Molecular Biology and Evolution

Total Page:16

File Type:pdf, Size:1020Kb

Molecular Biology and Evolution Molecular Biology and Evolution (ISSN 0737-4038) is a peer-reviewed Postal information journal published twelve times a year by Oxford University Press for the Molecular Biology and Evolution (ISSN 0737-4038) is published MOLECULAR BIOLOGY AND EVOLUTION Society for Molecular Biology and Evolution. monthly by Oxford University Press, 2001 Evans Road, Cary, NC Molecular Biology and Evolution (MBE) publishes research at the 27513-2009. Periodicals Postage Paid at Cary, NC, and additional interface between molecular and evolutionary biology. The journal mailing offices. POSTMASTER: Send address changes to Molecular (ISSN 0737-4038) publishes molecular evolutionary patterns, processes, and predictions at Biology and Evolution, Mercury Media Processing, 187 E. Albert all levels of taxonomic, functional, genomic, and phenotypic organization. St., Rahway, NJ 07065 USA. It also publishes new and improved methods, resources, and theories Founding Editors: Walter Fitch and Masatoshi Nei Environmental and ethical policies Editor in Chief: Sudhir Kumar Institute for Genomics and that are critical for advancing the molecular evolutionary research. MBE does not publish manuscripts containing largely descriptive work, Oxford Journals, a division of Oxford University Press, is committed Evolutionary Medicine, confi rmatory research, and discoveries with a limited scope or impact. to working with the global community to bring the highest quality Temple University, research to the widest possible audience. Oxford Journals will protect Philadelphia, PA, USA Membership in the Society for Molecular Biology and Evolution the environment by implementing environmentally friendly policies Individuals interested in becoming a member of the Society for and practices wherever possible. Please see http://www. [email protected] Molecular Biology and Evolution can obtain application forms from oxfordjournals.org/ethicalpolicies.html for further information on [email protected]. environmental and ethical policies. Editorial Assistant: Marjorie Gillis [email protected] Subscriptions Digital Object Identifi ers Editor’s Advisors: Barry Hall [email protected] A subscription to Molecular Biology and Evolution comprises 12 issues. For information on dois and to resolve them, please visit www.doi.org. Marcy Uyenoyama [email protected] All prices include postage; for subscribers outside the Americas, issues are sent air freight. Molecular Biology and Evolution Advance Access News Writer: Joseph Caspermeyer [email protected] Permissions Downloaded from https://academic.oup.com/mbe/article/33/2/i3/2579709 by guest on 30 September 2021 contains papers that have recently been accepted but have not yet been For information on how to request permissions to reproduce articles Editor’s Associate: Heather Rowe [email protected] included within an issue. Advance Access is updated daily. or information from this journal, please visit www.oxfordjournals.org/ Editors (Senior and Associate) Annual Subscription Rate (Volume 33, 12 issues, 2016) permissions. Institutional A list of senior and associate editors is available at Advertising Print edition and site-wide online access: US$1112.00/£635.00/E992.00 Advertising, inserts, and artwork enquiries should be addressed to www.oxfordjournals.org/molbev/editorial_board.html Print edition only: US$1021.00/£584.00/E912.00 Advertising and Special Sales, Oxford Journals, Oxford University Site-wide online access only: US$756.00/£431.00/E673.00 Press, Great Clarendon Street, Oxford, OX2 6DP, UK. Tel: +44 (0)1865 Information for Authors Please note: UK£ rate applies to UK and Rest of World, except US 354767; Fax: +44 (0)1865 353774; E-mail: [email protected]. Guidelines for author submissions are available at and Canada ($) and Europe (E). Payment for orders to be delivered http://www.oxfordjournals.org/our_journals/molbev/general_author_guidelines.html within Europe should be made in euros. There are other subscription rates available; for a complete listing, Granting of License please visit www.mbe.oxfordjournals.org/subscriptions. It is a condition of publication in the journal that authors grant an exclusive license to the Society for Molecular Biology and Full prepayment in the correct currency is required for all orders. Payment Evolution. This ensures that requests from third parties to reproduce SOCIETY FOR MOLECULAR BIOLOGY AND EVOLUTION should be in US dollars for orders being delivered to the USA or Canada; articles are handled efficiently and consistently and will also allow the Euros for orders being delivered within Europe (excluding the UK); GBP article to be as widely disseminated as possible. As part of the license www.smbe.org sterling for orders being delivered elsewhere (i.e. not being delivered to agreement, authors may use their own material in other publications USA, Canada, or Europe). All orders should be accompanied by full provided that the journal is acknowledged as the original place of COUNCIL payment and sent to your nearest Oxford Journals office. Subscriptions publication and Oxford University Press as the publisher. George Zhang, President are accepted for complete volumes only. Orders are regarded as firm, Statements and opinions expressed in publications of the Society for Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109. Email: [email protected] and payments are not refundable. Our prices include Standard Air as postage outside of the UK. Claims must be notified within four months Molecular Biology and Evolution or in presentations given during its Laura Landweber, President-elect of despatch/order date (whichever is later). Subscriptions in the EEC may regular meetings are those of the author(s) and do not necessarily reflect Department of Ecology & Evolutionary Biology, Princeton University, Princeton, NJ 08544. Email: lfl @princeton.edu be subject to European VAT. If registered, please supply details to avoid the official position of the Society for Molecular Biology and Evolution, Joe Felsenstein, Past President unnecessary charges. For subscriptions that include online versions, a the Editors, or the organizations with which the authors are affiliated. Department of Genome Sciences, University of Washington, Seattle, WA 98195. Email: [email protected] proportion of the subscription price may be subject to UK VAT. The Editor(s), publisher, and Society disclaim any responsibility or Subscribers in Canada, please add GST to the prices quoted. Personal rate liability for such material and do not guarantee, warrant, or endorse any James McInerney, Secretary product or service mentioned, including those by advertisers, nor do they Department of Biology, National University of Ireland, Kildare, Ireland. Email: [email protected] subscriptions are only available if payment is made by personal cheque or credit card, delivery is to a private address, and is for personal use only. guarantee any claim made by the manufacturer of such product or service. Juliette de Meaux, Treasurer Official positions of the Society are established only by its Council. Institute for Evolution and Biodiversity, University of Münster, Germany 48149. Email: [email protected] The current year and two previous years’ issues are available from Oxford Journals. Previous volumes can be obtained from the Periodicals Service Copyright © 2016 Society for Molecular Biology and Evolution Sandra Baldauf, Councillor (2014–2016) Company at http://www.periodicals.com/oxford.html or Periodicals Service Evolutionary Biology Centre, Uppsala University, Box 256, 751 05, Uppsala, Sweden. Email: [email protected] Company, 11 Main Street, Germantown, NY 12526, USA. E-mail: All rights reserved; no part of this publication may be reproduced, David Liberles, Councillor (2014–2016) [email protected]. Tel: (518) 537-4700. Fax: (518) 537-5899. stored in a retrieval system, or transmitted in any form or by any Department of Molecular Biology, University of Wyoming, Laramie, WY 82071. Email: [email protected] means, electronic, mechanical, photocopying, recording, or otherwise Contact information without prior written permission of the publisher or a license Maud Tenaillon, Councillor (2015–2017) Journals Customer Service Department, Oxford University Press, Great permitting restricted copying issued in the UK by the Copyright Department Quantitative Genetics and Evolution, Le Moulon, 91190 Gif-sur-Yvette, France. Email: [email protected] Clarendon Street, Oxford OX2 6DP, UK. E-mail: jnls.cust. Licensing Agency Ltd, 90 Tottenham Court Road, London W1P 9HE. Adam Eyre-Walker, Councillor [email protected]. Tel: +44 (0)1865 353907. Fax: + 44 (0)1865 353485. (2015–2017) Typeset by Cenveo Publisher Services, Bengaluru, India; Printed by CTPS School of Biological Sciences University of Sussex, Brighton BN1 9QG, United Kingdom. Email: [email protected] In the Americas, please contact: Journals Customer Service Department, Oxford University Press, 2001 Evans Road, Cary, NC 27513, USA. DIGIASIA Pte Ltd, Singapore. Emma Teeling, Councillor (2015–2017) E-mail: [email protected]. Tel: (800) 852-7323 (toll-free in USA/ School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland. Email: [email protected] Canada) or (919) 677-0977. Fax: (919) 677-1714. In Japan, please Indexing and Abstracting Kateryna Makova, Councillor (2015–2017) contact: Journals Customer Service Department, Oxford University Molecular Biology and Evolution is
Recommended publications
  • Review 2015–16 Review
