Systematic Biology

Volume 63, Number 1

January 2014

CONTENTS Scan to view this journal on your mobile device

REGULAR ARTICLES Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron

Alastair J. Potts, Terry A. Hedderson, and Guido W. Grimm ....................................................................................................................... 1

Volume 63 Number 1, pp. 1–117

Systematic Biology

Systematic Biology A JOURNAL OF THE

Society of Systematic Biologists

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

Adam D. Leaché, Rebecca B. Harris, Bruce Rannala, and Ziheng Yang...................................................................................................... 17 Accelerated Rate of Molecular Evolution for Vittarioid Ferns is Strong and Not Driven by Selection

Carl J. Rothfels and Eric Schuettpelz ........................................................................................................................................................... 31 Island Biogeography, the Effects of Taxonomic Effort and the Importance of Island Niche Diversity to Single-Island Endemic Species

Alan Gray and Stephen Cavers ....................................................................................................................................................................... 55 Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees

Michael DeGiorgio and James H. Degnan ......................................................................................................................................................66

Brian Tilston Smith, Michael G. Harvey, Brant C. Faircloth, Travis C. Glenn, and Robb T. Brumfield.................................................... 83 Timeframes of Speciation, Reticulation, and Hybridization in the Bulldog Bat Explained Through Phylogenetic Analyses of All Genetic Transmission Elements

Faisal Ali Anwarali Khan, Caleb D. Phillips, and Robert J. Baker ..............................................................................................................96

BOOK REVIEWS A Primer of Botanical Latin with Vocabulary

Peter D. Bostock ............................................................................................................................................................................................ 111 Mutation-Driven Evolution

Nicolas Galtier .............................................................................................................................................................................................. 113 The Eponym Dictionary of Amphibians The Eponym Dictionary of Reptiles The Eponym Dictionary of Mammals Whose Bird? Men and Women Commemorated in the Common Names of Birds

SYSTEMATIC BIOLOGY

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

David A. Morrison ........................................................................................................................................................................................ 115

January 2014

Cover Illustration: Sequence capture of ultraconserved elements (UCEs) promises to generate data for systematics studies in diverse organisms. In this issue, Smith et al. (pp. 83–95) demonstrate the utility of UCEs for phylogeography in five widespread Neotropical bird species. Across species, they find discordance in population trees, demographic histories, and the number of genetic species. This study demonstrates that UCEs are informative at shallow as well as deep timescales and that sequence capture of these markers is a straightforward way to generate genomic datasets for systematics. Bird photographs were taken by Kurazo Okada, Ciro Albano, and Luiz Carlos Ribenboim and are available at WikiAves (http://www.wikiaves.com.br).

VOLUME 63 NUMBER 1

JANUARY 2014

ONLINE ISSN 1076-836X PRINT ISSN 1063-5157

Published on behalf of the Society of Systematic Biologists http://systbiol.org/ Downloaded from https://academic.oup.com/sysbio/issue/63/1 by guest on 03 February 2018

sysbio_63_1_Cover.indd 1

10-12-2013 18:03:41

Systematic Biology

Information for Members and Subscribers

EDITOR-IN-CHIEF: Frank E. (Andy) Anderson, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901-6501, USA. Email: [email protected]. Phone: (618) 453-4136. Fax: (618) 453-2806.

Subscriptions. Subscriptions to Systematic Biology comprise 6 issues. Print prices include dispatch by Standard Air. Airmail rates are available on request. Systematic Biology Advance Access contains papers that have recently been accepted but have not yet been included within an issue. Advance Access is updated daily.

EDITORIAL OFFICE: Lulu Stader, [email protected] BOOK REVIEW EDITOR: David A. Morrison, Department of Parasitology (SWEPAR), National Veterinary Institute, SE-751 89 Uppsala, Sweden. Email: [email protected]. Books for review should be sent to the Book Review Editor. ASSOCIATE EDITORS: Cécile Ané, Robb Brumfield, Thomas Buckley, Michael Charleston, Benoit Dayrat, Erika Edwards, Dan Faith, Mark Fishbein, Peter Foster, Olivier Gascuel, Richard Glor, Luke Harmon, Mark Holder, Lars Jermiin, Karl Kjer, Laura Kubatko, Norman MacLeod, Roberta J. Mason-Gamer, Austin Mast, John McCormack, Thomas Near, Adrian Paterson, David Posada, Susanne S. Renner, Vincent Savolainen, Tanja Stadler, Edward Susko, Brian Wiegmann, Tiffani Williams EDITORIAL BOARD MEMBERS: Kenneth Angielczyk, Stephane Aris-Brosou, Jonathan Banks, Keith Barker, Timothy G. Barraclough, Bastien Boussau, Sean Brady, Jeremy Brown, David Bryant, Rob W. Bryson, Jr., Bryan Carstens, Cymon Cox, Karen Cranston, Rob Cruickshank, Frédéric Delsuc, Leonardo de Oliveira Martins, Alexei Drummond, Brant Faircloth, Mareike Fischer, Brant Faircloth, Mareike Fischer, Joe Gillespie, Richard Grenyer, Tracy Heath, Andrew Hipp, Robert Hirt, Sebastian Höhna, Boris Igic, Martyn Kennedy, Thorsten Lumbsch, David Marshall, Erick Matsen, Helene Morlon, Brian O’Meara, Bernard Pfeil, David Polly, R. Alexander Pyron, Chris Randle, Liam Revell, Andrew J. Roger, Sarah Samadi, John Schenk, Beth Shapiro, Stacey D. Smith, W. Leo Smith, Matthew Spencer, Felix Sperling, Shannon Straub, John Trueman, George D.F. Wilson, Felipe Zapata Manuscripts should be submitted online at http://mc.manuscriptcentral.com/systbiol. Correspondence about the journal should be sent to the Editorial Office at [email protected]

