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Systematic Biology Volume 63 Number 1, pp. 1–117 63 Number 1, Volume Systematic Biology Volume 63, Number 1 January 2014 CONTENTS Scan to view this journal Systematic Biology on your mobile device REGULAR ARTICLES A JOURNAL OF THE Constructing Phylogenies in the Presence Of Intra-Individual Site Polymorphisms (2ISPs) with a Focus on the Nuclear Ribosomal Cistron Society of Systematic Biologists Alastair J. Potts, Terry A. Hedderson, and Guido W. Grimm ....................................................................................................................... 1 The Infl uence 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 Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow BIOLOGY SYSTEMATIC Evolutionary Time Scales Brian Tilston Smith, Michael G. Harvey, Brant C. Faircloth, Travis C. Glenn, and Robb T. Brumfi eld ....................................................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 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 fi ve widespread Neotropical bird species. Across species, they fi nd 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 ONLINE ISSN 1076-836X JANUARY 2014 NUMBER 1 PRINT ISSN 1063-5157 Published on behalf of the Society of Systematic Biologists http:// systbiol.org/ sysbio_63_1_Cover.indd 1 10-12-2013 18:03:41 Systematic Biology Information for Members and Subscribers Subscriptions. Subscriptions to Systematic Biology comprise 6 issues. Print prices include dispatch by Standard Air. 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