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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...and the amount of genomic convergence. To our knowledge, we so far lacked study designs that could quantify genomic convergence accounting for both species relatedness and age of transition.Rodentia is the most diversified order of mammals with living representatives spanning 70 million years (MY) of evolution...
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Research: Lake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements
- Fu Xiang Quah,
- Miguel Vasconcelos Almeida,
- Moritz Blumer,
- Chengwei Ulrika Yuan,
- Bettina Fischer,
- Kirsten See,
- Ben Jackson,
- Richard Zatha,
- Bosco Rusuwa,
- George F. Turner,
- M. Emília Santos,
- Hannes Svardal,
- Martin Hemberg,
- Richard Durbin,
- and Eric Miska
Genome Res. May 2025 35: 1094-1107; Published in Advance April 10, 2025, doi:10.1101/gr.279674.124
...reference s, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)–based studies have revealed little...
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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
..., sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality “evolutionarily dead-ends.” We addressed this hypothesis in a comparative genomic study in spiders, in which sociality has...
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Research: Fusion, fission, and scrambling of the bilaterian genome in Bryozoa
- Thomas D. Lewin,
- Isabel Jiah-Yih Liao,
- Mu-En Chen,
- John D.D. Bishop,
- Peter W.H. Holland,
- and Yi-Jyun Luo
Genome Res. January 2025 35: 78-92; Published in Advance January 6, 2025, doi:10.1101/gr.279636.124
...that these rearrangements are present across the entire extant bryozoan phylum. This suggests that massive rearrangements had already occurred by the time of the last common ancestor of living lineages. However, we note that much of bryozoan diversity is represented only in the fossil record. Six of the seven orders...
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Mini-Review: Toward telomere-to-telomere cat genomes for precision medicine and conservation biology
- William J. Murphy and
- Andrew J. Harris
Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123
...-016-1090-1 ↵Aberdein D, Munday JS, Gandolfi B, Dittmer KE, Malik R, Garrick DJ, Lyons LA, 99 Lives Consortium. 2017. A FAS-ligand variant associated with autoimmune lymphoproliferative syndrome in cats. Mamm Genome 28: 47–55. doi:10.1007/s00335-016-9668-1 ↵Abkowitz JL, Linenberger ML, Newton MA, Shelton GH, Ott RL...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...Zan4, Hui Zhang1, Lu Li1, Keying Wen1 and Yaosheng Chen1 1State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, 510006 Guangzhou, China; 2Bio-X Institutes, Shanghai Jiao Tong University, 200240 Shanghai, China; 3Animal Breeding and Genomics, Wageningen University...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 6McDonnell Genome Institute, Washington University, St. Louis, Missouri 63108, USA; 7Department of Life Sciences, Texas A&M University, Corpus Christi, Texas 78412, USA; 8Developmental Biochemistry, Biozentrum...
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Research: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
- Gang Li,
- Brian W. Davis,
- Eduardo Eizirik,
- and William J. Murphy
Genome Res. January 2016 26: 1-11; Published in Advance October 30, 2015, doi:10.1101/gr.186668.114
...100 Nuclear Kodkod cat Tigrina-S.Am. Pampas cat Snow leopard Tiger Jaguar Leopard Lion 100 100 100 100 Nuclear Genome Tiger Snow leopard Jaguar Leopard Lion 100 100 100 100 Mito Jaguar Tiger Lion LeopardSnow leopard 0-0.15 0.10.05 0.20.15-0.1 Indochinese Sundaic Fishing catAsian leopard cat...
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Method: Detecting differential growth of microbial populations with Gaussian process regression
- Peter D. Tonner,
- Cynthia L. Darnell,
- Barbara E. Engelhardt,
- and Amy K. Schmid
Genome Res. February 2017 27: 320-333; Published in Advance November 18, 2016, doi:10.1101/gr.210286.116
..., supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.210286.116 . Freely available online through the Genome Research Open Access option. Received May 24, 2016. Accepted November 15, 2016. © 2017 Tonner et al.; Published by Cold...
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Research: Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
- Kevin Vanneste,
- Guy Baele,
- Steven Maere,
- and Yves Van de Peer
Genome Res. August 2014 24: 1334-1347; Published in Advance May 16, 2014, doi:10.1101/gr.168997.113
...Biotechnology and Bioinformatics, Ghent University, Ghent B-9052, Belgium; 3Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven B-3000, Belgium; 4Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0002, South Africa Ancient whole- duplications (WGDs...
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