Extracting abundance information from DNA-based data

The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to the reconstruction of diets and quantitative foodwebs, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, capture bias, capture noise, species pipeline biases, and pipeline noise all combine to inject error into DNA-based datasets. This review focuses on methods for correcting the latter two error sources, as the first two are addressed extensively in the ecological survey literature. To extract abundance information from DNA-based data, it is useful to distinguish two concepts. (1) Across-species quantification describes relative species abundances within a single sample. (2) In contrast, within-species quantification describes how the abundance of each individual species varies across sam...从基于DNA的测序数据（元条形码（metabarcoding）、宏基因组学（metagenomics））中精准提取物种丰度信息，可有效助力饮食结构重构、定量食物网构建、物种互作推断、种群动态与物种分布建模、环境状态及变化的生物监测，以及假阳性与假阴性结果的推断。然而，捕获偏差、捕获噪声、物种分析流程偏差与分析流程噪声共同会向基于DNA的数据集引入误差。本综述聚焦于校正后两类误差来源的方法，因前两类误差已在生态学调查文献中得到广泛探讨。若要从基于DNA的测序数据中提取丰度信息，需区分两个核心概念：(1) 跨物种定量，指单一样本内各物种的相对丰度；(2) 种内定量，与之相对，指单个物种的丰度在不同样本间的变化……