From metabarcoding to metaphylogeography: separating the wheat from the chaff.

Area of Science:

• Ecology and Evolutionary Biology
• Genetics
• Bioinformatics

Background:

• Metabarcoding is established for biodiversity assessment (α- and β-diversity).
• Hypervariable markers like COI offer untapped intraspecies (intra-MOTU) genetic information.
• COI is a traditional marker for population genetics and phylogeography.

Purpose of the Study:

• Introduce metaphylogeography: using metabarcoding for simultaneous intraspecies analysis.
• Develop and validate a computational protocol to clean metabarcoding data for phylogeographic inference.
• Assess intra- and interpopulation genetic variability across multiple species.

Main Methods:

• Developed a two-step cleaning protocol (denoising and abundance filtering) for COI metabarcoding data.
• Utilized entropy changes and sequence co-occurrence patterns for data cleaning.
• Applied the protocol to Mediterranean and Atlantic benthic community DNA, performing AMOVAs and haplotype network analyses.

Main Results:

• Successfully processed 563 MOTUs for phylogeographic inference.
• Genetic variability was primarily within samples but showed significant between-sea components.
• Identified intergroup differences in genetic variability within and between seas.
• Results for two species validated against Sanger sequencing data.

Conclusions:

• Metabarcoding data, after rigorous cleaning, can effectively infer intraspecies genetic variability for numerous species concurrently.
• Metaphylogeography offers a powerful new approach for basic biogeography, connectivity, and dispersal studies.
• This method has significant potential for applied fields like conservation genetics, invasion genetics, and protected area management.