Document Detail

Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome.
MedLine Citation:
PMID:  17989248     Owner:  NLM     Status:  MEDLINE    
Several recent studies have estimated that a large fraction of amino acid divergence between species of Drosophila was fixed by positive selection, using statistical approaches based on the McDonald-Kreitman test. However, little is known about associated selection coefficients of beneficial amino acid mutations. Recurrent selective sweeps associated with adaptive substitutions should leave a characteristic signature in genome variability data that contains information about the frequency and strength of selection. Here, I document a significant negative correlation between the level and the frequency of synonymous site polymorphism and the rate of protein evolution in highly recombining regions of the X chromosome of D. melanogaster. This pattern is predicted by recurrent adaptive protein evolution and suggests that adaptation is an important determinant of patterns of neutral variation genome-wide. Using a maximum likelihood approach, I estimate the product of the rate and strength of selection under a recurrent genetic hitchhiking model, lambda2N(e)s approximately 3 x 10(-8). Using an approach based on the McDonald-Kreitman test, I estimate that approximately 50% of divergent amino acids were driven to fixation by positive selection, implying that beneficial amino acid substitutions are of weak effect on average, on the order of 10(-5) (i.e., 2N(e)s approximately 40). Two implications of these results are that most adaptive substitutions will be difficult to detect in genome scans of selection and that population size (and genetic drift) may be an important determinant of the evolutionary dynamics of protein adaptation.
Peter Andolfatto
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Publication Detail:
Type:  Comparative Study; Journal Article     Date:  2007-11-07
Journal Detail:
Title:  Genome research     Volume:  17     ISSN:  1088-9051     ISO Abbreviation:  Genome Res.     Publication Date:  2007 Dec 
Date Detail:
Created Date:  2007-12-07     Completed Date:  2008-02-05     Revised Date:  2013-06-06    
Medline Journal Info:
Nlm Unique ID:  9518021     Medline TA:  Genome Res     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1755-62     Citation Subset:  IM    
Division of Biological Sciences, University of California San Diego, La Jolla, California 92093, USA.
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MeSH Terms
Amino Acid Substitution / genetics*
Codon / genetics
Drosophila melanogaster / genetics*
Evolution, Molecular*
Genetic Variation
Genome, Insect*
Insect Proteins / genetics
Models, Genetic
Molecular Sequence Data
Selection, Genetic*
X Chromosome / genetics
Reg. No./Substance:
0/Codon; 0/Insect Proteins
Erratum In:
Genome Res. 2008 Jan;18(1):197

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