Moeller David A, Tenaillon Maud I, Tiffin Peter
Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108, USA.
Genetics. 2007 Jul;176(3):1799-809. doi: 10.1534/genetics.107.070631. Epub 2007 May 4.
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.
对玉米野生祖先小颖玉米（Zea mays ssp. parviglumis）的核苷酸多样性调查显示，全基因组偏离了标准中性平衡（NE）模型。在此，我们研究了种群结构在多大程度上可能解释了在全物种样本中经常观察到的稀有多态性过剩现象。基于来自五个核基因座和两个叶绿体基因座的序列数据，我们在来自两个地理区域的七个亚种群中发现了显著的种群遗传结构。对全物种样本和特定亚种群样本的种群遗传参数估计值进行比较后发现，种群遗传细分影响了观察到的核苷酸多态性模式。特别是，相对于全物种样本，特定亚种群样本中的 Tajima's D 值显著更高（更接近零），因此更符合 NE 预期。尽管存在这些总体模式，但亚种群内多态性水平和模式与全物种样本及 NE 预期的差异程度在很大程度上取决于采样亚种群所在的地理区域（哈利斯科州与巴尔萨斯）。这可能是由于这些区域中亚种群的种群历史所致。总体而言，这些结果表明，在研究生态和农艺重要性状的遗传基础以及识别已成为选择目标的基因座时，明确考虑种群结构可能很重要。
