DOCSLIB.ORG

A Rooted Net of Life David Williams1*†, Gregory P Fournier2*†, Pascal Lapierre3, Kristen S Swithers1, Anna G Green1, Cheryl P Andam1 and J Peter Gogarten1*

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
A Rooted Net of Life David Williams1*†, Gregory P Fournier2*†, Pascal Lapierre3, Kristen S Swithers1, Anna G Green1, Cheryl P Andam1 and J Peter Gogarten1* Williams et al. Biology Direct 2011, 6:45 http://www.biology-direct.com/content/6/1/45 REVIEW Open Access A Rooted Net of Life David Williams1*†, Gregory P Fournier2*†, Pascal Lapierre3, Kristen S Swithers1, Anna G Green1, Cheryl P Andam1 and J Peter Gogarten1* Abstract Phylogenetic reconstruction using DNA and protein sequences has allowed the reconstruction of evolutionary histories encompassing all life. We present and discuss a means to incorporate much of this rich narrative into a single model that acknowledges the discrete evolutionary units that constitute the organism. Briefly, this Rooted Net of Life genome phylogeny is constructed around an initial, well resolved and rooted tree scaffold inferred from a supermatrix of combined ribosomal genes. Extant sampled ribosomes form the leaves of the tree scaffold. These leaves, but not necessarily the deeper parts of the scaffold, can be considered to represent a genome or pan- genome, and to be associated with members of other gene families within that sequenced (pan)genome. Unrooted phylogenies of gene families containing four or more members are reconstructed and superimposed over the scaffold. Initially, reticulations are formed where incongruities between topologies exist. Given sufficient evidence, edges may then be differentiated as those representing vertical lines of inheritance within lineages and those representing horizontal genetic transfers or endosymbioses between lineages. Reviewers: W. Ford Doolittle, Eric Bapteste and Robert Beiko. Open peer review reconstructed, revealing new aspects of the evolutionary Reviewed by W. Ford Doolittle, Eric Bapteste and Robert process. Beiko. For the full reviews, see the Reviewers’ Comments Substantial incongruities in gene histories and uneven section. taxonomic distributions of gene families within groups of organisms have challenged a tree-like bifurcating process Background as an adequate model to describe organismal evolution The use of DNA and protein sequence residues as charac- [4-6]. In addition, evidence is abundant that the evolu- ter states for phylogenetic reconstruction was a profound tionary history of Eukarya includes numerous primary, breakthrough in biology [1]. It has facilitated advances in secondary and tertiary endosymbiotic events often pro- population genetics and reconstructions of evolutionary viding important traits such as photosynthesis [7]. These histories encompassing all life with most of the molecular inferences have caused a shift in the consensus among diversity found among microorganisms [2]. While progress evolutionary biologists towards a view that the horizontal in theoretical aspects of reconstruction has allowed more transfer of genetic material relative to vertical inheritance confident and detailed inferences, it has also revealed the is a major source of evolutionary innovation [5,8,9]. With necessity for caution, as these inferences can be misleading a growing recognition for the need to represent more if methodologies are not applied with care. At the same than just the lines of vertical inheritance, various alterna- time, exponentially growing sequence databases including tive models have been suggested. These vary in detail but complete genome sequences [3] have allowed a more broadly describe a reticulated network representation of complete picture of biological lineages over time to be organismal relationships [4,6,10-12]. * Correspondence: [email protected]; [email protected]; The Rooted Net of Life [email protected] † Contributed equally In this manuscript we present a model, the Rooted Net of 1Department of Molecular and Cell Biology, University of Connecticut, Storrs, Life, in which the evolutionary relationships of organisms CT 06269-3125, USA aremorefullydescribedthaninexistingTreeofLife 2Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA concepts [13,14]. Importantly, we address the observation Full list of author information is available at the end of the article that organisms consist of many discrete evolutionary © 2011 Williams et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Williams et al. Biology Direct 2011, 6:45 Page 2 of 20 http://www.biology-direct.com/content/6/1/45 units: open reading frames, operons, plasmids, chromo- in practice, explicitly described by molecular phylogenies. somes and in some cases plastids and other organelles, As such, the ToCD is only knowable insofar that a verti- each with discrete and possibly different evolutionary his- cal signal is preserved; if all gene histories were domi- tories. These multiple histories are combined and plotted nated by random horizontal transfer, there would be no as a