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.面向种群管理与物种保护，学界亟需快速且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学技术，可实现种群与个体水平遗传混合比例的精准估算，同时能鉴定出“超级入侵”等位基因——这类等位基因的基因渐渗速率远超全基因组背景水平，其成因大概率为自然选择。诸如限制性酶切位点相关DNA（Restriction-site Associated DNA, RAD）测序这类技术，可发掘并分型大量SNP位点，但受Illumina短读长测序产出的连续序列长度限制，其应用存在一定局限。本研究提出一种全新方法——重叠双端RAD测序，可生成长度超过300~400 bp的RAD重叠群。这些重叠群可提供充足的侧翼序列，用于设计高通量SNP基因分型芯片，同时支持严格过滤以鉴定重复的旁系同源位点。本研究将该方法应用于5个本土西坡割喉鳟种群，这些种群此前被检测出存在不同程度（低水平）的引入种虹鳟（Rainbow Trout, RBT）遗传混合。本研究共生成77141条RAD重叠群，并利用这些数据对此前已鉴定的3180个物种特异性SNP位点进行过滤与基因分型。本研究得到的种群与个体水平遗传混合估算结果，与此前基于相同个体的微卫星标记估算结果总体一致。但我们发现，基于全基因组标记的混合估算值略低，其成因可能包括：特定基因组区域受到自然选择的排斥、微卫星标记与RAD测序获得的SNP位点位于不同基因组区域，以及微卫星位点数量过少（n=7）带来的抽样误差。此外，本研究还在杂交割喉鳟种群中鉴定出源自虹鳟的候选适应性“超级入侵”等位基因，这类等位基因在杂交种群中表现出极高的遗传混合比例。