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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...that the ape ancestral locus (hsa10) began to duplicate 5.6 (5.1–6.1) million years ago (MYA), creating an interstitial copy mapping to Pan Chr6 (hsa7) that is located 2 kbp away from an interstitial pCht satellite array. This interstitial spacer in the Pan lineage is ancestral to all other gorilla subterminal...
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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
...that there are many different, yet repeatedly selected, ways to adapt to aridity and that the degree of convergent evolution increases with both the age of the transitions and species relatedness.Repeated evolution, embracing parallel and convergent evolution, occurs when different lineages evolve similar traits...
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Research: Copy number variation alters local and global mutational tolerance
- Grace Avecilla,
- Pieter Spealman,
- Julia Matthews,
- Elodie Caudal,
- Joseph Schacherer,
- and David Gresham
Genome Res. August 2023 33: 1340-1353; Published in Advance August 31, 2023, doi:10.1101/gr.277625.122
...or duplication of segments of DNA. Amplification of segments of DNA sequence, a type of copy number variation (CNV), is an important source of rapid adaptive evolution. In the short term, gene amplification can result in increased gene expression, which provides a selective advantage facilitating adaptation...
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Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
- Kavitha Uthanumallian,
- Andrea Del Cortona,
- Susana M. Coelho,
- Olivier De Clerck,
- Sebastian Duchene,
- and Heroen Verbruggen
Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
...Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage Kavitha Uthanumallian1, Andrea Del Cortona2, Susana M. Coelho3, Olivier De Clerck2, Sebastian Duchene4,5 and Heroen Verbruggen1,6 1Melbourne Integrative Genomics, School of Bio...
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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
...that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative...
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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
...The grasshopper reveals long-term gene content conservation of the X Chromosome and temporal variation in X Chromosome evolution Xinghua Li1,2, Judith E. Mank3 and Liping Ban1 1Department of Grassland Resources and Ecology, College of Grassland Science and Technology, China Agricultural University...
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Research: Multi-species analysis of inflammatory response elements reveals ancient and lineage-specific contributions of transposable elements to NF-kB binding
- Liangxi Wang,
- Tiegh Taylor,
- Kumaragurubaran Rathnakumar,
- Nadiya Khyzha,
- Minggao Liang,
- Azad Alizada,
- Laura F. Campitelli,
- Sara E. Pour,
- Zain M. Patel,
- Lina Antounians,
- Ian C. Tobias,
- Huayun Hou,
- Timothy R. Hughes,
- Sushmita Roy,
- Jennifer A. Mitchell,
- Jason E. Fish,
- and Michael D. Wilson
Genome Res. July 2025 35: 1544-1559; Published in Advance June 6, 2025, doi:10.1101/gr.280357.124
...motifs capable of regulating target gene expression in vivo.Ancestral reconstruction reveals a stabilization of RELA motifs during MER81 evolutionThe enrichment of RELA binding in extant MER81 copies appears to be a common feature across cells and mammalian lineages. However, the extant copies of MER81...
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Research: Variation in the fitness impact of translationally optimal codons among animals
- Florian Bénitière,
- Tristan Lefébure,
- and Laurent Duret
Genome Res. March 2025 35: 446-458; Published in Advance February 10, 2025, doi:10.1101/gr.279837.124
...to the demand. This evolution most probably results from variation in the extent of adenosine-to-inosine modification at the first position of ANN anticodons, which affects the extent to which the WCp codon is preferred to the wobble one (Lim and Curran 2001).These observations suggest a straightforward model...
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Research: Long-read genomics reveal extensive nuclear-specific evolution and allele-specific expression in a dikaryotic fungus
- Rita Tam,
- Mareike Möller,
- Runpeng Luo,
- Zhenyan Luo,
- Ashley Jones,
- Sambasivam Periyannan,
- John P. Rathjen,
- and Benjamin Schwessinger
Genome Res. June 2025 35: 1364-1376; Published in Advance April 11, 2025, doi:10.1101/gr.280359.124
...attachment sites are not always positionally conserved. Each nucleus carries a unique array of rDNAs with more than 200 copies that harbor nucleus-specific sequence variations. The inter-haplotype diversity between the two nuclear s is shaped by large-scale structural variations linked to transposable...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...in shaping evolution of retroelement-associated TE-CRE landscapes in Atlantic salmon.Although retroelements dominate the salmon TE-CRE landscape, the role of DNA transposons such as DTA and DTT elements in TE-CRE evolution cannot be neglected owing to their high genomic copy numbers (Figs. 1, 3A). Indeed...

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