Contents

Vol. 197 No. 1 May 2014

GENETIC TOOLBOX REVIEWS

1–18 Resources for Functional Genomics Studies in Drosophila melanogaster Mohr, Stephanie E., Yanhui Hu, Kevin Kim, Benjamin E. Housden, and Norbert Perrimon

19–31 Genetic and Genomic Tools for the Marine Annelid Platynereis dumerilii Cover photo: The marine Zantke, Juliane, Stephanie Bannister, Vinoth Babu Veedin Rajan, Florian Raible, bristle worm Platynereis and Kristin Tessmar-Raible dumerilii is a long-standing invertebrate model system PRIMER for chronobiology, repro- 33–48 Budding Yeast for Budding Geneticists: A Primer on the Saccharomyces duction and regeneration. cerevisiae Model System Over the last decade, Duina, Andrea A., Mary E. Miller, and Jill B. Keeney Platynereis has also become an important reference INVESTIGATIONS species for the study of METHODS, TECHNOLOGY, AND RESOURCES evolutionary developmental 49–59 Exploiting the Extraordinary Genetic Polymorphism of Ciona for biology (evo-devo). Because of its retention of several Developmental Genetics with Whole Genome Sequencing ancient-type features, the Abdul-Wajid, Sarah, Michael T. Veeman, Shota Chiba, Thomas L. Turner, worm has sometimes been and William C. Smith symbolically referred to as 61–76 TargetOrtho: A Phylogenetic Footprinting Tool to Identify Transcription “ ” living fossil . In this issue, Factor Targets et al Bannister .(Genetics Glenwinkel, Lori, Di Wu, Gregory Minevich, and Oliver Hobert 197:77–89)presentthe first method for generating 77–89 TALENs Mediate Efficient and Heritable Mutation of Endogenous Genes targeted genome modifi- in the Marine Annelid Platynereis dumerilii cations in Platynereis. Bannister, Stephanie, Olga Antonova, Alessandra Polo, Claudia Lohs, Along with additional tools Natalia Hallay, Agne Valinciute, Florian Raible, and Kristin Tessmar-Raible (reviewed by Zantke, GENOME INTEGRITY AND TRANSMISSION Bannister et al., Genetics 197:19–31), this technique 91–106 High-Resolution Sex-Specific Linkage Maps of the Mouse Reveal Polarized marks a key event in the Distribution of Crossovers in Male Germline transition of Platynereis Liu, Eric Yi, Andrew P. Morgan, Elissa J. Chesler, Wei Wang, from a classical model to Gary A. Churchill, and Fernando Pardo-Manuel de Villena a functional molecular 107–119 Nascent DNA Synthesis During Homologous Recombination Is Synergistically model system. The cover image presents motifs of Promoted by the Rad51 Recombinase and DNA Homology the “living fossil” and its Mundia, Maureen M., Vatsal Desai, Alissa C. Magwood, and Mark D. Baker transition to a functional GENE EXPRESSION laboratory model. Artwork 121–132 Nuclear RNAi Contributes to the Silencing of Off-Target Genes and Repetitive courtesy of Florian Raible. Sequences in Caenorhabditis elegans See Bannister et al., Ge- Zhou, Xufei, Fei Xu, Hui Mao, Jiaojiao Ji, Meng Yin, Xuezhu Feng, netics 197:77–89; Zantke, and Shouhong Guang Bannister et al., Genetics 197:19–31. 133–145 Maintenance of Heterochromatin Boundary and Nucleosome Composition at Promoters by the Asf1 Histone Chaperone and SWR1-C Chromatin Remodeler in Saccharomyces cerevisiae Lu, Phoebe Y. T. and Michael S. Kobor 147–157 High Intake of Dietary Sugar Enhances Bisphenol A (BPA) Disruption and Reveals Ribosome-Mediated Pathways of Toxicity Branco, Alan T. and Bernardo Lemos

CELLULAR GENETICS 159–173 NsdD Is a Key Repressor of Asexual Development in Aspergillus nidulans Lee, Mi-Kyung, Nak-Jung Kwon, Jae Min Choi, Im-Soon Lee, Seunho Jung, and Jae-Hyuk Yu

175–192 Insight into Insulin Secretion from Transcriptome and Genetic Analysis of Insulin-Producing Cells of Drosophila Cao, Jian, Julie Ni, Wenxiu Ma, Vanessa Shiu, Luis A. Milla, Sangbin Park, Maria L. Spletter, Sheng Tang, Jun Zhang, Xing Wei, Seung K. Kim, and Matthew P. Scott

193–197 Degradation of Specific Nuclear Proteins Occurs in the Cytoplasm in Saccharomyces cerevisiae Chen, Li and Kiran Madura

