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Avian Vision and the Evolution of Egg Color Mimicry in The
evo_65_7_cover 6/22/11 7:16 PM Page 1 Volume 65, Number 7, July 2011 VOLUME 65, NUMBER 7, JULY 2011 EVOLUTION VOLUME 65, NUMBER 7, PAGES PERSPECTIVE INTERNATIONAL JOURNAL OF ORGANIC EVOLUTION Convergence, Adaptation, and Constraint Jonathan B. Losos 1827–1840 ORIGINAL ARTICLES 1827 Neutral Biodiversity Theory can Explain the Imbalance of Phylogenetic Trees but not the Tempo –2132 of their Diversification T. Jonathan Davies, Andrew P. Allen, Luís Borda-de-A´gua, Jim Regetz, and Carlos J. Melián 1841–1850 The Impact of Gene-Tree/Species-Tree Discordance on Diversification-Rate Estimation Frank T. Burbrink and R. Alexander Pyron 1851–1861 Dealing with Incomplete Taxon Sampling and Diversification of a Large Clade of Mushroom-Forming Fungi Martin Ryberg and Patrick Brandon Matheny 1862–1878 EVOLUTION Diversity and Demography in Beringia: Multilocus Tests of Paleodistribution Models Reveal the Complex History of Arctic Ground Squirrels Kurt E. Galbreath, Joseph A. Cook, Aren A. Eddingsaas, and Eric G. DeChaine 1879–1896 The Genetic Architecture of Adaptation Under Migration-Selection Balance Sam Yeaman and Michael C. Whitlock 1897–1911 The Influence of an Innovative Locomotor Strategy on the Phenotypic Diversification of Triggerfish (Family: Balistidae) Alex Dornburg, Brian Sidlauskas, Francesco Santini, Laurie Sorenson, Thomas J. Near, and Michael E. Alfaro 1912–1926 The Tempo and Mode of Evolution: Body Sizes of Island Mammals Pasquale Raia and Shai Meiri 1927–1934 Mammals Evolve Faster on Smaller Islands Virginie Millien 1935–1944 Evolutionary Advantage of Small Populations on Complex Fitness Landscapes Kavita Jain, Joachim Krug, and Su-Chan Park 1945–1955 Interspecific X-Chromosome and Mitochondrial DNA Introgression in the Iberian Hare: Selection or Allele Surfing? July 2011 José Melo-Ferreira, Paulo C. -
Telomere Length Is Repeatable, Shortens with Age and Reproductive
University of Groningen Telomere length is repeatable, shortens with age and reproductive success, and predicts remaining lifespan in a long-lived seabird Bichet, Coraline; Bouwhuis, Sandra; Bauch, Christina; Verhulst, Simon; Becker, Peter H.; Vedder, Oscar Published in: Molecular Ecology DOI: 10.1111/mec.15331 IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from it. Please check the document version below. Document Version Publisher's PDF, also known as Version of record Publication date: 2020 Link to publication in University of Groningen/UMCG research database Citation for published version (APA): Bichet, C., Bouwhuis, S., Bauch, C., Verhulst, S., Becker, P. H., & Vedder, O. (2020). Telomere length is repeatable, shortens with age and reproductive success, and predicts remaining lifespan in a long-lived seabird. Molecular Ecology, 29(2), 429-441. https://doi.org/10.1111/mec.15331 Copyright Other than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of the author(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons). The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license. More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne- amendment. Take-down policy If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. -
A Multiscale Tool to Explore Genomic Conservation
SynVisio: A Multiscale Tool to Explore Genomic Conservation A Thesis Submitted to the College of Graduate and Postdoctoral Studies in Partial Fulfillment of the Requirements for the degree of Master of Science in the Department of Computer Science University of Saskatchewan Saskatoon By Venkat Kiran Bandi ©Venkat Kiran Bandi, May/2020. All rights reserved. Permission to Use In presenting this thesis in partial fulfilment of the requirements for a Postgraduate degree from the University of Saskatchewan, I agree that the Libraries of this University may make it freely available for inspection. I further agree that permission for copying of this thesis in any manner, in whole or in part, for scholarly purposes may be granted by the professor or professors who supervised my thesis work or, in their absence, by the Head of the Department or the Dean of the College in which my thesis work was done. It is understood that any copying or publication or use of this thesis or parts thereof for financial gain shall not be allowed without my written permission. It is also understood that due recognition shall be given to me and to the University of Saskatchewan in any scholarly use which may be made of any material in my thesis. Requests for permission to copy or to make other use of material in this thesis in whole or part should be addressed to: Head of the Department of Computer Science 176 Thorvaldson Building 110 Science Place University of Saskatchewan Saskatoon, Saskatchewan Canada S7N 5C9 Or Dean College of Graduate and Postdoctoral Studies University of Saskatchewan 116 Thorvaldson Building, 110 Science Place Saskatoon, Saskatchewan S7N 5C9 Canada i Abstract Comparative analysis of genomes is an important area in biological research that can shed light on an organism's internal functions and evolutionary history. -
