Kinnersley Margie, Wenger Jared, Kroll Evgueny, Adams Julian, Sherlock Gavin, Rosenzweig Frank
Division of Biological Sciences, The University of Montana, Missoula, Montana, United States of America.
Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America.
PLoS Genet. 2014 Jun 26;10(6):e1004430. doi: 10.1371/journal.pgen.1004430. eCollection 2014 Jun.
A major goal of genetics is to define the relationship between phenotype and genotype, while a major goal of ecology is to identify the rules that govern community assembly. Achieving these goals by analyzing natural systems can be difficult, as selective pressures create dynamic fitness landscapes that vary in both space and time. Laboratory experimental evolution offers the benefit of controlling variables that shape fitness landscapes, helping to achieve both goals. We previously showed that a clonal population of E. coli experimentally evolved under continuous glucose limitation gives rise to a genetically diverse community consisting of one clone, CV103, that best scavenges but incompletely utilizes the limiting resource, and others, CV101 and CV116, that consume its overflow metabolites. Because this community can be disassembled and reassembled, and involves cooperative interactions that are stable over time, its genetic diversity is sustained by clonal reinforcement rather than by clonal interference. To understand the genetic factors that produce this outcome, and to illuminate the community's underlying physiology, we sequenced the genomes of ancestral and evolved clones. We identified ancestral mutations in intermediary metabolism that may have predisposed the evolution of metabolic interdependence. Phylogenetic reconstruction indicates that the lineages that gave rise to this community diverged early, as CV103 shares only one Single Nucleotide Polymorphism with the other evolved clones. Underlying CV103's phenotype we identified a set of mutations that likely enhance glucose scavenging and maintain redox balance, but may do so at the expense of carbon excreted in overflow metabolites. Because these overflow metabolites serve as growth substrates that are differentially accessible to the other community members, and because the scavenging lineage shares only one SNP with these other clones, we conclude that this lineage likely served as an "engine" generating diversity by creating new metabolic niches, but not the occupants themselves.
遗传学的一个主要目标是定义表型与基因型之间的关系，而生态学的一个主要目标是确定支配群落组装的规则。通过分析自然系统来实现这些目标可能很困难，因为选择压力会创造出在空间和时间上都变化的动态适应度景观。实验室实验进化提供了控制塑造适应度景观的变量的好处，有助于实现这两个目标。我们之前表明，在持续葡萄糖限制下实验进化的大肠杆菌克隆群体产生了一个基因多样化的群落，该群落由一个克隆CV103组成，它能最佳地清除但不能完全利用有限资源，以及其他克隆CV101和CV116，它们消耗其溢流代谢物。由于这个群落可以被拆解和重新组装，并且涉及随时间稳定的合作相互作用，其遗传多样性是通过克隆强化而非克隆干扰来维持的。为了理解产生这一结果的遗传因素，并阐明群落的潜在生理学，我们对祖先克隆和进化克隆的基因组进行了测序。我们在中间代谢中鉴定出祖先突变，这些突变可能预先决定了代谢相互依赖的进化。系统发育重建表明，产生这个群落的谱系早期就发生了分化，因为CV103与其他进化克隆仅共享一个单核苷酸多态性。在CV103的表型之下，我们鉴定出一组可能增强葡萄糖清除并维持氧化还原平衡的突变，但这样做可能是以溢流代谢物中排出的碳为代价的。由于这些溢流代谢物作为其他群落成员可不同程度获取的生长底物，并且由于清除谱系与其他这些克隆仅共享一个单核苷酸多态性，我们得出结论，这个谱系可能作为一个“引擎”，通过创造新的代谢生态位而非占据者本身来产生多样性。
