DOCSLIB.ORG

Evaluating, Accelerating and Extending the Multispecies Coalescent Model of Evolution

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Evaluating, Accelerating and Extending the Multispecies Coalescent Model of Evolution Huw Alexander Ogilvie December 2017 A thesis submitted for the degree of Doctor of Philosophy of The Australian National University. © Copyright by Huw Alexander Ogilvie 2017 All Rights Reserved Declaration The length of this thesis is 30,924 words, exclusive of footnotes, tables, figures, maps, bibli- ographies and appendices. The abstract, introduction and conclusion of the thesis are my own original work, with input and advice from my chair supervisor, Professor Craig Moritz. Each chapter was based on research conducted jointly with others, and all chapters have been published in or submitted to peer-reviewed journals. Chapter 1 was published in 2016 in Systematic Biology as “Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods” (volume 65, is- sue 3, pages 381–396). The authors are Huw A. Ogilvie, Joseph Heled, Dong Xie and Alexei J. Drummond. DX and AJD designed, conducted, and analysed the results of Experiment 1. JH and HAO analysed the results of Experiment 2, which was designed and conducted by JH. HAO designed, conducted, and analysed the results of Experiment 3. All authors contributed to the writing of the manuscript. Chapter 2 was published in 2017 in Molecular Biology and Evolution as “StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates” (vol- ume 34, issue 8, pages 2101–2114). The authors are Huw A. Ogilvie, Remco R. Bouckaert and Alexei J. Drummond. HAO and RRB wrote the StarBEAST2 software. HAO designed, conducted and analysed the results of all experiments with advice and input from AJD. The manuscript was written by HAO with advice and input from AJD. i Chapter 3 was published online in 2017 in Molecular Biology and Evolution as “Bayesian Inference of Species Networks from Multilocus Sequence Data”. The authors are Chi Zhang, Huw A. Ogilvie, Alexei J. Drummond and Tanja Stadler. The SpeciesNetwork software was written by HAO and CZ with input from AJD and TS. The birth-hybridization process was derived by TS and CZ. CZ designed, conducted and analysed the results of all experiments with input from HAO and AJD. The manuscript was written by CZ and HAO with input from TS and AJD. Chapter 4 has been submitted to Systematic Biology as “Inferring Species Trees Using Inte- grative Models of Species Evolution”. The authors are Huw A. Ogilvie, Timothy G. Vaughan, Nicholas J. Matzke, Graham J. Slater, Tanja Stadler, David Welch and Alexei J. Drummond. The integrative model of species evolution was formulated by AJD, TS and HAO. Software to support the model was developed by HAO with input from AJD. TGV designed, conducted and analysed the results of experiments to test the correctness of the implementation, with input from HAO. HAO designed, conducted and analysed the results of all other experiments with input from AJD, NJM and GJS. The manuscript with written by HAO with input from all other authors, and parts of the introduction were based on a grant application authored by and awarded to AJD, NJM, TS, TGV and DW. Huw Alexander Ogilvie, December 15th 2017 ii Acknowledgments This thesis is large and contains multitudes. By that I mean although I am the nominal author and wrote much of the text and code, it is the product of everyone who has supported me. Of course I rst have to thank my doctoral committee of Craig Moritz, Alexei Drummond and Jason Bragg. Each of them believed in me, and I hope I have absorbed some of their copious knowledge and wisdom in the process of completing my PhD. Thanks also to Tanja Stadler who, although not an ocial member of my committee, oversaw a good chunk of my PhD research. Prior to my PhD my honours supervisors Michael Djordjevic and Nijat Imin, and my honours examiners John Rathjen and Ulrike Mathesius, taught me much about research and academia — preparing me for what was to come. For the last ve years I have been part of a community of honours students, PhD students, and postdocs, and it was understood by everyone that we are all in this together. In alpha- betical order, the following people from this community made life and work much easier for me: Adam, Alex P, Alex G, Ana, Ariel, Armand, Bec, Bo, Chi, Christiana, Connie, Damien, Dan, David, Duncan, Eli, Fábio, Ian, Izzy, Jack, Jared, Jessica, Jessie, Jo, Joëlle, John, Jordan, Josh, Jūlija, Karen, Kelly, Kevin, Lauren, Leo, Liam, Louisa, Marta, Meenu, Megan, Michael T, Mitzy, Mozes, Nadia, Nick, Nicola, Ollie, Paul, Regina, Sally, Sasha, Stephen, Susan, Tim, Vero, Veronica, Veronika, Viri, and Xia. If anyone is missing from that list, it is because my memory is temporarily out-of-order as a side efect of writing a thesis. iii My parents, Teresa and Ian, my late