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For: Liu H, Zhang J. Is the mutation rate lower in genomic regions of stronger selective constraints? Mol Biol Evol 2022;39:6652438. [PMID: 35907247 PMCID: PMC9372563 DOI: 10.1093/molbev/msac169] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]  Open
Number Cited by Other Article(s)
1
Hara Y, Kuraku S. Intragenomic mutational heterogeneity: structural and functional insights from gene evolution. Trends Genet 2025:S0168-9525(25)00075-7. [PMID: 40328580 DOI: 10.1016/j.tig.2025.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 03/27/2025] [Accepted: 03/28/2025] [Indexed: 05/08/2025]
2
James JE, Lascoux M. Amino Acid Properties, Substitution Rates, and the Nearly Neutral Theory. Genome Biol Evol 2025;17:evaf025. [PMID: 39971341 PMCID: PMC11884779 DOI: 10.1093/gbe/evaf025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2024] [Revised: 02/05/2025] [Accepted: 02/12/2025] [Indexed: 02/21/2025]  Open
3
Waneka G, Pate B, Monroe JG, Sloan DB. Exploring the Relationship Between Gene Expression and Low-Frequency Somatic Mutations in Arabidopsis with Duplex Sequencing. Genome Biol Evol 2024;16:evae213. [PMID: 39365161 PMCID: PMC11489876 DOI: 10.1093/gbe/evae213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 09/07/2024] [Accepted: 09/10/2024] [Indexed: 10/05/2024]  Open
4
Liang X, Yang S, Wang D, Knief U. Characterization and distribution of de novo mutations in the zebra finch. Commun Biol 2024;7:1243. [PMID: 39358581 PMCID: PMC11447093 DOI: 10.1038/s42003-024-06945-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 09/24/2024] [Indexed: 10/04/2024]  Open
5
Polizzi B, Calvez V, Charlat S, Rajon E. (Epi)mutation Rates and the Evolution of Composite Trait Architectures. Am Nat 2024;204:E42-E56. [PMID: 39179232 DOI: 10.1086/731461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2024]
6
Beichman AC, Zhu L, Harris K. The Evolutionary Interplay of Somatic and Germline Mutation Rates. Annu Rev Biomed Data Sci 2024;7:83-105. [PMID: 38669515 DOI: 10.1146/annurev-biodatasci-102523-104225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
7
Wu K, Qin D, Qian Y, Liu H. A new era of mutation rate analyses: Concepts and methods. Zool Res 2024;45:767-780. [PMID: 38894520 PMCID: PMC11298668 DOI: 10.24272/j.issn.2095-8137.2024.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]  Open
8
Baduel P, Sammarco I, Barrett R, Coronado‐Zamora M, Crespel A, Díez‐Rodríguez B, Fox J, Galanti D, González J, Jueterbock A, Wootton E, Harney E. The evolutionary consequences of interactions between the epigenome, the genome and the environment. Evol Appl 2024;17:e13730. [PMID: 39050763 PMCID: PMC11266121 DOI: 10.1111/eva.13730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 03/30/2024] [Accepted: 05/22/2024] [Indexed: 07/27/2024]  Open
9
Quiroz D, Oya S, Lopez-Mateos D, Zhao K, Pierce A, Ortega L, Ali A, Carbonell-Bejerano P, Yarov-Yarovoy V, Suzuki S, Hayashi G, Osakabe A, Monroe G. H3K4me1 recruits DNA repair proteins in plants. THE PLANT CELL 2024;36:2410-2426. [PMID: 38531669 PMCID: PMC11132887 DOI: 10.1093/plcell/koae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/28/2024]
10
Waneka G, Pate B, Monroe JG, Sloan DB. Investigating low frequency somatic mutations in Arabidopsis with Duplex Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578196. [PMID: 38352550 PMCID: PMC10862904 DOI: 10.1101/2024.01.31.578196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
11
Livnat A, Love AC. Mutation and evolution: Conceptual possibilities. Bioessays 2024;46:e2300025. [PMID: 38254311 DOI: 10.1002/bies.202300025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 01/24/2024]
12
Horton JS, Taylor TB. Mutation bias and adaptation in bacteria. MICROBIOLOGY (READING, ENGLAND) 2023;169:001404. [PMID: 37943288 PMCID: PMC10710837 DOI: 10.1099/mic.0.001404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
13
Lynch M, Ali F, Lin T, Wang Y, Ni J, Long H. The divergence of mutation rates and spectra across the Tree of Life. EMBO Rep 2023;24:e57561. [PMID: 37615267 PMCID: PMC10561183 DOI: 10.15252/embr.202357561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023]  Open
14
Staunton PM, Peters AJ, Seoighe C. Somatic mutations inferred from RNA-seq data highlight the contribution of replication timing to mutation rate variation in a model plant. Genetics 2023;225:iyad128. [PMID: 37450609 PMCID: PMC10550316 DOI: 10.1093/genetics/iyad128] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 03/23/2023] [Accepted: 06/11/2023] [Indexed: 07/18/2023]  Open
15
Majic P, Payne JL. Developmental Selection and the Perception of Mutation Bias. Mol Biol Evol 2023;40:msad179. [PMID: 37556606 PMCID: PMC10443735 DOI: 10.1093/molbev/msad179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]  Open
16
Monroe JG, Murray KD, Xian W, Srikant T, Carbonell-Bejerano P, Becker C, Lensink M, Exposito-Alonso M, Klein M, Hildebrandt J, Neumann M, Kliebenstein D, Weng ML, Imbert E, Ågren J, Rutter MT, Fenster CB, Weigel D. Reply to: Re-evaluating evidence for adaptive mutation rate variation. Nature 2023;619:E57-E60. [PMID: 37495874 PMCID: PMC10371858 DOI: 10.1038/s41586-023-06315-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
17
Charlesworth B, Jensen JD. Population Genetic Considerations Regarding Evidence for Biased Mutation Rates in Arabidopsis thaliana. Mol Biol Evol 2023;40:msac275. [PMID: 36572441 PMCID: PMC9907473 DOI: 10.1093/molbev/msac275] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
18
Zhang J. What Has Genomics Taught An Evolutionary Biologist? GENOMICS, PROTEOMICS & BIOINFORMATICS 2023;21:1-12. [PMID: 36720382 PMCID: PMC10373158 DOI: 10.1016/j.gpb.2023.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/06/2023] [Accepted: 01/19/2023] [Indexed: 01/30/2023]
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