genet Volume TOC Title page 1

GENETICS

A PERIODICAL RECORD OF INVESTIGATIONSBEARING ON HEREDITY AND VARIATION

Founded in 1916

and published by

The Genetics Society of America

VOLUME 182, MAY–AUGUST 2009

GENETICS VOLUME 182, MAY–AUGUST 2009

EDITORIAL BOARD

Mark Johnston, Editor-in-ChiefWashington University School of Medicine

Montserrat Aguade

Universitat de Barcelona

Eric E. Alani

Cornell University

Brenda J. Andrews

University of Toronto

Robert R. H. Anholt

North Carolina State University

Elja Arjas

University of Helsinki

Norman Arnheim

University of Southern California

Bonnie Bartel

Rice University

William D. Beavis

Iowa State University

David Begun

University of California, Davis

Sharon E. Bickel

Dartmouth College

James A. Birchler

University of Missouri

Justin Borevitz

University of Chicago

Karl W. Broman

University of Wisconsin, Madison

Thomas P. Brutnell

Boyce Thompson Institute

Edward Buckler

Cornell University

Deborah Charlesworth

University of Edinburgh

Orna Cohen-Fix

NIDDK, National Institutes of Health

Monica Colaiacovo

Harvard Medical School

Gregory Copenhaver

University of North Carolina

Anna Di Rienzo


R. W. Doerge

Purdue University

JoAnne Engebrecht


Laurent Excoffier

University of Bern

Marcus W. Feldman

Stanford University

Stanley Fields

University of Washington

William M. Gelbart

Harvard University

Gregory C. Gibson

University of Queensland

Kent Golic

University of Utah

Susan Gottesman

National Institutes of Health-NCI

David I. Greenstein

University of Minnesota

David Jonah Grunwald

University of Utah

Chris Haley

Roslin Institute (Edinburgh)

Michael Hampsey

Robert Wood Johnson MedicalSchool-UMDNJ

Lawrence G. Harshman

University of Nebraska, Lincoln

Oliver Hobert

Columbia University

Ina Hoeschele

Virginia Polytechnic Institute and StateUniversity

Nancy Hollingsworth

Stony Brook University

M. Zafri Humayun

UMDNJ-New Jersey Medical School

Thomas C. Kaufman

Indiana University

Scott Keeney

Sloan-Kettering Institute

Kenneth J. Kemphues

Cornell University

Matias Kirst

University of Florida

Jeffrey Lawrence

University of Pittsburgh

David Leach

University of Edinburgh

Manyuan Long


Tony Long

University of California,Irvine

A. Javier Lopez

Carnegie Mellon University

Terry R. Magnuson

University of North Carolina, Chapel Hill

Barbara J. Meyer

University of California, Berkeley

Aaron P. Mitchell

Carnegie Mellon University

Spencer Muse

North Carolina State University

Michael Nachman

University of Arizona

Rasmus Nielsen

University of Copenhagen, Centre forBioinformatics

Michael Nonet

Washington University School of Medicine

Magnus Nordborg

University of Southern California

Peter J. Oefner

Stanford University

Andrew Paterson

University of Georgia

Norbert Perrimon


Patrick Phillips

University of Oregon

Lorraine Pillus

University of California, San Diego

David Rand

Brown University

Eric J. Richards

Boyce Thompson Institute for PlantResearch

Mark D. Rose

Princeton University

Matthew S. Sachs

Texas A&M University

Outi Savolainen

University of Oulu

Trudi Schupbach


Jeff Sekelsky


Linda Siracusa

Thomas Jefferson University

Gerald R. Smith

Fred Hutchinson Cancer Center

Hamish Gordon Spencer

University of Otago

Franklin W. Stahl

University of Oregon

Matthew Stephens


Gary Stormo

Washington University School ofMedicine

Venkatesan Sundaresan


Naoyuki Takahata

Graduate University for Advanced Studies

John Tamkun

University of California, Santa Cruz

David Threadgill


Marcy K. Uyenoyama

Duke University

Michel A. Veuille

Ecole Pratique des Hautes Etudes, Paris

Anne M. Villeneuve

Stanford University School of Medicine

Daniel F. Voytas

University of Minnesota

Lindi M. Wahl

Middlesex College

Jon Wakefield

University of Washington

Ned Wingreen


Hongyu Zhao

Yale University

William F. Dove, Perspectives EditorUniversity of Wisconsin, Madison

Adam S. Wilkins, Perspectives EditorUniversity of Cambridge

Mitsuhiro Yanagida, Perspectives EditorKyoto University

Patricia J. Pukkila, Genetics EducationEditor


Allan C. Spradling, Reviews EditorCarnegie Institution

Board of Senior Editors

Jef Boeke

Johns Hopkins School of Medicine

Susan Dutcher

Washington University School ofMedicine

R. Scott Hawley

Stowers Institute for Medical Research

Charles H. Langley


Ruth Lehmann

Skirball Institute of BiomolecularMedicine

Lauren M. McIntyre

University of Florida

John Wakeley

Harvard University

Fred Winston


Tracey DePellegrin Connelly, Executive EditorPublished at Baltimore, Maryland

by the Genetics Society of America

Pre-publication services and printing by Dartmouth Journal Services

VOLUME CONTENTS

to Volume 182, May–August 2009

Albert, Frank W., Orjan Carlborg, Irina Plyusnina, Francois Besnier, Daniela Hedwig,Susann Lautenschlager, Doreen Lorenz, Jenny McIntosh, Christof Neumann,Henning Richter, Claudia Zeising, Rimma Kozhemyakina, Olesya Shchepina, Jurgen

