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单核苷酸多态性(SNP)分子标记结合二代测序技术是研究群体遗传学强有力的工具,同时也是界定物种的最佳方法之一。与以往获取SNPs数据的常用方法相比,靶基因富集的方法可以用来富集不同物种的同源片段,甚至可以用于部分降解的DNA。本研究应用一套通用的脊椎动物单拷贝核基因标记,通过基因富集和Illumina测序获取鲱形目鲚属数千个SNPs位点。样本取自靠近长江入海口的沿海地区、长江干流和洞庭湖。用STRUCTURE和Bayes factor delimitation(*with genomic data,BFD*:一种新的物种界定工具)分析SNPs数据,发现洞庭湖的短颌鲚显著不同于其他采样点的样本,而从沿海地区采集的刀鲚与长江干流的个体之间的差异不明显(Bayes factor=11.3)。研究表明,基因富集可以用来获得非模式生物的SNPs数据,结合新的分析工具如BFD*可用于物种界定。
Single nucleotide polymorphism (SNP) molecular markers combined with second-generation sequencing is a powerful tool for studying population genetics and is one of the best ways to define species. Compared with the conventional methods for obtaining SNPs data, the target gene enrichment method can be used to enrich homologous fragments of different species and can even be used for partially degraded DNA. In this study, a common set of single-copy nuclear gene markers of vertebrates was used to obtain thousands of SNPs from the genus Meretrix by gene enrichment and Illumina sequencing. Samples taken from the coastal areas near the mouth of the Yangtze River, the Yangtze River and Dongting Lake. Analysis of SNPs using STRUCTURE and Bayes factor delimitation (* with genomic data, BFD *: a new species-defining tool) found that the short-jaw ridges in Dongting Lake were significantly different from those of the other sampling points, while the knives collected from the coastal areas There was no significant difference between individuals in the Yangtze River and those in the Yangtze River (Bayes factor = 11.3). Studies have shown that gene enrichment can be used to obtain SNPs for non-model organisms, combined with new analytical tools such as BFD * for species definition.