single reticulated network phylogenetic representa- connection between cellular and genetic history. Addi- tion in which misleading artifacts of reconstruction and tionally, the ToCD concept fails when a new cell is cre- loss of information due to the averaging of phylogenetic ated through the fusion of two cells. If this fusion is part signals are minimized. In some instances it may be possi- of the sexual life cycle, the principle of the ToCD is vio- ble to assign some edges as representative of ancestral lated, but the deviations may be inconsequential if phylo- vertical descent by genetic inheritance and other edges as geny is considered at a larger scale. However, instances reticulations due to horizontal genetic transfers. In other of symbioses that lead to lineage and/or cell fusions instances, this decision is less certain, for example, did between divergent partners (as in the serial endosymbio- the ancestor of the Thermotogales acquire the ribosome sis theory for eukaryogenesis, if mitochondria and plas- from a relative of the Aquificales, or did the Thermoto- tids are no longer considered individual cells) lead to gales acquire most of their genes from the clostridia? reticulations in the ToCD. Therefore, when all life is (See “Highways of Gene Sharing” below for details.) included, the ToCD does not represent a strictly bifurcat- Despite the distinct evolutionary histories among the ing process. genes in an organism, when they are found together in Bridging the gap between gene and species trees has an extant genome, they are assigned to the same terminal traditionally been approached via two methods: (1) super- node and edge that remains intact until their histories matrix methods, which seek to infer a species tree by the differ. This organism-genome definition includes his- concatenation of a large number of genes, integrating tories of endosymbioses, which evolved to a point of across many sites within aligned sequences to arrive at a bidirectional dependence e.g., mitochondria and plastids well-supported, comprehensive tree [17]; and (2) supertree with the “host” cell [7], but excludes parasitisms and methods, which integrate across phylogenies calculated for mutualisms in which partners are facultative or inter- many individual genes [18]. Both methods attempt to changeable e.g., the gut microflora of animals [15]. Ribo- arrive at a consensus phylogeny to approximate the spe- somal RNA and protein sequences are combined into a cies tree by overcoming the insufficient and occasionally supermatrix and used to infer a well-resolved phyloge- conflicting phylogenetic information that each molecular netic tree scaffold which we anticipate to mostly, but not unit (typically genes) can provide. However, if applied necessarily, approximate the vertical descent of a coher- indiscriminately, biased horizontal gene transfer can invali- ent biological entity (but see the “Endosymbioses” section date these methodologies, as multiple strong, distinct below). One terminal node may represent a group of phylogenetic patterns can exist within a dataset [10,19]. In sequenced genomes sharing very similar ribosomal this case, it is possible that the resulting phylogeny will sequences. All other genetic sequences including plas- not only be incorrect, but even contain bipartitions not mids and chromosomes are assigned to tips by member- supported by any subset of the data due to fallacious aver- ship within these ribosome-defined pan-genomes and are aging between signals [20]. While these approaches further grouped into homologous gene families across acknowledge that a comprehensive history of life must other tips. Reconstructed phylogenetic trees of each are take into account many individual gene histories, it is clear superimposed on top of the scaffold, forming reticula- that, at best, this is insufficient for capturing the true com- tions where necessary. plexity of the evolution of life. In supermatrix approaches, to avoid averaging over phy- The Ribosomal Tree Scaffold logenies with conflicting phylogenetic signal, gene families The complex relationship between individual genetic with conflicting gene phylogenies are usually removed. components and the evolutionary history of organisms This results in genome or species phylogenies that only must be well understood in order for a biologically mean- represent a small fraction of the genetic information ingful, comprehensive history of life to be assembled within each organism, the so-called “tree of one percent” from molecular data. Since species are propagated
Load more

Recommended publications
  • Cancer-Milestones December 2020
