Harrison Tia L, Stinchcombe John R, Frederickson Megan E
Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada.
Department of Biology, Queen's University, Kingston, Ontario K7L 3N6, Canada.
Mol Biol Evol. 2024 Dec 6;41(12). doi: 10.1093/molbev/msae245.
Rates of molecular evolution vary greatly among even closely related species. Although theory predicts that antagonistic interactions between species increase rates of molecular evolution, predictions for how mutualism affects evolutionary rates are mixed. We compared rates of molecular evolution between (i) mutualistic and non-mutualistic legumes, (ii) an independent set of symbiotic rhizobia and their non-symbiotic close relatives, and (iii) symbiotic and non-symbiotic clades within Ensifer, a diverse genus of bacteria with various lifestyles. We assembled transcriptomes de novo for 12 legume species and calculated dN/dS ratios at orthologous genes in all species to determine if genes in mutualistic plants evolve faster or slower than in their non-mutualistic relatives. We also calculated dN/dS ratios in genes known to be important for symbiosis. We found that mutualists have higher rates of molecular evolution genome-wide compared to non-mutualistic legumes, but this pattern did not hold in symbiosis genes. We next calculated dN/dS ratios in 14 bacteria species across the proteobacteria phylogeny that differ in whether they associate mutualistically with plants, using published data. In most pairs, symbiotic rhizobia show higher dN/dS values compared to their non-symbiotic relatives. Within a bacterial genus with many well-characterized mutualist species (Ensifer), we calculated dN/dS ratios in symbiotic and non-symbiotic clades and found that symbiotic lineages have higher rates of molecular evolution genome-wide, but not at genes on the symbiotic plasmid pSymB. Our results suggest that although mutualism between legumes and rhizobia is associated with elevated rates of molecular evolution genome-wide, symbiosis genes may be evolutionarily stagnant.
即使是亲缘关系很近的物种，其分子进化速率也有很大差异。虽然理论预测物种间的拮抗相互作用会提高分子进化速率，但关于共生关系如何影响进化速率的预测却莫衷一是。我们比较了以下几组的分子进化速率：（i）共生和非共生豆科植物；（ii）一组独立的共生根瘤菌及其非共生的近缘种；（iii）Ensifer属内的共生和非共生分支，Ensifer是一个具有多种生活方式的多样化细菌属。我们从头组装了12种豆科植物的转录组，并计算了所有物种直系同源基因的dN/dS比值，以确定共生植物中的基因进化速度比其非共生亲缘植物更快还是更慢。我们还计算了已知对共生很重要的基因的dN/dS比值。我们发现，与非共生豆科植物相比，共生植物在全基因组范围内具有更高的分子进化速率，但这种模式在共生基因中并不成立。接下来，我们利用已发表的数据，计算了14种变形菌门细菌的dN/dS比值，这些细菌在与植物共生关系上存在差异。在大多数配对中，共生根瘤菌的dN/dS值高于其非共生亲缘种。在一个有许多特征明确的共生菌种（Ensifer）的细菌属内，我们计算了共生和非共生分支的dN/dS比值，发现共生谱系在全基因组范围内具有更高分子进化速率，但在共生质粒pSymB上的基因并非如此。我们的结果表明，虽然豆科植物和根瘤菌之间的共生关系与全基因组范围内分子进化速率的提高有关，但共生基因在进化上可能停滞不前。
