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Reticulate Evolution and Phylogenetic Networks 6
CHAPTER Reticulate Evolution and Phylogenetic Networks 6 So far, we have modeled the evolutionary process as a bifurcating treelike process. The main feature of trees is that the flow of information in one lineage is independent of that in another lineage. In real life, however, many process- es—including recombination, hybridization, polyploidy, introgression, genome fusion, endosymbiosis, and horizontal gene transfer—do not abide by lineage independence and cannot be modeled by trees. Reticulate evolution refers to the origination of lineages through the com- plete or partial merging of two or more ancestor lineages. The nonvertical con- nections between lineages are referred to as reticulations. In this chapter, we introduce the language of networks and explain how networks can be used to study non-treelike phylogenetic processes. A substantial part of this chapter will be dedicated to the evolutionary relationships among prokaryotes and the very intriguing question of the origin of the eukaryotic cell. Networks Networks were briefly introduced in Chapter 4 in the context of protein-protein interactions. Here, we provide a more formal description of networks and their use in phylogenetics. As mentioned in Chapter 5, trees are connected graphs in which any two nodes are connected by a single path. In phylogenetics, a network is a connected graph in which at least two nodes are connected by two or more pathways. In other words, a network is a connected graph that is not a tree. All networks contain at least one cycle, i.e., a path of branches that can be followed in one direction from any starting point back to the starting point. -
Topology of Reticulate Evolution
Topology of Reticulate Evolution Kevin Joseph Emmett Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Graduate School of Arts and Sciences COLUMBIA UNIVERSITY 2016 ⃝c 2016 Kevin Joseph Emmett All Rights Reserved ABSTRACT Topology of Reticulate Evolution Kevin Joseph Emmett The standard representation of evolutionary relationships is a bifurcating tree. How- ever, many types of genetic exchange, collectively referred to as reticulate evolution, involve processes that cannot be modeled as trees. Increasing genomic data has pointed to the prevalence of reticulate processes, particularly in microorganisms, and underscored the need for new approaches to capture and represent the scale and frequency of these events. This thesis contains results from applying new techniques from applied and computa- tional topology, under the heading topological data analysis, to the problem of characterizing reticulate evolution in molecular sequence data. First, we develop approaches for analyz- ing sequence data using topology. We propose new topological constructions specific to molecular sequence data that generalize standard constructions such as Vietoris-Rips. We draw on previous work in phylogenetic networks and use homology to provide a quantitative measure of reticulate events. We develop methods for performing statistical inference using topological summary statistics. Next, we apply our approach to several types of molecular sequence data. First, we examine the mosaic genome structure in phages. We recover inconsistencies in existing morphology-based taxonomies, use a network approach to construct a genome-based repre- sentation of phage relationships, and identify conserved gene families within phage popu- lations. Second, we study influenza, a common human pathogen. -
Reticulate Evolutionary History in a Recent Radiation of Montane
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426362; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Reticulate Evolutionary History in a Recent Radiation of Montane 2 Grasshoppers Revealed by Genomic Data 3 4 VANINA TONZO1, ADRIÀ BELLVERT2 AND JOAQUÍN ORTEGO1 5 6 1 Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC); Avda. 7 Américo Vespucio, 26 – 41092; Seville, Spain 8 2 Department of Evolutionary Biology, Ecology and Environmental Sciences, and 9 Biodiversity Research Institute (IRBio), Universitat de Barcelona; Av. Diagonal, 643 – 10 08028; Barcelona, Spain 11 12 13 Author for correspondence: 14 Vanina Tonzo 15 Estación Biológica de Doñana, EBD-CSIC, 16 Avda. Américo Vespucio 26, E-41092 Seville, Spain 17 E-mail: [email protected] 18 Phone: +34 954 232 340 19 20 21 22 Running title: Reticulate evolution in a grasshopper radiation bioRxiv preprint doi: https://doi.org/10.1101/2021.01.12.426362; this version posted January 13, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 23 Abstract 24 Inferring the ecological and evolutionary processes underlying lineage and phenotypic 25 diversification is of paramount importance to shed light on the origin of contemporary 26 patterns of biological diversity. However, reconstructing phylogenetic relationships in 27 recent evolutionary radiations represents a major challenge due to the frequent co- 28 occurrence of incomplete lineage sorting and introgression. -