    www.nature.com/collections/cancer-milestones December 2020 Cancer Produced by: With support from: Nature Genetics and Nature Medicine Cancer MILESTONES S2 Foreword S3 Timeline S4 Routes to resistance S5 Tracking cancer in liquid biopsies S6 When cancer prevention went viral S7 A licence to kill S8 Sitting on the fence S9 Not a simple switch S10 Sequencing the secrets of the cancer genome S11 Unleashing the immune system against cancer S12 Engineering armed T cells for the fight S13 Oncohistones: epigenetic drivers of cancer S14 Tumour evolution: from linear paths to branched trees S15 Undruggable? Inconceivable S16 Good bacteria make for good cancer therapy S17 The AI revolution in cancer Credit: S.Fenwick/Springer Nature Limited CITING THE MILESTONES VISIT THE SUPPLEMENT ONLINE SUBSCRIPTIONS AND CUSTOMER SERVICES Nature Milestones in Cancer includes Milestone articles written The Nature Milestones in Cancer supplement can be found at Springer Nature, Subscriptions, by our editors and an online Collection of previously published www.nature.com/collections/cancer-milestones Cromwell Place, Hampshire International Business Park, material. To cite the full project, please use Nature Milestones: Lime Tree Way, Basingstoke, Cancer https://www.nature.com/collections/cancer-milestones CONTRIBUTING JOURNALS Hampshire RG24 8YJ, UK (2020). Should you wish to cite any of the individual Milestones, BMC Cancer, Nature, Nature Cancer, Nature Communications, Tel: +44 (0) 1256 329242 please list Author, A. Title. Nature Milestones: Cancer <Article URL> Nature Genetics, Nature Medicine, Nature Reviews Cancer, [email protected] (2020). For example, Milestone 1 is Valtierra, I. Routes to resistance. Nature Reviews Clinical Oncology, Nature Reviews Drug Discovery, Customer serviCes: www.nature.com/help Nature Milestones: Cancer https://www.nature.com/articles/ Nature Reviews Gastroenterology & Hepatology, d42859-020-00069-6 (2020).
    [Show full text]
  • Understanding Biological Design from Synthetic Circuits
    REVIEWS MODELLING Synthetic biology: understanding biological design from synthetic circuits Shankar Mukherji* and Alexander van Oudenaarden‡ Abstract | An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems — from synthetic promoters to the control of cell–cell interactions — has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics. 10–12 Modularity One of the most astounding findings of the Human potential clinical applications . In this Review, however, A property of a system such Genome Project was that our genome contains as many we focus on how synthetic circuits help us to under- that it can be broken down into genes as that of Drosophila melanogaster. This finding stand how natural biological systems are genetically discrete subparts that perform begged the question: how do you get one organism to assembled and how they operate in organisms from specific tasks independently of look like a fly and another like a human with the same microbes to mammalian cells. In this light, synthetic the other subparts. number of genes? One possibility is that the rich rep- circuits have been crucial as simplified test beds in Bioremediation ertoire of non-protein-coding sequences found in the which to refine our ideas of how similarly structured The treatment of pollution with genomes of complex organisms adds many new parts natural networks function, and they have served as microorganisms.
    [Show full text]
  • Michael Lynch
    1 Michael Lynch Center for Mechanisms of Evolution, Biodesign Institute Arizona State University Tempe, AZ 85287 Phone: 480-965-0868 Email: [email protected] Birth: 6 December 1951, Auburn, New York Undergraduate education: St. Bonaventure University, Biology - B.S., 1973. Graduate education: University of Minnesota, Ecology and Behavioral Biology - Ph.D., 1977 (advisor: J. Shapiro). Areas of Interest and Research: The integration of molecular and cellular biology, genetics, and evolution; population and quantitative genetics; molecular, genomic, and phenotypic evolution. Select Professional Activities and Service: Director, Biodesign Center for Mechanisms of Evolution, Arizona State University, 2017 – present. Professor, School of Life Sciences, Arizona State University, 2017 – present. Class of 1954 Professor, 2011 – 2017. Distinguished Professor, Indiana University, 2005 – 2017. Professor; Biology, Indiana University, 2001 – 2004. Adjunct Professor, Computer Science, Indiana University, 2014 – 2017. Adjunct Professor, Physics, Indiana University, 2015 – 2017. Professor; Biology, University of Oregon, 1989 – 2001. Director, Ecology and Evolution Program, Univ. of Oregon, 1989 – 1993, 1996 – 2000. Asst., Assoc., Full Professor; Ecology, Ethology, and Evolution; University of Illinois, 1977 – 1989. Co-director, NSF IGERT Training Grant in Evolution, Development, and Genomics, 1999 – 2004. Director, NSF Genetic Mechanisms of Evolution Training Grant, 1990 – 2000. President, Genetics Society of America, 2013. President, Society for Molecular Biology and Evolution, 2009. President, American Genetic Association, 2007. President, Society for the Study of Evolution, 2000. Chair-elect, Section on Biological Sciences American Association for the Advancement of Science, 2017-2020. Vice-president, Genetics Society of America, 2012. Vice-president, Society for the Study of Evolution, 1994. Council Member, Society for the Study of Evolution, 1991 – 1993.