grandparents, Graeme and Pix, and my brother Martin made me who I am today. My grandfather was a research scientist at CSIRO, and my admira- tion for him certainly predisposed me towards a career in science. In addition to my family and academic buddies, thanks to everyone I know in a non-science, non-blood-relative capacity (although one of them has a PhD, it’s in evolutionary compu- tation and not computational evolution). Especially Rico, Shan Shan, He Chuan, Robbie, John, Ben, Nick, Dzung, Darryl, Yin, Damien, Ron and Miri. Benji, the best dog in the world, helped too. I am legally required to acknowledge that “This research is supported by an Australian Government Research Training Program (RTP) Scholarship” iv Abstract So much research builds on evolutionary histories of species and genes. They are used in genomics to infer synteny, in ecology to describe and predict biodiversity, and in molecular biology to transfer knowledge acquired in model organisms to humans and crops. Beyond downstream applications, expanding our knowledge of life on Earth is important in its own right. From Naturalis Historia to On the Origin of Species, the acquisition of this knowledge has been a part of human development. Evolutionary histories are commonly represented as trees, where a common ancestor pro- gressively splits into descendant species or alleles. Time trees add more information by using height to represent genetic distance or elapsed time. Species and gene trees can be inferred from molecular sequences using methods which are explicitly model-based, or implicitly as- sume or are statistically consistent with a particular model of evolution. One such model, the multispecies coalescent (MSC), is the topic of my thesis. Under this model, separate trees are inferred for the species history and for each gene’s history. Gene trees are embedded within the species tree according to a coalescent process. Researchers often avoid the MSC when reconstructing time trees because of claims that available implementations are too computationally demanding. Instead, the species history is inferred using a single tree by concatenating the sequences from each gene. I began my thesis research by evaluating the effect of this approximation. In a realistic simulation based on pa- rameters inferred from empirical data, concatenation was grossly inaccurate, especially when estimating recent species divergence times. In a later simulation study I demonstrated that when using concatenation, credible intervals often excluded the true values. v To address reluctance towards using the MSC, I developed a faster implementation of the model. “StarBEAST2” is a Markov chain Monte Carlo (MCMC) method, meaning it char- acterizes the probability distribution over trees by randomly walking the parameter space. I improved computational performance by developing more efficient proposals used to traverse the space, and reducing the number of parameters in the model through analytical integration of population sizes. Despite its sophistication, the MSC has theoretical limitations. One is that the substitution rate is assumed to stay constant, or uncorrelated between lineages of different genes. How- ever substitution rates do vary and are associated with species traits like body size. I addressed this assumption in StarBEAST2 by extending the MSC to estimate substitution rates for each species. Another assumption is that genetic material cannot be transferred “horizontally”, but a more general model called the multispecies network coalescent (MSNC) permits introgres- sion of alleles across species boundaries. My collaborators and I have developed and evaluated an MCMC implementation of the the MSNC. My final thesis project was to combine the MSC with the fossilized birth-death (FBD) pro- cess, which models how species are fossilized and sampled through time. To demonstrate the utility of the FBD-MSC model, I used it to reconstruct the evolutionary history of Caninae (dogs and foxes) using fossil data and molecular sequences. vi Contents 0 Introduction 1 0.1 Inferring trees from data ............................ 2 0.2 Inferring species trees ............................. 4 0.3 Evaluating and accelerating the multispecies coalescent ............ 6 0.4 Extending the multispecies coalescent ..................... 8 1 Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods 13 1.1 Introduction ................................. 14 1.2 Methods .................................... 17 1.3 Results .................................... 25 1.4 Discussion and conclusions .......................... 38 1.5 Supplementary information and data ..................... 46 1.6 Acknowledgements .............................
Recommended publications
  • Paul J. Weitz, Commander of the Maiden Voyage of Challenger, Dies at 85 Scott Altman  John Blaha  Larry Bradley  ORLANDO – Paul J

