Renzette Nicholas, Kowalik Timothy F, Jensen Jeffrey D
Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.
Immunology and Microbiology Program, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA, 01655, USA.
Mol Ecol. 2016 Jan;25(1):403-13. doi: 10.1111/mec.13331. Epub 2015 Sep 3.
A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms.
群体遗传学的一个核心焦点一直是研究选择性和中性过程在塑造种内多样性模式中的作用。具体就选择而言，对高等生物的调查表明，背景选择和基因搭便车在塑造多态性分布方面的相对贡献存在相当大的差异，尽管这些分析很少扩展到细菌和病毒。在这里，我们通过分析种内多样性、种间差异和重组率之间的关系，研究一种普遍存在的病毒病原体——人类巨细胞病毒（HCMV）的进化。我们表明，多样性和差异之间存在很强的相关性，这与中性进化的预期一致。然而，在对差异进行校正后，种内多样性与重组率之间仍然存在显著的相关性，进一步的分析表明，这种相关性很大程度上是由于背景选择的影响。此外，少数以长链非编码RNA为中心的位点也显示出选择性清除的证据。这些数据表明，HCMV的进化由中性机制以及背景选择主导，将我们对连锁选择的理解扩展到了一类新型生物体。
