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Pinpointing the Origin of Mitochondria Zhang Wang Hanchuan, Hubei
Pinpointing the origin of mitochondria Zhang Wang Hanchuan, Hubei, China B.S., Wuhan University, 2009 A Dissertation presented to the Graduate Faculty of the University of Virginia in Candidacy for the Degree of Doctor of Philosophy Department of Biology University of Virginia August, 2014 ii Abstract The explosive growth of genomic data presents both opportunities and challenges for the study of evolutionary biology, ecology and diversity. Genome-scale phylogenetic analysis (known as phylogenomics) has demonstrated its power in resolving the evolutionary tree of life and deciphering various fascinating questions regarding the origin and evolution of earth’s contemporary organisms. One of the most fundamental events in the earth’s history of life regards the origin of mitochondria. Overwhelming evidence supports the endosymbiotic theory that mitochondria originated once from a free-living α-proteobacterium that was engulfed by its host probably 2 billion years ago. However, its exact position in the tree of life remains highly debated. In particular, systematic errors including sparse taxonomic sampling, high evolutionary rate and sequence composition bias have long plagued the mitochondrial phylogenetics. This dissertation employs an integrated phylogenomic approach toward pinpointing the origin of mitochondria. By strategically sequencing 18 phylogenetically novel α-proteobacterial genomes, using a set of “well-behaved” phylogenetic markers with lower evolutionary rates and less composition bias, and applying more realistic phylogenetic models that better account for the systematic errors, the presented phylogenomic study for the first time placed the mitochondria unequivocally within the Rickettsiales order of α- proteobacteria, as a sister clade to the Rickettsiaceae and Anaplasmataceae families, all subtended by the Holosporaceae family. -
Origin and Evolution of Eukaryotic Compartmentalization
TESI DOCTORAL UPF 2016 Origin and evolution of eukaryotic compartmentalization Alexandros Pittis Director Dr. Toni Gabaldon´ Comparative Genomics Group Bioinformatics and Genomics Department Centre for Genomic Regulation (CRG) To my father Stavros for the PhD he never did Acknowledgments Looking back at the years of my PhD in the Comparative Genomics group at CRG, I feel it was equally a process of scientific, as well as personal development. All this time I was very privileged to be surrounded by people that offered me their generous support in both fronts. And they were available in the very moments that I was fighting more myself than the unsolvable (anyway) comparative genomics puzzles. I hope that in the future I will have many times the chance to express them my appreciation, way beyond these few words. First, to Toni, my supervisor, for all his support, and patience, and confidence, and respect, especially at the moments that things did not seem that promising. He offered me freedom, to try, to think, to fail, to learn, to achieve that few enjoy during their PhD, and I am very thankful to him. Then, to my good friends and colleagues, those that I found in the group already, and others that joined after me. A very special thanks to Marinita and Jaime, for all their valuable time, and guidance and paradigm, which nevertheless I never managed to follow. They have both marked my phylogenomics path so far and I cannot escape. To Les and Salvi, my fellow students and pals at the time for all that we shared; to Gab and Fran and Dam, for -
Can We Understand Evolution Without Symbiogenesis?
