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Table of Contents | February 2010

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A juvenile stickleback head stained red for developing bone and blue for forming cartilage.

In this issue of PLoS Genetics, Hohenlohe et al. report the first high-density genome scan of stickleback fish to identify signatures of selection. Oceanic stickleback have repeatedly formed freshwater populations that have evolved rapidly in many characters, including the head and jaws. Previous work demonstrated that the same genes were behind parallel phenotypic changes in independent populations. Hohenlohe et al. show that this is a general pattern in stickleback evolution, with many genomic regions exhibiting parallel signatures in independently derived freshwater populations. These results show that parallel phenotypic evolution may often be caused by extensive parallel genomic changes.

Image Credit: Mark Currey (Center for Ecology and Evolutionary Biology, University of Oregon, USA)

Perspectives

Nucleoporins and Transcription: New Connections, New Questions

Kohta Ikegami, Jason D. Lieb

Wing Patterns in the Mist

Arnaud Martin, Durrell D. Kapan, Lawrence E. Gilbert

Review

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

Einat Hazkani-Covo, Raymond M. Zeller, William Martin

Research Articles

Bacterial Genes in the Aphid Genome: Absence of Functional Gene Transfer from Buchnera to Its Host

Naruo Nikoh, John P. McCutcheon, Toshiaki Kudo, Shin-ya Miyagishima, Nancy A. Moran, Atsushi Nakabachi

Cheating by Exploitation of Developmental Prestalk Patterning in Dictyostelium discoideum

Anupama Khare, Gad Shaulsky

Ku Regulates the Non-Homologous End Joining Pathway Choice of DNA Double-Strand Break Repair in Human Somatic Cells

Farjana Fattah, Eu Han Lee, Natalie Weisensel, Yongbao Wang, Natalie Lichter, Eric A. Hendrickson

Genome-Wide Association Study Reveals Multiple Loci Associated with Primary Tooth Development during Infancy

Demetris Pillas, Clive J. Hoggart, David M. Evans, Paul F. O'Reilly, Kirsi Sipilä, Raija Lähdesmäki, Iona Y. Millwood, Marika Kaakinen, Gopalakrishnan Netuveli, David Blane, Pimphen Charoen, Ulla Sovio, Anneli Pouta, Nelson Freimer, Anna-Liisa Hartikainen, Jaana Laitinen, Sarianna Vaara, Beate Glaser, Peter Crawford, Nicholas J. Timpson, Susan M. Ring, Guohong Deng, Weihua Zhang, Mark I. McCarthy, Panos Deloukas, Leena Peltonen, Paul Elliott, Lachlan J. M. Coin, George Davey Smith, Marjo-Riitta Jarvelin

Molecular Evolution and Functional Characterization of Drosophila Insulin-Like Peptides

Sebastian Grönke, David-Francis Clarke, Susan Broughton, T. Daniel Andrews, Linda Partridge

Cdk1 Targets Srs2 to Complete Synthesis-Dependent Strand Annealing and to Promote Recombinational Repair

Marco Saponaro, Devon Callahan, Xiuzhong Zheng, Lumir Krejci, James E. Haber, Hannah L. Klein, Giordano Liberi

Structure, Function, and Evolution of the Thiomonas spp. Genome

Florence Arsène-Ploetze, Sandrine Koechler, Marie Marchal, Jean-Yves Coppée, Michael Chandler, Violaine Bonnefoy, Céline Brochier-Armanet, Mohamed Barakat, Valérie Barbe, Fabienne Battaglia-Brunet, Odile Bruneel, Christopher G. Bryan, Jessica Cleiss-Arnold, Stéphane Cruveiller, Mathieu Erhardt, Audrey Heinrich-Salmeron, Florence Hommais, Catherine Joulian, Evelyne Krin, Aurélie Lieutaud, Didier Lièvremont, Caroline Michel, Daniel Muller, Philippe Ortet, Caroline Proux, Patricia Siguier, David Roche, Zoé Rouy, Grégory Salvignol, Djamila Slyemi, Emmanuel Talla, Stéphanie Weiss, Jean Weissenbach, Claudine Médigue, Philippe N. Bertin

Allelic Exchange of Pheromones and Their Receptors Reprograms Sexual Identity in Cryptococcus neoformans

Brynne C. Stanton, Steven S. Giles, Mark W. Staudt, Emilia K. Kruzel, Christina M. Hull

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

Paul A. Hohenlohe, Susan Bassham, Paul D. Etter, Nicholas Stiffler, Eric A. Johnson, William A. Cresko

Cdk2 Is Required for p53-Independent G₂/M Checkpoint Control

Jon H. Chung, Fred Bunz

The Genetic Interpretation of Area under the ROC Curve in Genomic Profiling

Naomi R. Wray, Jian Yang, Michael E. Goddard, Peter M. Visscher

A Genome-Wide Association Study Identifies Susceptibility Variants for Type 2 Diabetes in Han Chinese

