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Table of Contents: February 2011

COVER

Sister Act.

Image Credit: Alex Wild.
Issue Image

Leaf-cutter ants are widespread neotropical herbivores that farm a fungus for food using leaves. This obligate ant-fungus symbiosis forms the foundation of their complex societies and their colonies can contain millions of workers ranging in size from small fungus tenders to large soldiers. In this issue of PLoS Genetics, Suen et al. report the genome sequence of the leaf-cutter ant Atta cephalotes. Genome comparisons with other social and non-social insects reveal features of their obligate lifestyle. These include loss of genes involved in nutrient acquisition and amino acid biosynthesis, suggesting a role in helping to stabilize this ant-fungus mutualism over its ancient coevolutionary history.

Perspective

Break to Make a Connection

Takamune T. Saito, Monica P. Colaiácovo

Research Articles

Correlated Evolution of Nearby Residues in Drosophilid Proteins

Benjamin Callahan, Richard A. Neher, Doris Bachtrog, Peter Andolfatto, Boris I. Shraiman

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

Athma A. Pai, Jordana T. Bell, John C. Marioni, Jonathan K. Pritchard, Yoav Gilad

Single-Tissue and Cross-Tissue Heritability of Gene Expression Via Identity-by-Descent in Related or Unrelated Individuals

Alkes L. Price, Agnar Helgason, Gudmar Thorleifsson, Steven A. McCarroll, Augustine Kong, Kari Stefansson

A Population Genetic Approach to Mapping Neurological Disorder Genes Using Deep Resequencing

Rachel A. Myers, Ferran Casals, Julie Gauthier, Fadi F. Hamdan, Jon Keebler, Adam R. Boyko, Carlos D. Bustamante, Amelie M. Piton, Dan Spiegelman, Edouard Henrion, Martine Zilversmit, Julie Hussin, Jacklyn Quinlan, Yan Yang, Ronald G. Lafrenière, Alexander R. Griffing, Eric A. Stone, Guy A. Rouleau, Philip Awadalla

Meta-Analysis of Genome-Wide Association Studies in Celiac Disease and Rheumatoid Arthritis Identifies Fourteen Non-HLA Shared Loci

Alexandra Zhernakova, Eli A. Stahl, Gosia Trynka, Soumya Raychaudhuri, Eleanora A. Festen, Lude Franke, Harm-Jan Westra, Rudolf S. N. Fehrmann, Fina A. S. Kurreeman, Brian Thomson, Namrata Gupta, Jihane Romanos, Ross McManus, Anthony W. Ryan, Graham Turner, Elisabeth Brouwer, Marcel D. Posthumus, Elaine F. Remmers, Francesca Tucci, Rene Toes, Elvira Grandone, Maria Cristina Mazzilli, Anna Rybak, Bozena Cukrowska, Marieke J. H. Coenen, Timothy R. D. J. Radstake, Piet L. C. M. van Riel, Yonghong Li, Paul I. W. de Bakker, Peter K. Gregersen, Jane Worthington, Katherine A. Siminovitch, Lars Klareskog, Tom W. J. Huizinga, Cisca Wijmenga, Robert M. Plenge

MiRNA Control of Vegetative Phase Change in Trees

Jia-Wei Wang, Mee Yeon Park, Ling-Jian Wang, Yeonjong Koo, Xiao-Ya Chen, Detlef Weigel, R. Scott Poethig

Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins

Sergey Kryazhimskiy, Jonathan Dushoff, Georgii A. Bazykin, Joshua B. Plotkin

Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin–Dependent Regulation of AGAMOUS-LIKE36

Reza Shirzadi, Ellen D. Andersen, Katrine N. Bjerkan, Barbara M. Gloeckle, Maren Heese, Alexander Ungru, Per Winge, Csaba Koncz, Reidunn B. Aalen, Arp Schnittger, Paul E. Grini

Mapping of the Disease Locus and Identification of ADAMTS10 As a Candidate Gene in a Canine Model of Primary Open Angle Glaucoma

