Early evolution of mutualism is characterized by big and predictable adaptive changes, including the specialization of interacting partners, such as through deleterious mutations in genes not required for metabolic cross-feeding. We sought to investigate whether these early mutations improve cooperativity by manifesting in synergistic epistasis between genomes of the mutually interacting species. Specifically, we have characterized evolutionary trajectories of syntrophic interactions of Desulfovibrio vulgaris (Dv) with Methanococcus maripaludis (Mm) by longitudinally monitoring mutations accumulated over 1000 generations of nine independently evolved communities with analysis of the genotypic structure of one community down to the single-cell level. We discovered extensive parallelism across communities despite considerable variance in their evolutionary trajectories and the perseverance within many evolution lines of a rare lineage of Dv that retained sulfate-respiration (SR+) capability, which is not required for metabolic cross-feeding. An in-depth investigation revealed that synergistic epistasis across pairings of Dv and Mm genotypes had enhanced cooperativity within SR− and SR+ assemblages, enabling their coexistence within the same community. Thus, our findings demonstrate that cooperativity of a mutualism can improve through synergistic epistasis between genomes of the interacting species, enabling the coexistence of mutualistic assemblages of generalists and their specialized variants.

互利共生的早期进化以巨大且可预测的适应性变化为特征，包括相互作用伙伴的专业化，例如通过代谢交叉喂养不需要的基因的有害突变。我们试图研究这些早期突变是否通过在相互作用物种的基因组之间表现出协同上位性来改善协同性。具体来说，我们已经表征了Desulfovibrio vulgaris ( Dv ) 与Methanococcus maripaludis ( Mm) 通过纵向监测九个独立进化社区的 1000 多代积累的突变，分析一个社区的基因型结构，直至单细胞水平。我们发现群落之间存在广泛的平行性，尽管它们的进化轨迹存在相当大的差异，并且在保留硫酸盐呼吸 (SR+) 能力的罕见Dv谱系的许多进化线中坚持不懈，这不是代谢交叉喂养所必需的。一项深入的调查表明，跨Dv和Mm配对的协同上位性基因型增强了 SR- 和 SR+ 组合内的协同性，使它们能够在同一社区内共存。因此，我们的研究结果表明，互利共生的协同性可以通过相互作用物种的基因组之间的协同上位性来改善，从而使通才的互惠组合及其专门变体共存。