Data from: Geographically structured genetic variation in the Medicago lupulina – Ensifer mutualism

Gene flow between genetically differentiated populations can maintain variation in species interactions, especially when population structure is congruent between interacting species. However, large-scale empirical comparisons of the population structure of interacting species are rare, particularly in positive interspecific interactions (mutualisms). One agriculturally and ecologically important mutualism is the partnership between legume plants and rhizobia. Through characterizing and comparing the population genomic structure of the legume Medicago lupulina and two rhizobial species (Ensifer medicae and E. meliloti), we explored the spatial scale of population differentiation between interacting partners in their introduced range in North America. We found high proportions of E. meliloti in southeastern populations and high proportions of E. medicae in northwestern populations. Medicago lupulina and the Ensifer genus showed similar patterns of spatial genetic structure (isolation by distance). However, we detected no evidence of isolation by distance or population structure within either species of bacteria. Genome-wide nucleotide diversity within each of the two Ensifer species was low, suggesting limited introduction of strains, founder events, or severe bottlenecks. Our results suggest that there is potential for geographically structured coevolution between M. lupulina and the Ensifer genus, but not between M. lupulina and either Ensifer species.

遗传分化种群间的基因流（gene flow）可维持物种相互作用的遗传变异，当相互作用物种的种群结构（population structure）一致时，该效应尤为显著。然而，针对相互作用物种的种群结构开展大规模实证比较的研究极为匮乏，针对正种间相互作用（互利共生，mutualisms）的此类研究更是稀缺。
豆科植物（legume plants）与根瘤菌（rhizobia）的共生体系是一类兼具农业与生态重要性的互利共生关系。本研究通过对引入北美分布区的天蓝苜蓿（Medicago lupulina）以及两种剑菌属（Ensifer）根瘤菌——梅氏剑菌（Ensifer medicae）与苜蓿剑菌（Ensifer meliloti）——的种群基因组结构（population genomic structure）进行解析与比较，探究了相互作用伙伴间的种群分化空间尺度。
结果显示，东南种群中苜蓿剑菌占比极高，西北种群则以梅氏剑菌为优势类群。天蓝苜蓿与剑菌属整体呈现相似的空间遗传结构模式，即距离隔离（isolation by distance）效应。然而，我们未在任一根瘤菌物种中检测到距离隔离或种群结构的相关证据。
两种剑菌属物种的全基因组核苷酸多样性（genome-wide nucleotide diversity）均处于较低水平，这暗示菌株引入规模有限、存在奠基者效应（founder events）或经历了严重的瓶颈效应（bottlenecks）。
本研究结果表明，天蓝苜蓿与剑菌属整体存在地理结构化协同进化（coevolution）的潜力，但天蓝苜蓿与任一单种剑菌之间则不具备该潜力。