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doi:10.1534/genetics.107.070631
A more recent version of this article appeared on July 1, 2007.
REGULAR RESEARCH PAPERS |
Population structure and its effects on patterns of nucleotide polymorphism in teosinte (Zea mays ssp. parviglumis)
David A Moeller 1, Maud I Tenaillon 2 and Peter Tiffin 1*
1 University of Minnesota
2 CNRS
* To whom correspondence should be addressed. E-mail: ptiffin{at}umn.edu.
Submitted on January 7, 2007
Revised on March 19, 2007
Accepted on 19 April 2007
Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genome-wide departures from the standard neutral equilibrium (NE) model. Here we investigate the degree to which population structure may account for the excess of rare polymorphisms frequently observed in species-wide samples. Based on sequence data from five nuclear and two chloroplast loci, we found significant population genetic structure among seven subpopulations from two geographic regions. Comparisons of estimates of population genetic parameters from species-wide samples and subpopulation-specific samples showed that population genetic subdivision influenced observed patterns of nucleotide polymorphism. In particular, Tajima's D was significantly higher (closer to zero) in subpopulation-specific samples relative to species-wide samples, and therefore more closely corresponded to NE expectations. In spite of these overall patterns, the extent to which levels and patterns of polymorphism within subpopulations differed from species-wide samples and NE expectations depended strongly on the geographic region (Jalisco versus Balsas) from which subpopulations were sampled. This may be due to the demographic history of subpopulations in those regions. Overall, these results suggest that explicitly accounting for population structure may be important for studies examining the genetic basis of ecologically- and agronomically-important traits as well as for identifying loci that have been the targets of selection.
Key Words: demographic history, domestication, gene flow, maize, natural selection
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