    Paul J. Weitz, Commander of the Maiden Voyage of Challenger, Dies at 85 Scott Altman  John Blaha  Larry Bradley  ORLANDO – Paul J

    Paul Joseph Weitz was born in Erie, Pa., on July 25, 1932. He graduated from Harbor Creek High School in Harborcreek, Pa., which later renamed the school’s stadium a�er him. He is survived by his two children, Ma�hew and Cynthia. BOARD OF DIRECTORS Contact: FOR IMMEDIATE RELEASE Curtis Brown Laura Cutchens October 23, 2017 Chairman Based in Orlando, the Astronaut Scholarship Founda�on annually funds scholarships up to $10,000 50 students with Lisa Schott Execu�ve Vice President External Affairs Vice Chairman Astronaut Scholarship Founda�on support from astronauts from the Mercury, Gemini, Apollo, Skylab, Space Shu�le and Space Sta�on programs who Michael Neukamm Secretary Office: 407-403-5907 par�cipate in this educa�onal effort. ASF also accepts other contribu�ons. Vincent Cimino Treasurer Cell: 407-474-3196 Kevin Chilton [email protected] -30- Tammy Sudler www.astronautscholarship.org President & CEO James Lovell Chairman Emeritus Paul J. Weitz, Commander of the Maiden Voyage of Challenger, Dies at 85 Scott Altman John Blaha Larry Bradley ORLANDO – Paul J. Weitz, the re�red astronaut and naval aviator who returned from re�rement to Daniel Brandenstein command the maiden voyage of the space shu�le Challenger in 1983, died Monday (Oct. 23) at his Richard Covey Charles Duke home in Flagstaff, Az., according to friends. He was 85. Chris Ferguson Fred Gregory Joseph Han “Paul Weitz’s name will always be synonymous with the space shu�le Challenger. But he also will be Jeffrey Hoffman Charles Precourt remembered for defying the laws of gravity – and age.
  • JOHN NOVEMBRE, Phd

    JOHN NOVEMBRE, Phd

    JOHN NOVEMBRE, PhD The University of Chicago Department of Human Genetics 920 E 58th Steet CLSC 421 Chicago, IL 60637 Email: [email protected] Webpage: http://jnpopgen.org/ Curriculum Vitae Formatted to Guidelines for UChicago Biological Sciences Division ACADEMIC APPOINTMENTS 2017- Professor, University of Chicago, Department of Human Genetics, Department of Ecology and Evolutionary Biology (secondary appointment) 2013-2017 Associate Professor, University of Chicago, Department of Human Genetics, Department of Ecology and Evolutionary Biology (secondary appointment) 2012-2013 Associate Professor, University of California–Los Angeles, Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics 2008-2012 Assistant Professor, University of California–Los Angeles, Department of Ecology and Evolutionary Biology, Interdepartmental Program in Bioinformatics Ph.D.-Granting Committee, Program, Institute, and Center Appointments 2013- Committee on Evolutionary Biology, University of Chicago 2013- Committee on Genetics, Genomics, and Systems Biology, University of Chicago 2008-2013 Indepartmental Program in Bioinformatics, UCLA 2012-2009 Center for Society and Genetics, UCLA ACADEMIC TRAINING 2006-2008 Postdoctoral training, Department of Human Genetics University of Chicago, Chicago, IL. Advisor: Matthew Stephens 2006 PhD, Integrative Biology, designated emphasis in Computational Biology/Genomics University of California-Berkeley, Berkeley, CA. Advisor: Montgomery Slatkin Dissertation title: Statistical methods
  • Natural Selection and Coalescent Theory

