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Research: Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer
- Yang Liu,
- João Botelho,
- and Jaime Iranzo
Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
...by interfering with the propagation of MGEs, several empirical and theoretical observations suggest that the relation between defense systems and HGT might be more complex. First, the selection pressure to maintain defense systems in a population (and consequently their prevalence) generally increases...
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Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
- Jian-Hai Chen,
- Patrick Landback,
- Deanna Arsala,
- Alexander Guzzetta,
- Shengqian Xia,
- Jared Atlas,
- Dylan Sosa,
- Yong E. Zhang,
- Jingqiu Cheng,
- Bairong Shen,
- and Manyuan Long
Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
...million years). Despite this stable pace, we observe distinct patterns in phenotypic enrichment, pleiotropy, and selective pressures across gene ages. Young genes show significant enrichment in diseases related to the male reproductive system, indicating strong sexual selection. Young genes also exhibit...
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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
...dominated by genetic drift, with extremely low diversity, variable Tajima's D, and very high divergence from continental conspecifics. Increased dN/dS ratios over a wide range of genes in Orkney voles indicated -wide relaxation of purifying selection. We found evidence of hard sweeps on key genes...
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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
...of selection relative to drift (Ohta 1972, 1992; Charlesworth 2009; Chen et al. 2017), an idea supported by studies showing that populations with larger Ne experience stronger selection efficacy (Lynch and Conery 2003; Gossmann et al. 2012).View larger version: In this window In a new window Figure 1...
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Resource: Genetic features and genomic targets of human KRAB-zinc finger proteins
- Jonas de Tribolet-Hardy,
- Christian W. Thorball,
- Romain Forey,
- Evarist Planet,
- Julien Duc,
- Alexandre Coudray,
- Bara Khubieh,
- Sandra Offner,
- Cyril Pulver,
- Jacques Fellay,
- Michael Imbeault,
- Priscilla Turelli,
- and Didier Trono
Genome Res. August 2023 33: 1409-1423; Published in Advance September 20, 2023, doi:10.1101/gr.277722.123
...of selective pressures imposed on its sequence, hence is linked to the relative functional importance of the corresponding protein or protein domain for a given species. Typically, highly constrained coding regions correspond to loci whereas mutations are either associated with disease or are completely absent...
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Method: A general calculus of fitness landscapes finds genes under selection in cancers
- Teng-Kuei Hsu,
- Jennifer Asmussen,
- Amanda Koire,
- Byung-Kwon Choi,
- Mayur A. Gadhikar,
- Eunna Huh,
- Chih-Hsu Lin,
- Daniel M. Konecki,
- Young Won Kim,
- Curtis R. Pickering,
- Marek Kimmel,
- Lawrence A. Donehower,
- Mitchell J. Frederick,
- Jeffrey N. Myers,
- Panagiotis Katsonis,
- and Olivier Lichtarge
Genome Res. May 2022 32: 916-929; Published in Advance March 17, 2022, doi:10.1101/gr.275811.121
...selection (Greenman et al. 2007). A single-gene illustration is the TCGA-wide cohort integral of DNAH5, a large and frequently mutated gene that has not, to the best of our knowledge, been associated with cancer and that appears free of any selection pressure (P = 0.84) (Supplemental Fig. S2A...
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Research: Purifying selection on noncoding deletions of human regulatory loci detected using their cellular pleiotropy
- David W. Radke,
- Jae Hoon Sul,
- Daniel J. Balick,
- Sebastian Akle,
- Alzheimer's Disease Neuroimaging Initiative,
- Robert C. Green,
- and Shamil R. Sunyaev
Genome Res. June 2021 31: 935-946; Published in Advance May 7, 2021, doi:10.1101/gr.275263.121
...identifying feature. The classic example is the analysis of selective constraints on protein-coding genes evident from the depletion of missense or nonsense genetic variants. These advances, however, are not directly translatable to the analysis of noncoding DNA, which has increasingly become a focus of human...
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Research: The hourglass model of evolutionary conservation during embryogenesis extends to developmental enhancers with signatures of positive selection
- Jialin Liu,
- Rebecca R. Viales,
- Pierre Khoueiry,
- James P. Reddington,
- Charles Girardot,
- Eileen E.M. Furlong,
- and Marc Robinson-Rechavi
Genome Res. September 2021 31: 1573-1581; Published in Advance July 15, 2021, doi:10.1101/gr.275212.121
.... In terms of protein sequence, for example, the lower sequence evolution in the phylotypic period appears to be caused by both strong purifying selection and weak positive selection (Liu and Robinson-Rechavi 2018a,b; Coronado-Zamora et al. 2019). To investigate the underlying regulatory mechanisms, as well...
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Research: Less effective selection leads to larger genomes
- Tristan Lefébure,
- Claire Morvan,
- Florian Malard,
- Clémentine François,
- Lara Konecny-Dupré,
- Laurent Guéguen,
- Michèle Weiss-Gayet,
- Andaine Seguin-Orlando,
- Luca Ermini,
- Clio Der Sarkissian,
- N. Pierre Charrier,
- David Eme,
- Florian Mermillod-Blondin,
- Laurent Duret,
- Cristina Vieira,
- Ludovic Orlando,
- and Christophe Jean Douady
Genome Res. June 2017 27: 1016-1028; Published in Advance April 19, 2017, doi:10.1101/gr.212589.116
...; Supplemental Table S2; Supplemental Figs. S1, S3). This supports a scenario in which subterranean species do not experience higher rates of positive selection, but instead evolve under reduced purifying selection efficacy. We next tested the adaptive dN/dS increase scenario using polymorphism data. Under...
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Research: Human long intrinsically disordered protein regions are frequent targets of positive selection
- Arina Afanasyeva,
- Mathias Bockwoldt,
- Christopher R. Cooney,
- Ines Heiland,
- and Toni I. Gossmann
Genome Res. July 2018 28: 975-982; Published in Advance June 1, 2018, doi:10.1101/gr.232645.117
.... For example, functionally active parts of proteins are more susceptible to selective pressure, and active sites of enzymes evolve significantly slower than other parts of the protein (Dean et al. 2002). On the other hand, parts exposed to the solvent protein surface evolve much faster (Franzosa and Xia 2009...

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