Data from: Parallel genome-wide fixation of ancestral alleles in partially outcrossing experimental populations of Caenorhabditis elegans

Experimental evolution studies, coupled with new advances in DNA sequencing technology, have become a powerful tool for exploring how populations respond to selection at the genomic level. Recent experiments in microbes typically have found evidence for multiple novel mutations, which are usually fixed. In contrast, in animal model systems, evolutionary responses seem to involve more modest changes in the frequencies of pre-existing alleles, probably because these populations outcross and are usually initialized with greater levels of standing variation. In this experiment, I used whole-genome rese- quencing to estimate allele frequencies and look for novel substitutions in experimentally evolved popu- lations of Caenorhabditis elegans. These populations were founded with a fixed pair of deleterious mutations introgressed into multiple wild genetic backgrounds and allowed to evolve for 50 generations with a mixed mating system. There is evidence for some recombination between ancestral haplotypes, but selective sweeps seem to have resulted in the fixation of large chromosomal segments throughout most of the genome. In addition, a few new mutations were detected. Simulations suggest that strong selection and low outcrossing rates are likely explanations for the observed outcomes, consistent with earlier work show- ing large fitness increases in these populations over 50 generations. These results also show clear parallels to population genetic patterns in C. elegans in nature: recent selective sweeps, high linkage disequilibrium, and low effective recombination rates. Thus, the genomic consequences of selection depend heavily on the biology of the organism in question, including its mating system and levels of genetic variation.

实验进化研究结合DNA测序技术的最新进展，已成为探索种群在基因组水平响应选择过程的强大工具。针对微生物的近期相关实验通常可检测到多个新发突变的存在，且这些突变往往会在种群中被固定。与之形成鲜明对比的是，动物模型系统中的进化响应则更多表现为预先存在的等位基因频率发生小幅改变，这一现象可能源于此类种群采用异交繁殖策略，且初始种群携带更高水平的现存遗传变异。本实验采用全基因组重测序技术，对秀丽隐杆线虫（Caenorhabditis elegans）的实验进化种群进行等位基因频率估算，并搜寻其中的新发碱基替换。该实验种群以一对固定的有害突变为基础，将其渐渗至多个野生遗传背景中构建而成，并在混合交配系统下经历了50代的进化。有证据显示祖先单倍型之间存在一定程度的重组，但选择性清除似乎使得基因组大部分区域的大片染色体区段被固定下来。此外，本研究还检测到了少量新发突变。模拟实验结果表明，强选择作用与低异交率极有可能是本次观测到的进化结果的成因，这与此前的研究结论一致——该研究证实这些种群在50代的进化过程中适合度得到了大幅提升。本研究结果还与自然界中秀丽隐杆线虫的群体遗传模式存在显著相似性：近期发生的选择性清除、高连锁不平衡以及低有效重组率。由此可见，选择所产生的基因组效应在很大程度上取决于所研究生物的生物学特性，包括其交配系统与遗传变异水平。