    Natural Selection and Coalescent Theory

    Natural Selection and Coalescent Theory John Wakeley Harvard University INTRODUCTION The story of population genetics begins with the publication of Darwin’s Origin of Species and the tension which followed concerning the nature of inheritance. Today, workers in this field aim to understand the forces that produce and maintain genetic variation within and between species. For this we use the most direct kind of genetic data: DNA sequences, even entire genomes. Our “Great Obsession” with explaining genetic variation (Gillespie, 2004a) can be traced back to Darwin’s recognition that natural selection can occur only if individuals of a species vary, and this variation is heritable. Darwin might have been surprised that the importance of natural selection in shaping variation at the molecular level would be de-emphasized, beginning in the late 1960s, by scientists who readily accepted the fact and importance of his theory (Kimura, 1983). The motivation behind this chapter is the possible demise of this Neutral Theory of Molecular Evolution, which a growing number of population geneticists feel must follow recent observations of genetic variation within and between species. One hundred fifty years after the publication of the Origin, we are struggling to fully incorporate natural selection into the modern, genealogical models of population genetics. The main goal of this chapter is to present the mathematical models that have been used to describe the effects of positive selective sweeps on genetic variation, as mediated by gene genealogies, or coalescent trees. Background material, comprised of population genetic theory and simulation results, is provided in order to facilitate an understanding of these models.
  • Science Fiction Stories with Good Astronomy & Physics

    Science Fiction Stories with Good Astronomy & Physics

    Science Fiction Stories with Good Astronomy & Physics: A Topical Index Compiled by Andrew Fraknoi (U. of San Francisco, Fromm Institute) Version 7 (2019) © copyright 2019 by Andrew Fraknoi. All rights reserved. Permission to use for any non-profit educational purpose, such as distribution in a classroom, is hereby granted. For any other use, please contact the author. (e-mail: fraknoi {at} fhda {dot} edu) This is a selective list of some short stories and novels that use reasonably accurate science and can be used for teaching or reinforcing astronomy or physics concepts. The titles of short stories are given in quotation marks; only short stories that have been published in book form or are available free on the Web are included. While one book source is given for each short story, note that some of the stories can be found in other collections as well. (See the Internet Speculative Fiction Database, cited at the end, for an easy way to find all the places a particular story has been published.) The author welcomes suggestions for additions to this list, especially if your favorite story with good science is left out. Gregory Benford Octavia Butler Geoff Landis J. Craig Wheeler TOPICS COVERED: Anti-matter Light & Radiation Solar System Archaeoastronomy Mars Space Flight Asteroids Mercury Space Travel Astronomers Meteorites Star Clusters Black Holes Moon Stars Comets Neptune Sun Cosmology Neutrinos Supernovae Dark Matter Neutron Stars Telescopes Exoplanets Physics, Particle Thermodynamics Galaxies Pluto Time Galaxy, The Quantum Mechanics Uranus Gravitational Lenses Quasars Venus Impacts Relativity, Special Interstellar Matter Saturn (and its Moons) Story Collections Jupiter (and its Moons) Science (in general) Life Elsewhere SETI Useful Websites 1 Anti-matter Davies, Paul Fireball.

  • Coalescent from Wikipedia, the Free Encyclopedia This Article Is About the Novel

    Coalescent From Wikipedia, the free encyclopedia This article is about the novel. For the theory of genomics, see coalescent theory. Coalescent is a science- Coalescent fiction novel by Stephen Baxter. It is part one of the Destiny's Children series. The story is set in two main time periods: modern Britain, when George Poole finds that he has a previously unknown sister and follows a trail to a mysterious and ancient organisation in Rome (Puissant Order of Holy Mary Queen of Virgins); and the time of Regina, a girl growing up during the ending of Roman rule Hardcover edition cover in Britain, around AD Author Stephen Baxter 400. Cover artist EkhornForss Coalescent was Country United Kingdom nominated for the Arthur C. Clarke Award in 2004. Language English [1] Series Destiny's Children Xeelee Sequence Genre Science fiction novel Contents Publisher Gollancz Publication November 2003 1 Plot summary date 1.1 Part one Media type Print (hardback & paperback) 1.1.1 George Pages 480 pp Poole ISBN ISBN 0-575-07423-X 1.1.2 OCLC 52695764 Regina 1.2 Part two (https://www.worldcat.org/oclc/52695764) 1.2.1 Followed by 'Exultant' Lucia 1.2.2 Regina 1.3 Part three 1.3.1 George Poole 1.4 Part four 2 References 3 External links Plot summary The book consists of four distinct parts. The primary purpose of part one is the introduction of the characters, in ancient Britain and the present. Part two introduces a modern first-person view of the Order in Rome while following Regina's budding legacy centuries before.
  • Space Food and Nutrition