John Kuchtey, Lana M. Olson, Tommy Rinkoski, Edward O. MacKay, T. M. Iverson, Kirk N. Gelatt, Jonathan L. Haines, Rachel W. Kuchtey

Association between Common Variation at the FTO Locus and Changes in Body Mass Index from Infancy to Late Childhood: The Complex Nature of Genetic Association through Growth and Development

Ulla Sovio, Dennis O. Mook-Kanamori, Nicole M. Warrington, Robert Lawrence, Laurent Briollais, Colin N. A. Palmer, Joanne Cecil, Johanna K. Sandling, Ann-Christine Syvänen, Marika Kaakinen, Lawrie J. Beilin, Iona Y. Millwood, Amanda J. Bennett, Jaana Laitinen, Anneli Pouta, John Molitor, George Davey Smith, Yoav Ben-Shlomo, Vincent W. V. Jaddoe, Lyle J. Palmer, Craig E. Pennell, Tim J. Cole, Mark I. McCarthy, Marjo-Riitta Järvelin, Nicholas J. Timpson , Early Growth Genetics Consortium

Genome-Wide Association of Familial Late-Onset Alzheimer's Disease Replicates BIN1 and CLU and Nominates CUGBP2 in Interaction with APOE

Ellen M. Wijsman, Nathan D. Pankratz, Yoonha Choi, Joseph H. Rothstein, Kelley M. Faber, Rong Cheng, Joseph H. Lee, Thomas D. Bird, David A. Bennett, Ramon Diaz-Arrastia, Alison M. Goate, Martin Farlow, Bernardino Ghetti, Robert A. Sweet, Tatiana M. Foroud, Richard Mayeux , The NIA-LOAD/NCRAD Family Study Group

Mutations in Zebrafish lrp2 Result in Adult-Onset Ocular Pathogenesis That Models Myopia and Other Risk Factors for Glaucoma

Kerry N. Veth, Jason R. Willer, Ross F. Collery, Matthew P. Gray, Gregory B. Willer, Daniel S. Wagner, Mary C. Mullins, Ava J. Udvadia, Richard S. Smith, Simon W. M. John, Ronald G. Gregg, Brian A. Link

Risk Alleles for Systemic Lupus Erythematosus in a Large Case-Control Collection and Associations with Clinical Subphenotypes

Kimberly E. Taylor, Sharon A. Chung, Robert R. Graham, Ward A. Ortmann, Annette T. Lee, Carl D. Langefeld, Chaim O. Jacob, M. Ilyas Kamboh, Marta E. Alarcón-Riquelme, Betty P. Tsao, Kathy L. Moser, Patrick M. Gaffney, John B. Harley, Michelle Petri, Susan Manzi, Peter K. Gregersen, Timothy W. Behrens, Lindsey A. Criswell

The Cardiac Transcription Network Modulated by Gata4, Mef2a, Nkx2.5, Srf, Histone Modifications, and MicroRNAs

Jenny Schlesinger, Markus Schueler, Marcel Grunert, Jenny J. Fischer, Qin Zhang, Tammo Krueger, Martin Lange, Martje Tönjes, Ilona Dunkel, Silke R. Sperling

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

Steven A. Frese, Andrew K. Benson, Gerald W. Tannock, Diane M. Loach, Jaehyoung Kim, Min Zhang, Phaik Lyn Oh, Nicholas C. K. Heng, Prabhu B. Patil, Nathalie Juge, Donald A. MacKenzie, Bruce M. Pearson, Alla Lapidus, Eileen Dalin, Hope Tice, Eugene Goltsman, Miriam Land, Loren Hauser, Natalia Ivanova, Nikos C. Kyrpides, Jens Walter

Phosphoinositide Regulation of Integrin Trafficking Required for Muscle Attachment and Maintenance

