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Taxon Ordering in Phylogenetic Trees by Means of Evolutionary Algorithms Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2*
Cerutti et al. BioData Mining 2011, 4:20 http://www.biodatamining.org/content/4/1/20 BioData Mining RESEARCH Open Access Taxon ordering in phylogenetic trees by means of evolutionary algorithms Francesco Cerutti1,2, Luigi Bertolotti1,2, Tony L Goldberg3 and Mario Giacobini1,2* * Correspondence: mario. Abstract [email protected] 1 Department of Animal Production, Background: In in a typical “left-to-right” phylogenetic tree, the vertical order of taxa Epidemiology and Ecology, Faculty of Veterinary Medicine, University is meaningless, as only the branch path between them reflects their degree of of Torino, Via Leonardo da Vinci similarity. To make unresolved trees more informative, here we propose an 44, 10095, Grugliasco (TO), Italy innovative Evolutionary Algorithm (EA) method to search the best graphical Full list of author information is available at the end of the article representation of unresolved trees, in order to give a biological meaning to the vertical order of taxa. Methods: Starting from a West Nile virus phylogenetic tree, in a (1 + 1)-EA we evolved it by randomly rotating the internal nodes and selecting the tree with better fitness every generation. The fitness is a sum of genetic distances between the considered taxon and the r (radius) next taxa. After having set the radius to the best performance, we evolved the trees with (l + μ)-EAs to study the influence of population on the algorithm. Results: The (1 + 1)-EA consistently outperformed a random search, and better results were obtained setting the radius to 8. The (l + μ)-EAs performed as well as the (1 + 1), except the larger population (1000 + 1000). -
Revised Glossary for AQA GCSE Biology Student Book
Biology Glossary amino acids small molecules from which proteins are A built abiotic factor physical or non-living conditions amylase a digestive enzyme (carbohydrase) that that affect the distribution of a population in an breaks down starch ecosystem, such as light, temperature, soil pH anaerobic respiration respiration without using absorption the process by which soluble products oxygen of digestion move into the blood from the small intestine antibacterial chemicals chemicals produced by plants as a defence mechanism; the amount abstinence method of contraception whereby the produced will increase if the plant is under attack couple refrains from intercourse, particularly when an egg might be in the oviduct antibiotic e.g. penicillin; medicines that work inside the body to kill bacterial pathogens accommodation ability of the eyes to change focus antibody protein normally present in the body acid rain rain water which is made more acidic by or produced in response to an antigen, which it pollutant gases neutralises, thus producing an immune response active site the place on an enzyme where the antimicrobial resistance (AMR) an increasing substrate molecule binds problem in the twenty-first century whereby active transport in active transport, cells use energy bacteria have evolved to develop resistance against to transport substances through cell membranes antibiotics due to their overuse against a concentration gradient antiretroviral drugs drugs used to treat HIV adaptation features that organisms have to help infections; they -
Foucault's Darwinian Genealogy
genealogy Article Foucault’s Darwinian Genealogy Marco Solinas Political Philosophy, University of Florence and Deutsches Institut Florenz, Via dei Pecori 1, 50123 Florence, Italy; [email protected] Academic Editor: Philip Kretsedemas Received: 10 March 2017; Accepted: 16 May 2017; Published: 23 May 2017 Abstract: This paper outlines Darwin’s theory of descent with modification in order to show that it is genealogical in a narrow sense, and that from this point of view, it can be understood as one of the basic models and sources—also indirectly via Nietzsche—of Foucault’s conception of genealogy. Therefore, this essay aims to overcome the impression of a strong opposition to Darwin that arises from Foucault’s critique of the “evolutionistic” research of “origin”—understood as Ursprung and not as Entstehung. By highlighting Darwin’s interpretation of the principles of extinction, divergence of character, and of the many complex contingencies and slight modifications in the becoming of species, this essay shows how his genealogical framework demonstrates an affinity, even if only partially, with Foucault’s genealogy. Keywords: Darwin; Foucault; genealogy; natural genealogies; teleology; evolution; extinction; origin; Entstehung; rudimentary organs “Our classifications will come to be, as far as they can be so made, genealogies; and will then truly give what may be called the plan of creation. The rules for classifying will no doubt become simpler when we have a definite object in view. We possess no pedigrees or armorial bearings; and we have to discover and trace the many diverging lines of descent in our natural genealogies, by characters of any kind which have long been inherited. -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
