DNA metabarcoding assessment of Neotropical ichthyoplankton communities is marker-dependent

Area of Science:

• Ichthyology
• Molecular Ecology
• Environmental DNA (eDNA) analysis

Background:

• Ichthyoplankton studies are crucial for understanding fish reproductive dynamics and community structure.
• DNA metabarcoding offers a powerful tool for rapid, cost-effective, and simultaneous identification of multiple fish species.
• Challenges in DNA metabarcoding include marker selection, primer bias, database completeness, and accurate abundance inference.

Purpose of the Study:

• To compare the effectiveness of three DNA metabarcoding markers (COI, NeoFish, MiFish) for identifying Neotropical ichthyoplankton.
• To evaluate marker performance in terms of resolution, sensitivity, specificity, and relative read abundance (RRA) recovery.
• To assess the benefits of combining multiple markers for enhanced taxonomic coverage.

Main Methods:

• DNA metabarcoding analysis of 30 ichthyoplankton pools from a Neotropical river.
• Comparison of three molecular markers: standard COI fragment (650 bp) and two short 12S rRNA gene markers (NeoFish and MiFish, ~200 bp).
• Evaluation of marker performance metrics including detection rates, resolution, sensitivity, specificity, and RRA.

Main Results:

• The combined use of the three markers increased ichthyoplankton genera detection rates by 25%–87.5%.
• This multi-marker approach provided broader taxonomic coverage and more robust identification of complex communities.
• Relative read abundance (RRA) varied significantly depending on the marker used, highlighting potential biases in abundance estimations.

Conclusions:

• Combining COI, NeoFish, and MiFish markers significantly enhances the taxonomic resolution and coverage for Neotropical ichthyoplankton identification.
• Researchers should exercise caution when interpreting relative read abundance (RRA) as a proxy for species abundance in PCR-dependent metabarcoding protocols.
• Optimizing marker selection and database quality is essential for accurate and comprehensive fish community assessments using DNA metabarcoding.