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November 2018

The drawing depicts the importance of admixture for fast and repeated evolution of two ecotypes of the saltmarsh beetle Pogonus chalceus. Long- and short-winged ecotypes of P. chalceus have diverged repeatedly along the Atlantic European coast in response to contrasting hydrological regimes. The repeated evolution is driven by an initial ancient and singular divergence of the short-winged ecotype, after which it admixed with the ancestral long-winged population. This admixture resulted in a polymorphic population that survived during the most recent glacial maxima and from which both ecotypes currently diverge rapidly and repeatedly by the reassembly of these ancient alleles when habitats become available. See Van Belleghem et al.

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Image Credit: Steven M. Van Belleghem and Frederik Hendrickx

Research Articles

The tumor suppressor BRCA1-BARD1 complex localizes to the synaptonemal complex and regulates recombination under meiotic dysfunction in Caenorhabditis elegans

Qianyan Li, Takamune T. Saito, Marina Martinez-Garcia, Alison J. Deshong, Saravanapriah Nadarajan, Katherine S. Lawrence, Paula M. Checchi, Monica P. Colaiacovo, JoAnne Engebrecht

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Slower environmental change hinders adaptation from standing genetic variation

Thiago S. Guzella, Snigdhadip Dey, Ivo M. Chelo, Ania Pino-Querido, Veronica F. Pereira, Stephen R. Proulx, Henrique Teotónio

How many individuals share a mitochondrial genome?

Mikkel M. Andersen, David J. Balding

Dietary restriction improves intestinal cellular fitness to enhance gut barrier function and lifespan in D. melanogaster

Kazutaka Akagi, Kenneth A. Wilson, Subhash D. Katewa, Mauricio Ortega, Jesse Simons, Tyler A. Hilsabeck, Subir Kapuria, Amit Sharma, Heinrich Jasper, Pankaj Kapahi

Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer's disease

Nisha Rathore, Sree Ranjani Ramani, Homer Pantua, Jian Payandeh, Tushar Bhangale, Arthur Wuster, Manav Kapoor, Yonglian Sun, Sharookh B. Kapadia, Lino Gonzalez, Ali A. Zarrin, Alison Goate, David V. Hansen, Timothy W. Behrens, Robert R. Graham

An investigation of Y chromosome incorporations in 400 species of Drosophila and related genera

Eduardo G. Dupim, Gabriel Goldstein, Thyago Vanderlinde, Suzana C. Vaz, Flávia Krsticevic, Aline Bastos, Thadeo Pinhão, Marcos Torres, Jean R. David, Carlos R. Vilela, Antonio Bernardo Carvalho

Stereotypic generation of axial tenocytes from bipartite sclerotome domains in zebrafish

Roger C. Ma, Craig T. Jacobs, Priyanka Sharma, Katrinka M. Kocha, Peng Huang

A variably imprinted epiallele impacts seed development

Daniela Pignatta, Katherine Novitzky, P. R. V. Satyaki, Mary Gehring

Functional equivalence of germ plasm organizers

Pritesh Krishnakumar, Stephan Riemer, Roshan Perera, Thomas Lingner, Alexander Goloborodko, Hazem Khalifa, Franck Bontems, Felix Kaufholz, Mohamed A. El-Brolosy, Roland Dosch

Genotype to phenotype: Diet-by-mitochondrial DNA haplotype interactions drive metabolic flexibility and organismal fitness

Wen C. Aw, Samuel G. Towarnicki, Richard G. Melvin, Neil A. Youngson, Michael R. Garvin, Yifang Hu, Shaun Nielsen, Torsten Thomas, Russell Pickford, Sonia Bustamante, Antón Vila-Sanjurjo, Gordon K. Smyth, J. William O. Ballard

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

François Rousset, Lun Cui, Elise Siouve, Christophe Becavin, Florence Depardieu, David Bikard

Evidence that regulation of intramembrane proteolysis is mediated by substrate gating during sporulation in Bacillus subtilis

Fernando H. Ramírez-Guadiana, Christopher D. A. Rodrigues, Kathleen A. Marquis, Nathalie Campo, Rocío del Carmen Barajas-Ornelas, Kelly Brock, Debora S. Marks, Andrew C. Kruse, David Z. Rudner

