Rodríguez-Ezpeleta Naiara, Bradbury Ian R, Mendibil Iñaki, Álvarez Paula, Cotano Unai, Irigoien Xabier
Marine Research Division, AZTI, Txatxarramend ugartea z/g, Sukarrieta 48395, Bizkaia, Spain.
Department of Fisheries and Oceans, St. John's, NF A1C 5X1, Canada.
Mol Ecol Resour. 2016 Jul;16(4):991-1001. doi: 10.1111/1755-0998.12518. Epub 2016 Mar 22.
Restriction-site-associated DNA sequencing (RAD-seq) and related methods are revolutionizing the field of population genomics in nonmodel organisms as they allow generating an unprecedented number of single nucleotide polymorphisms (SNPs) even when no genomic information is available. Yet, RAD-seq data analyses rely on assumptions on nature and number of nucleotide variants present in a single locus, the choice of which may lead to an under- or overestimated number of SNPs and/or to incorrectly called genotypes. Using the Atlantic mackerel (Scomber scombrus L.) and a close relative, the Atlantic chub mackerel (Scomber colias), as case study, here we explore the sensitivity of population structure inferences to two crucial aspects in RAD-seq data analysis: the maximum number of mismatches allowed to merge reads into a locus and the relatedness of the individuals used for genotype calling and SNP selection. Our study resolves the population structure of the Atlantic mackerel, but, most importantly, provides insights into the effects of alternative RAD-seq data analysis strategies on population structure inferences that are directly applicable to other species.
限制性内切酶位点相关DNA测序（RAD-seq）及相关方法正在彻底改变非模式生物群体基因组学领域，因为即使没有基因组信息，它们也能产生数量空前的单核苷酸多态性（SNP）。然而，RAD-seq数据分析依赖于对单个位点存在的核苷酸变异的性质和数量的假设，选择不当可能导致SNP数量估计不足或高估，和/或导致基因型错误判定。以大西洋鲭（Scomber scombrus L.）及其近亲大西洋竹荚鱼（Scomber colias）为案例研究，我们在此探讨群体结构推断对RAD-seq数据分析中两个关键方面的敏感性：将 reads 合并到一个位点时允许的最大错配数，以及用于基因型判定和SNP选择的个体之间的亲缘关系。我们的研究解析了大西洋鲭的群体结构，但最重要的是，提供了关于RAD-seq数据分析替代策略对群体结构推断影响的见解，这些见解可直接应用于其他物种。
