Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations’ ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.

肺炎链球菌可分为许多菌株，每个菌株都是一组不同的分离株，它们共享相似的核心和附属基因组，它们在同一宿主内共同传播。先前的分析表明肺炎链球菌的短期疫苗相关动态菌株可能通过多基因座负频率依赖性选择 (NFDS) 介导，NFDS 将辅助基因座维持在平衡频率。长期模拟表明，NFDS 通过基于多态性频率、成对遗传距离和系统发育防止漂移引起的变异损失，稳定了克隆进化的多菌株种群。然而，允许在多位点 NFDS 下进化的分离株之间进行对称重组，产生了不同基因型的非结构化种群。当多位点 NFDS 与不对称的重组相结合时，观察到的数据的复制得到改善，有利于删除附属位点而不是插入。这种组合通过远交衰退将种群分离成品系，由具有减少的附属基因组的重组体产生，其适应性低于其亲本基因型。尽管重组的简单建模可能限制了这些模拟将基因组数据的某些特性保持为与缺乏重组的数据一样准确的能力，但不对称重组和多位点 NFDS 的组合可以从随机初始种群恢复多菌株种群结构。由于许多细菌会抑制插入其染色体，因此这种组合通常可能成为生态位内菌株共存的基础。不对称重组和多位点 NFDS 的结合可以从随机初始种群恢复多菌株种群结构。由于许多细菌会抑制插入其染色体，因此这种组合通常可能成为生态位内菌株共存的基础。不对称重组和多位点 NFDS 的结合可以从随机初始种群恢复多菌株种群结构。由于许多细菌会抑制插入其染色体，因此这种组合通常可能成为生态位内菌株共存的基础。