Data from: Network structure and local adaptation in coevolving bacteria-phage interactions

Numerous theoretical and experimental studies have investigated antagonistic coevolution between parasites and their hosts. Although experimental tests of theory from a range of biological systems are largely concordant regarding the influence of several driving processes, we know little as to how mechanisms acting at the smallest scales (individual molecular and phenotypic changes) may result in the emergence of structures at larger scales, such as coevolutionary dynamics and local adaptation. We capitalized on methods commonly employed in community ecology to quantify how the structure of community interaction matrices, so called ‘bipartite networks’, reflected observed coevolutionary dynamics, and how phages from these communities may or may not have adapted locally to their bacterial hosts. We found a consistent nested network structure for two phage types, one previously demonstrated to exhibit arms race coevolutionary dynamics and the other fluctuating coevolutionary dynamics. Both phages increased their host ranges through evolutionary time, but we found no evidence for a trade off with impact on bacteria. Finally, only bacteria from the arms race phage showed local adaptation, and we provide preliminary evidence that these bacteria underwent (sometimes different) molecular changes in the wzy gene associated with the LPS receptor, while bacteria coevolving with the fluctuating selection phage did not show local adaptation and had partial deletions of the pilF gene associated with Type IV pili. We conclude that the structure of phage-bacteria interaction networks is not necessarily specific to coevolutionary dynamics, and discuss hypotheses for why only one of the two phages was, nevertheless, locally adapted.

诸多理论与实验研究均已探讨了寄生虫与其宿主间的拮抗协同进化（antagonistic coevolution）关系。尽管针对多种生物系统开展的理论实验检验，在若干驱动过程的影响方面已基本达成共识，但我们仍不清楚，微观尺度（单个分子与表型改变）的作用机制如何催生宏观尺度的协同进化动态与本地适应等结构。我们采用群落生态学领域的常用方法，量化了群落相互作用矩阵（即所谓的「二部网络（bipartite networks）」）的结构如何反映观测到的协同进化动态，以及这些群落中的噬菌体是否对其细菌宿主产生了本地适应。我们发现两种噬菌体类型均呈现出一致的嵌套网络结构：其中一种此前被证实存在军备竞赛式协同进化动态，另一种则呈现波动型协同进化动态。两种噬菌体均随进化时间拓展了宿主范围，但未发现其对细菌产生适应性权衡（trade-off）的相关证据。最终，仅来自军备竞赛噬菌体的细菌呈现出本地适应特征；我们还提供了初步证据表明，这些细菌在与脂多糖（lipopolysaccharide，LPS）受体相关的wzy基因中发生了（有时存在差异的）分子改变，而与波动选择噬菌体协同进化的细菌则未表现出本地适应，且其与IV型菌毛（Type IV pili）相关的pilF基因存在部分缺失。我们的研究结论表明，噬菌体-细菌相互作用网络的结构并非必然与协同进化动态一一对应；此外，我们还针对为何仅两种噬菌体中的一种产生了本地适应这一问题，探讨了相关假说。