Identifying and reducing AFLP genotyping error: an example of tradeoffs when comparing population structure in broadcast spawning versus brooding oysters

Phylogeographic inferences about gene flow are strengthened through comparison of co-distributed taxa, but also depend on adequate genomic sampling. Amplified Fragment Length Polymorphisms (AFLP) provide a rapid and inexpensive source of multilocus allele frequency data for making genomically robust inferences. Every AFLP study initially generates markers with a range of locus-specific genotyping error rates and applies criteria to select a subset for analysis. However, there has been very little empirical evaluation of the best tradeoff between culling all but the lowest-error loci to minimize overall genotyping error versus the potential for increasing population genetic signal by retaining more loci. Here, we used AFLPs to compare population structure in co-distributed broadcast spawning (Crassostrea virginica) and brooding (Ostrea equestris) oyster species. Using existing methods for almost entirely automated marker selection and scoring, genotyping error tradeoffs were evaluated by...

针对基因流的系统地理学推断，可通过比较同域分布类群得到强化，但此类推断同时依赖于充足的基因组采样。扩增片段长度多态性（Amplified Fragment Length Polymorphisms, AFLP）可快速且低成本地获取多位点等位基因频率数据，为开展具有基因组可靠性的推断提供支撑。所有AFLP研究最初都会生成具有不同位点特异性基因分型错误率的分子标记，并通过设定筛选标准选取部分标记用于后续分析。然而，目前极少有实证研究对最优权衡方案开展评估：即究竟是剔除除低错误率位点外的所有标记以最小化整体基因分型误差，还是保留更多位点以提升群体遗传信号强度。本研究利用AFLP技术，对同域分布的体外产卵型（美洲牡蛎 *Crassostrea virginica*）与育幼型（*Ostrea equestris*）两种牡蛎的群体结构进行了比较分析。本研究采用近乎全自动化的标记筛选与评分方法，通过……对基因分型误差的权衡方案进行了评估。