    [Show full text]
  • Towards Population-Scale Long-Read Sequencing
    REVIEWS Towards population-scale long-read sequencing Wouter De Coster 1,2,5, Matthias H. Weissensteiner3,5 and Fritz J. Sedlazeck 4 ✉ Abstract | Long-read sequencing technologies have now reached a level of accuracy and yield that allows their application to variant detection at a scale of tens to thousands of samples. Concomitant with the development of new computational tools, the first population-scale studies involving long-read sequencing have emerged over the past 2 years and, given the continuous advancement of the field, many more are likely to follow. In this Review, we survey recent developments in population-scale long-read sequencing, highlight potential challenges of a scaled-up approach and provide guidance regarding experimental design. We provide an overview of current long-read sequencing platforms, variant calling methodologies and approaches for de novo assemblies and reference-based mapping approaches. Furthermore, we summarize strategies for variant validation, genotyping and predicting functional impact and emphasize challenges remaining in achieving long-read sequencing at a population scale. Genome-wide association Sequencing the DNA or mRNA of multiple individuals These studies highlighted that a substantial proportion studies of one or more species (that is, population-scale sequenc- of hidden variation can be discovered with long-read (GWAS). Studies involving a ing) aims to identify genetic variation at a population sequencing. Indeed, recent long-read sequencing stud- statistical approach in genetics level to address questions in the fields of evolutionary, ies of Icelandic and Chinese populations have already to identify variants that correlate with a certain agricultural and medical research. Previous popula- identified previously undetected variants associated with 11,12 phenotype (for example, a tion studies, including genome-wide association studies height, cholesterol level and anaemia .
    [Show full text]
  • How We Are Evolving New Analyses Suggest That Recent Human Evolution Has Followed a Di!Erent Course Than Biologists Would Have Expected
    XXXXXXXX 40 Scientific American, October 2010 Photograph/Illustration by Artist Name © 2010 Scientific American Jonathan K. Pritchard is professor of human genetics at the University of Chicago and a Howard Hughes Medical Institute investigator. He studies genetic variation within and between human populations and the processes that led to this variation. E VO LU T I O N How We Are Evolving New analyses suggest that recent human evolution has followed a di!erent course than biologists would have expected By Jonathan K. Pritchard IN BRIEF As early Homo sapiens spread out from Many scientists thus expected that sur- ural selection—that is, because those nome contains some examples of very Africa starting around 60,000 years ago, veys of our genomes would reveal con- who carry the mutations have greater strong, rapid natural selection, most of they encountered environmental chal- siderable evidence of novel genetic mu- numbers of healthy babies than those the detectable natural selection appears lenges that they could not overcome tations that have recently spread quickly who do not. to have occurred at a far slower pace with prehistoric technology. ïà¹ù¹ùïmyày´ïȹÈù¨Dï¹´åUĂ´Dï- But it turns out that although the ge- than researchers had envisioned. Illustrations by Owen Gildersleeve October 2010, ScientificAmerican.com 41 © 2010 Scientific American !"#$%&'$ "( )*%+$ %," !#-%&$ -".*' ("+ /!* in technologies for studying genetic variation, we were able to first time into the Tibetan plateau, a vast ex- begin to address these questions. panse of steppelands that towers some 14,000 The work is still under way, but the preliminary findings have feet above sea level.
