PCI

PCI computes the probability of correct identification for fungal species by evaluating ITS-based DNA barcodes to quantify identification accuracy for taxa including Annulohypoxylon and Hypoxylon.

Key Features:

• Species Identification: Assesses species diversity using DNA barcoding of the Internal Transcribed Spacer (ITS) region.
• Data Integration: Incorporates ITS sequences from field-collected samples and GenBank to evaluate biases in barcode analysis.
• Alignment Methods: Compares multiple sequence alignment methods against pairwise alignments and assesses their effects on identification, ensuring compatibility with workflows such as the Barcode of Life Data System (BOLD).
• Evolutionary Distance Insensitivity: Evaluates the impact of different evolutionary distance metrics and demonstrates robustness of automated identification across those metrics.
• Cryptic Species Detection: Supports detection of cryptic species and delineation of monophyletic clades through phylogenetic analysis.

Scientific Applications:

• Biodiversity Assessment: Facilitates comprehensive biodiversity assessments by accurately identifying fungal species, applicable to regions such as Thailand's Indo-Burma hotspot.
• Secondary Marker Requirement: Indicates that while ITS sequences are informative, secondary markers may be necessary to enhance fungal barcoding accuracy in certain genera.
• Error Mitigation: Uses statistical methods to mitigate potential misidentifications by experts and to evaluate identification reliability.

Methodology:

Collect teleomorphs and generate ITS sequences; analyze ITS sequences using multiple sequence alignment techniques and pairwise alignments; examine the impact of different evolutionary distance metrics; integrate ITS data from field samples and GenBank; and apply phylogenetic analyses to support species delineation.