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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
...a moderate signal for habitat-related convergent evolution of gene expression levels, whereas the Murinae_expr data set displays a stronger signal.Transcriptome convergence is associated with convergent shifts in kidney cell compositionTissue bulk RNA-seq data reflect variation in both expression per cell...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species Daniel Siqueira de Oliveira1,2,3, Anaïs Larue2, William Vilas Boas Nunes2, Francois Sabot4, Alejandra Bodelón5, María Pilar García Guerreiro5, Cristina Vieira2 and Claudia Marcia...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...in herbivory represents a convergent relaxation of selection on genes and functions that are important for the consumption of animal matter. Rapid evolution due to positive selection is transient and less likely to be detected by RERconverge than sustained relaxation of purifying selection (Kowalczyk et al...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., hinging on the precise binding of transcription factors (TFs) and cofactors to gene regulatory elements such as promoters and enhancers. Although it is relatively routine to profile -wide DNA binding landscapes of proteins, identifying the specific proteins that bind to, and regulate the transcription of...
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Research: The grasshopper genome reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution
- Xinghua Li,
- Judith E. Mank,
- and Liping Ban
Genome Res. July 2024 34: 997-1007; Published in Advance August 5, 2024, doi:10.1101/gr.278794.123
...a broader conservation across the class, with the exception of the Lepidoptera (Pease and Hahn 2012).Previous work has documented convergent gene content on the mammalian Y, avian W, and snake W Chromosomes (Bellott and Page 2021) and convergent evolution of mammalian X and avian Z Chromosome gene content...
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Research: Autism spectrum disorder risk genes have convergent effects on transcription and neuronal firing patterns in primary neurons
- Alekh Paranjapye,
- Rili Ahmad,
- Steven Su,
- Abraham J. Waldman,
- Jennifer E. Phillips-Cremins,
- Shuo Zhang,
- and Erica Korb
Genome Res. November 2025 35: 2433-2444; Published in Advance October 20, 2025, doi:10.1101/gr.280698.125
...-linked transcription regulators by depleting them in primary cultured neurons. We then define the resulting gene expression disruptions using RNA sequencing and test effects on neuronal firing using multielectrode array recordings. We identify shared gene expression signatures across many ASD risk genes that converge...
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Research: GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes
- Anguo Liu,
- Nini Wang,
- Guoxiang Xie,
- Yang Li,
- Xixi Yan,
- Xinmei Li,
- Zhenliang Zhu,
- Zhuohui Li,
- Jing Yang,
- Fanxin Meng,
- Mingle Dou,
- Weihuang Chen,
- Nange Ma,
- Yu Jiang,
- Yuanpeng Gao,
- and Yu Wang
Genome Res. October 2023 33: 1673-1689; Published in Advance October 26, 2023, doi:10.1101/gr.277784.123
...GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian s Anguo Liu1,2,7, Nini Wang1,3,7, Guoxiang Xie1,2,7, Yang Li1,2, Xixi Yan1,2, Xinmei Li1,2, Zhenliang Zhu2,4,5, Zhuohui Li1,2, Jing Yang2,4,5, Fanxin Meng1, Mingle Dou1,2, Weihuang Chen1, Nange...
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Method: Recovering gene regulatory networks in single-cell multi-omics data with PRISM-GRN
- Wenhao Zhang,
- Lan Cao,
- Xiaoxuan Gu,
- Yongyu Long,
- and Ying Wang
Genome Res. January 2026 36: 142-158; Published in Advance October 9, 2025, doi:10.1101/gr.280757.125
...of Mariculture Breeding, Xiamen University, Xiamen, Fujian 361000, China; 4Xiamen Key Laboratory of Big Data Intelligent Analysis and Decision, Xiamen, Fujian 361005, China Corresponding author: wangying@xmu.edu.cnAbstractUnderstanding gene regulatory networks (GRNs) is crucial for deciphering cellular...
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Method: Analysis of coding gene expression from small RNA sequencing
- Aygun Azadova,
- Anthonia Ekperuoh,
- Greg N. Brooke,
- and Antonio Marco
Genome Res. March 2026 36: 611-618; Published in Advance February 10, 2026, doi:10.1101/gr.281364.125
...the regulation of miR-10b and its targets in primary breast tumors. BMC Cancer 19: 86. doi:10.1186/s12885-019-5300-6 ↵Meunier J, Lemoine F, Soumillon M, Liechti A, Weier M, Guschanski K, Hu H, Khaitovich P, Kaessmann H. 2013. Birth and expression evolution of mammalian microRNA genes. Genome Res 23: 34–45. doi...

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