Inês Ribeiro, Lin Yuan, Guy Tanentzapf, James J. Dowling, Amy Kiger

Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella

Philipp Engel, Walter Salzburger, Marius Liesch, Chao-Chin Chang, Soichi Maruyama, Christa Lanz, Alexandra Calteau, Aurélie Lajus, Claudine Médigue, Stephan C. Schuster, Christoph Dehio

New Functions of Ctf18-RFC in Preserving Genome Stability outside Its Role in Sister Chromatid Cohesion

Lionel Gellon, David F. Razidlo, Olive Gleeson, Lauren Verra, Danae Schulz, Robert S. Lahue, Catherine H. Freudenreich

Srf1 Is a Novel Regulator of Phospholipase D Activity and Is Essential to Buffer the Toxic Effects of C16:0 Platelet Activating Factor

Michael A. Kennedy, Nazir Kabbani, Jean-Philippe Lambert, Leigh Anne Swayne, Fida Ahmed, Daniel Figeys, Steffany A. L. Bennett, Jennnifer Bryan, Kristin Baetz

Genome-Wide Association Study of Coronary Heart Disease and Its Risk Factors in 8,090 African Americans: The NHLBI CARe Project

Guillaume Lettre, Cameron D. Palmer, Taylor Young, Kenechi G. Ejebe, Hooman Allayee, Emelia J. Benjamin, Franklyn Bennett, Donald W. Bowden, Aravinda Chakravarti, Al Dreisbach, Deborah N. Farlow, Aaron R. Folsom, Myriam Fornage, Terrence Forrester, Ervin Fox, Christopher A. Haiman, Jaana Hartiala, Tamara B. Harris, Stanley L. Hazen, Susan R. Heckbert, Brian E. Henderson, Joel N. Hirschhorn, Brendan J. Keating, Stephen B. Kritchevsky, Emma Larkin, Mingyao Li, Megan E. Rudock, Colin A. McKenzie, James B. Meigs, Yang A. Meng, Tom H. Mosley Jr., Anne B. Newman, Christopher H. Newton-Cheh, Dina N. Paltoo, George J. Papanicolaou, Nick Patterson, Wendy S. Post, Bruce M. Psaty, Atif N. Qasim, Liming Qu, Daniel J. Rader, Susan Redline, Muredach P. Reilly, Alexander P. Reiner, Stephen S. Rich, Jerome I. Rotter, Yongmei Liu, Peter Shrader, David S. Siscovick, W. H. Wilson Tang, Herman A. Taylor Jr., Russell P. Tracy, Ramachandran S. Vasan, Kevin M. Waters, Rainford Wilks, James G. Wilson, Richard R. Fabsitz, Stacey B. Gabriel, Sekar Kathiresan, Eric Boerwinkle

Genome-Wide Association Studies of the PR Interval in African Americans

J. Gustav Smith, Jared W. Magnani, Cameron Palmer, Yan A. Meng, Elsayed Z. Soliman, Solomon K. Musani, Kathleen F. Kerr, Renate B. Schnabel, Steven A. Lubitz, Nona Sotoodehnia, Susan Redline, Arne Pfeufer, Martina Müller, Daniel S. Evans, Michael A. Nalls, Yongmei Liu, Anne B. Newman, Alan B. Zonderman, Michele K. Evans, Rajat Deo, Patrick T. Ellinor, Dina N. Paltoo, Christopher Newton-Cheh, Emelia J. Benjamin, Reena Mehra, Alvaro Alonso, Susan R. Heckbert, Ervin R. Fox , Candidate-gene Association Resource (CARe) Consortium

The Genome Sequence of the Leaf-Cutter Ant Atta cephalotes Reveals Insights into Its Obligate Symbiotic Lifestyle