DEVELOPMENTAL AND BEHAVIORAL GENETICS 199–205 The Origin of the Second Centriole in the Zygote of Drosophila melanogaster Blachon, Stephanie, Atul Khire, and Tomer Avidor-Reiss

207–220 Neuronal Migration Is Regulated by Endogenous RNAi and Chromatin-Binding Factor ZFP-1/AF10 in Caenorhabditis elegans Kennedy, Lisa M. and Alla Grishok

POPULATION AND EVOLUTIONARY GENETICS 221–236 Robust Forward Simulations of Recurrent Hitchhiking Uricchio, Lawrence H. and Ryan D. Hernandez

237–255 Fisher’s Geometrical Model Emerges as a Property of Complex Integrated Phenotypic Networks Martin, Guillaume

257–271 A Penalized-Likelihood Method to Estimate the Distribution of Selection Coefficients from Phylogenetic Data Tamuri, Asif U., Nick Goldman, and Mario dos Reis

273–283 The Fate of Chromosomes and Alleles in an Allohexaploid Brassica Population Mason, Annaliese S., Matthew N. Nelson, Junko Takahira, Wallace A. Cowling, Gustavo Moreira Alves, Arkaprava Chaudhuri, Ning Chen, Mohana E. Ragu, Jessica Dalton-Morgan, Olivier Coriton, Virginie Huteau, Frédérique Eber, Anne-Marie Chèvre, and Jacqueline Batley

285–289 SNP2GO: Functional Analysis of Genome-Wide Association Studies Szkiba, David, Martin Kapun, Arndt von Haeseler, and Miguel Gallach

291–299 Birth, Death, and Diversification of Mobile Promoters in Prokaryotes van Passel, Mark W.J., Harm Nijveen, and Lindi M. Wahl

301–315 The Effect of Mutation and Selection on Codon Adaptation in Escherichia coli Bacteriophage Chithambaram, Shivapriya, Ramanandan Prabhakaran, and Xuhua Xia

317–336 The Effect of Linkage on Establishment and Survival of Locally Beneficial Mutations Aeschbacher, Simon and Reinhard Bürger

337–349 Exploiting Population Samples to Enhance Genome-Wide Association Studies of Disease Kaufman, Shachar and Saharon Rosset

ii Contents 351–360 Stochastic Demography and the Neutral Substitution Rate in Class-Structured Populations Lehmann, Laurent

361–373 Parallel Geographic Variation in Drosophila melanogaster Reinhardt, Josie A., Bryan Kolaczkowski, Corbin D. Jones, David J. Begun, and Andrew D. Kern GENETICS OF COMPLEX TRAITS 375–387 Recovering Power in Association Mapping Panels with Variable Levels of Linkage Disequilibrium Rincent, Renaud, Laurence Moreau, Hervé Monod, Estelle Kuhn, Albrecht E. Melchinger, Rosa A. Malvar, Jesus Moreno-Gonzalez, Stéphane Nicolas, Delphine Madur, Valérie Combes, Fabrice Dumas, Thomas Altmann, Dominique Brunel, Milena Ouzunova, Pascal Flament, Pierre Dubreuil, Alain Charcosset, and Tristan Mary-Huard

389–399 A Novel Statistical Approach for Jointly Analyzing RNA-Seq Data from

F1 Reciprocal Crosses and Inbred Lines Zou, Fei, Wei Sun, James J. Crowley, Vasyl Zhabotynsky, Patrick F. Sullivan, and Fernando Pardo-Manuel de Villena

401–404 Efficient Imputation of Missing Markers in Low-Coverage Genotyping-by- Sequencing Data from Multiparental Crosses Huang, B. Emma, Chitra Raghavan, Ramil Mauleon, Karl W. Broman, and Hei Leung

405–420 Modular Skeletal Evolution in Sticklebacks Is Controlled by Additive and Clustered Quantitative Trait Loci Miller,CraigT.,AndrewM.Glazer,BrianR.Summers,BenjaminK.Blackman, Andrew R. Norman, Michael D. Shapiro, Bonnie L. Cole, Catherine L. Peichel, Dolph Schluter, and David M. Kingsley GENOME AND SYSTEMS BIOLOGY 421–432 Maintaining Two Mating Types: Structure of the Mating Type Locus and Its Role in Heterokaryosis in Podospora anserina Grognet, Pierre, Frédérique Bidard, Claire Kuchly, Laetitia Chan Ho Tong, Evelyne Coppin, Jinane Ait Benkhali, Arnaud Couloux, Patrick Wincker, Robert Debuchy, and Philippe Silar

CORRIGENDUM 433 Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae) Eckert, A. J., J. van Heerwaarden, J. L. Wegrzyn, C. D. Nelson, J. Ross-Ibarra

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