A Zebrafish Reporter Line Reveals Immune and Neuronal Expression of Endogenous Retrovirus
bioRxiv preprint doi: https://doi.org/10.1101/2021.01.21.427598; this version posted January 21, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. A zebrafish reporter line reveals immune and neuronal expression of endogenous retrovirus. Noémie Hamilton1,2*, Amy Clarke1, Hannah Isles1, Euan Carson1, Jean-Pierre Levraud3, Stephen A Renshaw1 1. The Bateson Centre, Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK 2. The Institute of Neuroscience, University of Sheffield, Sheffield, UK 3. Macrophages et Développement de l’Immunité, Institut Pasteur, CNRS UMR3738, 25 rue du docteur Roux, 75015 Paris *Corresponding author: [email protected] Abstract Endogenous retroviruses (ERVs) are fossils left in our genome from retrovirus infections of the past. Their sequences are part of every vertebrate genome and their random integrations are thought to have contributed to evolution. Although ERVs are mainly kept silenced by the host genome, they are found activated in multiple disease states such as auto-inflammatory disorders and neurological diseases. What makes defining their role in health and diseases challenging is the numerous copies in mammalian genomes and the lack of tools to study them. In this study, we identified 8 copies of the zebrafish endogenous retrovirus (zferv). We created and characterised the first in vivo ERV reporter line in any species. Using a combination of live imaging, flow cytometry and single cell RNA sequencing, we mapped zferv expression to early T cells and neurons. -
Population Substructure, Local Density, and Calf Winter Survival in Red Deer (Cervus Elaphus)
Edinburgh Research Explorer Population substructure, local density, and calf winter survival in red deer (Cervus elaphus) Citation for published version: Coulson, T, Albon, S, Guinness, F, Pemberton, J & CluttonBrock, T 1997, 'Population substructure, local density, and calf winter survival in red deer (Cervus elaphus)', Ecology, vol. 78, no. 3, pp. 852-863. https://doi.org/10.1890/0012-9658(1997)078[0852:PSLDAC]2.0.CO;2 Digital Object Identifier (DOI): 10.1890/0012-9658(1997)078[0852:PSLDAC]2.0.CO;2 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Ecology Publisher Rights Statement: RoMEO green General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 07. Oct. 2021 Population Substructure, Local Density, and Calf Winter Survival in Red Deer (Cervus Elaphus) Author(s): Tim Coulson, Steve Albon, Fiona Guinness, Josephine Pemberton and Tim Clutton- Brock Source: Ecology, Vol. 78, No. 3 (Apr., 1997), pp. 852-863 Published by: Ecological Society of America Stable URL: http://www.jstor.org/stable/2266064 . -
Evolution and Function of Drososphila Melanogaster Cis-Regulatory Sequences
Evolution and Function of Drososphila melanogaster cis-regulatory Sequences By Aaron Hardin A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michael Eisen, Chair Professor Doris Bachtrog Professor Gary Karpen Professor Lior Pachter Fall 2013 Evolution and Function of Drososphila melanogaster cis-regulatory Sequences This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License 2013 by Aaron Hardin 1 Abstract Evolution and Function of Drososphila melanogaster cis-regulatory Sequences by Aaron Hardin Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Michael Eisen, Chair In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods on the natural genetic variation in a population. This works integrates an investigation of the consequences of polymorphisms at three stages of gene regulation in the developing fly embryo: the diversity at cis-regulatory modules, the integration of transcription factor binding into changes in chromatin state and the effects of these inputs on the final phenotype of embryonic gene expression. i I dedicate this dissertation to Mela Hardin who has been here for me at all times, even when we were apart. ii Contents List of Figures iv List of Tables vi Acknowledgments vii 1 Introduction1 2 Within Species Diversity in cis-Regulatory Modules6 2.1 Introduction....................................6 2.2 Results.......................................8 2.2.1 Genome wide diversity in transcription factor binding sites......8 2.2.2 Genome wide purifying selection on cis-regulatory modules......9 2.3 Discussion.....................................9 2.4 Methods for finding polymorphisms...................... -
Science & Policy Meeting Jennifer Lippincott-Schwartz Science in The
