College of Wildlife Resources, Northeast Forestry University, China.
College of Wildlife Resources, Northeast Forestry University, China; State Forestry and Grassland Administration Detecting Center of Wildlife of China, China.
Forensic Sci Int Genet. 2019 May;40:85-95. doi: 10.1016/j.fsigen.2019.02.013. Epub 2019 Feb 13.
Species identification is fundamental to wildlife forensic practice. The desirability of molecular genetic methods is increasing rapidly. The sequence of a marker, rather than its particular diagnostic nucleotides, provides greater safety through comparisons between intra- and inter-specific pairwise genetic distances. However, it has not been well described how reliability of species assignment is influenced by distance computing methods and reference sample sizes. In this study, the influences were tested using 12 species from 4 genera of passerine birds and the sequences of partial Cytochrome b (Cyt b) and Cytochrome Oxidase subunit I (COI) genes. Results showed that different substitution types have different outcomes of pairwise genetic distance estimation and this influences the risk of false inclusion and exclusion. Transition (Ts) is the most effective substitution type to reveal optimal species resolution for both Cyt b and COI gene fragments no matter whether K2P and p-distance are used. Sample size required to accurately estimate pairwise distance is essentially determined by the genetic diversity of a species in reference to a given strictness of predefined acceptable accuracy. These findings suggest that for future forensic work on birds by use of Cyt b and COI gene fragments, transition should be used exclusively for marker validation and identification practice when targeting closely related species. Meanwhile, the reference database should sufficiently represent overall genetic diversity of the species. The minimum sample size should be estimated based on existing knowledge of genetic diversity. Special caution should be used for species assignment when only several reference data are available for animals that are considered likely to have high genetic diversity.
物种鉴定是野生动物法医实践的基础。分子遗传方法的需求正在迅速增加。标记的序列，而不是其特定的诊断核苷酸，通过比较种内和种间的遗传距离提供了更大的安全性。然而，对于距离计算方法和参考样本大小如何影响物种分配的可靠性，还没有很好地描述。在这项研究中，使用来自 4 个雀形目鸟类属的 12 个物种以及部分细胞色素 b（Cyt b）和细胞色素氧化酶亚基 I（COI）基因的序列测试了这些影响。结果表明，不同的替代类型对成对遗传距离估计有不同的结果，这会影响假包含和假排除的风险。无论是使用 K2P 还是 p-距离，转换（Ts）都是最有效的替代类型，可以揭示 Cyt b 和 COI 基因片段的最佳物种分辨率。准确估计成对距离所需的样本量本质上取决于物种的遗传多样性，而参考的是给定的可接受精度的严格程度。这些发现表明，对于未来使用 Cyt b 和 COI 基因片段对鸟类进行法医工作，在针对密切相关的物种进行标记验证和鉴定实践时，应专门使用转换；同时，参考数据库应充分代表物种的整体遗传多样性。最小样本量应根据遗传多样性的现有知识进行估计。当只有几个参考数据可用于被认为可能具有高遗传多样性的动物时，应特别注意物种分配。