Analysis of 7,815 cancer exomes reveals associations between mutational processes and somatic driver mutations

Rebecca C. Poulos, Yuen T. Wong, Regina Ryan, Herbert Pang, Jason W. H. Wong

Population genomics of grey wolves and wolf-like canids in North America

Mikkel-Holger S. Sinding, Shyam Gopalakrishan, Filipe G. Vieira, Jose A. Samaniego Castruita, Katrine Raundrup, Mads Peter Heide Jørgensen, Morten Meldgaard, Bent Petersen, Thomas Sicheritz-Ponten, Johan Brus Mikkelsen, Ulf Marquard-Petersen, Rune Dietz, Christian Sonne, Love Dalén, Lutz Bachmann, Øystein Wiig, Anders J. Hansen, M. Thomas P. Gilbert

A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events

Magali Jaillard, Leandro Lima, Maud Tournoud, Pierre Mahé, Alex van Belkum, Vincent Lacroix, Laurent Jacob

The zinc finger protein DCM1 is required for male meiotic cytokinesis by preserving callose in rice

Chao Zhang, Yi Shen, Ding Tang, Wenqing Shi, Dongmei Zhang, Guijie Du, Yihua Zhou, Guohua Liang, Yafei Li, Zhukuan Cheng

Function and regulation of the Caenorhabditis elegans Rab32 family member GLO-1 in lysosome-related organelle biogenesis

Caitlin Morris, Olivia K. Foster, Simran Handa, Kimberly Peloza, Laura Voss, Hannah Somhegyi, Youli Jian, My Van Vo, Marie Harp, Fiona M. Rambo, Chonglin Yang, Greg J. Hermann

Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization

Lusine Nazaryan-Petersen, Jesper Eisfeldt, Maria Pettersson, Johanna Lundin, Daniel Nilsson, Josephine Wincent, Agne Lieden, Lovisa Lovmar, Jesper Ottosson, Jelena Gacic, Outi Mäkitie, Ann Nordgren, Francesco Vezzi, Valtteri Wirta, Max Käller, Tina Duelund Hjortshøj, Cathrine Jespersgaard, Rayan Houssari, Laura Pignata, Mads Bak, Niels Tommerup, Elisabeth Syk Lundberg, Zeynep Tümer, Anna Lindstrand

Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation

Vamsi K. Gali, David Dickerson, Yuki Katou, Katsunori Fujiki, Katsuhiko Shirahige, Tom Owen-Hughes, Takashi Kubota, Anne D. Donaldson

Single-cell RNA-sequencing reveals transcriptional dynamics of estrogen-induced dysplasia in the ovarian surface epithelium

Nhung H. Vuong, David P. Cook, Laura A. Forrest, Lauren E. Carter, Pascale Robineau-Charette, Joshua M. Kofsky, Kendra M. Hodgkinson, Barbara C. Vanderhyden

Evolution at two time frames: Polymorphisms from an ancient singular divergence event fuel contemporary parallel evolution

Steven M. Van Belleghem, Carl Vangestel, Katrien De Wolf, Zoë De Corte, Markus Möst, Pasi Rastas, Luc De Meester, Frederik Hendrickx

Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish

Leonard Burg, Nicholas Palmer, Khrievono Kikhi, Evgeniya S. Miroshnik, Helen Rueckert, Eleanor Gaddy, Carlee MacPherson Cunningham, Kenny Mattonet, Shih-Lei Lai, Rubén Marín-Juez, Richard B. Waring, Didier Y. R. Stainier, Darius Balciunas

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

Stefanie Schöne, Melissa Bothe, Edda Einfeldt, Marina Borschiwer, Philipp Benner, Martin Vingron, Morgane Thomas-Chollier, Sebastiaan H. Meijsing

Telomere length-dependent transcription and epigenetic modifications in promoters remote from telomere ends

Ananda Kishore Mukherjee, Shalu Sharma, Suman Sengupta, Dhurjhoti Saha, Pankaj Kumar, Tabish Hussain, Vivek Srivastava, Sumitabho Deb Roy, Jerry W. Shay, Shantanu Chowdhury