    [Show full text]
  • Measuring the Societal Impact of Open Science – Presentation of a Research Project
    InformaatiotutkimusKATSAUS 34(4), 2015 Holmberg et al: Measuring... 1 Holmberg, K.*,1, Didegah, F. 1, Bowman, S. 1, Bowman, T.D. 1, & Kortelainen, T.2 Measuring the societal impact of open science – Presentation of a research project Address: 1Research Unit for the Sociology of Education, University of Turku 2Information Studies, University of Oulu Email: *[email protected] Introduction data, and 2) investigate novel quantitative indica- tors of research impact to incentivize researchers Research assessment has become increasingly in adopting the open science movement. important—especially in these economically challenging times—as funders of research try to Assessing impact of research identify researchers, research groups, and uni- versities that are most deserving of the limited Two approaches have traditionally been used to funds. The goal of any research assessment is to assess research impact: (1) assessments based on discover research that is of the highest quality and citations and (2) assessments based on publica- therefore more deserving of funding. As quality is tion venues. Both approaches have issues that are very difficult and time-consuming to assess and well-documented (e.g., Vanclay, 2012). Citations can be highly subjective, other approaches have have been found to not always reflect quality or been preferred for assessment purposes (especially intellectual debt as they can be created for many when assessing big data). Research assessments different reasons, some of which do not reflect usually focus on evaluating the level of impact a the scientific value of the cited article (Borgman research product has made; impact is therefore & Furner, 2002). In addition citations can take a used as a proxy for quality.
    [Show full text]
  • Denkanstöße 5/2021
    Denkanstöße 5 aus der Akademie Juli/2021 Eine Schriftenreihe der Berlin-Brandenburgischen Akademie der Wissenschaften Andreas Radbruch und Konrad Reinhart (Hrsg.) NACHHALTIGE MEDIZIN Berlin-Brandenburgische Akademie der Wissenschaften (BBAW) NACHHALTIGE MEDIZIN NACHHALTIGE MEDIZIN Andreas Radbruch und Konrad Reinhart (Hrsg.) Denkanstöße 5/Juli 2021 Herausgeber: Der Präsident der Berlin-Brandenburgischen Akademie der Wissenschaften Redaktion: Elke Luger, Roman Marek und Ute Tintemann Grafik: angenehme gestaltung/Thorsten Probst Druck: PIEREG Druckcenter Berlin GmbH © Berlin-Brandenburgische Akademie der Wissenschaften, 2021 Jägerstraße 22–23, 10117 Berlin, www.bbaw.de Lizenz: CC-BY-NC-SA ISBN: 978-3-949455-00-1 INHALTSVERZEICHNIS Vorwort ....................................................................... 7 Christoph Markschies Einführung in das Thema ...................................................... 9 Britta Siegmund, Max Löhning, Detlev Ganten und Roman M. Marek Einleitung – Wie kann Medizin „nachhaltig“ sein? ............................15 Andreas Radbruch und Konrad Reinhart NACHHALTIGE BIOMEDIZINISCHE FORSCHUNG Nachhaltigkeit in der Medizin: Einzelzellanalysen in Diagnostik und Therapie ................................20 Nikolaus Rajewsky Regenerative Therapien ......................................................26 Hans-Dieter Volk und Petra Reinke ‚genomDE’ – Eine Chance für die deutsche Genommedizin und -forschung ...............................................32 Karl Sperling und Hans-Hilger Ropers Gesundheit neu denken:
    [Show full text]
  • Prof. Lori B. Andrews