A General Criterion for Translating Phylogenetic Trees Into Linear Sequences
A general criterion for translating phylogenetic trees into linear sequences Proposal (474) to South American Classification Committee In most of the books, papers and check-lists of birds (e.g. Meyer de Schauensee 1970, Stotz et al. 1996; and other taxa e.g. Lewis et al. 2005, Haston et al. 2009, for plants), at least the higher taxa are arranged phylogenetically, with the “oldest” groups (Rheiformes/Tinamiformes) placed first, and the “modern” birds (Passeriformes) at the end. The molecular phylogenetic analysis of Hackett et al. (2008) supports this criterion. For this reason, it would be desirable that in the SACC list not only orders and families, but also genera within families and species within genera, are phylogenetically ordered. In spite of the SACC’s efforts in producing an updated phylogeny-based list, it is evident that there are differences in the way the phylogenetic information has been translated into linear sequences, mainly for node rotation and polytomies. This is probably one of the reasons why Douglas Stotz (Proposal #423) has criticized using sequence to show relationships. He considers that we are creating unstable sequences with little value in terms of understanding of relationships. He added, “We would be much better served by doing what most taxonomic groups do and placing taxa within the hierarchy in alphabetical order, making no pretense that sequence can provide useful information on the branching patterns of trees. This would greatly stabilize sequences and not cost much information about relationships”. However, we encourage creating sequences that reflect phylogeny as much as possible at all taxonomic levels (although we agree with Douglas Stotz that the translation of a phylogenetic tree into a simple linear sequence inevitably involves a loss of information about relationships that is present in the trees on which the sequence is based). -
Synthesis of Phylogeny and Taxonomy Into a Comprehensive Tree of Life
Synthesis of phylogeny and taxonomy into a comprehensive tree of life Cody E. Hinchliffa,1, Stephen A. Smitha,1,2, James F. Allmanb, J. Gordon Burleighc, Ruchi Chaudharyc, Lyndon M. Coghilld, Keith A. Crandalle, Jiabin Dengc, Bryan T. Drewf, Romina Gazisg, Karl Gudeh, David S. Hibbettg, Laura A. Katzi, H. Dail Laughinghouse IVi, Emily Jane McTavishj, Peter E. Midfordd, Christopher L. Owenc, Richard H. Reed, Jonathan A. Reesk, Douglas E. Soltisc,l, Tiffani Williamsm, and Karen A. Cranstonk,2 aEcology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109; bInterrobang Corporation, Wake Forest, NC 27587; cDepartment of Biology, University of Florida, Gainesville, FL 32611; dField Museum of Natural History, Chicago, IL 60605; eComputational Biology Institute, George Washington University, Ashburn, VA 20147; fDepartment of Biology, University of Nebraska-Kearney, Kearney, NE 68849; gDepartment of Biology, Clark University, Worcester, MA 01610; hSchool of Journalism, Michigan State University, East Lansing, MI 48824; iBiological Science, Clark Science Center, Smith College, Northampton, MA 01063; jDepartment of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045; kNational Evolutionary Synthesis Center, Duke University, Durham, NC 27705; lFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; and mComputer Science and Engineering, Texas A&M University, College Station, TX 77843 Edited by David M. Hillis, The University of Texas at Austin, Austin, TX, and approved July 28, 2015 (received for review December 3, 2014) Reconstructing the phylogenetic relationships that unite all line- published phylogenies are available only as journal figures, rather ages (the tree of life) is a grand challenge. The paucity of homologous than in electronic formats that can be integrated into databases and character data across disparately related lineages currently renders synthesis methods (7–9). -
18.4 Bacteria and Archaea Kingdom Eubacteria Domain Bacteria
18.4 Bacteria and Archaea Kingdom Eubacteria Domain Bacteria 18.4 Bacteria and Archaea Description Bacteria are single-celled prokaryotes. 18.4 Bacteria and Archaea Where do they live? Prokaryotes are widespread on Earth. ( Est. over 1 billion types of bacteria, and over 1030 individual prokaryote cells on earth.) Found in all land and ocean environments, even inside other organisms! 18.4 Bacteria and Archaea Common Examples • E. Coli • Tetanus bacteria • Salmonella bacteria • Tuberculosis bacteria • Staphylococcus • Streptococcus 18.4 Bacteria and Archaea Modes Of Nutrition • Bacteria may be heterotrophs or autotrophs 18.4 Bacteria and Archaea Bacteria Reproduce How? • by binary fission. • exchange genes during conjugation= conjugation bridge increases diversity. • May survive by forming endospores = specialized cell with thick protective cell wall. TEM; magnification 6000x • Can survive for centuries until environment improves. Have been found in mummies! 