity of cyanobacteria. Furthermore, they are one of the few prokaryotic phyla where multicellularity has evolved. Understanding when and how multicellularity evolved in these ancient organisms would provide fundamental information on the early history of life and further our knowledge of complex life forms. RESULTS We conducted and compared phylogenetic analyses of 16S rDNA sequences from a large sample of taxa representing the morphological and genetic diversity of cyanobacteria. We reconstructed ancestral character states on 10,000 phylogenetic trees. The results suggest that the majority of extant cyanobacteria descend from multicellular ancestors. Reversals to unicellularity occurred at least 5 times. Multicellularity was established again at least once within a single-celled clade. Comparison to the fossil record supports an early origin of multicellularity, possibly as early as the "Great Oxygenation Event" that occurred 2.45-2.22 billion years ago. CONCLUSIONS The results indicate that a multicellular morphotype evolved early in the cyanobacterial lineage and was regained at least once after a previous loss. Most of the morphological diversity exhibited in cyanobacteria today--including the majority of single-celled species--arose from ancient multicellular lineages. Multicellularity could have conferred a considerable advantage for exploring new niches and hence facilitated the diversification of new lineages.
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Affiliation(s)
- Bettina E Schirrmeister
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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23
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Gao ZY, Xu H, Chen KJ, Shi DZ, Li LZ, Zhou XZ. [Efficacy evaluation of Shengmai Injection in treating coronary heart disease based on random walk model]. ACTA ACUST UNITED AC 2010; 6:902-6. [PMID: 18782531 DOI: 10.3736/jcim20080905] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE To evaluate the clinical effects of Shengmai Injection in treating coronary heart disease (CHD) based on correct syndrome differentiation and incorrect syndrome differentiation. METHODS The patients' information was collected through a system of individual diagnosis and treatment of CHD. The score of main symptoms was calculated and recorded during the treatment. Patients were divided into two groups (incorrect syndrome and correct syndrome groups) on the basis of syndrome differentiation treatment or not. The clinical therapeutic effects of the two treatments were evaluated based on statistic theory combined with random walk method. RESULTS There were 273 patients in the correct syndrome group and 4 patients died (case-fatality rate was 1.47%). There were 297 patients in the incorrect syndrome group and 7 patients died (case-fatality rate was 2.36%). In the correct syndrome group, random fluctuation peak of comprehensive evaluation index, walk steps, positive growth rate of walk, ratio, random fluctuation power-law, increase rate and record times of comprehensive evaluation index were 1 472, 13 617, 0.108 1, 9.25, 0.674 2, 0.470 6 and 3 128 respectively, while in the incorrect syndrome group, 1 030, 14 588, 0.070 6, 14.16, 0.660 6, 0.312 8 and 3 293 respectively. The random fluctuation power-law in both groups exceeded 0.5. CONCLUSION There is a long-range correlation between the comprehensive evaluation index and therapeutic method as the CHD patients were treated with Shengmai Injection. The clinical therapeutic effects of Shengmai Injection under correct syndrome differentiation are better than the effects of Shengmai Injection under incorrect syndrome differentiation.
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Affiliation(s)
- Zhu-Ye Gao
- Department of Cardiology, Xiyuan Hospital, China Academy of Chinese Medical Sciences, Beijing 100091, China
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Genomes as documents of evolutionary history. Trends Ecol Evol 2010; 25:224-32. [DOI: 10.1016/j.tree.2009.09.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Revised: 09/18/2009] [Accepted: 09/21/2009] [Indexed: 02/02/2023]
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25
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Mann S, Li J, Chen YPP. Insights into bacterial genome composition through variable target GC content profiling. J Comput Biol 2010; 17:79-96. [PMID: 20078399 DOI: 10.1089/cmb.2009.0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This study presents a new computational method for guanine (G) and cytosine (C), or GC, content profiling based on the idea of multiple resolution sampling (MRS). The benefit of our new approach over existing techniques follows from its ability to locate significant regions without prior knowledge of the sequence, nor the features being sought. The use of MRS has provided novel insights into bacterial genome composition. Key findings include those that are related to the core composition of bacterial genomes, to the identification of large genomic islands (in Enterobacterial genomes), and to the identification of surface protein determinants in human pathogenic organisms (e.g., Staphylococcus genomes). We observed that bacterial surface binding proteins maintain abnormal GC content, potentially pointing to a viral origin. This study has demonstrated that GC content holds a high informational worth and hints at many underlying evolutionary processes. For online Supplementary Material, see www.liebertonline.com .
