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Research: The genomic consequences and persistence of sociality in spiders
- Jilong Ma,
- Jesper Bechsgaard,
- Anne Aagaard,
- Palle Villesen,
- Trine Bilde,
- and Mikkel Heide Schierup
Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
...sizes largely (Bechsgaard et al. 2019), causing increases in the strength of drift and reducing the efficacy of natural selection (Kimura et al. 1963). This substantiates the question of whether consequences of low Ne have impact on the evolutionary persistence of social lineages. Reports...
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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
..., Computational and Systems Biology, University of California Irvine, Irvine, California 92697, USA; 3Department of Biology, Texas A&M University, College Station, Texas 77843, USA; 4Center for Complex Biological Systems, University of California Irvine, Irvine, California 92697, USA Corresponding authors: mahul...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...drift, population bottlenecks, or selective pressures. From these, we observed that the vast majority of loci showed divergent alleles in individuals with African ancestry (n = 743, 99.1%), which is consistent with the greater genetic diversity observed in this population (The 1000 Genomes Project...
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Resource: The western redcedar genome reveals low genetic diversity in a self-compatible conifer
- Tal J. Shalev,
- Omnia Gamal El-Dien,
- Macaire M.S. Yuen,
- Shu Shengqiang,
- Shaun D. Jackman,
- René L. Warren,
- Lauren Coombe,
- Lise van der Merwe,
- Ada Stewart,
- Lori B. Boston,
- Christopher Plott,
- Jerry Jenkins,
- Guifen He,
- Juying Yan,
- Mi Yan,
- Jie Guo,
- Jesse W. Breinholt,
- Leandro G. Neves,
- Jane Grimwood,
- Loren H. Rieseberg,
- Jeremy Schmutz,
- Inanc Birol,
- Matias Kirst,
- Alvin D. Yanchuk,
- Carol Ritland,
- John H. Russell,
- and Joerg Bohlmann
Genome Res. October 2022 32: 1952-1964; Published in Advance September 15, 2022, doi:10.1101/gr.276358.121
..., Vancouver, British Columbia V6T 1Z4, Canada; 2Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt; 3Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; 4Canada's Michael Smith Genome Sciences Centre...
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Research: Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion
- James Hadfield,
- Simon R. Harris,
- Helena M.B. Seth-Smith,
- Surendra Parmar,
- Patiyan Andersson,
- Philip M. Giffard,
- Julius Schachter,
- Jeanne Moncada,
- Louise Ellison,
- María Lucía Gallo Vaulet,
- Marcelo Rodríguez Fermepin,
- Frans Radebe,
- Suyapa Mendoza,
- Sander Ouburg,
- Servaas A. Morré,
- Konrad Sachse,
- Mirja Puolakkainen,
- Suvi J. Korhonen,
- Chris Sonnex,
- Rebecca Wiggins,
- Hamid Jalal,
- Tamara Brunelli,
- Patrizia Casprini,
- Rachel Pitt,
- Cathy Ison,
- Alevtina Savicheva,
- Elena Shipitsyna,
- Ronza Hadad,
- Laszlo Kari,
- Matthew J. Burton,
- David Mabey,
- Anthony W. Solomon,
- David Lewis,
- Peter Marsh,
- Magnus Unemo,
- Ian N. Clarke,
- Julian Parkhill,
- and Nicholas R. Thomson
Genome Res. July 2017 27: 1220-1229; Published in Advance June 6, 2017, doi:10.1101/gr.212647.116
...(Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/. Research 1220 Genome Research 27:1220–1229 Published by Cold Spring Harbor Laboratory Press; ISSN 1088-9051/17; www..org www..org Chlamydia trachomatis is the world’s most prevalent bacterial sexually transmitted...
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Perspective: What does our genome encode?
- John A. Stamatoyannopoulos
Genome Res. September 2012 22: 1602-1611; doi:10.1101/gr.146506.112
...the information content of the human and other complex genomes, including the very definition of the gene. Here I discuss and place in context many of the leading findings of ENCODE, as well as trends that are shaping the generation and interpretation of ENCODE data. Finally, I consider prospects for the future...
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Research: Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis
- Cristel G. Thomas,
- Wei Wang,
- Richard Jovelin,
- Rajarshi Ghosh,
- Tatiana Lomasko,
- Quang Trinh,
- Leonid Kruglyak,
- Lincoln D. Stein,
- and Asher D. Cutter
Genome Res. May 2015 25: 667-678; Published in Advance March 17, 2015, doi:10.1101/gr.187237.114
...is thought to interact with selection to shape chromosome-scale patterns of genetic diversity (Cutter and Choi 2010; Cutter and Payseur 2013). Consequently, selection, self-fertilization, and gene flow all likely interact to control diversity and divergence in ways requiring genomic-scale population...
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Research: High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome
- Houssam Hajjoul,
- Julien Mathon,
- Hubert Ranchon,
- Isabelle Goiffon,
- Julien Mozziconacci,
- Benjamin Albert,
- Pascal Carrivain,
- Jean-Marc Victor,
- Olivier Gadal,
- Kerstin Bystricky,
- and Aurélien Bancaud
Genome Res. November 2013 23: 1829-1838; Published in Advance September 27, 2013, doi:10.1101/gr.157008.113
..., University Pierre et Marie Curie-Paris 6, 75252 Paris Cedex 05, France Chromosome dynamics are recognized to be intimately linked to genomic transactions, yet the physical principles governing spatial fluctuations of chromatin are still a matter of debate. Using high-throughput single-particle tracking, we...
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PERSPECTIVE: Drosophila melanogaster: A case study of a model genomic sequence and its consequences
- Michael Ashburner and
- Casey M. Bergman
Genome Res. December 2005 15: 1661-1667; doi:10.1101/gr.3726705
...Drosophila melanogaster : A case study of a model genomic sequence and its consequences Michael Ashburner 2 and Casey M. Bergman 1 Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, United Kingdom Abstract The sequencing...
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Research: Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments
- Barbara Dunn,
- Chandra Richter,
- Daniel J. Kvitek,
- Tom Pugh,
- and Gavin Sherlock
Genome Res. May 2012 22: 908-924; Published in Advance February 27, 2012, doi:10.1101/gr.130310.111
..., but also because they appear to have a common origin (Legras et al. 2007). To understand the consequences of selection during domestication we need to have a broader understanding of the levels of genetic diversity among wine yeasts. Furthermore, detailed characterization of genomic differences may shed...

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