Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing

Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of ‘super invasive’ alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.种群管理与生物保护领域迫切需要快速、低成本的全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）发掘与基因分型方法。在杂交种群中，能够识别并分型数千个物种特异性标记的基因组技术，可实现种群与个体水平混血比例的精准估算，同时鉴定出“超级入侵”等位基因——这类等位基因的渐渗速率高于全基因组背景水平，推测由自然选择驱动。诸如限制性酶切位点相关DNA（restriction-site-associated DNA, RAD）测序的技术虽可发掘并分型大量SNP，但受Illumina短读长测序产出的连续序列长度限制，其应用仍存在局限。本研究提出一种全新策略：重叠双端RAD测序，可生成长度超过300~400碱基对（base pair, bp）的RAD重叠群。这些重叠群可提供足够的侧翼序列，用于设计高通量SNP基因分型芯片，并通过严格过滤识别重复的旁系同源位点。我们将该方法应用于5个本土西坡割喉鳟种群，这些种群此前已被检测出不同程度（低水平）的引入种虹鳟（rainbow trout, RBT）混血现象。本研究共获得77141个RAD重叠群，并利用这些数据筛选并分型了3180个此前已鉴定的物种特异性SNP位点。种群与个体水平的混血估算结果，与基于相同个体的微卫星（microsatellite）评估结果总体一致。不过我们观察到，基于全基因组标记的混血估算值略低于微卫星方法的结果，这可能源于多方面因素：特定基因组区域受到自然选择排斥、微卫星标记与RAD来源SNP的基因组位置存在差异，以及微卫星位点数量较少（n=7）带来的抽样误差。此外，我们还在杂交鳟种群中鉴定出来自RBT的候选适应性超级入侵等位基因，其在种群中的混血比例异常偏高。