ASAP

ASAP performs species delimitation by automatically partitioning single-locus sequence alignments to propose species partitions based on pairwise genetic distances.

Key Features:

• Automatic partitioning of single-locus alignments: Partitions single-locus sequence alignments into candidate species groups grounded in evolutionary theory.
• Hierarchical clustering on pairwise genetic distances: Employs a hierarchical clustering algorithm that relies solely on pairwise genetic distances and avoids phylogenetic tree reconstruction.
• Scoring system: Implements a novel scoring system that ranks proposed species partitions without requiring prior information on intraspecific diversity.
• Efficiency and scalability: Capable of processing up to 10,000 sequences in minutes, enabling analysis of large barcode datasets.
• Comparative evaluation: Performance has been compared with ABGD, PTP, and GMYC across COI barcode data sets and via Monte-Carlo simulations under a multispecies coalescent framework.

Scientific Applications:

• Integrative taxonomy: Provides rapid initial species hypotheses to be tested with additional data in integrative taxonomic workflows.
• Biodiversity research: Enables delimitation of species-level units in large-scale DNA barcode surveys.
• Conservation biology: Supports identification of genetically distinct units for conservation prioritization.
• Ecological studies: Facilitates species-level diversity and community composition analyses using single-locus sequence data.

Methodology:

Computational methods explicitly include automatic partitioning of single-locus sequence alignments, hierarchical clustering using pairwise genetic distances, a scoring system to rank partitions, and comparative evaluations using Monte-Carlo simulations within a multispecies coalescent framework.