Comparison of Larval Fish Detections Using Morphology-Based Taxonomy versus High-Throughput Sequencing for Invasive...

Area of Science:

• Ecology
• Genetics
• Ichthyology

Background:

• Invasive species detection is crucial for ecosystem management, but traditional methods like morphology-based taxonomy can be error-prone and miss early introductions.
• DNA barcoding combined with high-throughput sequencing (HTS) presents a potentially more sensitive and accurate alternative for species identification, especially for cryptic or early life stages.

Purpose of the Study:

• To quantify and compare the relative error rates of species detection between morphology-based and HTS-based taxonomic identification methods.
• To assess the effectiveness of HTS in detecting invasive and rare aquatic species, specifically ichthyoplankton in the Laurentian Great Lakes.

Main Methods:

• Ichthyoplankton samples were collected from the Port of Duluth, Minnesota, a known "hot-spot" for aquatic non-native species introductions.
• Taxonomic identification was performed using both traditional morphology-based methods and DNA barcoding coupled with high-throughput sequencing (HTS).
• Discrepancies between the two methods were analyzed to determine error rates and identify sources of taxonomic misidentification.

Main Results:

• HTS identified 28 species, while morphology identified 30 species, with 27 common to both. Family-level agreement was 76%, but species-level agreement dropped to 42%.
• The majority of taxonomic errors were attributed to morphology-based identification; HTS-based taxonomy demonstrated low error rates.
• Detection probabilities for non-native fish larvae using HTS were comparable to optimized surveys for juveniles and adults.

Conclusions:

• HTS-based DNA barcoding is a more accurate and reliable method for identifying ichthyoplankton and detecting invasive aquatic species compared to morphology-based taxonomy.
• Classifying taxonomic errors by comparing HTS results with morphology is a vital step towards integrating HTS into routine biodiversity and invasive species surveillance programs.
• This approach enhances the sensitivity and accuracy of detecting rare or newly introduced species in vulnerable aquatic ecosystems.