Can We Understand Evolution Without Symbiogenesis? Francisco Carrapiço …symbiosis is more than a mere casual and isolated biological phenomenon: it is in reality the most fundamental and universal order or law of life. Hermann Reinheimer (1915) Abstract This work is a contribution to the literature and knowledge on evolu- tion that takes into account the biological data obtained on symbiosis and sym- biogenesis. Evolution is traditionally considered a gradual process essentially consisting of natural selection, conducted on minimal phenotypical variations that are the result of mutations and genetic recombinations to form new spe- cies. However, the biological world presents and involves symbiotic associations between different organisms to form consortia, a new structural life dimension and a symbiont-induced speciation. The acknowledgment of this reality implies a new understanding of the natural world, in which symbiogenesis plays an important role as an evolutive mechanism. Within this understanding, symbiosis is the key to the acquisition of new genomes and new metabolic capacities, driving living forms’ evolution and the establishment of biodiversity and complexity on Earth. This chapter provides information on some of the key figures and their major works on symbiosis and symbiogenesis and reinforces the importance of these concepts in our understanding of the natural world and the role they play in the establishing of the evolutionary complexity of living systems. In this context, the concept of the symbiogenic superorganism is also discussed. Keywords Evolution · Symbiogenesis · Symbiosis · Symbiogenic superorgan- ism · New paradigm F. Carrapiço (*) Centre for Ecology Evolution and Environmental Change (CE3C); Centre for Philosophy of Science, Department of Plant Biology, Faculty of science, University of Lisbon, Lisbon, Portugal e-mail: [email protected] © Springer International Publishing Switzerland 2015 81 N. -
The Origin of Plastids By: Cheong Xin Chan, Ph.D
A Collaborative Learning Space for Science ABOUT FACULTY STUDENTS INTERMEDIATE CELL ORIGINS AND METABOLISM | Lead Editor: Gary Cote, Mario De Tullio The Origin of Plastids By: Cheong Xin Chan, Ph.D. & Debashish Bhattacharya, Ph.D. (Rutgers, The State University of New Jersey) © 2010 Nature Education Citation: Chan, C. X. & Bhattacharya, D. (2010) The Origin of Plastids. Nature Education 3(9):84 Plastids are core components of photosynthesis in plants and algae. Scientists are currently debating the events leading to the appearance of plastids in eukaryotic cells. Organelles, called plastids, are the main sites of photosynthesis in eukaryotic cells. Chloroplasts, as well as any other pigment containing cytoplasmic organelles that enables the harvesting and conversion of light and carbon dioxide into food and energy, are plastids. Found mainly in eukaryotic cells, plastids can be grouped into two distinctive types depending on their membrane structure: primary plastids and secondary plastids. Primary plastids are found in most algae and plants, and secondary, more-complex plastids are typically found in plankton, such as diatoms and dinoflagellates. Exploring the origin of plastids is an exciting field of research because it enhances our understanding of the basis of photosynthesis in green plants, our primary food source on planet Earth. Primary Plastids and Endosymbiosis Where did plastids originate? Their origin is explained by endosymbiosis, the act of a unicellular heterotrophic protist engulfing a free-living photosynthetic cyanobacterium and retaining it, instead of digesting it in the food vacuole (Margulis 1970; McFadden 2001; Kutschera & Niklas 2005). The captured cell (the endosymbiont) was then reduced to a functional organelle bound by two membranes, and was transmitted vertically to subsequent generations. -
Lynn Margulis
BIOGRAPHY THE INDOMITABLE EVOLUTIONIST: LYNN MARGULIS MEENAKSHI PANT The evolutionary “To me, the human move to take responsibility interest in science. In 1957, she graduated biologist Lynn for the living Earth is laughable — the rhetoric with a degree in Liberal Arts, and moved to Margulis is best of the powerless. The planet takes care of us, the University of Wisconsin to study Biology known for her not we of it. Our self-inflated moral imperative under Walter Plaut (who was to become her work on the Serial to guide a wayward Earth, or heal our sick supervisor) and Hans Ris. In 1960, she graduated Endosymbiotic planet, is evidence of our immense capacity with an MS degree in Zoology and Genetics. Theory (SET) to for