Kratzsch, Lyudmila Trut, Daniel Teupser, Joachim Thiery, Torsten Schoneberg, Leif

Andersson and Svante Paabo, Genetic architecture of tameness in a rat model of animaldomestication .................................................................................................................................... 541—554

Arunkumar, K. P., Kazuei Mita and J. Nagaraju, The silkworm Z chromosome is enriched intestis-specific genes ........................................................................................................................ 493—501

Barazesh, Solmaz, Cima Nowbakht and Paula McSteen, sparse inflorescence1, barreninflorescence1 and barren stalk1 promote cell elongation in maize inflorescence development 403—406

Bauman, Lara E., Janet S. Sinsheimer, Eric M. Sobel and Kenneth Lange, Mixed effectsmodels for quantitative trait loci mapping with inbred strains .................................................. 411

Berry, S. D., S. R. Davis, E. M. Beattie, N. L. Thomas, A. K. Burrett, H. E. Ward, A. M.Stanfield, M. Biswas, A. E. Ankersmit-Udy, P. E. Oxley, J. L. Barnett, J. F. Pearson, Y. van

der Does, A. H. K. MacGibbon, R. J. Spelman, K. Lehnert and R. G. Snell, Mutation inbovine b-carotene oxygenase 2 affects milk color ....................................................................... 923—926

Blachon, Stephanie, Xuyu Cai, Kela A. Roberts, Kevin Yang, Andrey Polyanovsky,Allen Church and Tomer Avidor-Reiss, A proximal centriole-like structure is present inDrosophila spermatids and can serve as a model to study centriole duplication ..................... 133—144

Blekhman, Ran, Alicia Oshlack and Yoav Gilad, Segmental duplications contribute togene expression differences between humans and chimpanzees .............................................. 627—630

Blumenstiel, Justin P., Aaron C. Noll, Jennifer A. Griffiths, Anoja G. Perera, Kendra

N. Walton, William D. Gilliland, R. Scott Hawley and Karen Staehling-Hampton,Identification of EMS-induced mutations in Drosophila melanogaster by whole-genomesequencing ..................................................................................................................................... 25—32

Boggs, Nathan A., Kathleen G. Dwyer, Paurush Shah, Amanda A. McCulloch, Jesper

Bechsgaard, Mikkel H. Schierup, Mikhail E. Nasrallah and June B. Nasrallah,Expression of distinct self-incompatibility specificities in Arabidopsis thaliana .......................... 1313—1321

Boysen, Jacob H., Saranna Fanning, Justin Newberg, Robert F. Murphy and Aaron P.Mitchell, Detection of protein–protein interactions through vesicle targeting .................... 33—39

Bozas, Ana, Kelly J. Beumer, Jonathan K. Trautman and Dana Carroll, Genetic analysisof zinc-finger nuclease-induced gene targeting in Drosophila .................................................. 641—651

Brandvain, Yaniv, and Michael J. Wade, The functional transfer of genes from themitochondria to the nucleus: The effects of selection, mutation, population size and rate ofself-fertilization .............................................................................................................................. 1129—1139

Brenner, Sydney, In the beginning was the worm .................................................................... 413—415

Campos, Gustavo de los, Hugo Naya, Daniel Gianola, Jose Crossa, Andres Legarra,Eduardo Manfredi, Kent Weigel and Jose Miguel Cotes, Predicting quantitative traitswith regression models for dense molecular markers and pedigree ......................................... 375—385

Carpenter, Adelaide T. C., The joys of truly joint research, with the Great TranslocationHunt as an example ...................................................................................................................... 929—934

Castillon, Alicia, Hui Shen and Enamul Huq, Blue light induces degradation of thenegative regulator phytochrome interacting factor 1 to promote photomorphogenic de-velopment of Arabidopsis seedlings ............................................................................................. 161—171

Chanet, Soline, Nicolas Vodovar, Veronique Mayau and Francxois Schweisguth,Genome engineering-based analysis of Bearded family genes reveals both functional re-dundancy and a nonessential function in lateral inhibition in Drosophila .............................. 1101—1108

Chau, Johnnie, Laura Shapiro Kulnane and Helen K. Salz, Sex-lethal facilitates thetransition from germline stem cell to committed daughter cell in the Drosophila ovary ....... 121—132

Chaudhary, Bhupendra, Lex Flagel, Robert M. Stupar, Joshua A. Udall, Neetu Verma,Nathan M. Springer and Jonathan F. Wendel, Reciprocal silencing, transcriptional biasand functional divergence of homeologs in polyploid cotton (Gossypium) ............................ 503—517

Chun, Hyonho, and Sunduz Kelesx, Expression quantitative trait loci mapping withmultivariate sparse partial least squares regression .................................................................... 79—90

Concha, Carolina, and Maxwell J. Scott, Sexual development in Lucilia cuprina (Diptera,Calliphoridae) is controlled by the transformer gene ................................................................ 785—798