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Affiliation(s)
- Scott Mann
- Faculty of Science and Technology, Deakin University, Melbourne, Victoria, Australia
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26
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Mann S, Chen YPP. Bacterial genomic G+C composition-eliciting environmental adaptation. Genomics 2010; 95:7-15. [DOI: 10.1016/j.ygeno.2009.09.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Revised: 08/18/2009] [Accepted: 09/01/2009] [Indexed: 01/12/2023]
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Ragan MA, Beiko RG. Lateral genetic transfer: open issues. Philos Trans R Soc Lond B Biol Sci 2009; 364:2241-51. [PMID: 19571244 DOI: 10.1098/rstb.2009.0031] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Lateral genetic transfer (LGT) is an important adaptive force in evolution, contributing to metabolic, physiological and ecological innovation in most prokaryotes and some eukaryotes. Genomic sequences and other data have begun to illuminate the processes, mechanisms, quantitative extent and impact of LGT in diverse organisms, populations, taxa and environments; deep questions are being posed, and the provisional answers sometimes challenge existing paradigms. At the same time, there is an enhanced appreciation of the imperfections, biases and blind spots in the data and in analytical approaches. Here we identify and consider significant open questions concerning the role of LGT in genome evolution.
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Affiliation(s)
- Mark A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia.
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Galtier N, Daubin V. Dealing with incongruence in phylogenomic analyses. Philos Trans R Soc Lond B Biol Sci 2009; 363:4023-9. [PMID: 18852109 DOI: 10.1098/rstb.2008.0144] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Incongruence between gene trees is the main challenge faced by phylogeneticists in the genomic era. Incongruence can occur for artefactual reasons, when we fail to recover the correct gene trees, or for biological reasons, when true gene trees are actually distinct from each other, and from the species tree. Horizontal gene transfers (HGTs) between genomes are an important process of bacterial evolution resulting in a substantial amount of phylogenetic conflicts between gene trees. We argue that the (bacterial) species tree is still a meaningful scientific concept even in the case of HGTs, and that reconstructing it is still a valid goal. We tentatively assess the amount of phylogenetic incongruence caused by HGTs in bacteria by comparing bacterial datasets to a metazoan dataset in which transfers are presumably very scarce or absent.We review existing phylogenomic methods and their ability to return to the user, both the vertical (speciation/extinction history) and horizontal (gene transfers) phylogenetic signals.
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Affiliation(s)
- Nicolas Galtier
- CNRS UMR 5554, Institut des Sciences de l'Evolution, Université Montpellier 2, CC64, Place E. Bataillon, 34095 Montpellier, France.
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Abstract
This chapter discusses the pros and cons of the existing computational methods for the detection of horizontal (or lateral) gene transfer and highlights the genome-wide studies utilizing these methods. The impact of horizontal gene transfer (HGT) on prokaryote genome evolution is discussed.
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30
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Jordan FM, Gray RD, Greenhill SJ, Mace R. Matrilocal residence is ancestral in Austronesian societies. Proc Biol Sci 2009; 276:1957-64. [PMID: 19324748 DOI: 10.1098/rspb.2009.0088] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The nature of social life in human prehistory is elusive, yet knowing how kinship systems evolve is critical for understanding population history and cultural diversity. Post-marital residence rules specify sex-specific dispersal and kin association, influencing the pattern of genetic markers across populations. Cultural phylogenetics allows us to practise 'virtual archaeology' on these aspects of social life that leave no trace in the archaeological record. Here we show that early Austronesian societies practised matrilocal post-marital residence. Using a Markov-chain Monte Carlo comparative method implemented in a Bayesian phylogenetic framework, we estimated the type of residence at each ancestral node in a sample of Austronesian language trees spanning 135 Pacific societies. Matrilocal residence has been hypothesized for proto-Oceanic society (ca 3500 BP), but we find strong evidence that matrilocality was predominant in earlier Austronesian societies ca 5000-4500 BP, at the root of the language family and its early branches. Our results illuminate the divergent patterns of mtDNA and Y-chromosome markers seen in the Pacific. The analysis of present-day cross-cultural data in this way allows us to directly address cultural evolutionary and life-history processes in prehistory.
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Affiliation(s)
- Fiona M Jordan
- Department of Anthropology, University College London, 14 Taviton Street, London WC1H 0BW, UK.
