Data from: Evaluating the performance of selection scans to detect selective sweeps in domestic dogs

Selective breeding of dogs has resulted in repeated artificial selection on breed-specific morphological phenotypes. A number of quantitative trait loci associated with these phenotypes have been identified in genetic mapping studies. We analyzed the population genomic signatures observed around the causal mutations for 12 of these loci in 25 dog breeds, for which we genotyped 25 individuals in each breed. By measuring the population frequencies of the causal mutations in each breed, we identified those breeds in which specific mutations most likely experienced positive selection. These instances were then used as positive controls for assessing the performance of popular statistics to detect selection from population genomic data. We found that artificial selection during dog domestication has left characteristic signatures in the haplotype and nucleotide polymorphism patterns around selected loci that can be detected in the genotype data from a single population sample. However, the sensitivity and accuracy at which such signatures were detected varied widely between loci, the particular statistic used, and the choice of analysis parameters. We observed examples of both hard and soft selective sweeps and detected strong selective events that removed genetic diversity almost entirely over regions >10 Mbp. Our study demonstrates the power and limitations of selection scans in populations with high levels of linkage disequilibrium due to severe founder effects and recent population bottlenecks.

犬类选择性育种的过程，引发了针对品种特异性形态表型的多轮人工选择。诸多与这类表型相关的数量性状位点（quantitative trait loci, QTL）已通过遗传定位研究得以鉴定。我们针对其中12个位点的因果突变周边区域的群体基因组特征开展了分析，分析样本涵盖25个犬品种，且每个品种均完成了25个个体的基因分型。通过测定各品种中因果突变的群体频率，我们鉴定出了特定突变极可能经历正向选择的犬品种。这些鉴定出的案例随后被用作阳性对照，用于评估常用群体基因组选择检测统计方法的性能。研究发现，犬类驯化过程中的人工选择在受选择位点周边的单倍型与核苷酸多态性模式中留下了特征性标记，这类标记可通过单一份群体样本的基因型数据被检测到。不过，这类标记的检测灵敏度与准确度，会因位点、所采用的统计方法以及分析参数的不同而存在显著差异。我们同时观测到了硬选择清除（hard selective sweep）与软选择清除（soft selective sweep）的案例，并检测到了在超过10兆碱基对的区域内几乎完全清除遗传多样性的强烈选择事件。本研究阐明了在因严重奠基者效应与近期群体瓶颈而呈现高度连锁不平衡的群体中，选择扫描方法的效能与局限性。