Conde, Francisco, Esther Refolio, Violeta Cordon-Preciado, Felipe Cortes-Ledesma,Luis Aragon, Andres Aguilera and Pedro A. San-Segundo, The Dot1 histone methyl-transferase and the Rad9 checkpoint adaptor contribute to cohesin-dependent double-strandbreak repair by sister chromatid recombination in Saccharomyces cerevisiae ............................... 437—446

Copic, Alenka, Mariana Dorrington, Silvere Pagant, Justine Barry, Marcus C. S. Lee,Indira Singh, John L. Hartman, IV and Elizabeth A. Miller, Genomewide analysis revealsnovel pathways affecting endoplasmic reticulum homeostasis, protein modification andquality control ............................................................................................................................... 757—769

Corrigendum ................................................................................................................................. 1399

Cox, Allison, Cheryl L. Ackert-Bicknell, Beth L. Dumont, Yueming Ding, Jordana

Tzenova Bell, Gudrun A. Brockmann, Jon E. Wergedal, Carol Bult, Beverly Paigen,Jonathan Flint, Shirng-Wern Tsaih, Gary A. Churchill and Karl W. Broman, A newstandard genetic map for the laboratory mouse ......................................................................... 1335—1344

Cziko, Anne-Marie J., Cathal T. McCann, Iris C. Howlett, Scott A. Barbee, Rebecca P.Duncan, Rene Luedemann, Daniela Zarnescu, Konrad E. Zinsmaier, Roy R. Parker and

Mani Ramaswami, Genetic modifiers of dFMR1 encode RNA granule components inDrosophila ..................................................................................................................................... 1051—1060

Daines, Bryce, Hui Wang, Yumei Li, Yi Han, Richard Gibbs and Rui Chen, High-throughput multiplex sequencing to discover copy number variants in Drosophila ............... 935—941

da Silva, Jack, Amino acid covariation in a functionally important human immunodeficiencyvirus type 1 protein region is associated with population subdivision ....................................... 265—275

Dassah, MaryAnn, Sophie Patzek, Valerie M. Hunt, Pedro E. Medina and Alan M.Zahler, A genetic screen for suppressors of a mutated 59 splice site identifies factorsassociated with later steps of spliceosome assembly ................................................................... 725—734

Davis, Diana E., Hyun Cheol Roh, Krupa Deshmukh, Janelle J. Bruinsma, Daniel L.Schneider, James Guthrie, J. David Robertson and Kerry Kornfeld, The cation diffusionfacilitator gene cdf-2 mediates zinc metabolism in Caenorhabditis elegans .................................. 1015—1033

Deminoff, Stephen J., Vidhya Ramachandran and Paul K. Herman, Distal recognitionsites in substrates are required for efficient phosphorylation by the cAMP-dependent proteinkinase ............................................................................................................................................. 529—539

Deng, Xinxian, S. Kiran Koya, Ying Kong and Victoria H. Meller, Coordinatedregulation of heterochromatic genes in Drosophila melanogaster males ...................................... 481—491

Dorfman, Marc, Jose-Eduardo Gomes, Sean O’Rourke and Bruce Bowerman, Using RNAinterference to identify specific modifiers of a temperature-sensitive, embryonic-lethalmutation in the Caenorhabditis elegans ubiquitin-like Nedd8 protein modification pathwayE1-activating gene rfl-1 .................................................................................................................. 1035—1049

Dumont, Beth L., Karl W. Broman and Bret A. Payseur, Variation in genomicrecombination rates among heterogeneous stock mice ............................................................. 1345—1349

Eckert, Andrew J., Andrew D. Bower, Jill L. Wegrzyn, Barnaly Pande, Kathleen D.Jermstad, Konstantin V. Krutovsky, J. Bradley St. Clair and David B. Neale,Association genetics of coastal Douglas fir (Pseudotsuga menziesii var. menziesii, Pinaceae). I.Cold-hardiness related traits ......................................................................................................... 1289—1302

Edwards, Alexis C., and Trudy F. C. Mackay, Quantitative trait loci for aggressive behaviorin Drosophila melanogaster ............................................................................................................... 889—897

Eisman, Robert C., Melissa A. S. Phelps and Thomas C. Kaufman, Centrosomin: Acomplex mix of long and short isoforms is required for centrosome function during earlydevelopment in Drosophila melanogaster ........................................................................................ 979—997

Emmons, Richard B., Heather Genetti, Stephen Filandrinos, Jillian Lokere and Chao-ting Wu, Molecular genetic analysis of Suppressor 2 of zeste identifies key functional domains 999—1013

Favor, Jack, Alan Bradley, Nathalie Conte, Dirk Janik, Walter Pretsch, Peter

Reitmeir, Michael Rosemann, Wolfgang Schmahl, Johannes Wienberg and Irmgard

Zaus, Analysis of Pax6 contiguous gene deletions in the mouse, Mus musculus, identifiesregions distinct from Pax6 responsible for extreme small-eye and belly-spotting phenotypes 1077—1088

Fiumera, Heather L., Maitreya J. Dunham, Scott A. Saracco, Christine A. Butler,Jessica A. Kelly and Thomas D. Fox, Translocation and assembly of mitochondrially codedSaccharomyces cerevisiae cytochrome c oxidase subunit Cox2 by Oxa1 and Yme1 in the absenceof Cox18 ......................................................................................................................................... 519—528