    LORI B. ANDREWS, J.D. IIT Chicago-Kent College of Law • 565 West Adams Street • Chicago, Illinois 60661 312-906-5359 (phone) • 312-906-5388 (fax) • [email protected] EMPLOYMENT: CHICAGO-KENT COLLEGE OF LAW, ILLINOIS INSTITUTE OF TECHNOLOGY, August 1993 – Present Distinguished Professor of Law, 2000 – Present Professor of Law, 1993 – 2000 ILLINOIS INSTITUTE OF TECHNOLOGY INSTITUTE FOR SCIENCE, LAW AND TECHNOLOGY Director, June 1998 – present ILLINOIS INSTITUTE OF TECHNOLOGY Associate Vice President, June 1998 – June 2012 PRINCETON UNIVERSITY, January 2002 – May 2002 Visiting Professor, Public and International Affairs UNIVERSITY OF CHICAGO Senior Scholar, Center for Clinical Medical Ethics, July 1987 – June 2001 Adjunct Professor, School of Law and Graduate School of Business, at various points between 1980 and 1993. CASE WESTERN RESERVE UNIVERSITY SCHOOL OF LAW, January 2000 – June 2000 Ben C. Green Visiting Professor AMERICAN BAR FOUNDATION, April 1980 – September 1997 Research Fellow UNIVERSITY OF HOUSTON LAW CENTER, January 1992 Visiting Professor (taught a three-credit genetics and law course over intersession) AMERICAN BAR ASSOCIATION, September 1978 – April 1980 Assistant Director, Legal Services Group EDUCATION: YALE LAW SCHOOL–Juris Doctor, 1978 Teaching Assistant, Constitutional Law with Professor Eugene Rostow Summer Associate, Cravath, Swaine & Moore, New York YALE UNIVERSITY–Bachelor of Arts, summa cum laude, 1975 Phi Beta Kappa Departmental Honors in Psychology Lori B. Andrews - 2 BOOKS: I Know Who You Are and I Saw What You Did: Social Networks and the Death of Privacy (Simon and Schuster 2012, paperback 2013). Published in Japanese (East Press Co. Ltd., 2013), Arabic (Obeikan Research & Development, 2015), Korean (Youngjin, 2016), and Chinese (Hangzhou Blue Lion Cultural & Creative, 2016).
    [Show full text]
  • Integrating Inclusive Inheritance Into an Extended Theory of Evolution
    REVIEWS Beyond DNA: integrating inclusive inheritance into an extended theory of evolution Étienne Danchin*‡, Anne Charmantier§, Frances A. Champagne||, Alex Mesoudi¶, Benoit Pujol*‡ and Simon Blanchet*# Abstract | Many biologists are calling for an ‘extended evolutionary synthesis’ that would ‘modernize the modern synthesis’ of evolution. Biological information is typically considered as being transmitted across generations by the DNA sequence alone, but accumulating evidence indicates that both genetic and non-genetic inheritance, and the interactions between them, have important effects on evolutionary outcomes. We review the evidence for such effects of epigenetic, ecological and cultural inheritance and parental effects, and outline methods that quantify the relative contributions of genetic and non-genetic heritability to the transmission of phenotypic variation across generations. These issues have implications for diverse areas, from the question of missing heritability in human complex-trait genetics to the basis of major evolutionary transitions. Modern synthesis When Charles Darwin was born in 1809, the idea causes, one of which is that heritability estimates are 10 The merging of Darwinism with that species change over time — that is, evolve — had incorrect , or at least misinterpreted, mainly because genetics that occurred from already emerged1. However, it was only half a century non-genetic heritability is often confounded with the 1930s to the 1950s. later, when Darwin published On the Origin of Species2, purely genetic effects. There is increasing awareness that the theory of evolution profoundly transformed that non-genetic information can also be inherited our understanding of life. Darwin understood that across generations (reviewed in REFS 8,11–13). The natural selection can only affect traits in which there is concepts of ‘general heritability’ (REF.