The Effect of Disturbance on Plant Com Unities in Tundra Regio S of the Soviet Union
The Effect of Disturbance on Plant Communities in Tundra Regions of the Soviet Union Item Type Technical Report Authors Yurtsev, B.A.; Korobkov, A.A.; Matveyeva, N.V.; Druzhinina, O.A.; Zharkova, Yu. G. Publisher University of Alaska. Institute of Arctic Biology Download date 05/10/2021 11:09:08 Link to Item http://hdl.handle.net/11122/1496 THE EFFECT OF DISTURBANCE ON PLANT COM UNITIES IN TUNDRA REGIO S OF THE SOVIET UNION Three Papers with Annotated Lists BIOLOGICAL PAPERS OF THE UNIVERSITY OF ALASKA Number20 June 1979 HE EFFECT OF DISTURBA CE ON PLANT COMMUNITIES IN TUNDRA REGIONS OF THE SOVIET UNION Three Papers with Annotated Lists BIOLOGICAL PAPERS OF THE UNIVERSITY OF ALASKA Number20 June 1979 Editor GEORGE C. WEST Division of Life Science University of Alaska Fairbanks, Alaska Price of this issue $3.00 Printed by Ken Wray's Prine Shop, lnc. Anchorage, Alaska TABLE OF CO TE TS An Annotated List of Plants Inhabiting Sires of Natural and A thr pogenic Disturbances ofTun dra Cover: South astern most Chukchi Peninsula -B.A. Yurtsev and A.A. Korobkov page l An Annotated List of Plants Inhabiting Sites of Natural and Anthropogenic Disturbances of Tundra Cover in Western Taimyr: The Settlement of Kresty- N.V. Maweyeva page 18 A Study of Plant Communities of Anthropogenic Habitats in rhe Area of the Vorkuta Industrial Center - O .A. Druz;hinina and Yu. G. Zharkova page 30 Editor's NoLe The original Russtan language manuscrtpts were translated hy 00ris Love and Barbara Murray. Funding for translation and preparation of camera ready copy for thts tssue of the Btological Papers was provided through the U.S. -
Horizontal Gene Transfer and Recombination Analysis of SARS-Cov-2 Genes Helps Discover Its Close Relatives and Shed Light on Its Origin
bioRxiv preprint doi: https://doi.org/10.1101/2020.12.03.410233; this version posted December 3, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin Vladimir Makarenkov1*, Bogdan Mazoure2*, Guillaume Rabusseau2,3 and Pierre Legendre4 1. Département d’informatique, Université du Québec à Montréal, Montréal, QC, Canada 2. Montreal Institute for Learning Algorithms (Mila), Montréal, QC, Canada 3. Département d'informatique et de recherche opérationnelle, Université de Montréal, Montréal, QC, Canada 4. Département de sciences biologiques, Université de Montréal, C. P. 6128, succursale Centre-ville, Montréal, QC, H3C 3J7 Canada *Both authors contributed equally to this manuscript. Vladimir Makarenkov is the corresponding author of this manuscript (email: [email protected]) Abstract Background The SARS-CoV-2 pandemic is among the most dangerous infectious diseases that have emerged in recent history. Human CoV strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. -
Reticulate Evolution Everywhere
Reticulate Evolution Everywhere Nathalie Gontier Abstract Reticulation is a recurring evolutionary pattern found in phylogenetic reconstructions of life. The pattern results from how species interact and evolve by mechanisms and processes including symbiosis; symbiogenesis; lateral gene transfer (that occurs via bacterial conjugation, transformation, transduction, Gene Transfer Agents, or the movements of transposons, retrotransposons, and other mobile genetic elements); hybridization or divergence with gene flow; and infec- tious heredity (induced either directly by bacteria, bacteriophages, viruses, pri- ons, protozoa and fungi, or via vectors that transmit these pathogens). Research on reticulate evolution today takes on inter- and transdisciplinary proportions and is able to unite distinct research fields ranging from microbiology and molecular genetics to evolutionary biology and the biomedical sciences. This chapter sum- marizes the main principles of the diverse reticulate evolutionary mechanisms and situates them into the chapters that make up this volume. Keywords Reticulate evolution · Symbiosis · Symbiogenesis · Lateral Gene Transfer · Infectious agents · Microbiome · Viriome · Virolution · Hybridization · Divergence with gene flow · Evolutionary patterns · Extended Synthesis 1 Reticulate Evolution: Patterns, Processes, Mechanisms According to the Online Etymology Dictionary (http://www.etymonline.com), the word reticulate is an adjective that stems from the Latin words “re¯ticulātus” (having a net-like pattern) and re¯ticulum (little net). When scholars identify the evolution of life as being “reticulated,” they first and foremost refer to a recurring evolutionary pattern. N. Gontier (*) AppEEL—Applied Evolutionary Epistemology Lab, University of Lisbon, Lisbon, Portugal e-mail: [email protected] © Springer International Publishing Switzerland 2015 1 N. Gontier (ed.), Reticulate Evolution, Interdisciplinary Evolution Research 3, DOI 10.1007/978-3-319-16345-1_1 2 N. -