Forche, Anja, P. T. Magee, Anna Selmecki, Judith Berman and Georgiana May, Evolutionin Candida albicans populations during a single passage through a mouse host ...................... 799—811

Gabay-Laughnan, Susan, Evgeny V. Kuzmin, Jessica Monroe, Leah Roark and Kathleen

J. Newton, Characterization of a novel thermosensitive restorer of fertility for cytoplasmicmale sterility in maize ................................................................................................................... 91—103

Galhardo, Rodrigo S., Robert Do, Masami Yamada, Errol C. Friedberg, P. J. Hastings,Takehiko Nohmi and Susan M. Rosenberg, DinB upregulation is the sole role of the SOSresponse in stress-induced mutagenesis in Escherichia coli .......................................................... 55—68

Gao, Hong, and Marcus W. Feldman, Complementation and epistasis in viral coinfectiondynamics ........................................................................................................................................ 251—263

Garcıa-Bellido, Antonio, and Jose F. de Celis, The complex tale of the achaete–scutecomplex: A paradigmatic case in the analysis of gene organization and function duringdevelopment .................................................................................................................................. 631—639

Georis, Isabelle, Andre Feller, Jennifer J. Tate, Terrance G. Cooper and Evelyne

Dubois, Nitrogen catabolite repression-sensitive transcription as a readout of tor pathwayregulation: The genetic background, reporter gene and GATA factor assayed determine theoutcomes ........................................................................................................................................ 927

Goll, Mary G., Ryan Anderson, Didier Y. R. Stainier, Allan C. Spradling and Marnie E.Halpern, Transcriptional silencing and reactivation in transgenic zebrafish .......................... 747—755

Gros, Pierre-Alexis, and Olivier Tenaillon, Selection for chaperone-like mediatedgenetic robustness at low mutation rate: Impact of drift, epistasis and complexity ................. 555—564

Gros, Pierre-Alexis, Herve Le Nagard and Olivier Tenaillon, The evolution of epistasisand its links with genetic robustness, complexity and drift in a phenotypic model of adaptation 277—293

Haag, Christoph R., Seanna J. McTaggart, Anaıs Didier, Tom J. Little and Deborah

Charlesworth, Nucleotide polymorphism and within-gene recombination in Daphniamagna and D. pulex, two cyclical parthenogens ........................................................................... 313—323

Habier, D., R. L. Fernando and J. C. M. Dekkers, Genomic selection using low-densitymarker panels ................................................................................................................................ 343—353

Handel, Adam E., and Sreeram V. Ramagopalan, Public health implications of epigenetics 1397—1398

Hao, Weilong, and G. Brian Golding, Does gene translocation accelerate the evolution oflaterally transferred genes? ........................................................................................................... 1365—1375

Hines, Karrie A., Diane E. Cryderman, Kaitlin M. Flannery, Hongbo Yang, Michael W.Vitalini, Tulle Hazelrigg, Craig A. Mizzen and Lori L. Wallrath, Domains of HP1required for Drosophila melanogaster heterochromatin spreading ............................................... 967—977

Honda, Shinji, and Eric U. Selker, Tools for fungal proteomics: MultifunctionalNeurospora vectors for gene replacement, protein expression and protein purification ....... 11—23

Hontz, Robert D., Rachel O. Niederer, Joseph M. Johnson and Jeffrey S. Smith, Geneticidentification of factors that modulate ribosomal DNA transcription in Saccharomyces cerevisiae 105—119

Howell, Elaine C., Susan J. Armstrong and Dmitry A. Filatov, Evolution of neo-sexchromosomes in Silene diclinis ...................................................................................................... 1109—1115

Huang, Guohong, Stephen D. Dougherty and Scott E. Erdman, Conserved WCPL andCX4C domains mediate several mating adhesin interactions in Saccharomyces cerevisiae .......... 173—189

Huang, Li, Steven Brooks, Wanlong Li, John Fellers, James C. Nelson and Bikram Gill,Evolution of new disease specificity at a simple resistance locus in a crop–weed complex:Reconstitution of the Lr21 gene in wheat ................................................................................... 595—602

Ikeda, Hajime, Noriyuki Fujii and Hiroaki Setoguchi, Molecular evolution of phyto-chromes in Cardamine nipponica (Brassicaceae) suggests the involvement of PHYE in localadaptation ...................................................................................................................................... 603—614

Kerwin, Christine L., and Dennis D. Wykoff, Candida glabrata PHO4 is necessary andsufficient for Pho2-independent transcription of phosphate starvation genes ........................ 471—479

Kim, Hye-Ryun, Keon-Sang Chae, Kap-Hoon Han and Dong-Min Han, The nsdC geneencoding a putative C2H2-type transcription factor is a key activator of sexual development inAspergillus nidulans ......................................................................................................................... 771—783

Koehn, Demelza R., Stuart J. Haring, Jaime M. Williams and Robert E. Malone,Tethering recombination initiation proteins in Saccharomyces cerevisiae promotes double strandbreak formation ............................................................................................................................. 447—458

Kopp, Michael, and Joachim Hermisson, The genetic basis of phenotypic adaptation I:Fixation of beneficial mutations in the moving optimum model .............................................. 233—249