    [Show full text]
  • Ambiguity and Scientific Authority: Population Classification In
    ASRXXX10.1177/0003122416685812American Sociological ReviewPanofsky and Bliss 6858122017 American Sociological Review 2017, Vol. 82(1) 59 –87 Ambiguity and Scientific © American Sociological Association 2017 DOI: 10.1177/0003122416685812 Authority: Population journals.sagepub.com/home/asr Classification in Genomic Science Aaron Panofskya and Catherine Blissb Abstract The molecularization of race thesis suggests geneticists are gaining greater authority to define human populations and differences, and they are doing so by increasingly defining them in terms of U.S. racial categories. Using a mixed methodology of a content analysis of articles published in Nature Genetics (in 1993, 2001, and 2009) and interviews, we explore geneticists’ population labeling practices. Geneticists use eight classification systems that follow racial, geographic, and ethnic logics of definition. We find limited support for racialization of classification. Use of quasi-racial “continental” terms has grown over time, but more surprising is the persistent and indiscriminate blending of classification schemes at the field level, the article level, and within-population labels. This blending has led the practical definition of “population” to become more ambiguous rather than standardized over time. Classificatory ambiguity serves several functions: it helps geneticists negotiate collaborations among researchers with competing demands, resist bureaucratic oversight, and build accountability with study populations. Far from being dysfunctional, we show the ambiguity of population definition is linked to geneticists’ efforts to build scientific authority. Our findings revise the long-standing theoretical link between scientific authority and standardization and social order. We find that scientific ambiguity can function to produce scientific authority. Keywords genetics, race, ethnicity, geography, standardization, ambiguity, authority One of the most commented upon puzzles of genetics shows race not to be a scientific con- the postgenomic era is the paradox of race.
    [Show full text]
  • Life & Physical Sciences
    2018 Media Kit Life & Physical Sciences Impactful Springer Nature brands, influential readership and content that drives discovery. ASTRONOMY SPRINGER NATURE .................................2 BEHAVIORAL SCIENCES BIOMEDICAL SCIENCES OUR AUDIENCE & REACH ........................3 BIOPHARMA CELLULAR BIOLOGY ADVERTISING SOLUTIONS & CHEMISTRY EARTH SCIENCES PARTNERING OPPORTUNITIES .................6 ELECTRONICS JOURNAL AUDIENCE & CALENDARS .........8 ENERGY ENGINEERING SCIENTIFIC DISCIPLINES ......................17 ENVIRONMENTAL SCIENCES GENETICS A-Z JOURNAL LIST ...............................19 IMMUNOLOGY, MICROBIOLOGY LIFE SCIENCES MATERIALS SCIENCES MEDICINE METHODS, PROTOCOLS MULTIDISCIPLINARY NEUROLOGY, NEUROSCIENCE ONCOLOGY, CANCER RESEARCH PHARMACOLOGY PHYSICS PLANT SCIENCES SPRINGER NATURE SPRINGER NATURE QUALITY CONTENT Springer Nature is a leading publisher of scientific, scholarly, professional and educational content. For more than a century, our brands have set the scientific agenda. We’ve published ground-breaking work on many fundamental achievements, including the splitting of the atom, the structure of DNA, and the discovery of the hole in the ozone layer, as well as the latest advances in stem-cell research and the results of the ENCODE project. Our dominance in the scientific publishing market comes from a company-wide philosophy to uphold the highest level of quality for our readers, authors and commercial partners. Our family of trusted scientific brands receive 131 MILLION* page views each month reaching an audience
    [Show full text]
  • The Functional Genomics of Inbreeding Depression: a New Approach to an Old Problem Author(S): Ken N
    The Functional Genomics of Inbreeding Depression: A New Approach to an Old Problem Author(s): Ken N. Paige Source: BioScience, Vol. 60, No. 4 (April 2010), pp. 267-277 Published by: Oxford University Press on behalf of the American Institute of Biological Sciences Stable URL: http://www.jstor.org/stable/10.1525/bio.2010.60.4.5 Accessed: 03-08-2015 15:55 UTC Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at http://www.jstor.org/page/ info/about/policies/terms.jsp JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. Oxford University Press and American Institute of Biological Sciences are collaborating with JSTOR to digitize, preserve and extend access to BioScience. http://www.jstor.org This content downloaded from 130.126.52.115 on Mon, 03 Aug 2015 15:55:53 UTC All use subject to JSTOR Terms and Conditions 21st Century Directions in Biology The Functional Genomics of Inbreeding Depression: A New Approach to an Old Problem KEN N. PAIGE The fitness consequences of inbreeding have attracted the attention of biologists since the time its harmful effects were first recognized by Charles Darwin. Although inbreeding depression has been a central theme in biological research for over a century, little is known about its underlying molecular basis.
    [Show full text]