Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

Area of Science:

• Biodiversity research
• Genomics
• Entomology

Background:

• Over 80% of animal species are unknown, primarily small, diverse tropical organisms.
• Morphological identification is slow for species-rich, abundant taxa.
• Low-cost, accessible DNA barcoding is needed for rapid species discovery.

Purpose of the Study:

• To demonstrate MinION sequencing for large-scale species discovery in the hyperdiverse Phoridae fly family.
• To develop and validate a cost-effective MinION DNA barcoding pipeline.
• To assess the accuracy and utility of MinION for identifying molecular operational taxonomic units (mOTUs).

Main Methods:

• Sequenced 7059 Phoridae specimens using an optimized low-cost MinION pipeline.
• Utilized 1D sequencing and resequencing for increased barcoding capacity.
• Performed morphological verification of identified mOTUs.

Main Results:

• Discovered over 650 new phorid species from a single trap in Uganda, exceeding current regional records.
• Achieved high accuracy (99.99%) and low Ns (0.46%) with MinION barcodes.
• Confirmed 93% congruence between mOTUs and morphology, with 90% of species in the genus Megaselia.

Conclusions:

• A single African site may host ~1000 phorid species, with potential Afrotropical diversity exceeding 200,000.
• Low-cost MinION sequencing is suitable for rapid, large-scale species discovery in hyperdiverse taxa.
• This technology can reveal unknown biodiversity, especially in biodiverse countries with limited lab resources.