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The Evolutionary Fate and Consequences of Duplicate Genes
Michael Lynch,1*and John S. Conery2
Gene duplication has generally been viewed as a necessary source of
material for the origin of evolutionary novelties, butit is unclear
how often gene duplicates arise and how frequentlythey evolve new
functions. Observations from the genomic databasesfor several
eukaryotic species suggest that duplicate genes ariseat a very high
rate, on average 0.01 per gene per million years.Most duplicated genes
experience a brief period of relaxed selectionearly in their history,
with a moderate fraction of them evolvingin an effectively neutral
manner during this period. However,the vast majority of gene
duplicates are silenced within a fewmillion years, with the few
survivors subsequently experiencingstrong purifying selection.
Although duplicate genes may onlyrarely evolve new functions, the
stochastic silencing of suchgenes may play a significant role in the
passive origin of newspecies.
1 Department of Biology, University of Oregon,
Eugene, OR 97403, USA.
2 Department of Computer and
Information Science, University of Oregon, Eugene, OR 97403, USA.
*
To whom correspondence should be addressed. E-mail:
mlynch{at}oregon.uoregon.edu
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|Abstract »|Full Text »|PDF »
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|Abstract »|Full Text »|PDF »
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|Abstract »|Full Text »|PDF »
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