Population Genomics of Daphnia pulex
Population Genomics of Daphnia pulex
复制标题
DOI：
10.1534/genetics.116.190611
复制
发表时间：
2017-05-01
期刊：
影响因子：
3.3
通讯作者：
Jia, Zhiyuan
中科院分区：
文献类型：
--
作者：
Lynch, Michael;Gutenkunst, Ryan;Jia, Zhiyuan
使用数据从83个菌株从一个单一的人口，人口基因组学的微甲壳类动物蚤状水蚤的描述和目前的知识相比，只有其他研究充分的无脊椎动物，果蝇。这两个物种在有效群体大小和突变率方面非常相似，尽管重组的一些特征似乎不同，在D中短距离（< 100 bp）的连锁不平衡升高。melanogaster和D.蚤。研究人群与Hardy-Weinberg平衡下的预期密切相关，并反映了有效人群大小变化范围不超过两倍的既往人群历史。四倍冗余的沉默位点和内含子位点的限制区域似乎以一种近乎中性的方式进化，为群体遗传分析提供了一个强有力的工具。氨基酸置换位点主要处于强纯化选择下，UTR和基因间区域中的大部分位点也是如此，但是在这些位点处的大多数SNP（频率上升至> 0.05）似乎以接近中性的方式进化。所有形式的基因组位点（包括密码子内的替换位点，以及基因间和UTR区域）似乎都经历了与D.黑腹，但这可能部分是最近的人口变化的结果。这些结果确立了D. pulex是未来自然种群进化基因组学研究的一个优秀系统。
Using data from 83 isolates from a single population, the population genomics of the microcrustacean Daphnia pulex are described and compared to current knowledge for the only other well-studied invertebrate, Drosophila melanogaster. These two species are quite similar with respect to effective population sizes and mutation rates, although some features of recombination appear to be different, with linkage disequilibrium being elevated at short (< 100 bp) distances in D. melanogaster and at long distances in D. pulex. The study population adheres closely to the expectations under Hardy-Weinberg equilibrium, and reflects a past population history of no more than a twofold range of variation in effective population size. Fourfold redundant silent sites and a restricted region of intronic sites appear to evolve in a nearly neutral fashion, providing a powerful tool for population genetic analyses. Amino acid replacement sites are predominantly under strong purifying selection, as are a large fraction of sites in UTRs and intergenic regions, but the majority of SNPs at such sites that rise to frequencies > 0.05 appear to evolve in a nearly neutral fashion. All forms of genomic sites (including replacement sites within codons, and intergenic and UTR regions) appear to be experiencing an similar to 23 x higher level of selection scaled to the power of drift in D. melanogaster, but this may in part be a consequence of recent demographic changes. These results establish D. pulex as an excellent system for future work on the evolutionary genomics of natural populations.