Searching journal content for articles similar to Mallick et al. 19 (5): 922.

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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...the accuracy of the detection of positive selection (Grossman et al. 2010).In this study, we investigated the genomic interplay between selection and genetic drift leading to the island syndrome in a system with an exceptionally long and clear history of population isolation. Common voles (Microtus arvalis...
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Method: Direct detection of natural selection in Bronze Age Britain
- Iain Mathieson and
- Jonathan Terhorst
Genome Res. November/December 2022 32: 2057-2067; Published in Advance October 31, 2022, doi:10.1101/gr.276862.122
...and genomic variation. Compared with demographic inference, this is more challenging, because studies of natural selection typically require larger sample sizes than studies of population history, which can integrate information from across the .Although some recent studies have used aDNA to study selection...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...nt. For example, the dot plot for the fourth genomic region of CHROMOSOME_X (122,781–250,556) is very dense and appears black owing to the high similarity between the 54-mers. In contrast, white areas indicate discordance. Regions are grouped by sequence similarity rather than their genomic position...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...encodes a real protein. Such filtering will be particularly important when an annotation method is known to produce many false-positive predictions, and yet, the choice of metrics and thresholds may be ad hoc. The best approach will likely involve selecting metrics and tuning thresholds to maximize...
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Resource: High-quality assembly of the Chinese white truffle genome and recalibrated divergence time estimate provide insight into the evolutionary dynamics of Tuberaceae
- Jacopo Martelossi,
- Jacopo Vujovic,
- Yue Huang,
- Alessia Tatti,
- Kaiwei Xu,
- Federico Puliga,
- Yuanxue Chen,
- Omar Rota Stabelli,
- Fabrizio Ghiselli,
- Xiaoping Zhang,
- and Alessandra Zambonelli
Genome Res. November 2025 35: 2601-2616; Published in Advance August 21, 2025, doi:10.1101/gr.280368.124
...be explained by negative selection against long insertions in gene-dense genomic regions (Buckley et al. 2017; Ruggieri et al. 2022; Martelossi et al. 2024). Similarly to what was previously observed in the fungus Pleurotus ostreatus (Jacq.) P. Kumm. (Castanera et al. 2016), we found evidence of NAHR between...
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Research: Ancient dog introgression into the Iberian wolf genome may have facilitated adaptation to human-dominated landscapes
- Diana Lobo,
- Hernán E. Morales,
- Cock Van Oosterhout,
- José Vicente López-Bao,
- Pedro Silva,
- Luis Llaneza,
- Carolina Pacheco,
- Diana Castro,
- Germán Hernández-Alonso,
- George Pacheco,
- John Archer,
- M. Thomas P. Gilbert,
- Nuno Ferrand,
- and Raquel Godinho
Genome Res. March 2025 35: 432-445; Published in Advance February 14, 2025, doi:10.1101/gr.279093.124
...University, E-33600 Mieres, Spain; 8A.RE.NA, Asesores en Recursos Naturales, 27003 Lugo, Spain; 9University Museum, Norwegian University of Science and Technology, 7012 Trondheim, Norway; 10Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology, University of Johannesburg, 2006 South...
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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
...sequences were consistently depleted in highly brain-biased TF binding motif (Fig. 2G). One interpretation of these results may be that the evolutionary arms race between genomic “parasites” and the host results in selection pressure to “avoid” having sequences that function as, or can evolve into, CREs...
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Research: Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
- Wilfried M. Guiblet,
- Michael DeGiorgio,
- Xiaoheng Cheng,
- Francesca Chiaromonte,
- Kristin A. Eckert,
- Yi-Fei Huang,
- and Kateryna D. Makova
Genome Res. July 2021 31: 1136-1149; Published in Advance June 29, 2021, doi:10.1101/gr.269589.120
...strand of exons, suggesting that G4 structures on the nontranscribed strand are not maintained by natural selection. Thus, both stable and unstable G4s are unlikely to be functional, and stable G4s may be strongly avoided, in this group of genic components. Because such G4s can form at the level of RNA...
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Research: The human genome contains over a million autonomous exons
- Nicholas Stepankiw,
- Ally W.H. Yang,
- and Timothy R. Hughes
Genome Res. November 2023 33: 1865-1878; Published in Advance November 9, 2023, doi:10.1101/gr.277792.123
...(“Frame 2”) positions are shown. (C) Line plots depicting the distribution of mRNA exon lengths and the percent of mRNA exons at each length recovered by exon trapping. Plots have a 9 bp smoothing window applied. (D) Boxplots depicting GC content of trapped internal exons from different genomic regions. y...
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Method: Ultrafast genome-wide inference of pairwise coalescence times
- Regev Schweiger and
- Richard Durbin
Genome Res. July 2023 33: 1023-1031; Published in Advance August 10, 2023, doi:10.1101/gr.277665.123
...extensions infer the coalescence time of two homologous chromosomes at each genomic position. This inference is used in reconstructing demographic histories, detecting selection signatures, studying -wide associations, constructing ancestral recombination graphs, and more. Inference of coalescence times...
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