Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment

• Published in: Ecology and evolution 2024-07, Vol.14 (7), p.e11631-n/a
• Main Authors: Turanov, S. V., Koltsova, M. A., Rutenko, O. A.
• Format: Article
• Language: English
• Subjects: Anthropogenic factors; aquatic biodiversity; Aquatic ecosystems; Aquatic environment; Biodiversity; Changing environments; COI; Conserved sequence; Crustaceans; Data analysis; Deoxyribonucleic acid; DNA; DNA barcoding; Ecological Genetics; Ecological studies; Ecosystem management; eDNA metabarcoding; Environmental changes; Environmental DNA; Genetic diversity; Genetic markers; Genetic testing; Genetic variability; Genomes; Human influences; intraspecific diversity; Invasive species; Mitochondrial DNA; Mollusks; Neural networks; Nucleotide sequence; NUMTs; Peter I, Tsar of Russia (1672-1725); Population; Shellfish; Taxonomy
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.11631

Intraspecific genetic variation is important for the assessment of organisms' resistance to changing environments and anthropogenic pressures. Aquatic DNA metabarcoding provides a non‐invasive method in biodiversity research, including investigations at the within‐species level. Through the analysis of eDNA samples collected from the Peter the Great Gulf of the Japan Sea, in this study, we aimed to evaluate the identification of Amplicon Sequence Variants (ASVs) in marine eDNA among abundant species of the Zostera sp. community: Hexagrammos octogrammus, Pholidapus dybowskii (Teleostei: Perciformes), and Pandalus latirostris (Arthropoda: Decapoda). These species were collected from two distant locations to produce mock communities and gather aquatic eDNA both on the community and individual level. Our approach highlights the efficacy of eDNA metabarcoding in capturing haplotypic diversity and the potential for this methodology to track genetic diversity accurately, contributing to conservation efforts and ecosystem management. Additionally, our results elucidate the impact of nuclear mitochondrial DNA segments (NUMTs) on the reliability of metabarcoding data, indicating the necessity for cautious interpretation of such data in ecological studies. Moreover, we analyzed 83 publicly available COI sequence datasets from common groups of multicellular organisms (Mollusca, Echinodermata, Crustacea, Polychaeta, and Actinopterygii). The results reflect the decrease in population diversity that arises from using the metabarcode compared to the COI barcode. Intraspecific genetic variation is crucial for understanding organisms' resilience to environmental changes. This study utilized aquatic DNA metabarcoding to assess genetic diversity within the Zostera sp. community in the Japan Sea. By analyzing eDNA samples, we identified Amplicon Sequence Variants (ASVs) in Hexagrammos octogrammus, Pholidapus dybowskii, and Pandalus latirostris. Our findings emphasize the effectiveness of eDNA metabarcoding in capturing haplotypic diversity and highlight the impact of nuclear mitochondrial DNA segments on data reliability.