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ARTICLE: Copy number variation and evolution in humans and chimpanzees
- George H. Perry,
- Fengtang Yang,
- Tomas Marques-Bonet,
- Carly Murphy,
- Tomas Fitzgerald,
- Arthur S. Lee,
- Courtney Hyland,
- Anne C. Stone,
- Matthew E. Hurles,
- Chris Tyler-Smith,
- Evan E. Eichler,
- Nigel P. Carter,
- Charles Lee,
- and Richard Redon
Genome Res. November 2008 18: 1698-1710; Published in Advance September 4, 2008, doi:10.1101/gr.082016.108
...duplications. By adapting population genetic analyses for use with copy number data, we identified functional categories of genes that have likely evolved under purifying or positive selection for copy number changes. In particular, duplications and deletions of genes with inflammatory response and cell...
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Research: Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
- Željka Pezer,
- Bettina Harr,
- Meike Teschke,
- Hiba Babiker,
- and Diethard Tautz
Genome Res. August 2015 25: 1114-1124; Published in Advance July 6, 2015, doi:10.1101/gr.187187.114
...these populations, implying a more or less constant accumulation of differences over time. Such progressive divergence is predicted by the neutral model of evolution, which assumes that mutations, drift, and purifying selection shape molecular evolution, while adaptive mutations are expected to be rare (Kimura 1983...
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Research: The impact of widespread regulatory neofunctionalization on homeolog gene evolution following whole-genome duplication in maize
- Thomas E. Hughes,
- Jane A. Langdale,
- and Steven Kelly
Genome Res. August 2014 24: 1348-1355; Published in Advance April 30, 2014, doi:10.1101/gr.172684.114
...selection prevails over positive selection in human copy number variant evolution. Genome Res 18: 1711–1723. Ohno S. 1970. Evolution by gene duplication. Springer, Berlin. Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, et al. 2009...
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Letter: Human capacitance to dosage imbalance: Coping with inefficient selection
- Ariel Fernández and
- Jianping Chen
Genome Res. December 2009 19: 2185-2192; Published in Advance October 9, 2009, doi:10.1101/gr.094441.109
...capacitance (Fig. 3A) can be attributed to family size (gene copy number) effects. The number of paralogs is a determinant of dosage-related purifying selection. Whatever the divergence topology within the family, dosage imbalance is dependent on family size since the number of surviving paralogs determines...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...demonstrate that many mitochondrial-coding NUMTs exhibit signs of long-term selection. In a subset of these NUMT genes, we detected evolutionary signals consistent with adaptive evolution, including one human NUMT shared among seven ape species. These findings suggest that NUMT insertions may occasionally...
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Research: Candida albicans isolates contain frequent heterozygous structural variants and transposable elements within genes and centromeres
- Ursula Oggenfuss,
- Robert T. Todd,
- Natthapon Soisangwan,
- Bailey Kemp,
- Alison Guyer,
- Annette Beach,
- and Anna Selmecki
Genome Res. April 2025 35: 824-838; Published in Advance October 22, 2024, doi:10.1101/gr.279301.124
...(Hartmann et al. 2017; Yang et al. 2019; Fouché et al. 2023). SVs can influence gene expression, for example by the insertion or deletion of regulatory elements upstream of a gene (Butelli et al. 2012). Deleterious SVs are typically eliminated from populations by strong purifying selection (Elyashiv et al...
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Research: Hydra has mammal-like mutation rates facilitating fast adaptation despite its nonaging phenotype
- Arne Sahm,
- Konstantin Riege,
- Marco Groth,
- Martin Bens,
- Johann Kraus,
- Martin Fischer,
- Hans Kestler,
- Christoph Englert,
- Ralf Schaible,
- Matthias Platzer,
- and Steve Hoffmann
Genome Res. December 2024 34: 2217-2228; Published in Advance December 4, 2024, doi:10.1101/gr.279025.124
...of nonsynonymous variants (dN) as an indicator of selection, against that of synonymous variants (dS) representing the genetic drift. Therefore, a dN/dS ratio >>1 indicates positive selection, ∼1 indicates neutral evolution or genetic drift, and ≪1 negative selection (Kimura 1980). In line with this, our single...
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Research: Causes and consequences of a complex recombinational landscape in the ant Cardiocondyla obscurior
- Mohammed Errbii,
- Jürgen Gadau,
- Kerstin Becker,
- Lukas Schrader,
- and Jan Oettler
Genome Res. June 2024 34: 863-876; Published in Advance June 5, 2024, doi:10.1101/gr.278392.123
..., that is, the ratio of nonsynonymous (dN) to synonymous (dS) substitutions (Webster and Hurst 2012). In regions of low recombination, increased genetic interference should compromise both positive selection for advantageous variants and purifying selection against deleterious ones (Betancourt et al. 2009...
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Research: Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
- Tim Downing,
- Hideo Imamura,
- Saskia Decuypere,
- Taane G. Clark,
- Graham H. Coombs,
- James A. Cotton,
- James D. Hilley,
- Simonne de Doncker,
- Ilse Maes,
- Jeremy C. Mottram,
- Mike A. Quail,
- Suman Rijal,
- Mandy Sanders,
- Gabriele Schönian,
- Olivia Stark,
- Shyam Sundar,
- Manu Vanaerschot,
- Christiane Hertz-Fowler,
- Jean-Claude Dujardin,
- and Matthew Berriman
Genome Res. December 2011 21: 2143-2156; Published in Advance October 28, 2011, doi:10.1101/gr.123430.111
....6 per Mb) (Tajima 1983) and an excess of rare alleles (FS = 1.72) (Fu 1997) could be due to a pattern of clonal reproduction as well as purifying selection, which had a limited power to remove mildly deleterious variants. Comparing the proportions of nonsynonymous and synonymous mutations in our 17...
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Research: Convergent origination of a Drosophila-like dosage compensation mechanism in a reptile lineage
- Ray Marin,
- Diego Cortez,
- Francesco Lamanna,
- Madapura M. Pradeepa,
- Evgeny Leushkin,
- Philippe Julien,
- Angélica Liechti,
- Jean Halbert,
- Thoomke Brüning,
- Katharina Mössinger,
- Timo Trefzer,
- Christian Conrad,
- Halie N. Kerver,
- Juli Wade,
- Patrick Tschopp,
- and Henrik Kaessmann
Genome Res. December 2017 27: 1974-1987; Published in Advance November 13, 2017, doi:10.1101/gr.223727.117
...(potentially haploinsufficient genes) retained ancestral expression patterns. However, the almost complete erosion of all other Y genes triggered the evolution of a highly efficient dosage compensation system, in which the loss of Y gene copies was compensated by a global twofold up-regulation of ancestral X...
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