Society of Systematic Biologists URL: http://systematicbiology.org President: Jack Sites, Brigham Young University, Department of Biology, Provo, UT 84602, USA. Email: jack_sites@ byu.edu. President-Elect: Paul Lewis, Department of Ecology and Evolutionary Biology, University of Connecticut, 75 N. Eagleville Road, Unit 3043, Storrs, Connecticut 06269, USA. Past President: L. Lacey Knowles, University of Michigan Museum of Zoology and Department of Ecology and Evolutionary Biology, 1109 Geddes Ave., Ann Arbor, MI 48109-1079, USA. Email: [email protected]. Executive Vice President: Susanne Renner, Department of Biology, University of Munich. Systematische Botanik, Menzinger Str. 67, 80638, Muenchen, Deutschland. Email: [email protected]. Treasurer: H. Bradley Shaffer, University of California, Los Angeles, Department of Ecology and Evolutionary Biology, 621 Charles E. Young Drive South, Room LS5120, Box 951606, Los Angeles, CA 90095-1606, USA. Email: brad. [email protected]. Awards Director: Sean Brady, Smithsonian Institution, National Museum of Natural History, Department of Entomology, 10th & Constitution NW, Washington, DC 20560-0188, USA. Email: [email protected]. Publication Chairperson: Ronald W. DeBry, Department of Biological Sciences, ML006, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA. Email: [email protected]. Phone: (513) 556-9743. Fax: (513) 556-5299. Program Director: Bryan Carstens, Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, 318 W. 12th Avenue, Columbus, OH 43210-1293. Email: [email protected]. The Council: 2013: Cécile Ané, Erika J. Edwards, Luke Harmon, Kathleen Pryer, Alexis Stamatakis; 2014: Bryan Carstens, Karen Cranston, Mark Holder, Brian O’Meara, Stacey D. Smith; 2015: Mike Steel, Dan Rabosky, Susan Perkins, Chelsea Specht, Tracy Heath. Ex Officio: President, President-Elect, most recent Past-President, Executive Vice President, Treasurer, Program Chairperson, Editor, Editor-Elect. Trustees: Joel Cracraft, David M. Hillis, Vicki Funk. Honorary Members: J.S. Farris, J. Felsenstein, V.A. Funk, Ch. Michener, G. Nelson, and D.L. Swofford.