Fuu-Jen Tsai, Chi-Fan Yang, Ching-Chu Chen, Lee-Ming Chuang, Chieh-Hsiang Lu, Chwen-Tzuei Chang, Tzu-Yuan Wang, Rong-Hsing Chen, Chiung-Fang Shiu, Yi-Min Liu, Chih-Chun Chang, Pei Chen, Chien-Hsiun Chen, Cathy S. J. Fann, Yuan-Tsong Chen, Jer-Yuarn Wu

Genome-Wide Identification of Binding Sites Defines Distinct Functions for Caenorhabditis elegans PHA-4/FOXA in Development and Environmental Response

Mei Zhong, Wei Niu, Zhi John Lu, Mihail Sarov, John I. Murray, Judith Janette, Debasish Raha, Karyn L. Sheaffer, Hugo Y. K. Lam, Elicia Preston, Cindie Slightham, LaDeana W. Hillier, Trisha Brock, Ashish Agarwal, Raymond Auerbach, Anthony A. Hyman, Mark Gerstein, Susan E. Mango, Stuart K. Kim, Robert H. Waterston, Valerie Reinke, Michael Snyder

Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics Approach

Matteo Fumagalli, Uberto Pozzoli, Rachele Cagliani, Giacomo P. Comi, Nereo Bresolin, Mario Clerici, Manuela Sironi

Use of DNA–Damaging Agents and RNA Pooling to Assess Expression Profiles Associated with BRCA1 and BRCA2 Mutation Status in Familial Breast Cancer Patients

Logan C. Walker, Bryony A. Thompson, Nic Waddell, kConFab Investigators, Sean M. Grimmond, Amanda B. Spurdle

Analysis of the Legionella longbeachae Genome and Transcriptome Uncovers Unique Strategies to Cause Legionnaires' Disease

Christel Cazalet, Laura Gomez-Valero, Christophe Rusniok, Mariella Lomma, Delphine Dervins-Ravault, Hayley J. Newton, Fiona M. Sansom, Sophie Jarraud, Nora Zidane, Laurence Ma, Christiane Bouchier, Jerôme Etienne, Elizabeth L. Hartland, Carmen Buchrieser

Proteasome Nuclear Activity Affects Chromosome Stability by Controlling the Turnover of Mms22, a Protein Important for DNA Repair

Shay Ben-Aroya, Neta Agmon, Karen Yuen, Teresa Kwok, Kirk McManus, Martin Kupiec, Philip Hieter

Genome-Wide Association Study in Asian Populations Identifies Variants in ETS1 and WDFY4 Associated with Systemic Lupus Erythematosus

Wanling Yang, Nan Shen, Dong-Qing Ye, Qiji Liu, Yan Zhang, Xiao-Xia Qian, Nattiya Hirankarn, Dingge Ying, Hai-Feng Pan, Chi Chiu Mok, Tak Mao Chan, Raymond Woon Sing Wong, Ka Wing Lee, Mo Yin Mok, Sik Nin Wong, Alexander Moon Ho Leung, Xiang-Pei Li, Yingyos Avihingsanon, Chun-Ming Wong, Tsz Leung Lee, Marco Hok Kung Ho, Pamela Pui Wah Lee, Yuk Kwan Chang, Philip H. Li, Ruo-Jie Li, Lu Zhang, Wilfred Hing Sang Wong, Irene Oi Lin Ng, Chak Sing Lau, Pak Chung Sham, Yu Lung Lau

A Single Nucleotide Polymorphism within the Acetyl-Coenzyme A Carboxylase Beta Gene Is Associated with Proteinuria in Patients with Type 2 Diabetes

Shiro Maeda, Masa-aki Kobayashi, Shin-ichi Araki, Tetsuya Babazono, Barry I. Freedman, Meredith A. Bostrom, Jessica N. Cooke, Masao Toyoda, Tomoya Umezono, Lise Tarnow, Torben Hansen, Peter Gaede, Anders Jorsal, Daniel P. K. Ng, Minoru Ikeda, Toru Yanagimoto, Tatsuhiko Tsunoda, Hiroyuki Unoki, Koichi Kawai, Masahito Imanishi, Daisuke Suzuki, Hyoung Doo Shin, Kyong Soo Park, Atsunori Kashiwagi, Yasuhiko Iwamoto, Kohei Kaku, Ryuzo Kawamori, Hans-Henrik Parving, Donald W. Bowden, Oluf Pedersen, Yusuke Nakamura