self-delusion. Rather, we need to protect She then began her research career in the explain the origins ourselves from ourselves.” University of California, under the guidance of of eukaryotic Max Alfert, earning her doctoral degree in 1965. cells. This article Lynn was offered her first job — a research presents key facets his very courageous statement that assistantship and the position of a lecturer in in the life of Tchallenges the self-acclaimed supremacy Brandeis University — even before she could this avant-garde of humans over nature was made by Lynn finish her dissertation. However, it was only biologist and her Margulis (refer Fig.1). She is believed to be work that has one of the most creative scientific theorists after she had been awarded a PhD that she changed the way of the modern era, who transformed the idea moved to Boston University, where she taught we perceive life on of how life evolved on Earth. -
Events with Lynn Margulies Collegium Helveticum STW/D13
Events with Lynn Margulies Prof. Dr. Lynn Margulis Collegium Helveticum STW/D13 Schmelzbergstrasse 25 8092 Zurich T 01 632 3385 F 01 632 1204 Lynn Margulis ist Distinguished University Professor des Departements Geowissenschaften der Universität von Massachusetts in Amherst und wissenschaftlicher Gast des Collegium Helveticum im Sommersemester 2001. My conversion to science occurred in the College of the University of Chicago. No class accepted more than 24 students, labs were frequent, and tests - suggestive only - didn't «count». Rather, a 9-hour final examination in June was the sole requirement for the final grade, and June seemed infinitely distant from that first day of class in autumn. Since textbooks were an anathema to learning, we read unabridged and uncompromised original works. We ignorant chickens accessed the great scientists: Isaac Newton, Francis Bacon, Galileo Galilei, Charles Darwin, Gregor Mendel, Hans Spemann, August Weismann, and the neo-Darwinists. The preoccupation of the great Natural Sciences II class was «What is heredity? What links the generations? How do the materials in fused egg and sperm generate the development of an animal? How does variation in evolution arise? How do organisms originate? Why do they evolve?» These haunting questions drive me still. Ever since I learned about the idea that variation in evolution arises by symbiogenesis, I have worked on it. Symbiosis, coined by the German botanist Anton deBary (1873), refers simply to physical contact between different kinds of organisms - in his words, «living together of differently named organisms.» Cohabitation, long-term living together, it was asserted by many, results in symbiogenesis. Symbiogenesis, the concept developed by the Russian, K. -
Serial Endosymbiosis Or Singular Event at the Origin of Eukaryotes?
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by UCL Discovery Serial endosymbiosis or singular event at the origin of eukaryotes? Nick Lane Department of Genetics, Evolution and Environment, University College London Darwin Building, Gower Street, London WC1E 6BT, United Kingdom [email protected] Abstract ‘On the Origin of Mitosing Cells’ heralded a new way of seeing cellular evolution, with symbiosis at its heart. Lynn Margulis (then Sagan) marshalled an impressive array of evidence for endosymbiosis, from cell biology to atmospheric chemistry and Earth history. Despite her emphasis on symbiosis, she saw plenty of evidence for gradualism in eukaryotic evolution, with multiple origins of mitosis and sex, repeated acquisitions of plastids, and putative evolutionary intermediates throughout the microbial world. Later on, Margulis maintained her view of multiple endosymbioses giving rise to other organelles such as hydrogenosomes, in keeping with the polyphyletic assumptions of the serial endosymbiosis theory. She stood at the threshold of the phylogenetic era, and anticipated its potential. Yet while predicting that the nucleotide sequences of genes would enable a detailed reconstruction of eukaryotic evolution, Margulis did not, and could not, imagine the radically different story that would eventually emerge from comparative genomics. The last eukaryotic common ancestor now seems to have been essentially a modern eukaryotic cell that had already evolved mitosis, meiotic sex, organelles and endomembrane systems. The long search for missing evolutionary intermediates has failed to turn up a single example, and those discussed by Margulis turn out to have evolved reductively from more complex ancestors. -
Endosymbiosis, a Proven Theory Or Evolution Myth?