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A single class of ARF GTPase activated by several pathway-specific ARF-GEFs regulates essential membrane traffic in Arabidopsis

Manoj K. Singh, Sandra Richter, Hauke Beckmann, Marika Kientz, York-Dieter Stierhof, Nadine Anders, Florian Fäßler, Michael Nielsen, Christian Knöll, Alexis Thomann, Mirita Franz-Wachtel, Boris Macek, Karen Skriver, Peter Pimpl, Gerd Jürgens

Capitalizing on the heterogeneous effects of CFTR nonsense and frameshift variants to inform therapeutic strategy for cystic fibrosis

Neeraj Sharma, Taylor A. Evans, Matthew J. Pellicore, Emily Davis, Melis A. Aksit, Allison F. McCague, Anya T. Joynt, Zhongzhu Lu, Sangwoo T. Han, Arianna F. Anzmann, Anh-Thu N. Lam, Abigail Thaxton, Natalie West, Christian Merlo, Laura B. Gottschalk, Karen S. Raraigh, Patrick R. Sosnay, Calvin U. Cotton, Garry R. Cutting

Functional regulatory mechanism of smooth muscle cell-restricted LMOD1 coronary artery disease locus

Vivek Nanda, Ting Wang, Milos Pjanic, Boxiang Liu, Trieu Nguyen, Ljubica Perisic Matic, Ulf Hedin, Simon Koplev, Lijiang Ma, Oscar Franzén, Arno Ruusalepp, Eric E. Schadt, Johan L. M. Björkegren, Stephen B. Montgomery, Michael P. Snyder, Thomas Quertermous, Nicholas J. Leeper, Clint L. Miller

The Hsp70 co-chaperone Ydj1/HDJ2 regulates ribonucleotide reductase activity

Isaac T. Sluder, Nitika, Laura E. Knighton, Andrew W. Truman

Spen limits intestinal stem cell self-renewal

Maheva Andriatsilavo, Marine Stefanutti, Katarzyna Siudeja, Carolina N. Perdigoto, Benjamin Boumard, Louis Gervais, Alexandre Gillet-Markowska, Lara Al Zouabi, François Schweisguth, Allison J. Bardin

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Genetic variants influence on the placenta regulatory landscape

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FOXO1 regulates uterine epithelial integrity and progesterone receptor expression critical for embryo implantation

Yasmin M. Vasquez, Xiaoqiu Wang, Margeaux Wetendorf, Heather L. Franco, Qianxing Mo, Tianyuan Wang, Rainer B. Lanz, Steven L. Young, Bruce A. Lessey, Thomas E. Spencer, John P. Lydon, Francesco J. DeMayo

Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima

Markus G. Stetter, Kevin Thornton, Jeffrey Ross-Ibarra

Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ

Colby L. Samstag, Jake G. Hoekstra, Chiu-Hui Huang, Mark J. Chaisson, Richard J. Youle, Scott R. Kennedy, Leo J. Pallanck

Loss of the Mia40a oxidoreductase leads to hepato-pancreatic insufficiency in zebrafish

Anna M. Sokol, Barbara Uszczynska-Ratajczak, Michelle M. Collins, Michal Bazala, Ulrike Topf, Pia R. Lundegaard, Sreedevi Sugunan, Stefan Guenther, Carsten Kuenne, Johannes Graumann, Sherine S. L. Chan, Didier Y. R. Stainier, Agnieszka Chacinska

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Evidence for gene-environment correlation in child feeding: Links between common genetic variation for BMI in children and parental feeding practices

Saskia Selzam, Tom A. McAdams, Jonathan R. I. Coleman, Susan Carnell, Paul F. O’Reilly, Robert Plomin, Clare H. Llewellyn

Modulation of Drosophila post-feeding physiology and behavior by the neuropeptide leucokinin

Meet Zandawala, Maria E. Yurgel, Michael J. Texada, Sifang Liao, Kim F. Rewitz, Alex C. Keene, Dick R. Nässel

Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay

Michael J. Roach, Daniel L. Johnson, Joerg Bohlmann, Hennie J. J. van Vuuren, Steven J. M. Jones, Isak S. Pretorius, Simon A. Schmidt, Anthony R. Borneman

Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity

Oliver Hahn, Thomas M. Stubbs, Wolf Reik, Sebastian Grönke, Andreas Beyer, Linda Partridge

Mutations in Kinesin family member 6 reveal specific role in ependymal cell ciliogenesis and human neurological development

Mia J. Konjikusic, Patra Yeetong, Curtis W. Boswell, Chanjae Lee, Elle C. Roberson, Rungnapa Ittiwut, Kanya Suphapeetiporn, Brian Ciruna, Christina A. Gurnett, John B. Wallingford, Vorasuk Shotelersuk, Ryan S. Gray

Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay

Carrie L. Simms, Kyusik Q. Kim, Liewei L. Yan, Jessica Qiu, Hani S. Zaher

A suppressor of a wtf poison-antidote meiotic driver acts via mimicry of the driver’s antidote

María Angélica Bravo Núñez, Jeffrey J. Lange, Sarah E. Zanders

Stress-responsive and metabolic gene regulation are altered in low S-adenosylmethionine

Wei Ding, Daniel P. Higgins, Dilip K. Yadav, Adwait A. Godbole, Read Pukkila-Worley, Amy K. Walker

Nucleosome positions establish an extended mutation signature in melanoma

Alexander J. Brown, Peng Mao, Michael J. Smerdon, John J. Wyrick, Steven A. Roberts

A natural antisense lncRNA controls breast cancer progression by promoting tumor suppressor gene mRNA stability

Mahdieh Jadaliha, Omid Gholamalamdari, Wei Tang, Yang Zhang, Ana Petracovici, Qinyu Hao, Aamira Tariq, Tae Gyoon Kim, Sarah E. Holton, Deepak K. Singh, Xiao Ling Li, Susan M. Freier, Stefan Ambs, Rohit Bhargava, Ashish Lal, Supriya G. Prasanth, Jian Ma, Kannanganattu V. Prasanth

BLM prevents instability of structure-forming DNA sequences at common fragile sites

Hailong Wang, Shibo Li, Huimin Zhang, Ya Wang, Shuailin Hao, Xiaohua Wu

Mek1 coordinates meiotic progression with DNA break repair by directly phosphorylating and inhibiting the yeast pachytene exit regulator Ndt80

Xiangyu Chen, Robert Gaglione, Trevor Leong, Lauren Bednor, Teresa de los Santos, Ed Luk, Michael Airola, Nancy M. Hollingsworth

Danger signals activate a putative innate immune system during regeneration in a filamentous fungus

Elizabeth Medina-Castellanos, José Manuel Villalobos-Escobedo, Meritxell Riquelme, Nick D. Read, Cei Abreu-Goodger, Alfredo Herrera-Estrella

De novo mutations in the GTP/GDP-binding region of RALA, a RAS-like small GTPase, cause intellectual disability and developmental delay

Susan M. Hiatt, Matthew B. Neu, Ryne C. Ramaker, Andrew A. Hardigan, Jeremy W. Prokop, Miroslava Hancarova, Darina Prchalova, Marketa Havlovicova, Jan Prchal, Viktor Stranecky, Dwight K. C. Yim, Zöe Powis, Boris Keren, Caroline Nava, Cyril Mignot, Marlene Rio, Anya Revah-Politi, Parisa Hemati, Nicholas Stong, Alejandro D. Iglesias, Sharon F. Suchy, Rebecca Willaert, Ingrid M. Wentzensen, Patricia G. Wheeler, Lauren Brick, Mariya Kozenko, Anna C. E. Hurst, James W. Wheless, Yves Lacassie, Richard M. Myers, Gregory S. Barsh, Zdenek Sedlacek, Gregory M. Cooper

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Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators

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Downregulation of ERG and FLI1 expression in endothelial cells triggers endothelial-to-mesenchymal transition

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Correction

Topic Page

Selfish genetic elements

J. Arvid Ågren, Andrew G. Clark