Close relatives in population samples: Evaluation of the consequences for genetic stock identification

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using Genetic Stock Identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that non-representative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated propo...

在众多生态、保护及管理相关场景中，明确混合种群样本内个体的起源均为关键环节。可借助遗传种群识别（Genetic Stock Identification, GSI）方法对遗传数据开展分析：该方法通过个体指派（Individual Assignment, IA）确定单个个体的起源，并利用混合种群分析（Mixed Stock Analysis, MSA）估算种群比例。此类分析需依赖参考基线中的等位基因频率数据。未知个体或混合比例会依据其多位点基因型在特定基线样本中出现的似然性，被指派至源种群。在设计并实施遗传种群识别分析时，对基线所涵盖的种群进行代表性采样至关重要。本研究以大西洋鲑（Salmo salar）的模拟基因型与实测基因型为材料，探究家系采样对遗传种群识别分析的影响。研究结果表明，若因非代表性采样导致参考基线中纳入近缘个体，则可能会对估算的种群比例（原文此处截断）引入偏差。