18.4 Bacteria and Archaea • Bacteria Diagram – plasmid = small piece of genetic material, can replicate independently of the chromosome – flagellum = different than in eukaryotes, but for movement – pili = used to stick the bacteria to eachpili other or surfaces plasma membrance flagellum chromosome cell wall plasmid This diagram shows the typical structure of a prokaryote. Archaea and bacteria look very similar, although they have important molecular differences. 18.4 Bacteria and Archaea • Classified by: their need for oxygen, how they gram stain, and their shapes 18.4 Bacteria and Archaea Main Groups by Shapes – rod-shaped, called bacilli – spiral, called spirilla or spirochetes – spherical, called cocci Spirochaeta: spiral Lactobacilli: rod-shaped Enterococci: spherical 18.4 Bacteria and Archaea • Main Groups by their need for oxygen. -
Ten Misunderstandings About Evolution a Very Brief Guide for the Curious and the Confused by Dr
Ten Misunderstandings About Evolution A Very Brief Guide for the Curious and the Confused By Dr. Mike Webster, Dept. of Neurobiology and Behavior, Cornell Lab of Ornithology, Cornell University ([email protected]); February 2010 The current debate over evolution and “intelligent design” (ID) is being driven by a relatively small group of individuals who object to the theory of evolution for religious reasons. The debate is fueled, though, by misunderstandings on the part of the American public about what evolutionary biology is and what it says. These misunderstandings are exploited by proponents of ID, intentionally or not, and are often echoed in the media. In this booklet I briefly outline and explain 10 of the most common (and serious) misunderstandings. It is impossible to treat each point thoroughly in this limited space; I encourage you to read further on these topics and also by visiting the websites given on the resource sheet. In addition, I am happy to send a somewhat expanded version of this booklet to anybody who is interested – just send me an email to ask for one! What are the misunderstandings? 1. Evolution is progressive improvement of species Evolution, particularly human evolution, is often pictured in textbooks as a string of organisms marching in single file from “simple” organisms (usually a single celled organism or a monkey) on one side of the page and advancing to “complex” organisms on the opposite side of the page (almost invariably a human being). We have all seen this enduring image and likely have some version of it burned into our brains. -
The Unicellular and Colonial Organisms Prokaryotic And
The Unicellular and Colonial Organisms Prokaryotic and Eukaryotic Cells As you know, the building blocks of life are cells. Prokaryotic cells are those cells that do NOT have a nucleus. They mostly include bacteria and archaea. These cells do not have membrane-bound organelles. Eukaryotic cells are those that have a true nucleus. That would include plant, animal, algae, and fungal cells. As you can see, to the left, eukaryotic cells are typically larger than prokaryotic cells. Today in lab, we will look at examples of both prokaryotic and eukaryotic unicellular organisms that are commonly found in pond water. When examining pond water under a microscope… The unpigmented, moving microbes will usually be protozoans. Greenish or golden-brown organisms will typically be algae. Microorganisms that are blue-green will be cyanobacteria. As you can see below, living things are divided into 3 domains based upon shared characteristics. Domain Eukarya is further divided into 4 Kingdoms. Domain Kingdom Cell type Organization Nutrition Organisms Absorb, Unicellular-small; Prokaryotic Photsyn., Archaeacteria Archaea Archaebacteria Lacking peptidoglycan Chemosyn. Unicellular-small; Absorb, Bacteria, Prokaryotic Peptidoglycan in cell Photsyn., Bacteria Eubacteria Cyanobacteria wall Chemosyn. Ingestion, Eukaryotic Unicellular or colonial Protozoa, Algae Protista Photosynthesis Fungi, yeast, Fungi Eukaryotic Multicellular Absorption Eukarya molds Plantae Eukaryotic Multicellular Photosynthesis Plants Animalia Eukaryotic Multicellular Ingestion Animals Prokaryotic Organisms – the archaea, non-photosynthetic bacteria, and cyanobacteria Archaea - Microorganisms that resemble bacteria, but are different from them in certain aspects. Archaea cell walls do not include the macromolecule peptidoglycan, which is always found in the cell walls of bacteria. Archaea usually live in extreme, often very hot or salty environments, such as hot mineral springs or deep-sea hydrothermal vents. -
Biology Chapter 19 Kingdom Protista Domain Eukarya Description Kingdom Protista Is the Most Diverse of All the Kingdoms
