Data from: Reliable wolf-dog hybrid detection in Europe using a reduced SNP panel developed for non-invasively collected samples

Background: Understanding the processes that lead to hybridization of wolves and dogs is of scientific and management importance, particularly over large geographical scales, as wolves can disperse great distances. However, a method to efficiently detect hybrids in routine wolf monitoring is lacking. Microsatellites offer only limited resolution due to the low number of markers showing distinctive allele frequencies between wolves and dogs. Moreover, calibration across laboratories is time-consuming and costly. In this study, we selected a panel of 96 ancestry informative markers for wolves and dogs, derived from the Illumina CanineHD Whole-Genome BeadChip (174K). We designed very short amplicons for genotyping on a microfluidic array, thus making the method suitable also for non-invasively collected samples. Results: Genotypes based on 93 SNPs from wolves sampled throughout Europe, purebred and non-pedigree dogs, and suspected hybrids showed that the new panel accurately identifies parental individuals, first-generation hybrids and first-generation backcrosses to wolves, while second- and third-generation backcrosses to wolves were identified as advanced hybrids in almost all cases. Our results support the hybrid identity of suspect individuals and the non-hybrid status of individuals regarded as wolves. We also show the adequacy of these markers to assess hybridization at a European-wide scale and the importance of including samples from reference populations. Conclusions: We showed that the proposed SNP panel is an efficient tool for detecting hybrids up to the third-generation backcrosses to wolves across Europe. Notably, the proposed genotyping method is suitable for a variety of samples, including non-invasive and museum samples, making this panel useful for wolf-dog hybrid assessments and wolf monitoring at both continental and different temporal scales.

研究背景：解析灰狼与家犬的杂交机制兼具科学研究与管理实践价值，在大地理尺度下尤为关键，因灰狼具备长距离扩散的能力。但目前仍缺乏可应用于常规灰狼监测的高效杂交个体检测手段。微卫星标记（Microsatellites）的分辨率有限，仅能识别少数在灰狼与家犬间呈现显著等位基因频率差异的位点，且跨实验室的校准流程耗时耗本。本研究基于Illumina CanineHD全基因组芯片（Illumina CanineHD Whole-Genome BeadChip，174K位点），筛选出一套包含96个灰狼与家犬祖先信息标记的基因分型面板。我们设计了极短的扩增子（amplicon）以适配微流控阵列的基因分型流程，使该方法亦可用于非侵入式采集的样本。
研究结果：对全欧洲范围内采集的灰狼、纯种及非纯种家犬，以及疑似杂交个体的93个单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点进行基因分型，结果显示这套新型标记面板可准确识别亲本个体、一代杂交个体以及回交至灰狼的第一代回交个体，而几乎所有回交至灰狼的第二、三代回交个体均被归类为高级杂交个体。本研究结果验证了疑似个体的杂交身份，以及被认定为灰狼的个体并非杂交个体的结论。同时证实，该套标记足以在欧洲全域范围内评估杂交事件，且纳入参考种群样本具有重要意义。
研究结论：本研究表明，所提出的SNP标记面板是一款高效的杂交个体检测工具，可用于检测欧洲范围内直至回交至灰狼第三代的杂交个体。值得注意的是，该基因分型方法适配多种样本类型，包括非侵入式样本与博物馆馆藏样本，使得这套标记面板可用于跨大陆及不同时间尺度的灰狼-家犬杂交评估与灰狼监测工作。