    Review 2015–16 Review 2015–16 AR cover 1.indd 1 3/2/2017 3:00:03 PM TO PRINT.indd 82 3/2/2017 1:56:30 PM Inside A year in view 4 A note from the President 11 A note from the Executive Secretary 13 We explore 17 We award 27 We engage 31 We advise 49 We support 55 New members 61 Donations 73 Bereavements 78 Accounts 80 This report covers the period from March 2015 to December 2016 TO PRINT.indd 1 3/2/2017 1:53:07 PM 156 new entries added to the Dictionary of Irish Biography 61 maps from Irish Historic Towns Atlas now available online 10 volumes of Documents on Irish Foreign Policy to date 6 US-Ireland Research Innovation Award winners 1 prehistoric bear bone excavated with RIA grants TO PRINT.indd 2 3/2/2017 1:53:08 PM 19 1,400 visits on 1,500 events and meetings Culture Night 2016 13,300 followers on Twitter 20,100 books sold 100,000,000 stamps inspired by A History of Ireland in 100 Objects 38,500 visitors 70,000 441,900 in research grants awarded downloads € of 1916 Portraits and Lives TO PRINT.indd 3 3/2/2017 1:53:09 PM US-Ireland Research Innovation Awards 2016: L–R Eddie Cullen, Ulster Bank; Minister for Jobs, Enterprise and Innovation, Mary Mitchell O’Connor, TD; Shaun Murphy, KPMG and James O’Connor, American Chamber of Commerce. Participant at Inspiring Ireland London Collection Day, organised by the Digital Repository of Ireland in March 2016.
    [Show full text]
  • An Open Letter to the Government of Ireland
    An Open Letter to the Government of Ireland As scientists in Ireland and Irish scientists abroad, we are committed to making our contribution to Ireland’s recovery by doing the best and most innovative research possible. However, we are deeply concerned about the research policies implemented by the current government. The policy of sustained investment in scientific excellence that helped build a vibrant scientific community in Ireland over the past fifteen years has given way to a short- sighted drive for commercialisable research in a very limited set of prescribed areas. Along with an investment in research that is below the EU average, steadily decreasing core grants to universities, and a constant demand to increase student numbers, these policies are creating a perfect storm for scientific research and education in Ireland and are undermining our abilities to carry out worldclass research, to retain scientific talent in the country and also to educate future scientists and build a real and sustainable knowledge economy. Innovation needs a strong core in basic research A wealth of economic research shows that sustained investment in basic research pays huge dividends economically, not just through the generation of intellectual property and the development of new companies, but also by building human capital and by attracting companies that hope to benefit from a vibrant research community. Countries with long- established and functional research systems that successfully underpin economic development rely on a well-balanced mix between basic and applied research. The Irish Government’s current investment in applied research is welcome and forms an essential part of an overall strategy to generate economic return from scientific research.
    [Show full text]
  • Science Gallery Dublin Annual Review 01.01.15–31.12.15
    SCIENCE GALLERY DUBLIN ANNUAL REVIEW ANNUAL DUBLIN GALLERY SCIENCE 01.01.15–31.12.15 Science Gallery Dublin 01.01.15–31.12.15 Annual Review Contents 01 Introduction 33 Research and 55 Financial Report Evaluation 05 Background 37 Communications 59 Governance and Leadership 07 Exhibitions 43 The Global Science 61 Governance Board Gallery Network III IV 17 Plans for 2016 47 Touring 65 Leonardo Group 19 Events 49 Commercial 67 Science Gallery Activity Dublin Supporters 25 Education 51 Supporters and Learning and Collaborators 66 64 65 01 Introduction 2015 SCIENCE GALLERY DUBLIN ANNUAL REVIEW 63 62 60 61 Science Gallery at Trinity College Dublin is a porous Google Field Trip Day grant in Ireland in 2015, enabling 59 membrane — a creative platform for people, projects us to bring over 2,000 students to Science Gallery Dublin 58 57 Is the measured self a better and ideas — between the university and the wider from schools across Ireland. As one of only five successful 56 community. From the local to the global, our programmes consortiums in the Science Learning+ funding programme, 54 55 are embedded in a boundaryless world of artists, scientists, established by the National Science Foundation in the US 52 53 self? How are we reconfiguring designers and engineers — transdisciplinary agents of and Wellcome Trust in the UK, we began a groundbreaking 51 change tackling the big global challenges of the future. research and practice collaboration with colleagues in 50 In 2015, through themes like LIFELOGGING, HOME\SICK, the Exploratorium and University of Washington in the 49 48 the traditional ideas of home SECRET and TRAUMA, we investigated some of the most US.