Botany Orary
TAXONOMY AND CULTIVAR DEVELOPMENT OF POA PRATENSIS L. David P. Byres 1 13 BOTANY ORARY PhD. University of Edinburgh 1984 1) Declaration. This thesis was composed by myself, and the work described herein is my own. David P. Byres CONTENTS Acknowledgements . • I \/ Abstract . Section A . Taxonomy. Chapter 1. Introduction. 1.1 Introduction ..........................................1 1.2 Taxonomy .............................................1 1.3 Cultivar Development ............................... 4 Chapter 2. Literature Review : Taxonomy 2.1 Introduction ............. .............................7 2.2 History of the Taxonomic Treatment of of Poa pratensis L. s.1............ ....... 10 2.3 Taxonomic Characters used by previous workers .........14 Chapter 3. Materials and Methods. 3.1 Environmental Variation .................... 20 3.2 Population and Herbarium Studies .......... ............26 3.3 Taxonomic Analysis of Biotypes and Cultivars... ... ... 36 3.4 Statistical Analysis ..................................37 Chapter 4. Effect of Environmental Variation on Morphology. 4.1 Introduction .......................................... 38 4.2 Results ........................................ .......38 Chapter 5. Study of Poa pratensis Populations. 5.1 Introduction .......................................... 49 5.2 Results ........................ 49 Chapter 6. Study of Herbarium Material. 6.1 Introduction ......................................... 60 6.2 Results ....................... 60 Chapter 7. Morphological Examination of Biotypes and -
Non-Genetic Inheritance: Evolution Above the Organismal Level
BioSystems 200 (2021) 104325 Contents lists available at ScienceDirect BioSystems journal homepage: http://www.elsevier.com/locate/biosystems Non-genetic inheritance: Evolution above the organismal level Anton V. Sukhoverkhov a,*, Nathalie Gontier b a Department of Philosophy, Kuban State Agrarian University, Kalinina St. 13, 350044, Krasnodar, Russia b Applied Evolutionary Epistemology Lab, Centro de Filosofia das Ci^encias, Departamento de Historia´ e Filosofia das Ci^encias, Faculdade de Ci^encias, Universidade de Lisboa, 1749-016, Lisboa, Portugal ARTICLE INFO ABSTRACT Keywords: The article proposes to further develop the ideas of the Extended Evolutionary Synthesis by including into Non-genetic inheritance evolutionary research an analysis of phenomena that occur above the organismal level. We demonstrate that the Social plasticity current Extended Synthesis is focused more on individual traits (genetically or non-genetically inherited) and less Community traits on community system traits (synergetic/organizational traits) that characterize transgenerational biological, Reticulate evolution ecological, social, and cultural systems. In this regard, we will consider various communities that are made up of Extended evolutionary synthesis interacting populations, and for which the individual members can belong to the same or to different species. Examples of communities include biofilms,ant colonies, symbiotic associations resulting in holobiont formation, and human societies. The proposed model of evolution at the level of communities revises classic theorizing on the major transitions in evolution by analyzing the interplay between community/social traits and individual traits, and how this brings forth ideas of top-down regulations of bottom-up evolutionary processes (collabo ration of downward and upward causation). The work demonstrates that such interplay also includes reticulate interactions and reticulate causation. -
Exploring Reticulate Evolution and Its Consequences for Phylogenetic Reconstruction
phylogenetworks EXPLORING RETICULATE EVOLUTION AND ITS CONSEQUENCES FOR PHYLOGENETIC RECONSTRUCTION Bastienne Vriesendorp Promotor: Prof. dr. M.S.M. Sosef Hoogleraar Biosystematiek Wageningen Universiteit Co-promotoren: Dr. F.T. Bakker Universitair Docent, leerstoelgroep Biosystematiek Wageningen Universiteit Dr. R.G. van den Berg Universitair Hoofddocent, leerstoelgroep Biosystematiek Wageningen Universiteit Promotiecommissie: Prof. dr. J.A.M. Leunissen (Wageningen Universiteit) Prof. dr. E.F. Smets (Universiteit Leiden) Prof. dr. P.H. van Tienderen (Universiteit van Amsterdam) Dr. P.H. Hovenkamp (Universiteit Leiden) Dit onderzoek is uitgevoerd binnen de onderzoekschool Biodiversiteit phylogenetworks EXPLORING RETICULATE EVOLUTION AND ITS CONSEQUENCES FOR PHYLOGENETIC