Annual Subscription Rate (Volume 63, 6 issues, 2014) Members. Membership and print edition: £42/$63/E57. Institutional. Print and online access: £230/$345/E345; print edition only: £212/$317/E317; site-wide online access only: £165/$247/E247. Corporate. Print and online access: £288/$431/E431; print edition only: £265/$397/E397; site-wide online access only: £206/$309/E309. Please note: UK£ rate applies to UK and Rest of World, except US and Canada (US$) and Europe (EurE). There are other subscription rates available; for a complete listing, please visit http://www.oxfordjournals.org/our_journals/sysbio/access_purchase/price_list.html. Full prepayment in the correct currency is required for all orders. Payment should be in US dollars for orders being delivered to the USA or Canada; Euros for orders being delivered within Europe (excluding the UK); GBP Sterling for orders being delivered elsewhere (i.e., not being delivered to USA, Canada, or Europe). All orders should be accompanied by full payment and sent to your nearest Oxford Journals office. Subscriptions are accepted for complete volumes only. Orders are regarded as firm, and payments are not refundable. Our prices include dispatch by Standard Air. Claims must be notified within four months of despatch/order date (whichever is later). Subscriptions in the EEC may be subject to European VAT. If registered, please supply details to avoid unnecessary charges. For subscriptions that include online versions, a proportion of the subscription price may be subject to UK VAT. Subscribers in Canada, please add GST to the prices quoted. Personal rate 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. The current year and two previous years’ issues are available from Oxford Journals. Previous volumes can be obtained from the Periodicals Service Company, 11 Main Street, Germantown, NY 12526, USA. E-mail: [email protected]. Tel: (518) 537-4700. Fax: (518) 537-5899. Contact information. Journals Customer Service Department, Oxford Journals, Great Clarendon Street, Oxford OX2 6DP, UK. E-mail: [email protected]. Tel: +44 (0)1865 353907. Fax: +44 (0)1865 353485. In the Americas, please contact: Journals Customer Service Department, Oxford Journals, 2001 Evans Road, Cary, NC 27513, USA. E-mail: [email protected]. Tel: (800) 852-7323 (toll-free in USA/Canada) or (919) 677-0977. Fax: (919) 677-1714. In Japan, please contact: Journals Customer Service Department, Oxford Journals, 4-5-10-8F Shiba, Minato-ku, Tokyo, 108-8386, Japan. E-mail: [email protected]. Tel: (81) 3 5444 5858. Fax: (81) 3 3454 2929. Methods of payment. Payment should be made: by cheque (to Oxford Journals, Cashiers Office, Great Clarendon Street, Oxford, OX2 6DP, UK); by bank transfer [to Barclays Bank Plc, Oxford Office, Oxford (bank sort code 20-65-18) (UK); overseas only Swift code BARC GB22 (GB£ Sterling Account no. 70299332, IBAN GB89BARC20651870299332; US$ Dollars Account no. 66014600, IBAN GB27BARC20651866014600; EUE EURO Account no. 78923655, IBAN GB16BARC20651878923655]; or by credit card (Mastercard, Visa, Switch or American Express). Postal information. Systematic Biology (Print ISSN: 1063-5157; Online ISSN 1076-836X) is published six times a year in January, March, May, July, September, and November, by Oxford University Press, 2001 Evans Road, Cary, NC27513-2009, USA. Periodicals Postage Paid at Cary, NC, and additional mailing offices. POSTMASTER: Send address changes to Systematic Biology, Journals Customer Service Department, Oxford University Press, 2001 Evans Road, Cary, NC 27513-2009. Environmental and ethical policies. Oxford Journals, a division of Oxford University Press, is committed to working with the global community to bring the highest quality research to the widest possible audience. Oxford Journals will protect the environment by implementing

environmentally friendly policies and practices wherever possible. Please see http://www.oxfordjournals.org/ethicalpolicies.html for further information on Oxford Journals’ environmental and ethical policies. Paper statement. This journal is printed on FSC- and SFI®-certified paper as part of an ongoing effort to promote the responsible management of the world’s forests for the social, economic, and ecological needs of present and future generations. Digital object identifiers. For information on dois and to resolve them, please visit www.doi.org. Permissions. For information on how to request permissions to reproduce articles or information from this journal, please visit www. oxfordjournals.org/permissions. Advertising. Advertising, inserts, and artwork enquiries should be addressed to Advertising and Special Sales, Oxford Journals, Oxford University Press, Great Clarendon Street, Oxford, OX2 6DP, UK. Tel: +44 (0)1865 354767; Fax: +44 (0)1865 353774; E-mail: jnlsadvertising@ oup.com. Disclaimer. Statements of fact and opinion in the articles in Systematic Biology are those of the respective authors and contributors and not of the Society of Systematic Biologists or Oxford University Press. Neither Oxford University Press nor Systematic Biology make any representation, express or implied, in respect of the accuracy of the material in this journal and cannot accept any legal responsibility or liability for any errors or omissions that may be made. The reader should make her or his own evaluation as to the appropriateness or otherwise of any experimental technique described. Indexing/Abstracting. Chemical Abstracts Service, ISI, GenBank, Biosis, USDA National Agricultural Library, Abstracts in Anthropology, Abstracts on Hygiene and Communicable Diseases, Agbiotech News and Information, Agroforestry Abstracts, CAB Abstracts, MEDLINE, ProQuest 5000 International, ProQuest Biology Journals, ProQuest Central, ProQuest Discovery, ProQuest Health & Medical Complete, ProQuest International Academic Research Library, ProQuest News & Magazines, ProQuest Pharma Collection, ProQuest Research Library. Copyright © 2014 Society of Systematic Biologists All rights reserved; no part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise without prior written permission of the publisher or a license permitting restricted copying issued in the UK by the Copyright Licensing Agency Ltd, 90 Tottenham Court Road, London W1P 9HE. Instructions for Authors. Full instructions for manuscript preparation and submission can be found at: http://www.oxfordjournals.org/ our_journals/sysbio/for_authors/ Typeset by Cenveo publisher services, Bangalore, India. Printed by The Sheridan Press, Hanover, PA, USA. Oxford University Press is a department of the University of Oxford. It furthers the University’s objective of excellence in research, scholarship, and education by publishing worldwide.

SYSBIO06301M Downloaded from https://academic.oup.com/sysbio/issue/63/1 by guest on 03 February 2018

sysbio_63_1_Cover.indd Sec1:2

10-12-2013 18:03:43