    Space Food and Nutrition

    Educational Product National Aeronautics and Educators Grades K–8 Space Administration EG-1999-02-115-HQEG-1998-12-115-HQ SPACE FOOD AND NUTRITION An Educator’s Guide With Activities in Science and Mathematics Space and Food Nutrition—An Educator’s Guide With Activities in Science and Mathematics is available in electronic format through NASA Spacelink—one of the Agency’s electronic resources specifically developed for use by the educational community. The system may be accessed at the following address: http://spacelink.nasa.gov/products SPACE FOOD AND NUTRITION An Educator’s Guide With Activities in Science and Mathematics National Aeronautics and Space Administration This publication is in the Public Domain and is not protected by copyright. Permission is not required for duplication. EG-1999-02-115-HQ Space Food and Nutrition An Educator’s Guide With Activities in Science and Mathematics Acknowledgments National Aeronautics and Space Administration Special thanks to the following Office of Human Resources and Education contributors and reviewers Education Division Washington, D.C. Charles T. Bourland, Ph.D. System Manager, Space Station Food Education Working Group Flight Crew Support Division NASA Johnson Space Center NASA Johnson Space Center Houston, Texas Debbie A. Brown Writers ISS Education Liaison Angelo A. Casaburri Education Working Group Aerospace Education Services Program NASA Johnson Space Center NASA Johnson Space Center Houston, Texas Gregory L. Vogt, Ed.D. Crew Educational Affairs Liaison Cathy A. Gardner Education Working Group Dickinson Independent School District NASA Johnson Space Center Dickinson, Texas Karol L. Yeatts, Ed.D. Editor 1998 Einstein Fellow Jane A. George Miami Dade County Public Schools Teaching From Space Program Miami, Florida NASA Headquarters Washington, D.C.
  • The Drink Tank Sixth Annual Giant Sized Annualgarcia@Computerhistory.Orgeditors: James Bacon & Chris Garcia

    The Drink Tank Sixth Annual Giant Sized [email protected]: James Bacon & Chris Garcia

    The Drink Tank Sixth Annual Giant Sized Annual [email protected] Editors: James Bacon & Chris Garcia A Noise from the Wind Stephen Baxter had got me through the what he’ll be doing. I first heard of Stephen Baxter from Jay night. So, this is the least Giant Giant Sized Crasdan. It was a night like any other, sitting in I remember reading Ring that next Annual of The Drink Tank, but still, I love it! a room with a mostly naked former ballerina afternoon when I should have been at class. I Dedicated to Mr. Stephen Baxter. It won’t cover who was in the middle of what was probably finished it in less than 24 hours and it was such everything, but it’s a look at Baxter’s oevre and her fifth overdose in as many months. This was a blast. I wasn’t the big fan at that moment, the effect he’s had on his readers. I want to what we were dealing with on a daily basis back though I loved the novel. I had to reread it, thank Claire Brialey, M Crasdan, Jay Crasdan, then. SaBean had been at it again, and this time, and then grabbed a copy of Anti-Ice a couple Liam Proven, James Bacon, Rick and Elsa for it was up to me and Jay to clean up the mess. of days later. Perhaps difficult times made Ring everything! I had a blast with this one! Luckily, we were practiced by this point. Bottles into an excellent escape from the moment, and of water, damp washcloths, the 9 and the first something like a month later I got into it again, 1 dialed just in case things took a turn for the and then it hit.
  • Extrait De La Publication Gravité