    [Show full text]
  • Science Gallery Dublin Annual Review 01.01.19– 31.12.19 1 2019 Science Gallery Dublin Annual Review
    2019 SCIENCE GALLERY DUBLIN ANNUAL REVIEW SCIENCE GALLERY DUBLIN ANNUAL REVIEW 01.01.19– 31.12.19 1 2019 SCIENCE GALLERY DUBLIN ANNUAL REVIEW Introduction 01 01 / INTRODUCTION 04 02 / BACKGROUND 06 CONTENTS 03 / EXHIBITIONS 08 03 / OPEN LABS 10 03 / PERFECTION 14 03 / PLASTIC 18 04 / EVENTS 22 05 / RESEARCH AND LEARNING 26 06 / VISITOR SURVEYS 30 07 / THE SCIENCE GALLERY NETWORK 32 08 / SCIENCE GALLERY INTERNATIONAL 34 09 / TOURING 36 10 / COMMUNICATIONS 38 11 / COMMERCIAL ACTIVITY 40 12 / SUPPORTERS AND COLLABORATORS 42 13 / FINANCIAL REPORT 44 14 / GOVERNANCE AND LEADERSHIP 48 15 / GOVERNANCE BOARD 50 16 / LEONARDO GROUP 54 17 / PLANS FOR 2020 56 2 3 2019 SCIENCE GALLERY DUBLIN ANNUAL REVIEW Introduction 01 At the time of writing this introduction we are living in a Its deep integration within Trinity College Dublin brings University of Melbourne, the exhibition was re-curated In a similar way, every single one of our partners very different world to the one we are used to. Schools, scholars, researchers, students, and visitors together in Dublin, and was complemented by a series of events and sponsors contributes in a fundamental way to universities, and almost all businesses are closed. Citizens in ways that are mutually beneficial—leading to new drawing on research done at Trinity College Dublin. our activities—but when when taken into account can freely move only within a 2km radius from their home. research publications, award-winning educational collectively they make Science Gallery possible, PLASTIC was designed with sustainability at its core. It is The havoc brought by the COVID-19 pandemic is reshaping modules, and front-page mentions in the national news.
    [Show full text]
  • English TD, Minister for Skills, Research and Innovation and Prof James O’Donnell, Trinity College Dublin
    Front cover image Winner of the SFI Image of the Year Competition 2014. This image entitled ‘Starship Enterprise,’ taken by Dr Anthony Maher, won SFI’s Research Image of the Year competition at the SFI Science Summit in Athlone. Dr Anthony Maher is a Pharmaceutical Executive and former researcher at the Synthesis and Solid State Pharmaceutical Centre (SSPC) in University of Limerick. Dr Maher is a member of Kerry’s Senior Football All Ireland winning team 2014. Description Most of the medicines that we take are made up of compacted powders - the individual particles are in fact tiny crystals of the active compound. Some compounds are known to have a number of different crystal forms, known as polymorphs. The different polymorphs of a compound have different physical and chemical properties, inferring a relative stability hierarchy. One aspect of the research at the Synthesis and Solid State Pharmaceutical Centre (SSPC) focuses on understanding polymorphic compounds and the mechanisms that control their properties, such as crystal structure, purity, shape and size, and exploiting these mechanisms in order to increase the range of medicines available to the public. This optical micrograph image shows a form II piracetam crystal (rough, dissolving) undergoing a polymorphic transformation to a more stable form III crystal (smooth, defined faces) in methanol at 25°C. SCIENCE FOUNDATION IRELAND ANNUAL REPORT 2014 1 Table of Contents Key Statistics 2 Vision 4 Mission 4 Core Values 4 Agenda 2020 5 Chairman’s Statement 6 Director General’s Statement 10 The Year in Review 2014 16 Overview 2014 Activities 20 Governance and Oversight 36 Organisational Structure 41 Financial Statements 2014 47 Grant Commitments and Payment Analysis 2014 65 2 SCIENCE FOUNDATION IRELAND ANNUAL REPORT 2014 Ireland 1st 17th (of 94 countries) Science Week reached over 250,000 people through over 800 events in Nanosciences in the European research rankings for Ireland 2014, based on funding generated out of European funding programmes.
