Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA.
Mol Biol Evol. 2022 Feb 3;39(2). doi: 10.1093/molbev/msab368.
Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality-encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality-most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.
群体遗传学旨在阐明塑造遗传变异的力量，通常基于基因组变异的单一快照。然而，利用多个采样时间来研究等位基因频率的变化，可以帮助澄清中性和非中性力量在短时间尺度上的相对作用。本研究比较了最近采集的黑腹果蝇自然种群样本的全基因组序列变异，与大约 35 年前从同一地点采集的样本进行了比较——这涵盖了大约 500 代的进化。这些时间点之间的等位基因频率变化表明，局部有效种群大小相对较小，约为 10000，明显小于该物种的全球有效种群大小。一些基因座显示出比中性情况下基因组中任何地方都更强的等位基因频率变化——最显著的是串联旁系同源基因 Cyp6a17 和 Cyp6a23，它们受到与拟除虫菊酯杀虫剂抗性相关的结构变异的影响。我们发现，在旧样本和新样本之间存在大量的遗传分化的异常值，但与窗口分化相比，可能有更多的适应目标影响了 SNP 水平的分化。我们还发现了证据表明纬度等位基因频率梯度的加强：在以前确定为渐变异常值的 SNP 上，与北部相关的等位基因频率平均增加了近 2.5%，但在随机 SNP 上没有观察到这种模式。该项目强调了利用多个采样时间点来研究进化在自然种群中如何运作的科学潜力，通过量化遗传变异在生态相关时间尺度上的变化来实现这一目标。
