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Originally published as Genetics Published Articles Ahead of Print on May 4, 2007.
Genetics, Vol. 176, 1799-1809, July 2007, Copyright © 2007
doi:10.1534/genetics.107.070631
Population Structure and Its Effects on Patterns of Nucleotide Polymorphism in Teosinte (Zea mays ssp. parviglumis)
David A. Moeller*,1,
Maud I. Tenaillon
and
Peter Tiffin*,2
* Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108 and UMR de Génétique Végétale, CNRS-INRA-UPS-INA PG, 91190 Gif-sur-Yvette, France
2 Corresponding author: Department of Plant Biology, University of Minnesota, 1445 Gortner Ave., St. Paul, MN 55108.
E-mail: ptiffin{at}umn.edu
Surveys of nucleotide diversity in the wild ancestor of maize, Zea mays ssp. parviglumis, have revealed genomewide 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. On the basis of 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 vs. 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.
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