    [Show full text]
  • Six Reference-Quality Genomes Reveal Evolution of Bat Adaptations
    Article Six reference-quality genomes reveal evolution of bat adaptations https://doi.org/10.1038/s41586-020-2486-3 David Jebb1,2,3,25, Zixia Huang4,25, Martin Pippel1,3,25, Graham M. Hughes4, Ksenia Lavrichenko5, Paolo Devanna5, Sylke Winkler1, Lars S. Jermiin4,6,7, Emilia C. Skirmuntt8, Aris Katzourakis8, Received: 14 October 2019 Lucy Burkitt-Gray9, David A. Ray10, Kevin A. M. Sullivan10, Juliana G. Roscito1,2,3, Accepted: 9 June 2020 Bogdan M. Kirilenko1,2,3, Liliana M. Dávalos11,12, Angelique P. Corthals13, Megan L. Power4, Gareth Jones14, Roger D. Ransome14, Dina K. N. Dechmann15,16,17, Andrea G. Locatelli4, Published online: 22 July 2020 Sébastien J. Puechmaille18,19, Olivier Fedrigo20, Erich D. Jarvis20,21,22, Michael Hiller1,2,3,26 ✉, Open access Sonja C. Vernes5,23,26 ✉, Eugene W. Myers1,3,24,26 ✉ & Emma C. Teeling4,26 ✉ Check for updates Bats possess extraordinary adaptations, including fight, echolocation, extreme longevity and unique immunity. High-quality genomes are crucial for understanding the molecular basis and evolution of these traits. Here we incorporated long-read sequencing and state-of-the-art scafolding protocols1 to generate, to our knowledge, the frst reference-quality genomes of six bat species (Rhinolophus ferrumequinum, Rousettus aegyptiacus, Phyllostomus discolor, Myotis myotis, Pipistrellus kuhlii and Molossus molossus). We integrated gene projections from our ‘Tool to infer Orthologs from Genome Alignments’ (TOGA) software with de novo and homology gene predictions as well as short- and long-read transcriptomics to generate highly complete gene annotations. To resolve the phylogenetic position of bats within Laurasiatheria, we applied several phylogenetic methods to comprehensive sets of orthologous protein-coding and noncoding regions of the genome, and identifed a basal origin for bats within Scrotifera.
    [Show full text]
  • CONNECTIONS Alumni Magazine Going Global
    UCD2009-2010 CONNECTIONS alumni magazine Going Global ... with CHARISMA, INFLUENCE and a DEGREE from UCD ALUMNI ACHIEVERS in 2009 ______ Brian O’Driscoll George Lee Ryan Tubridy Niall Breslin Joan Burton Rob Kearney Neil Jordan Derval O’Rourke Brendan Gleeson Cracking the Code women in science GOthe L&H AHEAD debate AND ARGUE 5 49 | CONTENTS | 21 GOING GLOBAL UNIVERSITY PEOPLE 6 Charisma, influence A Year in the and a degree from Spotlight … ALUMNI UCD: all you need to ACHIEVERS in conquer the world. All 2009 (page 50). over the globe, UCD Why not alumni are making THE DNA OF UCD GO AHEAD their mark. Meet the BIG IDEAS are AND ARGUE ALUMNI SERVING hatched on campus (page 54) IRELAND ABROAD (page 22). – is the L&H (page 6). Check out UCD professors a breeding ground for three SCIENTISTS ask who’s SHAPING argumentative types? Is PUBLIC THINKING? who have cut a swathe in 5 politics bred in the bone at global scientific research (page 26). Still in touch – the Belfield? HALF THE DÁIL (page 10). Read missives alumni who CALL ARE UCD ALUMNI (page 58). from medics who left ON THEIR UCD The bust means boom … when UCD to PRACTISE CONTEMPORARIES it means GETTING BACK MEDICINE IN (page 30) and TO EDUCATION (page 64). NORTH AMERICA the FAMOUS FICTIONAL FINDER AND (page 14). See how ALUMNI created by Joyce, KEEPER The the CLASS OF 1994 Flann O’ Brien, Maeve Binchy riches of the has fared: 15 years out and more (page 32). Colour university of university they have on Campus … EVERY archives settled all over the PICTURE TELLS A STORY uncovered world (page 16).
