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在海洋脊椎动物eDNA研究中对分类学分类器的全面评估

Philipp E Bayer^1,2, Adam Bennett^1,2, Georgia Nester^1,2,3

¹Minderoo Foundation, Perth, Western Australia, Australia.

Molecular ecology resources

|April 17, 2025

概括

环境DNA (eDNA) 的元编码有助于调查海洋脊椎动物的生物多样性. 推使用MMSeqs2进行分类学分类,改善物种识别和减少错误阳性,以便进行可靠的eDNA分析.

科学领域:

海洋生物学海洋生物学
生物信息学是一种生物信息学.
保护科学保护科学

背景情况:

环境DNA (eDNA) 的元编码对于海洋脊椎动物生物多样性调查至关重要.
有许多计算工具和生物信息学方法用于eDNA分析.
需要可靠的基准来提高eDNA研究的准确性和可重复性.

研究的目的:

为了全面评估海洋脊椎动物eDNA元编码的九个分类学分类器.
评估澳大利亚海洋脊椎动物中三种线粒体标记物 (12S rDNA,16S rDNA,COI) 的性能.
建立最佳实践,以提高基于eDNA的生物多样性监测的可靠性.

主要方法:

利用模拟数据集与精心策划的参考和排除数据库来模仿各种物种组成.
在12S rDNA,16S rDNA和COI线粒体标记器中测试了9个分类学分类器.
采用阳性和阴性对照数据集来评估分类器的性能和对错误阳性的敏感性.

主要成果:

使用线粒体标记物识别了19%至89%的海洋脊椎动物物种.
对于12S和16SrDNA标记物,MMSeqs2和Metabuli的表现优于BLAST (10-11%高于F1得分).
纯粹的贝叶斯分类器 (例如,Mothur) 表现出色,除了COI,MMSeqs2表现出色.
与Kraken2.2相比,MMSeqs2和BLAST对虚假阳性反应的敏感性较低.

结论:

建议MMSeqs2用于海洋脊椎动物的分类学分类,由于改进了物种分配和减少了虚假阳性.
强调分类器选择对于准确的eDNA生物多样性评估的重要性.
旨在提高eDNA作为海洋脊椎动物保护工具的可靠性.

关键词:

环境 DNA DNA 环境 DNA 机器学习是机器学习.海洋生物多样性海洋生物多样性顺序对齐的顺序对齐.分类学分类器是分类学分类器.

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