    Extrait De La Publication Gravité

    Extrait de la publication Gravité Stephen Baxter Extrait de la publication Stephen Baxter – Gravité Le Bélial’ vous propose volontairement des fichiers dépourvus de dispositifs de gestion des droits numériques (DRM) et autres moyens techniques visant la limitation de l’utilisation et de la copie de ces fichiers. • Si vous avez acheté ce fichier, nous vous en remercions. Vous pouvez, comme vous le feriez avec un véritable livre, le transmettre à vos proches si vous souhaitez le leur faire découvrir. Afin que nous puissions continuer à distribuer nos livres numériques sans DRM, nous vous prions de ne pas le diffuser plus largement, via le web ou les réseaux peer-to-peer. • Si vous avez acquis ce fichier d’une autre manière, nous vous demandons de ne pas le diffuser. Notez que, si vous souhaitez soutenir l’auteur et les éditions du Bélial’, vous pouvez acheter légalement ce fichier sur notre plateforme e.belial.fr ou chez votre libraire numérique préféré. 2 Stephen Baxter – Gravité Ouvrage publié sur la direction d’Olivier Girard. Traduit de l’anglais par Guillaume Fournier Titre original : Raft ISBN : 978-2-84344-391-6 Code SODIS : en cours d’attribution Parution : octobre 2011 Version : 1.0 — 26/10/2011 Illustration de couverture © 2008, Manchu © 1991 by Karin Lowachee © 2008, Le Bélial’, pour la première édition française © 2011, Le Bélial’, pour la présente édition 3 Stephen Baxter – Gravité Introduction à la baxterologie Ce livre est particulier. S’il s’agit du treizième roman de Stephen Baxter publié en français, c’est surtout le premier qu’il écrivit. Paru outre-Manche en 1991, Raft, pour utiliser son titre anglais, est le volet initial d’une série fondatrice dans l’œuvre de notre auteur, le « cycle des Xeelees », série qui compte quatre romans (Timelike Infinity, Flux et Ring étant les trois autres) auxquels s’ajoute à ce jour un recueil de nouvelles, Vacuum Diagrams, lauréat du prestigieux prix Philip K.
  • Alternate Historical Fiction

    Alternate Historical Fiction

    Alternate Historical Fiction "Sometimes it's possible, just barely possible, to imagine a version of this world different from the existing one." Ben H. Winters, Underground Airlines Voyage The Peshawar Lancers by Stephen Baxter by S. M. Stirling An intense novel explores what On an alternate Earth might have happened if irrevocably transformed by a President Kennedy had lived violent spray of comets in the and a manned mission to Mars 1870s, the planet is controlled had been dispatched, by two superpowers--the British combining historical figures and Empire and Russia--who appear events with memorable to be heading for a deadly characters who experience the showdown, unless superspy trials and tribulations of this Captain Alfred King can stop it. aspiring mission. The Impeachment of How Few Remain Abraham Lincoln by Harry Turtledove In 1883, the United States, still by Stephen L. Carter smarting from its defeat at the The best-selling author of The hands of the Confederacy, Emperor of Ocean Park returns to the battlefields, with imagines a world where the the Apache, outlaw gangs, and 16th President survives his 1865 European forces becoming assassination only to be involved in the conflict, in a new charged with overstepping his novel of alternative history.. Constitutional authority during the Civil War, a case that is aided by a black college graduate who is entangled in a violent political conspiracy. Clash of Eagles by Alan Smale Fallout General Gaius Marcellinus of the by Todd Strasser Roman Empire is shocked by When an unthinkable nuclear the fighting skills shown by attack occurs in an alternate- Native Americans when he reality 1962, Scott is forced into commands the invasion of the his father's bomb shelter with newly-discovered North his family and neighbors, where American continent.
  • THE COLLECTED POEMS of HENRIK IBSEN Translated by John Northam