Labbe, Pierrick, Nicolas Sidos, Michel Raymond and Thomas Lenormand, Resistancegene replacement in the mosquito Culex pipiens: Fitness estimation from long-term cline series 303—312

LeBel, Catherine, Emanuel Rosonina, David C. F. Sealey, Fiona Pryde, David Lydall,Laura Maringele and Lea A. Harrington, Telomere maintenance and survival inSaccharomyces cerevisiae in the absence of telomerase and RAD52 ............................................... 671—684

Legrand, Delphine, Maud I. Tenaillon, Pat Matyot, Justin Gerlach, Daniel Lachaise

and Marie-Louise Cariou, Species-wide genetic variation and demographic history ofDrosophila sechellia, a species lacking population structure ......................................................... 1197—1206

Li, Wenyun, and Zehua Chen, Multiple-interval mapping for quantitative trait loci with aspike in the trait distribution ........................................................................................................ 337—342

Li, Yubin, and Hugo K. Dooner, Excision of Helitron transposons in maize .......................... 399—402

Li, Zheng, Sanwen Huang, Shiqiang Liu, Junsong Pan, Zhonghua Zhang, Qianyi Tao,Qiuxiang Shi, Zhiqi Jia, Weiwei Zhang, Huiming Chen, Longting Si, Lihuang Zhu and

Run Cai, Molecular isolation of the M gene suggests that a conserved-residue conversioninduces the formation of bisexual flowers in cucumber plants ................................................. 1381—1385

Lohmueller, Kirk E., Carlos D. Bustamante and Andrew G. Clark, Methods for humandemographic inference using haplotype patterns from genomewide single-nucleotide poly-morphism data .............................................................................................................................. 217—231

Lynch, Michael, Estimation of allele frequencies from high-coverage genome-sequencingprojects ........................................................................................................................................... 295—301

Manichaikul, Ani, and Karl W. Broman, Binary trait mapping in experimental crosses withselective genotyping ...................................................................................................................... 863—874

Marcus, Jeffrey M., and Tia M. Hughes, Drosophila transposon insertions as unknownsfor structured inquiry recombination mapping exercises in an undergraduate genetics course 417—422

Matzkin, Luciano M., and Therese A. Markow, Transcriptional regulation of metabolismassociated with the increased desiccation resistance of the cactophilic Drosophila mojavensis 1279—1288

Mazourek, Michael, Elizabeth T. Cirulli, Sarah M. Collier, Laurie G. Landry,Byoung-Cheorl Kang, Edmund A. Quirin, James M. Bradeen, Peter Moffett and Molly

M. Jahn, The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of diseaseresistance in the Solanaceae ......................................................................................................... 1351—1364

McGrath, Casey L., Claudio Casola and Matthew W. Hahn, Minimal effect of ectopicgene conversion among recent duplicates in four mammalian genomes ................................ 615—622

McNamee, Laura M., and Michael H. Brodsky, p53-independent apoptosis limits DNAdamage-induced aneuploidy ........................................................................................................ 423—435

Merritt, Thomas J. S., Caitlin Kuczynski, Efe Sezgin, Chen-Tseh Zhu, Seiji Kumagai and

Walter F. Eanes, Quantifying interactions within the NADP(H) enzyme network in Drosophilamelanogaster ..................................................................................................................................... 565—574

Messer, Philipp W., Measuring the rates of spontaneous mutation from deep and large-scalepolymorphism data ....................................................................................................................... 1219—1232

Methods, technology and resources: Drivers of discovery .......................................................... 1

Moorad, Jacob A., and David W. Hall, Mutation accumulation, soft selection and themiddle-class neighborhood .......................................................................................................... 1387—1389

Muirhead, Christina A., and John Wakeley, Modeling multiallelic selection using a Moranmodel ............................................................................................................................................. 1141—1157

Myrick, Kyl V., Francxois Huet, Stephanie E. Mohr, Ines Alvarez-Garcıa, Jeffrey T. Lu,Mark A. Smith, Madeline A. Crosby and William M. Gelbart, Large-scale functionalannotation and expanded implementations of the PfwHyg hybrid transposon in the Drosophilamelanogaster genome ...................................................................................................................... 653—660

Ni, Jian-Quan, Lu-Ping Liu, Richard Binari, Robert Hardy, Hye-Seok Shim, Amanda

Cavallaro, Matthew Booker, Barret D. Pfeiffer, Michele Markstein, Hui Wang,Christians Villalta, Todd R. Laverty, Lizabeth A. Perkins and Norbert Perrimon, ADrosophila resource of transgenic RNAi lines for neurogenetics ............................................. 1089—1100

Omilian, Angela R., and Michael Lynch, Patterns of intraspecific DNA variation in theDaphnia nuclear genome ............................................................................................................. 325—336

Palstra, Friso P., Michael F. O’Connell and Daniel E. Ruzzante, Age structure, changingdemography and effective population size in Atlantic salmon (Salmo salar) ............................ 1233—1249

Pauklin, Siim, Julia S. Burkert, Julie Martin, Fekret Osman, Sandra Weller, Simon J.Boulton, Matthew C. Whitby and Svend K. Petersen-Mahrt, Alternative induction ofmeiotic recombination from single-base lesions of DNA deaminases ....................................... 41—54