SUMMER 2014 ISSUE 27 encounters page 9 Science in the desert EMBO | EMBL Anniversary Science & Policy Meeting pageS 2 – 3 ANNIVERSARY TH page 8 Interview Jennifer E M B O 50 Lippincott-Schwartz H ©NI Membership expansion EMBO News New funding for senior postdoctoral In perspective Georgina Ferry’s enlarges its membership into evolution, researchers. EMBO Advanced Fellowships book tells the story of the growth and ecology and neurosciences on the offer an additional two years of financial expansion of EMBO since 1964. occasion of its 50th anniversary. support to former and current EMBO Fellows. PAGES 4 – 6 PAGE 11 PAGES 16 www.embo.org HIGHLIGHTS FROM THE EMBO|EMBL ANNIVERSARY SCIENCE AND POLICY MEETING transmissible cancer: the Tasmanian devil facial Science meets policy and politics tumour disease and the canine transmissible venereal tumour. After a ceremony to unveil the 2014 marks the 50th anniversary of EMBO, the 45th anniversary of the ScienceTree (see box), an oak tree planted in soil European Molecular Biology Conference (EMBC), the organization of obtained from countries throughout the European member states who fund EMBO, and the 40th anniversary of the European Union to symbolize the importance of European integration, representatives from the govern- Molecular Biology Laboratory (EMBL). EMBO, EMBC, and EMBL recently ments of France, Luxembourg, Malta, Spain combined their efforts to put together a joint event at the EMBL Advanced and Switzerland took part in a panel discussion Training Centre in Heidelberg, Germany, on 2 and 3 July 2014. The moderated by Marja Makarow, Vice President for Research of the Academy of Finland. -
A Burst of Protein Sequence Evolution and a Prolonged Period of Asymmetric Evolution Follow Gene Duplication in Yeast
Downloaded from genome.cshlp.org on October 3, 2021 - Published by Cold Spring Harbor Laboratory Press Letter A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast Devin R. Scannell1,2 and Kenneth H. Wolfe Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland It is widely accepted that newly arisen duplicate gene pairs experience an altered selective regime that is often manifested as an increase in the rate of protein sequence evolution. Many details about the nature of the rate acceleration remain unknown, however, including its typical magnitude and duration, and whether it applies to both gene copies or just one. We provide initial answers to these questions by comparing the rate of protein sequence evolution among eight yeast species, between a large set of duplicate gene pairs that were created by a whole-genome duplication (WGD) and a set of genes that were returned to single-copy after this event. Importantly, we use a new method that takes into account the tendency for slowly evolving genes to be retained preferentially in duplicate. We show that, on average, proteins encoded by duplicate gene pairs evolved at least three times faster immediately after the WGD than single-copy genes to which they behave identically in non-WGD lineages. Although the high rate in duplicated genes subsequently declined rapidly, it has not yet returned to the typical rate for single-copy genes. In addition, we show that although duplicate gene pairs often have highly asymmetric rates of evolution, even the slower members of pairs show evidence of a burst of protein sequence evolution immediately after duplication. -
Resource Summer 2017
ISSUE 55 Summer 2017 resourc e The Newsletter of Scotland’s National Academy Image © Gary Doak Photography Our Patron, Her Majesty The Queen, visited the RSE in July to present the 2017 Royal Medals. Her Majesty is pictured with past and present recipients of RSE Royal Medals. (Details inside) Also featured in this issue: Wilfred Owen’s Edinburgh 1917 –2017 International Relations with Japan New CEO at the RSE resourc e Summer 2017 The Royal Visit 2017 We were highly honoured to welcome Her Majesty The Queen to the RSE on Friday 7 July 2017 to present this year’s Royal Medals. Her Majesty was greeted, at the door to 22 George Street, by The Rt Hon Lord Provost and Lord Lieutenant of the City of Edinburgh, Frank Ross. The RSE Royal Medals were instituted by Her Majesty in 2000, to mark the Millennium, and have been awarded since then with her express approval. These accolades are awarded for distinction and international repute in any of the following categories: Life Sciences; Physical and Engineering Sciences; Arts, Humanities and Social Sciences; Business and Commerce. Medals were awarded to: Professor Peter Boyle CorrFRSE FMEDSci (below left), President, International Prevention Research Institute and Director, the University of Strathclyde Institute of Global Public Health, for his outstanding contribution to global cancer control and public health policy; Professor Tessa Holyoake FRSE FMedSci, Director (below right), Paul O’Gorman Leukaemia Research Centre, University of Glasgow, for her outstanding contribution to the field of Life Sciences through her discovery of the existence of cancer stem cells in chronic myeloid leukaemia and her development of a new therapy for this condition; Mr Donald Runnicles OBE (above), Chief Conductor, BBC Scottish Symphony Orchestra, for his outstanding contribution to the art of music at the highest international level. -
General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models