    THE COLLECTED POEMS of HENRIK IBSEN Translated by John Northam

    1 THE COLLECTED POEMS OF HENRIK IBSEN Translated by John Northam 2 PREFACE With the exception of a relatively small number of pieces, Ibsen’s copious output as a poet has been little regarded, even in Norway. The English-reading public has been denied access to the whole corpus. That is regrettable, because in it can be traced interesting developments, in style, material and ideas related to the later prose works, and there are several poems, witty, moving, thought provoking, that are attractive in their own right. The earliest poems, written in Grimstad, where Ibsen worked as an assistant to the local apothecary, are what one would expect of a novice. Resignation, Doubt and Hope, Moonlight Voyage on the Sea are, as their titles suggest, exercises in the conventional, introverted melancholy of the unrecognised young poet. Moonlight Mood, To the Star express a yearning for the typically ethereal, unattainable beloved. In The Giant Oak and To Hungary Ibsen exhorts Norway and Hungary to resist the actual and immediate threat of Prussian aggression, but does so in the entirely conventional imagery of the heroic Viking past. From early on, however, signs begin to appear of a more personal and immediate engagement with real life. There is, for instance, a telling juxtaposition of two poems, each of them inspired by a female visitation. It is Over is undeviatingly an exercise in romantic glamour: the poet, wandering by moonlight mid the ruins of a great palace, is visited by the wraith of the noble lady once its occupant; whereupon the ruins are restored to their old splendour.
  • The Geography of Recent Genetic Ancestry Across Europe

    The Geography of Recent Genetic Ancestry Across Europe

    The Geography of Recent Genetic Ancestry across Europe. Peter Ralph1 and Graham Coop2 1 Department of Evolution and Ecology & Center for Population Biology, University of California, Davis. 2 Department of Molecular and Computational Biology, University of Southern California. To whom correspondence should be addressed: [email protected],[email protected] Abstract The recent genealogical history of human populations is a complex mosaic formed by individual migration, large-scale population movements, and other demographic events. Population genomics datasets can provide a window into this recent history, as rare traces of recent shared genetic ancestry are detectable due to long segments of shared genomic material. We make use of genomic data for 2257 Europeans (in the POPRES dataset) to conduct one of the first surveys of recent genealogical ancestry over the past three thousand years at a continental scale. We detected 1.9 million shared long genomic segments, and used the lengths of these to infer the distri- bution of shared ancestors across time and geography. We find that a pair of modern Europeans living in neighboring populations share around 2{12 genetic common ancestors from the last 1500 years, and upwards of 100 genetic ancestors from the previous 1000 years. These numbers drop off exponentially with geographic distance, but since these genetic ancestors are a tiny fraction of common genealogical ancestors, individuals from opposite ends of Europe are still expected to share millions of common genealogical ancestors over the last 1000 years. There is also substantial regional variation in the number of shared genetic ancestors. For example, there are especially high numbers of common ancestors shared between many eastern populations which date roughly to the migration period (which includes the Slavic and Hunnic expansions into that region).
  • Conrad, Failure, and Irony in O'neill's

    Conrad, Failure, and Irony in O'neill's

    Global Posts building CUNY Communities since 2009 http://tags.commons.gc.cuny.edu The Border that Beckons and Mocks: Conrad, Failure, and Irony in O’Neill’s Beyond the Horizon The horizon is a border that cannot be crossed. “Beyond the horizon” is thus a meaningful locution only in the language of metaphor, where, like “the end of the rainbow,” it beckons and mocks, promising delight and abundance even as it emphasizes limitation.1 Eugene O’Neill’s Robert Mayo, poet manqué and protagonist of Beyond the Horizon, is drawn to the metaphor but curiously unequal to it.2 Place- bound by circumstance (as he realizes) and torpid by nature (as he does not), he cannot ground the metaphor in his own experience or animate it with his own imagination. His principal mode of conceptualizing life “beyond the horizon” is imitative. Specifically, Robert tries and fails to reify the metaphor after the fashion of Joseph Conrad, whose biography is a record of traversed national borders and whose fiction, abstractly a sustained negotiation of borders between description and metaphor, more concretely concerns experiences at sea, on land, and, yes, at the borders between. Robert, perennially a failure, fails thrice in this enterprise: he is unable to leave the hard-scrabble farm he loathes, to imagine life beyond the farm, and to enrich the life he does lead with the benefits of a vibrant imagination. The borders that circumscribe his life are both imaginative and geographical, and they are absolute. In this way O’Neill backhandedly thematizes the centrality of living to literature, making a Conradian play out of un-Conradian materials.