Pogorzala, Leah, Shona Mookerjee and Elaine A. Sia, Evidence that Msh1p plays multipleroles in mitochondrial base excision repair ................................................................................ 699—709

Ratnakumar, Sooraj, Nataly Kacherovsky, Erin Arms and Elton T. Young, Snf1controls the activity of Adr1 through dephosphorylation of Ser230 ......................................... 735—745

Ray, Jessica L., Klaus Harms, Odd-Gunnar Wikmark, Irina Starikova, Pal J. Johnsen

and Kaare M. Nielsen, Sexual isolation in Acinetobacter baylyi is locus-specific and varies10,000-fold over the genome ........................................................................................................ 1165—1181

Roegiers, Fabrice, Joshua Kavaler, Nicholas Tolwinski, Yu-Ting Chou, Hong Duan,Fernando Bejarano, Diana Zitserman and Eric C. Lai, Frequent unanticipated alleles oflethal giant larvae in Drosophila second chromosome stocks ..................................................... 407—410

Rogers, Alan R., and Chad Huff, Linkage disequilibrium between loci with unknown phase 839—844

Saıdou, Abdoul-Aziz, Cedric Mariac, Vivianne Luong, Jean-Louis Pham, Gilles

Bezancxon and Yves Vigouroux, Association studies identify natural variation at PHYClinked to flowering time and morphological variation in pearl millet ...................................... 899—910

Salathe, Marcel, Jeremy Van Cleve and Marcus W. Feldman, Evolution of stochasticswitching rates in asymmetric fitness landscapes ........................................................................ 1159—1164

Sanetra, Matthias, Frederico Henning, Shoji Fukamachi and Axel Meyer, A micro-satellite-based genetic linkage map of the cichlid fish, Astatotilapia burtoni (Teleostei): Acomparison of genomic architectures among rapidly speciating cichlids ................................ 387—397

Sellem, Carole H., Elodie Bovier, Severine Lorin and Annie Sainsard-Chanet,Mutations in two zinc-cluster proteins activate alternative respiratory and gluconeogenicpathways and restore senescence in long-lived respiratory mutants of Podospora anserina ....... 69—78

Shalaby, Nevine A., Annette L. Parks, Eric J. Morreale, Marisa C. Osswalt, Kristen M.Pfau, Eric L. Pierce and Marc A. T. Muskavitch, A screen for modifiers of notch signalinguncovers Amun, a protein with a critical role in sensory organ development ......................... 1061—1076

Shang, Junjun, Yong Tao, Xuewei Chen, Yan Zou, Cailin Lei, Jing Wang, Xiaobing Li,Xianfeng Zhao, Meijun Zhang, Zhike Lu, Jichen Xu, Zhukuan Cheng, Jianmin Wan and

Lihuang Zhu, Identification of a new rice blast resistance gene, Pid3, by genomewidecomparison of paired nucleotide-binding site–leucine-rich repeat genes and their pseudo-gene alleles between the two sequenced rice genomes .............................................................. 1303—1311

Shi, Jiaqin, Ruiyuan Li, Dan Qiu, Congcong Jiang, Yan Long, Colin Morgan, Ian

Bancroft, Jianyi Zhao and Jinling Meng, Unraveling the complex trait of crop yield withquantitative trait loci mapping in Brassica napus ......................................................................... 851—861

Shringarpure, Suyash, and Eric P. Xing, mStruct: Inference of population structure inlight of both genetic admixing and allele mutations ................................................................. 575—593

Siriaco, Giorgia, Renate Deuring, Mariacristina Chioda, Peter B. Becker and John W.Tamkun, Drosophila ISWI regulates the association of histone H1 with interphase chromo-somes in Vivo .................................................................................................................................. 661—669

Sivanantharajah, Lovesha, and Anthony Percival-Smith, Analysis of the sequence andphenotype of Drosophila Sex combs reduced alleles reveals potential functions of conservedprotein motifs of the Sex combs reduced protein ...................................................................... 191—203

Slatkin, Montgomery, Epigenetic inheritance and the missing heritability problem .......... 845—850

Stamenova, Radostina, Patrick H. Maxwell, Alison E. Kenny and M. Joan Curcio, Rrm3protects the Saccharomyces cerevisiae genome from instability at nascent sites of retrotranspo-sition ............................................................................................................................................... 711—723

Stadler, Thomas, Bernhard Haubold, Carlos Merino, Wolfgang Stephan and Peter

Pfaffelhuber, The impact of sampling schemes on the site frequency spectrum innonequilibrium subdivided populations ..................................................................................... 205—216

Steiner, Walter W., Estelle M. Steiner, Angela R. Girvin and Lauren E. Plewik, Novelnucleotide sequence motifs that produce hotspots of meiotic recombination in Schizosacchar-omyces pombe .................................................................................................................................... 459—469

Stinchcombe, John R., Cynthia Weinig, Katy D. Heath, Marcus T. Brock and Johanna

Schmitt, Polymorphic genes of major effect: Consequences for variation, selection andevolution in Arabidopsis thaliana ................................................................................................... 911—922

Sun, Song, Otto G. Berg, John R. Roth and Dan I. Andersson, Contribution of geneamplification to evolution of increased antibiotic resistance in Salmonella typhimurium .......... 1183—1195