2012 Microreviews in Cell and Molecular Biology kj Endosymbiosis, a Proven Theory or Evolution Myth? Author: Kyle McCall Major: Biology Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, OK 74078, USA Key Words: Mitochondria, Chloroplasts, Endosymbiosis, Evolution, Eukaryotic cells The Endosymbiotic theory is a theory that explains the evolution of the mitochondria and chloroplast, which are organelles of eukaryotic cells. This theory originated at the end of the 1800s by Andreas Schimper, and later published by Lynn Margulis in the 1960’s in her book “Symbiosis in Cell Evolution.” According to this theory, these organelles originated as separate prokaryotic organisms, which were taken inside the cell as endosymbionts. Theory states that Mitochondria developed from proteobacteria (in particular, Rickettsiales or close relatives) and chloroplasts from cyanobacteria. There has been much debate about this theory and many questions have emerged because of it.. Is it truly possible for simple prokaryotes to evolve and also succeed as a complex eukaryote? Introduction located in the nucleus. Many originate from the bacterial Konstantin Mereschkowsky first suggested that endosymbiont. plastids were originally endosymbionts in 1905- the same idea for mitochondria was suggested by Ivan Wallin in Recent Progress the 1920s. These theories were initially dismissed on the Interest in this theory of mitochondria evolution was assumption that they did not contain DNA. This was retouched once scientists discovered that mitochondria proven false in the 1960s, leading Hans Ris to resurrect have their own genomes. Finding that they do not follow the idea. the Mendelian rules, and are able to synthesize their own Endosymbiosis is a debate that has been widely proteins. -
Endosymbiosis and Its Implications for Evolutionary Theory
Endosymbiosis and its implications for evolutionary theory Maureen A. O’Malley1 Department of Philosophy, University of Sydney, Sydney, NSW 2006, Australia Edited by W. Ford Doolittle, Dalhousie University, Halifax, NS, Canada, and approved March 24, 2015 (received for review December 21, 2014) Historically, conceptualizations of symbiosis and endosymbiosis and neo-Darwinian evolutionary theory form the contemporary have been pitted against Darwinian or neo-Darwinian evolutionary focus. Although her main arguments do not withstand much theory. In more recent times, Lynn Margulis has argued vigorously analysis, macroevolutionary considerations do seem to offer an along these lines. However, there are only shallow grounds for explanatory niche for endosymbiotic innovations. However, I will finding Darwinian concepts or population genetic theory incom- show that, when organelle-producing endosymbiotic relationships patible with endosymbiosis. But is population genetics suffi- are scrutinized further, the explanatory focus shifts to metabolism ciently explanatory of endosymbiosis and its role in evolution? and its evolutionary consequences. In the final part of the paper, I Population genetics “follows” genes, is replication-centric, and is will revisit the implications for evolutionary theory when addi- concerned with vertically consistent genetic lineages. It may also tional explanatory resources are gained for the modern synthesis have explanatory limitations with regard to macroevolution. Even from a metabolic interpretation of endosymbiosis. so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead Historical Claims About Endosymbiosis be asking how explanatory of evolution endosymbiosis is, and ex- There is a long history of researchers who have theorized about actly which features of evolution it might be explaining. -
The Origin of Plastids By: Cheong Xin Chan, Ph.D
A Collaborative Learning Space for Science View metadata, citation and similar papers at core.ac.uk ABOUT FACULTY STUDENTS brought to you by CORE provided by University of Queensland eSpace INTERMEDIATE CELL ORIGINS AND METABOLISM | Lead Editor: Gary Cote, Mario De Tullio The Origin of Plastids By: Cheong Xin Chan, Ph.D. & Debashish Bhattacharya, Ph.D. (Rutgers, The State University of New Jersey) © 2010 Nature Education Citation: Chan, C. X. & Bhattacharya, D. (2010) The Origin of Plastids. Nature Education 3(9):84 Plastids are core components of photosynthesis in plants and algae. Scientists are currently debating the events leading to the appearance of plastids in eukaryotic cells. Organelles, called plastids, are the main sites of photosynthesis in eukaryotic cells. Chloroplasts, as well as any other pigment containing cytoplasmic organelles that enables the harvesting and conversion of light