    [Show full text]
  • Investing in Biotechnology Research
    Science Foundation Ireland (SFI) Investing in Biotechnology Research Research for Ireland’s Future www.sfi.ie Science Foundation Ireland (SFI) the National Foundation for Excellence in Scientific Research Investing in Biotechnology Research Science Foundation Ireland (SFI) invests in academic research and research teams that generate new knowledge, leading-edge technologies and competitive enterprises in the fields of science and engineering underpinning Biotechnology, Information & Communications Technology, and Sustainable Energy & Energy- Efficient Technologies. Since its establishment, SFI has contributed to the development and growth of a critical mass of individual investigators and research groups in these broad areas. Today, SFI funds over 300 Principal Investigators across multiple diverse disciplines and continues to encourage growth in these numbers to deliver the targets set out in the Irish Government’s Strategy for Science, Technology & Innovation 2006- 2013. Through these investments, Ireland’s research landscape has become diverse, yet highly interconnected. SFI Centres for Science, Engineering & Technology (CSETs) and Strategic Research Clusters (SRCs) bring together researchers in diverse disciplines such as physics, chemistry, engineering, material science, and biochemistry, and serve as examples of the opportunities for interdisciplinary work and cross-fertilisation of ideas that are presented across the sectors supported by SFI. The addition of new researchers, the growth of collaborative activity and the development
    [Show full text]
  • Science Gallery Dublin Annual Review 01.01.19– 31.12.19 1 2019 Science Gallery Dublin Annual Review
    2019 SCIENCE GALLERY DUBLIN ANNUAL REVIEW SCIENCE GALLERY DUBLIN ANNUAL REVIEW 01.01.19– 31.12.19 1 2019 SCIENCE GALLERY DUBLIN ANNUAL REVIEW Introduction 01 01 / INTRODUCTION 04 02 / BACKGROUND 06 CONTENTS 03 / EXHIBITIONS 08 03 / OPEN LABS 10 03 / PERFECTION 14 03 / PLASTIC 18 04 / EVENTS 22 05 / RESEARCH AND LEARNING 26 06 / VISITOR SURVEYS 30 07 / THE SCIENCE GALLERY NETWORK 32 08 / SCIENCE GALLERY INTERNATIONAL 34 09 / TOURING 36 10 / COMMUNICATIONS 38 11 / COMMERCIAL ACTIVITY 40 12 / SUPPORTERS AND COLLABORATORS 42 13 / FINANCIAL REPORT 44 14 / GOVERNANCE AND LEADERSHIP 48 15 / GOVERNANCE BOARD 50 16 / LEONARDO GROUP 54 17 / PLANS FOR 2020 56 2 3 2019 SCIENCE GALLERY DUBLIN ANNUAL REVIEW Introduction 01 At the time of writing this introduction we are living in a Its deep integration within Trinity College Dublin brings University of Melbourne, the exhibition was re-curated In a similar way, every single one of our partners very different world to the one we are used to. Schools, scholars, researchers, students, and visitors together in Dublin, and was complemented by a series of events and sponsors contributes in a fundamental way to universities, and almost all businesses are closed. Citizens in ways that are mutually beneficial—leading to new drawing on research done at Trinity College Dublin. our activities—but when when taken into account can freely move only within a 2km radius from their home. research publications, award-winning educational collectively they make Science Gallery possible, PLASTIC was designed with sustainability at its core. It is The havoc brought by the COVID-19 pandemic is reshaping modules, and front-page mentions in the national news.
    [Show full text]