Supplementary Data File 1

A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution, yet to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode experimental evolution animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. By varying the concentration of ivermectin in a liquid culture environment, we are able to precisely vary the effects of selection on these genes in populations with millions of individuals, yielding the largest animal experimental evolution study to date. The frequency of each barcode was determined at multiple time points via sequencing at deep coverage and then used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits.进化遗传学的一项基本原理是，单个基因座上选择的方向与强度随环境而异。带条形码的进化谱系追踪（barcoded evolutionary lineage tracking）是一种可用于实验进化研究中高通量测定选择作用的有力方法，但迄今为止该方法大多局限于微生物系统研究，主要因为条形码在动物体内的随机整合受限于生殖系的物理与分子保护机制。本研究借助秀丽隐杆线虫（Caenorhabditis elegans）中近年开发的TARDIS条形码系统（TARDIS barcoding system，Stevenson等人，2023），构建了首个随机插入基因组条形码的实验进化动物模型，并利用该系统精准测定了驱虫剂伊维菌素（anthelmintic compound ivermectin）的浓度对伊维菌素抗性基因盒选择强度的影响。此前已有研究证实，神经元表达的谷氨酸门控氯离子通道（GluCl channels）的三重敲除——avr-14、avr-15与glc-1——可赋予动物高浓度伊维菌素抗性。通过调控液体培养环境中的伊维菌素浓度，我们可在百万级个体的种群中精准调控这些基因所受选择的作用强度，由此开展了迄今为止规模最大的动物实验进化研究。我们通过高深度测序在多个时间点测定了每个条形码的频率，进而估算种群中各谱系的适合度（fitness）。低浓度伊维菌素环境下，抗性突变存在较高的适合度代价，会快速被野生型基因型淘汰；但当伊维菌素浓度超过2纳摩尔（2nM）时，选择天平便会向抗性突变倾斜。这种抗性权衡可能源于抗性个体的发育速率受阻。我们的研究结果表明，利用高通量条形码方法可通过秀丽隐杆线虫获得高精度的适合度估算结果，从而为进化与经济重要性状提供全新的研究视角。