The Scale of Population Structure in Arabidopsis thaliana

Alexander Platt, Matthew Horton, Yu S. Huang, Yan Li, Alison E. Anastasio, Ni Wayan Mulyati, Jon Ågren, Oliver Bossdorf, Diane Byers, Kathleen Donohue, Megan Dunning, Eric B. Holub, Andrew Hudson, Valérie Le Corre, Olivier Loudet, Fabrice Roux, Norman Warthmann, Detlef Weigel, Luz Rivero, Randy Scholl, Magnus Nordborg, Joy Bergelson, Justin O. Borevitz

Transcriptional Rewiring of the Sex Determining dmrt1 Gene Duplicate by Transposable Elements

Amaury Herpin, Ingo Braasch, Michael Kraeussling, Cornelia Schmidt, Eva C. Thoma, Shuhei Nakamura, Minoru Tanaka, Manfred Schartl

Uncoupling of Satellite DNA and Centromeric Function in the Genus Equus

Francesca M. Piras, Solomon G. Nergadze, Elisa Magnani, Livia Bertoni, Carmen Attolini, Lela Khoriauli, Elena Raimondi, Elena Giulotto

Nuclear Pore Proteins Nup153 and Megator Define Transcriptionally Active Regions in the Drosophila Genome

Juan M. Vaquerizas, Ritsuko Suyama, Jop Kind, Kota Miura, Nicholas M. Luscombe, Asifa Akhtar

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade

Simon W. Baxter, Nicola J. Nadeau, Luana S. Maroja, Paul Wilkinson, Brian A. Counterman, Anna Dawson, Margarita Beltran, Silvia Perez-Espona, Nicola Chamberlain, Laura Ferguson, Richard Clark, Claire Davidson, Rebecca Glithero, James Mallet, W. Owen McMillan, Marcus Kronforst, Mathieu Joron, Richard H. ffrench-Constant, Chris D. Jiggins

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in Heliconius erato

Brian A. Counterman, Felix Araujo-Perez, Heather M. Hines, Simon W. Baxter, Clay M. Morrison, Daniel P. Lindstrom, Riccardo Papa, Laura Ferguson, Mathieu Joron, Richard H. ffrench-Constant, Christopher P. Smith, Dahlia M. Nielsen, Rui Chen, Chris D. Jiggins, Robert D. Reed, Georg Halder, Jim Mallet, W. Owen McMillan

Mutations in SLC29A3, Encoding an Equilibrative Nucleoside Transporter ENT3, Cause a Familial Histiocytosis Syndrome (Faisalabad Histiocytosis) and Familial Rosai-Dorfman Disease

Neil V. Morgan, Mark R. Morris, Hakan Cangul, Diane Gleeson, Anna Straatman-Iwanowska, Nicholas Davies, Stephen Keenan, Shanaz Pasha, Fatimah Rahman, Dean Gentle, Maaike P. G. Vreeswijk, Peter Devilee, Margaret A. Knowles, Serdar Ceylaner, Richard C. Trembath, Carlos Dalence, Erol Kismet, Vedat Köseoğlu, Hans-Christoph Rossbach, Paul Gissen, David Tannahill, Eamonn R. Maher

DNA Binding of Centromere Protein C (CENPC) Is Stabilized by Single-Stranded RNA

Yaqing Du, Christopher N. Topp, R. Kelly Dawe

Genetic and Functional Dissection of HTRA1 and LOC387715 in Age-Related Macular Degeneration

Zhenglin Yang, Zongzhong Tong, Yuhong Chen, Jiexi Zeng, Fang Lu, Xufang Sun, Chao Zhao, Kevin Wang, Lisa Davey, Haoyu Chen, Nyall London, Daisuke Muramatsu, Francesca Salasar, Ruben Carmona, Daniel Kasuga, Xiaolei Wang, Matthew Bedell, Manjuxia Dixie, Peiquan Zhao, Ruifu Yang, Daniel Gibbs, Xiaoqi Liu, Yan Li, Cai Li, Yuanfeng Li, Betsy Campochiaro, Ryan Constantine, Donald J. Zack, Peter Campochiaro, Yinbin Fu, Dean Y. Li, Nicholas Katsanis, Kang Zhang

Replication and Active Demethylation Represent Partially Overlapping Mechanisms for Erasure of H3K4me3 in Budding Yeast

Marta Radman-Livaja, Chih Long Liu, Nir Friedman, Stuart L. Schreiber, Oliver J. Rando

Deletion of the Huntingtin Polyglutamine Stretch Enhances Neuronal Autophagy and Longevity in Mice

Shuqiu Zheng, Erin B. D. Clabough, Sovan Sarkar, Marie Futter, David C. Rubinsztein, Scott O. Zeitlin

A Kinase-Independent Role for the Rad3^ATR-Rad26^ATRIP Complex in Recruitment of Tel1^ATM to Telomeres in Fission Yeast

Lakxmi Subramanian, Toru M. Nakamura

Human and Non-Human Primate Genomes Share Hotspots of Positive Selection

David Enard, Frantz Depaulis, Hugues Roest Crollius

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