Takano-Kai, Noriko, Hui Jiang, Takahiko Kubo, Megan Sweeney, Takashi Matsumoto,Hiroyuki Kanamori, Badri Padhukasahasram, Carlos Bustamante, Atsushi Yoshi-

mura, Kazuyuki Doi and Susan McCouch, Evolutionary history of GS3, a gene conferringgrain length in rice ........................................................................................................................ 1323—1334

Taylor, Jesse E., The genealogical consequences of fecundity variance polymorphism ....... 813—837

Traven, Ana, Traude H. Beilharz, Tricia L. Lo, Franziska Lueder, Thomas Preiss and

Jorg Heierhorst, The Ccr4-Pop2-NOT mRNA deadenylase contributes to septin organiza-tion in Saccharomyces cerevisiae ....................................................................................................... 955—966

Tripathi, Namita, Margarete Hoffmann, Detlef Weigel and Christine Dreyer,Linkage analysis reveals the independent origin of poeciliid sex chromosomes and a case ofatypical sex inheritance in the guppy (Poecilia reticulata) ........................................................... 365—374

Tucker, Chandra L., Leslie A. Peteya, Adrianne M. C. Pittman and Jing Zhong, A genetictest for yeast two-hybrid bait competency using RanBPM .......................................................... 1377—1379

Valdar, William, Christopher C. Holmes, Richard Mott and Jonathan Flint, Mappingin structured populations by resample model averaging ........................................................... 1263—1277

Votintseva, Antonina A., and Dmitry A. Filatov, Evolutionary strata in a small mating-type-specific region of the smut fungus Microbotryum violaceum ................................................. 1391—1396

Watanabe, Satoshi, Rumiko Hideshima, Zhengjun Xia, Yasutaka Tsubokura, Shusei

Sato, Yumi Nakamoto, Naoki Yamanaka, Ryoji Takahashi, Masao Ishimoto, Toyoaki

Anai, Satoshi Tabata and Kyuya Harada, Map-based cloning of the gene associated withthe soybean maturity locus E3 ...................................................................................................... 1251—1262

Wegmann, Daniel, Christoph Leuenberger and Laurent Excoffier, Efficient approxi-mate Bayesian computation coupled with Markov chain Monte Carlo without likelihood ..... 1207—1218

Weiler, Karen S., The multi-AT-hook chromosomal protein of Drosophila melanogaster, D1, isdispensable for viability ................................................................................................................. 145—159

Yan, Zhun, Nicolas M. Berbenetz, Guri Giaever and Corey Nislow, Precise gene-dosealleles for chemical genetics ......................................................................................................... 623—626

Yanchukov, Alexey, One- and two-locus population models with differential viabilitybetween sexes: Parallels between haploid parental selection and genomic imprinting .......... 1117—1127

Zetterberg, Henrik, Magnus Bath, Madeleine Zetterberg, Peter Bernhardt and Ola

Hammarsten, The Szilard hypothesis on the nature of aging revisited ................................... 3—9

Zhang, Li-Feng, Yuya Ogawa, Janice Y. Ahn, Satoshi H. Namekawa, Susana S. Silva and

Jeannie T. Lee, Telomeric RNAs mark sex chromosomes in stem cells .................................... 685—698

Zhang, Xu, and Justin O. Borevitz, Global analysis of allele-specific expression inArabidopsis thaliana ........................................................................................................................ 943—954

Zhong, Shengqiang, Jack C. M. Dekkers, Rohan L. Fernando and Jean-Luc Jannink,Factors affecting accuracy from genomic selection in populations derived from multipleinbred lines: A barley case study .................................................................................................. 355—364

Zhu, Chengsong, and Jianming Yu, Nonmetric multidimensional scaling corrects forpopulation structure in association mapping with different sample types ............................... 875—888

A new standard genetic map for the laboratory mouse, pp. 1335–1344

Allison Cox, Cheryl L. Ackert-Bicknell, Beth L. Dumont, Yueming Ding, Jordana Tzenova Bell, Gudrun A. Brockmann, Jon E. Wergedal, Carol Bult, Beverly Paigen, Jonathan Flint, Shirng-Wern Tsaih, Gary A. Churchill and Karl W. Broman

Genetic maps continue to be relevant. They remain a critical tool formapping genes underlying complex traits, and they provide insights into fundamental processes of recombination. This group of investigatorsproduces an improved genetic map of the laboratory mouse genome that is fully integrated with the physical map of the genome. In theprocess of creating the new map, they correct numerous errors thathad accumulated in the mouse map. They demonstrate the impact ofthese improvements by remapping several historical QTLs.

Genetic modifiers of dFMR1 encode RNA granule componentsin Drosophila, pp. 1051–1060

Anne-Marie J. Cziko, Cathal T. McCann, Iris C. Howlett, Scott A. Barbee,Rebecca P. Duncan, Rene Luedemann, Daniela Zarnescu, Konrad E. Zinsmaier, Roy R. Parker and Mani Ramaswami

Fragile-X Mental Retardation Protein (FMRP) is a translational repressor that in neurons probably prevents translation of synaptic RNAs until athreshold of activation is reached. FMRP is also believed to be required formicroRNA-mediated translational repression. This article describes a geneticscreen that reveals likely new components of the fragile-X pathway that,like FMRP, can modify dendritic structure. The authors come to theunexpected conclusion that FMRP is not essential for microRNA function.