RECONSTRUCTION Bastienne Vriesendorp Proefschrift ter verkrijging van de graad van doctor op gezag van de rector magnificus van Wageningen Universiteit Prof. dr. M.J. Kropff in het openbaar te verdedigen op woensdag 12 september 2007 des namiddags te vier uur in de Aula Bastienne Vriesendorp (2007) Phylogenetworks: Exploring reticulate evolution and its consequences for phylogenetic reconstruction PhD thesis Wageningen University, The Netherlands With references – with summaries in English and Dutch ISBN 978-90-8504-703-2 aan mijn ouders CONTENTS chapter 1 General Introduction 9 chapter 2 Hybridization: History, terminology and evolutionary significance 15 chapter 3 Reconstructing patterns of reticulate evolution in angiosperms: what can we do? 41 chapter 4 Mosaic DNA -
Living Organisms Author Their Read-Write Genomes in Evolution
biology Review Living Organisms Author Their Read-Write Genomes in Evolution James A. Shapiro ID Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA; [email protected]; Tel.: +1-773-702-1625 Academic Editor: Andrés Moya Received: 23 August 2017; Accepted: 28 November 2017; Published: 6 December 2017 Abstract: Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with “non-coding” DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called “non-coding” RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations. -
Flora of North America North of Mexico
Flora of North America North of Mexico Edited by FLORA OF NORTH AMERICA EDITORIAL COMMITTEE VOLUME 24 MagnoUophyta: Commelinidae (in part): Foaceae, part 1 Edited by Mary E. Barkworth, Kathleen M. Capéis, Sandy Long, Laurel K. Anderton, and Michael B. Piep Illustrated by Cindy Talbot Roché, Linda Ann Vorobik, Sandy Long, Annaliese Miller, Bee F Gunn, and Christine Roberts NEW YORK OXFORD • OXFORD UNIVERSITY PRESS » 2007 Oxford Univei;sLty Press, Inc., publishes works that further Oxford University's objective of excellence in research, scholarship, and education. Oxford New York /Auckland Cape Town Dar es Salaam Hong Kong Karachi Kuala Lumpur Madrid Melbourne Mexico City Nairobi New Delhi Shanghai Taipei Toronto Copyright ©2007 by Utah State University Tlie account of Avena is reproduced by permission of Bernard R. Baum for the Department of Agriculture and Agri-Food, Government of Canada, ©Minister of Public Works and Government Services, Canada, 2007. The accounts of Arctophila, Dtipontui, Scbizacbne, Vahlodea, xArctodiipontia, and xDiipoa are reproduced by permission of Jacques Cayouette and Stephen J. Darbyshire for the Department of Agriculture and Agri-Food, Government of Canada, ©Minister of Public Works and Government Services, Canada, 2007. The accounts of Eremopoa, Leitcopoa, Schedoiioms, and xPucciphippsia are reproduced by permission of Stephen J. Darbyshire for the Department of Agriculture and Agri-Food, Government of Canada, ©Minister of Public Works and Government Services, Canada, 2007. Published by Oxford University Press, Inc. 198 Madison Avenue, New York, New York 10016 www.oup.com Oxford is a registered trademark of Oxford University Press All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of Utah State University. -
Diplomarbeit
Diplomarbeit vorgelegt zur Erlangung des Grades eines Diplom-Biologen an der Fakultät für Biologie und Biotechnologie der Ruhr-Universität Bochum Phylogenie der Brandpilzgattung Urocystis von Sascha Lotze-Engelhard Angefertigt im LS Evolution und Biodiversität der Pflanzen, AG Geobotanik Bochum im Dezember 2010 Referent: Prof. Dr. D. Begerow Koreferent: Prof. Dr. R. Tollrian 2 ҅Fungi have a profound impact on global ecosystems. They modify our habitats and are essential for many ecosystem functions. Fungi form soil, recycle nutrients, decay wood, enhance plant growth and cull plants from their environment. They feed us, poison us, parasitize us and cure us. They destroy our crops, homes and libraries, but they also produce valuable biochemicals, such as ethanol and antibiotics. For both practical and intellectual reasons it is important to provide a phylogeny of Fungi on which a classi- fication can be firmly based. ҆ (Blackwell u.a. 2006) Inhaltsverzeichnis 3 Inhaltsverzeichnis Inhaltsverzeichnis ........................................................................................................... 3 Abbildungsverzeichnis .................................................................................................... 6 Tabellenverzeichnis ........................................................................................................ 7 Abkürzungsverzeichnis .................................................................................................. 8 1 Einleitung ............................................................................................................