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31
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Boussau B, Guéguen L, Gouy M. Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria. BMC Evol Biol 2008; 8:272. [PMID: 18834516 PMCID: PMC2584045 DOI: 10.1186/1471-2148-8-272] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 10/03/2008] [Indexed: 01/09/2023] Open
Abstract
Background Despite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria. Results To get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found. Conclusion Methods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.
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Affiliation(s)
- Bastien Boussau
- Université de Lyon; Université Lyon 1; CNRS; INRIA; Laboratoire de Biométrie et Biologie Evolutive, 43 boulevard du 11 novembre 1918, Villeurbanne F-69622, France.
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Affiliation(s)
- Bruce Rannala
- Genome Center and Department of Evolution and Ecology, University of California, Davis, California 95616;
| | - Ziheng Yang
- Department of Biology, University College London, London WC1E 6BT United Kingdom; Laboratory of Biometrics, Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo, Japan;
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Martins LDO, Leal E, Kishino H. Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. PLoS One 2008; 3:e2651. [PMID: 18612422 PMCID: PMC2440540 DOI: 10.1371/journal.pone.0002651] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2008] [Accepted: 06/07/2008] [Indexed: 11/18/2022] Open
Abstract
Genomic regions participating in recombination events may support distinct topologies, and phylogenetic analyses should incorporate this heterogeneity. Existing phylogenetic methods for recombination detection are challenged by the enormous number of possible topologies, even for a moderate number of taxa. If, however, the detection analysis is conducted independently between each putative recombinant sequence and a set of reference parentals, potential recombinations between the recombinants are neglected. In this context, a recombination hotspot can be inferred in phylogenetic analyses if we observe several consecutive breakpoints. We developed a distance measure between unrooted topologies that closely resembles the number of recombinations. By introducing a prior distribution on these recombination distances, a Bayesian hierarchical model was devised to detect phylogenetic inconsistencies occurring due to recombinations. This model relaxes the assumption of known parental sequences, still common in HIV analysis, allowing the entire dataset to be analyzed at once. On simulated datasets with up to 16 taxa, our method correctly detected recombination breakpoints and the number of recombination events for each breakpoint. The procedure is robust to rate and transition∶transversion heterogeneities for simulations with and without recombination. This recombination distance is related to recombination hotspots. Applying this procedure to a genomic HIV-1 dataset, we found evidence for hotspots and de novo recombination.
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Leigh JW, Susko E, Baumgartner M, Roger AJ. Testing Congruence in Phylogenomic Analysis. Syst Biol 2008; 57:104-15. [DOI: 10.1080/10635150801910436] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Jessica W. Leigh
- Department of Biochemistry and Molecular Biology, Dalhousie University Halifax NS, Canada B3H 1X5; E-mail: (A.J.R.)
| | - Edward Susko
- Department of Mathematics and Statistics and Genome Atlantic, Dalhousie University Halifax NS, Canada B3H 3J5
| | - Manuela Baumgartner
- Department für Biologie I, Botanik, Ludwig-Maximilians-Universität München Menzingerstraße 67, D-80638 München, Germany
| | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University Halifax NS, Canada B3H 1X5; E-mail: (A.J.R.)
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Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. COMPARATIVE GENOMICS 2008. [DOI: 10.1007/978-3-540-87989-3_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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Abstract
How much horizontal gene transfer (HGT) between species influences bacterial phylogenomics is a controversial issue. This debate, however, lacks any quantitative assessment of the impact of HGT on phylogenies and of the ability of tree-building methods to cope with such events. I introduce a Markov model of genome evolution with HGT, accounting for the constraints on time -- an HGT event can only occur between concomitantly living species. This model is used to simulate multigene sequence data sets with or without HGT. The consequences of HGT on phylogenomic inference are analyzed and compared to other well-known phylogenetic artefacts. It is found that supertree methods are quite robust to HGT, keeping high levels of performance even when gene trees are largely incongruent with each other. Gene tree incongruence per se is not indicative of HGT. HGT, however, removes the (otherwise observed) positive relationship between sequence length and gene tree congruence to the estimated species tree. Surprisingly, when applied to a bacterial and a eukaryotic multigene data set, this criterion rejects the HGT hypothesis for the former, but not the latter data set.
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Affiliation(s)
- Nicolas Galtier
- Institut des Sciences de l'Evolution (UM2-CNRS), Université Montpellier 2, Montpellier, France.
