JAMP

JAMP processes community DNA metabarcoding data, including COI amplicon datasets, to extract haplotypes and assess intraspecific genetic diversity for biomonitoring and phylogeographic analyses.

Key Features:

• Modular integration: Integrates functions from USEARCH, VSEARCH, and CUTADAPT within the R programming environment for flexible analysis.
• Haplotype extraction: Employs sequence denoising strategies used in microbial research combined with abundance-based filtering to extract haplotypes from COI amplicon datasets.
• OTU clustering with intraspecific retention: Clusters reads into operational taxonomic units (OTUs) while retaining intraspecific diversity information.
• Error mitigation and filtering calibration: Applies denoising and abundance-based filtering to address sequencing errors and to balance sensitivity versus specificity.
• Application scope: Tailored for freshwater macroinvertebrate metabarcoding data but adaptable to other taxa.
• Automation and summary statistics: Automates folder creation and generation of summary statistics within the R environment.

Scientific Applications:

• Biomonitoring: Enables assessment of species composition and underlying intraspecific genetic diversity in ecological monitoring studies.
• Phylogeographic studies: Provides haplotype distributions and population-structure information to support hypotheses about taxon dispersal.
• Population genetics: Identifies population structure and potentially isolated populations or taxa that merit targeted phylogeographic or conservation analysis.

Methodology:

Integrates USEARCH, VSEARCH, and CUTADAPT within R, applies sequence denoising strategies and abundance-based filtering to address sequencing errors, extracts haplotypes from COI amplicon datasets, and clusters reads into OTUs while retaining intraspecific diversity.