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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 Pelican are two phylogenetic methods. EVE models the evolution of expression toward two optima depending on the condition (theta1 vs. theta2). Pelican looks for differences in amino acid usage at a given site between two conditions (here, p1 vs. p2). DESeq2, when used accounting for family effects, models...
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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
..., in which gene families with functions associated with host localization, acceptance, and usage are proposed to evolve. In this context, cactophilic Drosophila species serve as an excellent model to study host shift evolution, because they use a wide range of cacti as hosts, and many species display...
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Research: Evidence for compensatory evolution within pleiotropic regulatory elements
- Zane Kliesmete,
- Peter Orchard,
- Victor Yan Kin Lee,
- Johanna Geuder,
- Simon M. Krauß,
- Mari Ohnuki,
- Jessica Jocher,
- Beate Vieth,
- Wolfgang Enard,
- and Ines Hellmann
Genome Res. October 2024 34: 1528-1539; Published in Advance September 10, 2024, doi:10.1101/gr.279001.124
...). These observations imply that a simple model of purifying selection alone is insufficient to explain the effect of pleiotropy on CRE evolution and suggest a role for compensatory evolution.Zooming into tissue effects, in line with previous investigations on brain evolution (Kuma et al. 1995; Wang et al. 2007...
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Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
- Fangyuan Yang,
- Li-Jun Cao,
- Petr Nguyen,
- Zhong-Zheng Ma,
- Jin-Cui Chen,
- Wei Song,
- and Shu-Jun Wei
Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
...), these sex chromosome–autosome (SA) fusions occur relatively frequently, suggesting possible evolutionary advantages. Here, we investigated how SA fusion affects chromosome features and molecular evolution in leafroller moths (Lepidoptera: Tortricidae). Phylogenomic analysis showed that Tortricidae diverged...
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Method: Modeling and predicting cancer clonal evolution with reinforcement learning
- Stefan Ivanovic and
- Mohammed El-Kebir
Genome Res. July 2023 33: 1078-1088; Published in Advance June 21, 2023, doi:10.1101/gr.277672.123
...by , noting the fact that there are multiple ways of generating each tree (Fig. 1B). This leads to the following problem, which we describe in more detail in the Methods.Problem 1 (Independent Clonal Evolution).Given a cohort of tumor phylogenies for n tumors on m mutations, find model parameters θ...
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Research: Transposable elements drive the evolution of metazoan zinc finger genes
- Jonathan N. Wells,
- Ni-Chen Chang,
- John McCormick,
- Caitlyn Coleman,
- Nathalie Ramos,
- Bozhou Jin,
- and Cédric Feschotte
Genome Res. August 2023 33: 1325-1339; Published in Advance September 15, 2023, doi:10.1101/gr.277966.123
...subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that, in tetrapods, the targeting and repression of lineage-specific transposable elements (TEs) plays a critical role in the evolution of the Krüppel...
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Method: Contamination detection in sequencing studies using the mitochondrial phylogeny
- Hansi Weissensteiner,
- Lukas Forer,
- Liane Fendt,
- Azin Kheirkhah,
- Antonio Salas,
- Florian Kronenberg,
- and Sebastian Schoenherr
Genome Res. February 2021 31: 309-316; Published in Advance January 15, 2021, doi:10.1101/gr.256545.119
...the mtDNA and identify the mitochondrial copy number within a mixture as a critical component for the overall accuracy. The haplocheck tool is available both as a command-line tool and as a cloud web service producing interactive reports that facilitates the navigation through the phylogeny...
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Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
- Scott Ferguson,
- Ashley Jones,
- Kevin Murray,
- Rose Andrew,
- Benjamin Schwessinger,
- and Justin Borevitz
Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
...Plant evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence Scott Ferguson1,4, Ashley Jones1,4, Kevin Murray1,2, Rose Andrew3, Benjamin Schwessinger1 and Justin Borevitz1 1Research School of Biology, Australian National University, Canberra...
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Method: Leveraging protein language models for accurate multiple sequence alignments
- Claire D. McWhite,
- Isabel Armour-Garb,
- and Mona Singh
Genome Res. July 2023 33: 1145-1153; Published in Advance July 6, 2023, doi:10.1101/gr.277675.123
...based on substitution matrices to measure amino acid similarities. Although successful, standard methods struggle on sets of proteins with low sequence identity: the so-called twilight zone of protein alignment. For these difficult cases, another source of information is needed. Protein language models...
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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
...that extreme heterogamety will accelerate Fast-X evolution (Charlesworth et al. 1987) and the evolution of dosage compensation (Charlesworth 1996), empirical tests of this remain rare (Pal and Vicoso 2015).Grasshoppers were an early genetic model, and Walter Sutton proposed the chromosome theory of heredity...

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