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Stevenson B, Choy HA, Pinne M, Rotondi ML, Miller MC, Demoll E, Kraiczy P, Cooley AE, Creamer TP, Suchard MA, Brissette CA, Verma A, Haake DA. Leptospira interrogans endostatin-like outer membrane proteins bind host fibronectin, laminin and regulators of complement. PLoS One 2007; 2:e1188. [PMID: 18000555 PMCID: PMC2063517 DOI: 10.1371/journal.pone.0001188] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2007] [Accepted: 10/24/2007] [Indexed: 11/19/2022] Open
Abstract
The pathogenic spirochete Leptospira interrogans disseminates throughout its hosts via the bloodstream, then invades and colonizes a variety of host tissues. Infectious leptospires are resistant to killing by their hosts' alternative pathway of complement-mediated killing, and interact with various host extracellular matrix (ECM) components. The LenA outer surface protein (formerly called LfhA and Lsa24) was previously shown to bind the host ECM component laminin and the complement regulators factor H and factor H-related protein-1. We now demonstrate that infectious L. interrogans contain five additional paralogs of lenA, which we designated lenB, lenC, lenD, lenE and lenF. All six genes encode domains predicted to bear structural and functional similarities with mammalian endostatins. Sequence analyses of genes from seven infectious L. interrogans serovars indicated development of sequence diversity through recombination and intragenic duplication. LenB was found to bind human factor H, and all of the newly-described Len proteins bound laminin. In addition, LenB, LenC, LenD, LenE and LenF all exhibited affinities for fibronectin, a distinct host extracellular matrix protein. These characteristics suggest that Len proteins together facilitate invasion and colonization of host tissues, and protect against host immune responses during mammalian infection.
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Affiliation(s)
- Brian Stevenson
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky College of Medicine, Lexington, Kentucky, United States of America.
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Liu J, Glazko G, Mushegian A. Protein repertoire of double-stranded DNA bacteriophages. Virus Res 2006; 117:68-80. [PMID: 16490276 DOI: 10.1016/j.virusres.2006.01.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2005] [Revised: 01/11/2006] [Accepted: 01/18/2006] [Indexed: 01/21/2023]
Abstract
The complexity and diversity of phage gene sets, which are produced by rapid evolution of phage genomes and rampant gene exchanges among phages, hamper the efforts to decipher the evolutionary relationships between individual phage proteins and reconstruct the complete set of evolutionary events leading to the known phages. To start unraveling the natural history of phages, we built the phage orthologous groups (POGs), a natural system of phage protein families that includes 6378 genes from 164 complete genome sequences of double-stranded DNA bacteriophages. Phage proteomes have high POG coverage: on average, 39 genes per phage genome belong to POGs, which is close to half of all genes in most phages. In an agreement with the notion of phage role in horizontal gene transfer, we see many cases of likely gene exchange between phages and their microbial hosts. At the same time, about 80% of all POGs are highly specific to phage genomes and are not commonly found in microbial genomes, indicating coherence and large degree of evolutionary independence of phage gene sets. The information on orthologous genes is essential for evolutionary classification of known bacteriophages and for reconstruction of ancestral phage genomes.
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Affiliation(s)
- Jing Liu
- Stowers Institute for Medical Research, 1000 E 50th St., Kansas City, MO 64110, USA
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Ouzounis CA. Ancestral state reconstructions for genomes. Curr Opin Genet Dev 2005; 15:595-600. [PMID: 16216489 DOI: 10.1016/j.gde.2005.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2005] [Accepted: 09/28/2005] [Indexed: 11/26/2022]
Abstract
The recent expansion of phylogenetic analysis from the traditional field of molecular evolution, analyzing histories of genes, to the nascent field of "genomic evolution", analyzing histories of entire genomes, enables the construction of trees based on genome information, the quantification of the key processes that shape genome content and, ultimately, plausible parsimony reconstructions of ancestral genomes. Thus, when genomes are considered as phylogenetic characters, it is possible to reconstruct not only the history of species but also the ancestral states in terms of genome structure or function. In the future, we might be able to accurately reconstruct--or retrodict--a chain of events that led to the emergence of a specific genome sequence and, ultimately, to synthesize ancestral genomes at will, creating a "Jurassic database" of genomes.
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Affiliation(s)
- Christos A Ouzounis
- Computational Genomics Group, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.
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