Biology Chapter 19 Kingdom Protista Domain Eukarya Description Kingdom Protista is the most diverse of all the kingdoms. Protists are eukaryotes that are not animals, plants, or fungi. Some unicellular, some multicellular. Some autotrophs, some heterotrophs. Some with cell walls, some without. Didinium protist devouring a Paramecium protist that is longer than it is! Read about it on p. 573! Where Do They Live? • Because of their diversity, we find protists in almost every habitat where there is water or at least moisture! Common Examples • Ameba • Algae • Paramecia • Water molds • Slime molds • Kelp (Sea weed) Classified By: (DON’T WRITE THIS DOWN YET!!! • Mode of nutrition • Cell walls present or not • Unicellular or multicellular Protists can be placed in 3 groups: animal-like, plantlike, or funguslike. Didinium, is a specialist, only feeding on Paramecia. They roll into a ball and form cysts when there is are no Paramecia to eat. Paramecia, on the other hand are generalists in their feeding habits. Mode of Nutrition Depends on type of protist (see Groups) Main Groups How they Help man How they Hurt man Ecosystem Roles KEY CONCEPT Animal-like protists = PROTOZOA, are single- celled heterotrophs that can move. Oxytricha Reproduce How? • Animal like • Unicellular – by asexual reproduction – Paramecium – does conjugation to exchange genetic material Animal-like protists Classified by how they move. macronucleus contractile vacuole food vacuole oral groove micronucleus cilia • Protozoa with flagella are zooflagellates. – flagella help zooflagellates swim – more than 2000 zooflagellates • Some protists move with pseudopods = “false feet”. – change shape as they move –Ex. amoebas • Some protists move with pseudopods. -
Structural Biology of the C-Terminal Domain Of
STRUCTURAL BIOLOGY OF THE C-TERMINAL DOMAIN OF EUKARYOTIC REPLICATION FACTOR MCM10 By Patrick David Robertson Dissertation Submitted to the Faculty of the Graduate School of Vanderbilt University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biological Sciences August, 2010 Nashville, Tennessee Approved: Brandt F. Eichman Walter J. Chazin James G. Patton Hassane Mchaourab To my wife Sabrina, thank you for your enduring love and support ii ACKNOWLEDGMENTS I would like to begin by expressing my sincerest gratitude to my mentor and Ph.D. advisor, Dr. Brandt Eichman. In addition to your excellent guidance and training, your passion for science has been a source of encouragement and inspiration over the past five years. I consider working with you to be a great privilege and I am grateful for the opportunity. I would also like to thank the members of my thesis committee: Drs. Walter Chazin, Ellen Fanning, James Patton, and Hassane Mchaourab. My research and training would not have been possible without your insight, advice and intellectual contributions. I would like to acknowledge all of the members of the Eichman laboratory, past and present, for their technical assistance and camaraderie over the years. I would especially like to thank Dr. Eric Warren for his contributions to the research presented here, as well for his friendship of the years. I would also like to thank Drs. Benjamin Chagot and Sivaraja Vaithiyalingam from the Chazin laboratory for their expert assistance and NMR training. I would especially like to thank my parents, Joyce and David, my brother Jeff, and the rest of my family for their love and encouragement throughout my life. -
Darwin's “Tree of Life”
Icons of Evolution? Why Much of What Jonathan Wells Writes about Evolution is Wrong Alan D. Gishlick, National Center for Science Education DARWIN’S “TREE OF LIFE” mon descent. Finally, he demands that text- books treat universal common ancestry as PHYLOGENETIC TREES unproven and refrain from illustrating that n biology, a phylogenetic tree, or phyloge- “theory” with misleading phylogenies. ny, is used to show the genealogic relation- Therefore, according to Wells, textbooks Iships of living things. A phylogeny is not should state that there is no evidence for com- so much evidence for evolution as much as it mon descent and that the most recent research is a codification of data about evolutionary his- refutes the concept entirely. Wells is complete- tory. According to biological evolution, organ- ly wrong on all counts, and his argument is isms share common ancestors; a phylogeny entirely based on misdirection and confusion. shows how organisms are related. The tree of He mixes up these various topics in order to life shows the path evolution took to get to the confuse the reader into thinking that when current diversity of life. It also shows that we combined, they show an endemic failure of can ascertain the genealogy of disparate living evolutionary theory. In effect, Wells plays the organisms. This is evidence for evolution only equivalent of an intellectual shell game, put- in that we can construct such trees at all. If ting so many topics into play that the “ball” of evolution had not happened or common ances- evolution gets lost. try were false, we would not be able to discov- THE CAMBRIAN EXPLOSION er hierarchical branching genealogies for ells claims that the Cambrian organisms (although textbooks do not general- Explosion “presents a serious chal- ly explain this well).