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Research: Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous–Paleogene boundary
- Kevin Vanneste,
- Guy Baele,
- Steven Maere,
- and Yves Van de Peer
Genome Res. August 2014 24: 1334-1347; Published in Advance May 16, 2014, doi:10.1101/gr.168997.113
...and developmental genes, is most likely guarded against loss through dosagebalance constraints on the stoichiometry of duplicated pathways and/ormacromolecular complexes (Maere et al. 2005; Freeling and Thomas 2006; Birchler and Veitia 2010). Resolution of dosagebalance constraints over time can thus provide...
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LETTER: Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes
- Brian C. Thomas,
- Brent Pedersen,
- and Michael Freeling
Genome Res. July 2006 16: 934-946; Published in Advance June 7, 2006, doi:10.1101/gr.4708406
...; this mechanism also helps explain the initial survival of the tetraploid. The third explanation predicts that some genes, even though they are duplicated, cannot be deleted one-by-one following tetraploidy without incurring an unfit phenotype: this is the prediction of the gene balance hypothesis. The gene...
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Letter: Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention
- Andrew L. Hufton,
- Susanne Mathia,
- Helene Braun,
- Udo Georgi,
- Hans Lehrach,
- Martin Vingron,
- Albert J. Poustka,
- and Georgia Panopoulou
Genome Res. November 2009 19: 2036-2051; Published in Advance August 24, 2009, doi:10.1101/gr.093237.109
...evolutionary patterns. These results demonstrate that subfunctionalization of conserved cis -regulation has not been the primary determinate of gene duplicate retention in vertebrates. Instead, the data support the gene balance hypothesis, which proposes that duplicate retention has been driven by selection...
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Research: Gene duplication and genetic innovation in cereal genomes
- Hui Guo,
- Yuannian Jiao,
- Xu Tan,
- Xiyin Wang,
- Xianzhong Huang,
- Huizhe Jin,
- and Andrew H. Paterson
Genome Res. February 2019 29: 261-269; Published in Advance January 16, 2019, doi:10.1101/gr.237511.118
...-006-0232-3 ↵Freeling M, Thomas BC. 2006. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res 16: 805–814. doi:10.1101/gr.3681406 ↵Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate...
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Research: Differential retention and divergent resolution of duplicate genes following whole-genome duplication
- Casey L. McGrath,
- Jean-Francois Gout,
- Parul Johri,
- Thomas G. Doak,
- and Michael Lynch
Genome Res. October 2014 24: 1665-1675; Published in Advance August 1, 2014, doi:10.1101/gr.173740.114
...to phenotypic innovations and increased morphological complexity (Ohno 1970; Freeling 2008). Indeed, it has long been suggested that duplicated genes provide the raw material for evolving new functions, so that the thousands of duplicated genes created by a WGD represent unique opportunities to increase...
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Research: Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus
- Eli Rodgers-Melnick,
- Shrinivasrao P. Mane,
- Palitha Dharmawardhana,
- Gancho T. Slavov,
- Oswald R. Crasta,
- Steven H. Strauss,
- Amy M. Brunner,
- and Stephen P. DiFazio
Genome Res. January 2012 22: 95-105; Published in Advance October 5, 2011, doi:10.1101/gr.125146.111
...the degenerative process of subfunctionalization may be counterbalanced by a selective drive to retain highly connected proteins, as predicted by the gene balance hypothesis (Birchler et al. 2005; Freeling 2009; Birchler and Veitia 2010). Salicoid duplicates are longer and more broadly expressed Salicoid duplicate...
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Research: The contributions from the progenitor genomes of the mesopolyploid Brassiceae are evolutionarily distinct but functionally compatible
- Yue Hao,
- Makenzie E. Mabry,
- Patrick P. Edger,
- Michael Freeling,
- Chunfang Zheng,
- Lingling Jin,
- Robert VanBuren,
- Marivi Colle,
- Hong An,
- R. Shawn Abrahams,
- Jacob D. Washburn,
- Xinshuai Qi,
- Kerrie Barry,
- Christopher Daum,
- Shengqiang Shu,
- Jeremy Schmutz,
- David Sankoff,
- Michael S. Barker,
- Eric Lyons,
- J. Chris Pires,
- and Gavin C. Conant
Genome Res. May 2021 31: 799-810; Published in Advance April 16, 2021, doi:10.1101/gr.270033.120
...experienced a recent selective sweep. We propose a “mix and match” model of allopolyploidy, in which sub origin drives homoeolog loss propensities but where genes from different subs function together without difficulty.Fifty years ago, Ohno (1970) published a forceful opus on the role of gene duplication...
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Research: Recruitment of histone modifications to assist mRNA dosage maintenance after degeneration of cytosine DNA methylation during animal evolution
- Andrew Ying-Fei Chang and
- Ben-Yang Liao
Genome Res. September 2017 27: 1513-1524; Published in Advance July 18, 2017, doi:10.1101/gr.221739.117
...for this article.] Gene duplication frequently occurs during evolution (Lynch and Conery 2000), and it is an important mechanism that underlies the origin of organismal complexity (Freeling and Thomas 2006; Wagner et al. 2007). However, the resulting increase in total gene product from genes involved...
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Research: Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
- Orla M. Keane,
- Christina Toft,
- Lorenzo Carretero-Paulet,
- Gary W. Jones,
- and Mario A. Fares
Genome Res. November 2014 24: 1830-1841; Published in Advance August 22, 2014, doi:10.1101/gr.176792.114
...) and gene balance (Birchler et al. 2005; Freeling and Thomas 2006), has been proposed to allow the persistence of genes in duplicate for longer periods of time, thereby providing opportunity for innovation throughmutation (Gu et al. 2003; Fares et al. 2013). This claim is supported by larger fitness effects...
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LETTER: Many or most genes in Arabidopsis transposed after the origin of the order Brassicales
- Michael Freeling,
- Eric Lyons,
- Brent Pedersen,
- Maqsudul Alam,
- Ray Ming,
- and Damon Lisch
Genome Res. December 2008 18: 1924-1937; Published in Advance October 3, 2008, doi:10.1101/gr.081026.108
...interactive gene products following paleotetraploidy in Arabidopsis, as predicted by the Gene Balance Hypothesis ( Birchler and Veitia 2007 ). In this case, selection operates to prevent imbalanced gene product dosage. For the same reason, selection would be expected to disfavor both tandem duplications...

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