Garret Suen, Clotilde Teiling, Lewyn Li, Carson Holt, Ehab Abouheif, Erich Bornberg-Bauer, Pascal Bouffard, Eric J. Caldera, Elizabeth Cash, Amy Cavanaugh, Olgert Denas, Eran Elhaik, Marie-Julie Favé, Jürgen Gadau, Joshua D. Gibson, Dan Graur, Kirk J. Grubbs, Darren E. Hagen, Timothy T. Harkins, Martin Helmkampf, Hao Hu, Brian R. Johnson, Jay Kim, Sarah E. Marsh, Joseph A. Moeller, Mónica C. Muñoz-Torres, Marguerite C. Murphy, Meredith C. Naughton, Surabhi Nigam, Rick Overson, Rajendhran Rajakumar, Justin T. Reese, Jarrod J. Scott, Chris R. Smith, Shu Tao, Neil D. Tsutsui, Lumi Viljakainen, Lothar Wissler, Mark D. Yandell, Fabian Zimmer, James Taylor, Steven C. Slater, Sandra W. Clifton, Wesley C. Warren, Christine G. Elsik, Christopher D. Smith, George M. Weinstock, Nicole M. Gerardo, Cameron R. Currie

Nucleosomes Containing Methylated DNA Stabilize DNA Methyltransferases 3A/3B and Ensure Faithful Epigenetic Inheritance

Shikhar Sharma, Daniel D. De Carvalho, Shinwu Jeong, Peter A. Jones, Gangning Liang

Whole-Genome Comparison Reveals Novel Genetic Elements That Characterize the Genome of Industrial Strains of Saccharomyces cerevisiae

Anthony R. Borneman, Brian A. Desany, David Riches, Jason P. Affourtit, Angus H. Forgan, Isak S. Pretorius, Michael Egholm, Paul J. Chambers

Pathogenic VCP/TER94 Alleles Are Dominant Actives and Contribute to Neurodegeneration by Altering Cellular ATP Level in a Drosophila IBMPFD Model

Ya-Chu Chang, Wan-Tzu Hung, Yun-Chin Chang, Henry C. Chang, Chia-Lin Wu, Ann-Shyn Chiang, George R. Jackson, Tzu-Kang Sang

A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease

Iuliana Ionita-Laza, Joseph D. Buxbaum, Nan M. Laird, Christoph Lange

Quantitative Models of the Mechanisms That Control Genome-Wide Patterns of Transcription Factor Binding during Early Drosophila Development

Tommy Kaplan, Xiao-Yong Li, Peter J. Sabo, Sean Thomas, John A. Stamatoyannopoulos, Mark D. Biggin, Michael B. Eisen

Mapping a New Spontaneous Preterm Birth Susceptibility Gene, IGF1R, Using Linkage, Haplotype Sharing, and Association Analysis

Ritva Haataja, Minna K. Karjalainen, Aino Luukkonen, Kari Teramo, Hilkka Puttonen, Marja Ojaniemi, Teppo Varilo, Bimal P. Chaudhari, Jevon Plunkett, Jeffrey C. Murray, Steven A. McCarroll, Leena Peltonen, Louis J. Muglia, Aarno Palotie, Mikko Hallman

Targeted Sister Chromatid Cohesion by Sir2

Ching-Shyi Wu, Yu-Fan Chen, Marc R. Gartenberg

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

Alexandra C. Nica, Leopold Parts, Daniel Glass, James Nisbet, Amy Barrett, Magdalena Sekowska, Mary Travers, Simon Potter, Elin Grundberg, Kerrin Small, Åsa K. Hedman, Veronique Bataille, Jordana Tzenova Bell, Gabriela Surdulescu, Antigone S. Dimas, Catherine Ingle, Frank O. Nestle, Paola di Meglio, Josine L. Min, Alicja Wilk, Christopher J. Hammond, Neelam Hassanali, Tsun-Po Yang, Stephen B. Montgomery, Steve O'Rahilly, Cecilia M. Lindgren, Krina T. Zondervan, Nicole Soranzo, Inês Barroso, Richard Durbin, Kourosh Ahmadi, Panos Deloukas, Mark I. McCarthy, Emmanouil T. Dermitzakis, Timothy D. Spector , The MuTHER Consortium