| INVESTIGATION General Methods for Evolutionary Quantitative Genetic Inference from Generalized Mixed Models Pierre de Villemereuil,* Holger Schielzeth,†,‡ Shinichi Nakagawa,§ and Michael Morrissey**,1 *Laboratoire d’Écologie Alpine, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5553, Université Joseph Fourier, 38041 Grenoble Cedex 9, France, †Department of Evolutionary Biology, Bielefeld University, 33615 Bielefeld, Germany, ‡Institute of Ecology, Friedrich Schiller University, 07743 Jena, Germany, §Evolution and Ecology Research Centre, University of New South Wales, Sydney, New South Wales 2052, Australia, and **School of Evolutionary Biology, University of St. Andrews, St. Andrews KY16 9TH, United Kingdom ORCID IDs: 0000-0002-8791-6104 (P.d.V.); 0000-0002-9124-2261 (H.S.); 0000-0002-7765-5182 (S.N.); 0000-0001-6209-0177 (M.M.) ABSTRACT Methods for inference and interpretation of evolutionary quantitative genetic parameters, and for prediction of the response to selection, are best developed for traits with normal distributions. Many traits of evolutionary interest, including many life history and behavioral traits, have inherently nonnormal distributions. The generalized linear mixed model (GLMM) framework has become a widely used tool for estimating quantitative genetic parameters for nonnormal traits. However, whereas GLMMs provide inference on a statistically convenient latent scale, it is often desirable to express quantitative genetic parameters on the scale upon which traits are measured. The parameters of fitted GLMMs, despite being on a latent scale, fully determine all quantities of potential interest on the scale on which traits are expressed. We provide expressions for deriving each of such quantities, including population means, phenotypic (co)variances, variance components including additive genetic (co)variances, and parameters such as heritability. -
Program Book
The Genetics Society of America Conferences 55th Annual Drosophila Research Conference March 26–30, 2014 • San Diego, CA PROGRAM GUIDE 2014 Drosophila Program Cover.indd 1 1/21/14 11:33 AM Meeting Organizers Daniela Drummond-Barbosa, Johns Hopkins University Elissa Lei, NIH/National Institute of Diabetes and Digestive and Kidney Diseases Mihaela Serpe, NIH/Eunice Kennedy Shriver National Institute of Child Health and Human Development Mark Van Doren, Johns Hopkins University Drosophila Board of Directors Officers President Amy Bejsovec President-Elect 2014 Ken Irvine President-Elect 2015 David Bilder Past-President 2012 Michael O’Connor Past-President 2011 Liz Gavis & Elections Chair Treasurer Deborah Andrew Regional Representatives International Representatives Canada Laura Nilson Australia/Oceana Gary Hime Great Lakes Helen Salz Asia Shigeo Hiyashi Northwest Leo Pallanck Europe Daniel St. Johnston Southeast Steve Crews Latin America Mariana Melani California Angelika Stathopoulos Heartland Giovanni Bosco Primary Undergraduate Institution New England Eric Baehrecke Representative Mid-Atlantic Jessica Triesman Midwest Seth Blair Alexis Nagengast Sponsored by: The Genetics Society of America 9650 Rockville Pike, Bethesda, Maryland 20814-3998 Telephone: (301) 634-7300 • Fax: (301) 634-7079 E-mail: [email protected] • Web site: genetics-gsa.org Conference Web site: genetics-gsa.org/drosophila/2014 1 Table of Contents Schedule of Events ............................................................................................................................... -
Issues of Authorship Prac Ce and Policy in Experimental Science
Issues of authorship pracce and policy in experimental science research labs Cassandra Extavour Associate Professor Organismic and Evoluonary Biology Harvard University Members of the research team Principal Invesgator Graduate Postdocs Students Research Undergraduate Assistants Students Members of the research team have different goals Principal Invesgator Graduate Postdocs Students Research Undergraduate Assistants Students Authorship has different values for different members of the team Principal Invesgator Graduate Postdocs Students Research Undergraduate Assistants Students Authorship order has specific meaning, which is different in different fields of scholarship RESEARCH ARTICLE 5015 • DevelopmentAuthorship is merited if you have contributed substanally 138, 5015-5026 (2011) doi:10.1242/dev.073395 © 2011.to Published by The Company of Biologists Ltd Notch/Delta– Experimental design signalling is not required for segment generation– Carrying out experiments in the basally branching insect Gryllus bimaculatus– Analyzing data – Wring the manuscript Franz Kainz1,2, Ben Ewen-Campen1, Michael Akam2 and Cassandra G. Extavour1,* – Obtaining funding for the research • SUMMARYWho decides who has contributed substanally? First authorArthropods: carried out and vertebrates display a segmental body organisation along all Last authoror part of the : senior author anterior-posterior axis. Whether this reflects– aDifferent team members may differ in their definion of shared, ancestral developmental genetic mechanism for segmentation is uncertain. In vertebrates, segments are formed bulk of experimental and/sequentially by a segmentation ‘clock’ of oscillating gene expression involving Notch= PI. Usually major pathway components. Recent studies in or analycal work. Usually spiders and“substanal” basal insects have suggested that segmentation in these arthropodscontributor of intellectual also involves Notch-based signalling. These grad student or postdoc.