and carbon dioxide into food and energy, are plastids. Found mainly in eukaryotic cells, plastids can be grouped into two distinctive types depending on their membrane structure: primary plastids and secondary plastids. Primary plastids are found in most algae and plants, and secondary, more-complex plastids are typically found in plankton, such as diatoms and dinoflagellates. Exploring the origin of plastids is an exciting field of research because it enhances our understanding of the basis of photosynthesis in green plants, our primary food source on planet Earth. Primary Plastids and Endosymbiosis Where did plastids originate? Their origin is explained by endosymbiosis, the act of a unicellular heterotrophic protist engulfing a free-living photosynthetic cyanobacterium and retaining it, instead of digesting it in the food vacuole (Margulis 1970; McFadden 2001; Kutschera & Niklas 2005). -
Microbiology
Microbiology SENIOR CONTRIBUTING AUTHORS NINA PARKER, SHENANDOAH UNIVERSITY MARK SCHNEEGURT, WICHITA STATE UNIVERSITY ANH-HUE THI TU, GEORGIA SOUTHWESTERN STATE UNIVERSITY BRIAN M. FORSTER, SAINT JOSEPH'S UNIVERSITY PHILIP LISTER, CENTRAL NEW MEXICO COMMUNITY COLLEGE OpenStax Rice University 6100 Main Street MS-375 Houston, Texas 77005 To learn more about OpenStax, visit https://openstax.org. Individual print copies and bulk orders can be purchased through our website. ©2018 Rice University. Textbook content produced by OpenStax is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0). Under this license, any user of this textbook or the textbook contents herein must provide proper attribution as follows: - If you redistribute this textbook in a digital format (including but not limited to PDF and HTML), then you must retain on every page the following attribution: “Download for free at https://openstax.org/details/books/microbiology.” - If you redistribute this textbook in a print format, then you must include on every physical page the following attribution: “Download for free at https://openstax.org/details/books/microbiology.” - If you redistribute part of this textbook, then you must retain in every digital format page view (including but not limited to PDF and HTML) and on every physical printed page the following attribution: “Download for free at https://openstax.org/details/books/microbiology.” - If you use this textbook as a bibliographic reference, please include https://openstax.org/details/books/microbiology in your citation. For questions regarding this licensing, please contact [email protected]. Trademarks The OpenStax name, OpenStax logo, OpenStax book covers, OpenStax CNX name, OpenStax CNX logo, OpenStax Tutor name, Openstax Tutor logo, Connexions name, Connexions logo, Rice University name, and Rice University logo are not subject to the license and may not be reproduced without the prior and express written consent of Rice University. -
Lynn Margulis Doctora Honoris Causa LYNN MARGULIS
Doctora Honoris Causa Lynn Margulis Doctora Honoris Causa LYNN MARGULIS Discurs llegit a la cerimònia d’investidura celebrada a la sala d’actes del Rectorat el dia 6 de juny de 2007 Editat i imprès pel Servei de Publicacions de la Universitat Autònoma de Barcelona 08193 Bellaterra (Barcelona) Imprès a Catalunya 2 PRESENTACIÓ DE LYNN MARGULIS PER ISABEL ESTEVE MARTÍNEZ Excelentísimo y Magnífico Señor Rector, Muy honorables autoridades, Queridos colegas, Es para a mí una gran satisfacción, tanto en el terreno académico como en el per - sonal, presentar a la profesora Lynn Margulis al Claustro de la Universidad Autónoma de Barcelona para su investidura como doctora honoris causa . Ha sido muy difícil expresar en pocas palabras una trayectoria tan intensa, tanto a nivel científico como docente, y que deje a la vez traslucir su generosa personalidad. La profesora Lynn Margulis se doctoró en el Departamento de Genética de la Universidad de California, Berkeley, en el año 1963, y tal vez esta fecha deba ser con - siderada el punto de partida de una brillante carrera científica. Durante los años sesenta demostró una extraordinaria capacidad de síntesis al reunir centenares de hipó - tesis y experimentos dispersos para formular de una manera coherente la teoría de la endosimbiosis para explicar el origen de la célula eucariota. En los años siguien - tes, viajó incansablemente para defender dicha teoría, actualmente aceptada y que constituye una de las bases más importantes de la moderna biología celular. Su valiosa aportación a la ciencia puede descubrirse a través de los libros que ha escrito y pueden tomarse como referencia para descubrir esta faceta de su perso - nalidad.