High-throughput multiplex sequencing to discover copynumber variants in Drosophila, pp. 935–941

Bryce Daines, Hui Wang, Yumei Li, Yi Han, Richard Gibbs and Rui Chen

This article presents the use of high-throughput DNA sequencing foridentifying copy number variation, an approach that promises to becomethe method of choice for such studies. The authors demonstrate that lowsequence coverage is sufficient for identifying and mapping largedeletions at kilobase resolution. They show how multiplexing is a goodalternative to microarrays because of its greater resolution at acomparable (and rapidly declining) cost.

Domains of heterochromatin protein 1 required for Drosophilamelanogaster heterochromatin spreading, pp. 967–977

Karrie A. Hines, Diane E. Cryderman, Kaitlin M. Flannery, Hongbo Yang,Michael W. Vitalini, Tulle Hazelrigg, Craig A. Mizzen and Lori L. Wallrath

Heterochromatin, which makes up a significant fraction of the genomein nearly all eukaryotes, can spread along the chromosome and silencegene expression. Studying the mechanism of heterochromatinspreading has been challenging due to the repetitive DNA sequencesthat underlie heterochromatin. These investigators employ the lacrepressor to establish heterochromatin domains amenable for analysisof spreading. They identify domains of heterochromatin protein 1required for spreading, and unexpectedly reveal multiple mechanismsof spreading. Taken together, their findings provide new insights intothe mechanisms of transcriptional control by chromatin.

Measuring the rates of spontaneous mutation from deep and large-scale polymorphism data, pp. 1219–1232

Philipp W. Messer

Mutations are the foundation of genetic diversity, yet we remain uncertainabout their rates and patterns. This is because new mutations are difficultto assess experimentally, since they occur at extremely low rates inindividuals. Indirect estimates of mutation rates from levels of divergenceor heterozygosity suffer from unknown selective and demographic biasesand disregard deleterious mutations. The author demonstrates howunbiased mutation rate estimates can be obtained from polymorphismdata gathered from deep sequencing projects. This promises to facilitatethe assessment of several long-standing problems of evolutionary biology.

Modeling multiallelic selection using a Moran model, pp. 1141–1157

Christina A. Muirhead and John Wakeley

Mechanisms of natural selection are of great interest to evolutionarybiologists, but available population genetics models are oftendiscouragingly oversimplified. This article presents a new mathematicalmethod of modeling complex multiallelic selection that greatly simplifiesthe task of analyzing novel modes of selection and is much less reliant onsimplifying assumptions than previous models based on diffusionapproximations to Wright-Fisher reproduction.

Contribution of gene amplification to evolution of increasedantibiotic resistance in Salmonella typhimurium, pp. 1183–1195

Song Sun, Otto G. Berg, John R. Roth and Dan I. Andersson

These investigators study evolution of resistance to a �-lactamantibiotic. They expose Salmonella typhimurium carrying a �-lactamase-encoding gene to increasing concentrations ofthe antibiotic. The predominant response is amplification of the �-lactamase gene. Some lineages subsequently acquire mutations thatreduce expression of porins involved in drug uptake, whereuponselection for the �-lactamase gene amplification relaxes and its copynumber becomes reduced. These findings suggest that geneamplification facilitates the acquisition of stable adaptive mutations byincreasing the number of selected target genes in the population.

Global analysis of allele-specific expression in Arabidopsisthaliana, pp. 943–954

Xu Zhang and Justin O. Borevitz

The level of gene expression is a complex trait controlled by cis- and trans-acting genetic factors. Dissection of these two sources of geneticvariation promises to shed light on how gene regulatory networksevolved. These investigators find that genes subject to these two differentclasses of variation are distinct in their local sequence polymorphisms,associated epigenetic marks, and gene expression specificity.

This Month in Genetics Research

Evaluation of risk prediction updates from commercialgenome-wide scans, Genet. Med. 11: 588–594

Cecile Jansenns

Is “personalized medicine” ready for prime time? Several companiescurrently offer online genetic tests to predict an individual's risk of commondiseases, but those predictions may be premature, because susceptibilitygenes for common diseases are still being discovered, potentially makingpredictions of risk outdated. The authors of this article investigate theextent to which updating of risk predictions results in reclassification ofindividuals from below- to above-average disease risk, or vice versa. They conclude that updating risk factors may produce contradictoryinformation about an individual's risk status over time, which isundesirable if lifestyle and nutritional recommendations vary accordingly.

Massively parallel sequencing: The next big thing in geneticmedicine, Am. J. Hum. Genet. 85: 142–154

Tracy Tucker, Marco Marra and Jan M. Friedman

“Next generation” DNA sequencing technologies are rapidly changinghow we identify mutations. The first people to man the barricades of thistechnological revolution have been experimentalists (e.g., GENETICS 182:25–32, and articles in this issue by Messer and by Daines et al.), but ourapplied and clinical comrades are quickly taking up the cause. This articlein our sister publication describes how application of massively parallelDNA sequencing in the clinic promises to provide a way to determine theetiology of many diseases by screening the genomes of thousands ofpeople for pathogenic mutations and genomic signatures of novelinfectious agents. The authors lay out the significant practical and ethicalchallenges to implementation of this transformative technology.

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