Omilian Angela R, Lynch Michael
Department of Biology, Indiana University, Bloomington, Indiana 47405, USA.
Genetics. 2009 May;182(1):325-36. doi: 10.1534/genetics.108.099549. Epub 2009 Mar 19.
Understanding nucleotide variation in natural populations has been a subject of great interest for decades. However, many taxonomic groups, especially those with atypical life history attributes remain unstudied, and Drosophila is the only arthropod genus for which DNA polymorphism data are presently abundant. As a result of the recent release of the complete genome sequence and a wide variety of new genomic resources, the Daphnia system is quickly becoming a promising new avenue for expanding our knowledge of nucleotide variation in natural populations. Here, we examine nucleotide variation in six protein-coding loci for Daphnia pulex and its congeners with particular emphasis on D. pulicaria, the closest extant relative of D. pulex. Levels of synonymous intraspecific variation, pi(s), averaged 0.0136 for species in the Daphnia genus, and are slightly lower than most prior estimates in invertebrates. Tests of neutrality indicated that segregating variation conforms to neutral model expectations for the loci that we examined in most species, while K(a)/K(s) ratios revealed strong purifying selection. Using a full maximum-likelihood coalescent-based method, the ratio of the recombination rate to the mutation rate (c/u), averaged 0.5255 for species of the Daphnia genus. Lastly, a divergence population-genetics approach was used to investigate gene flow and divergence between D. pulex and D. pulicaria.
几十年来，了解自然种群中的核苷酸变异一直是一个备受关注的课题。然而，许多分类群，尤其是那些具有非典型生活史特征的分类群仍未得到研究，而果蝇是目前唯一拥有丰富DNA多态性数据的节肢动物属。由于最近公布了完整的基因组序列以及各种各样新的基因组资源，水蚤系统正迅速成为一个有前景的新途径，以扩展我们对自然种群中核苷酸变异的认识。在这里，我们研究了蚤状溞及其同属物种六个蛋白质编码基因座的核苷酸变异，特别关注蚤状溞现存最近的亲缘物种——美洲蚤状溞。蚤状溞属物种的同义种内变异水平（π(s)）平均为0.0136，略低于此前对无脊椎动物的大多数估计。中性检验表明，在我们研究的大多数物种中，分离变异符合所检测基因座的中性模型预期，而Ka/Ks比率显示出强烈的纯化选择。使用基于完全最大似然合并的方法，蚤状溞属物种的重组率与突变率之比（c/u）平均为0.5255。最后，采用分化种群遗传学方法研究了蚤状溞和美洲蚤状溞之间的基因流和分化。
