Suffering makes you weaker: limited evolutionary adaptation in competitively inferior populations

Data collected from an experimental evolution project.<br>54 evolution lines, including 18 <i>E. coli</i> monoculture lines, 18 <i>P. fluorescens</i> monoculture lines and 18 coculture lines were studied. Each line were propagated at three temperatures. Nine incubators were used in this study, and randomly divided into three blocks. The three incubators in each block were set 19, 26 and 31°C. There were two within-incubator replicate microcosms for each species composition. Therefore, a total of 36 evolution lines were established for each species (2 culture types × 3 blocks × 3 temperatures × 2 within-incubator replicates).<br>Population density was measured as colony formation units per ml.<br>Fitness of each evolved population against it ancestral strain at each of the three temperatures (19, 26 or 31°C) was measured by competition experiment. Fitness of evolved <i>E. coli</i> populations and their ancestor, all of the strain REL606, relative to a reference strain, REL606Ara+, was measured by head-to-head competition assays. Fitness of evolved and ancestral <i>P. fluorescens</i> populations, all of the strain SBW25EeZY6KX, was measured against a reference strain SBW25. Relative fitness of each tested population against the reference strain was estimated from the Malthusian parameters. Fitness of each evolved population relative to its ancestor (change in fitness during the evolution experiment) was calculated as difference between the two, analogous to the selection coefficient index.<br>Population-level competitive effect of an effect species on a response species could be estimated by the relative yield (RY) of the response species, that is, the ratio of its biomass in cocultures to that in monocultures. Interspecific effects of the ancestral and evolved <i>E. coli</i> (B REL606) populations on the ancestral <i>P. fluorescens</i> (SBW25EeZY6KX) strain were measured. And RY of the response population was calculated. The difference in competitive effects between evolved <i>E. coli</i> and the ancestral strain was then estimated as RY of ancestral <i>P. fluorescence</i> in the presence of evolved <i>E. coli</i> minus that in the presence of ancestral <i>E. coli</i>. This was termed as “change in interspecific effect”. Changes in interspecific effects of <i>P. fluorescens</i> populations were measured using the same method.

本数据集源自一项实验进化研究项目。本研究共纳入54个进化谱系，包括18株大肠杆菌（E. coli）单培养谱系、18株荧光假单胞菌（P. fluorescens）单培养谱系及18株共培养谱系。所有谱系均在三种温度条件下进行传代培养。本研究使用9台培养箱，随机划分为3个区组，每个区组内的3台培养箱分别设置为19℃、26℃和31℃。针对每种物种组合，每台培养箱内设置2个重复微宇宙体系。因此，针对每类实验物种，共构建了36个进化谱系（2种培养模式×3个区组×3个温度×2个培养箱内重复体系）。
种群密度以每毫升菌落形成单位（colony formation units, CFU）进行测定。
在三种温度（19℃、26℃、31℃）下，通过竞争实验分别测定各进化种群相对于其祖先菌株的适合度。对于进化的大肠杆菌种群及其祖先菌株（均为REL606株），其相对于参考菌株REL606Ara+的适合度通过一对一竞争实验进行测定。对于进化的及祖先的荧光假单胞菌种群（均为SBW25EeZY6KX株），其相对于参考菌株SBW25的适合度通过竞争实验测定。各待测种群相对于参考菌株的相对适合度通过马尔萨斯参数进行估算。将各进化种群相对于其祖先菌株的适合度（即进化实验过程中适合度的变化量）计算为二者的差值，该指标类似于选择系数。
某作用物种对响应物种的种群水平竞争效应，可通过响应物种的相对产量（relative yield, RY）进行估算，即共培养体系中该物种的生物量与单培养体系中该物种生物量的比值。本研究测定了祖先及进化的大肠杆菌（REL606株）种群对祖先荧光假单胞菌（SBW25EeZY6KX株）菌株的种间相互作用效应，并计算了响应种群的相对产量。进化大肠杆菌与祖先大肠杆菌的竞争效应差异，通过祖先荧光假单胞菌在进化大肠杆菌存在条件下的相对产量减去其在祖先大肠杆菌存在条件下的相对产量进行估算，该差值被定义为“种间效应变化量”。针对荧光假单胞菌种群的种间效应变化，采用相同方法进行测定。