A Comprehensive Survey of Progress in Fungal Taxonomy: Morphological Roots to Molecular Phylogenetics and Bioinformatic Frontiers

Abstract

The field of fungal taxonomy has undergone a transformative evolution with the advent of molecular phylogenetics and bioinformatics. This review surveys the significant strides made from traditional morphological classification to contemporary molecular approaches, which have improved species identification accuracy and resolved long-standing taxonomic ambiguities. We examine the integration of DNA barcoding with morphological techniques, leading to the discovery of new species and a refined understanding of fungal biodiversity. Furthermore, we delve into the potential of bioinformatics platforms and tools in advancing fungal taxonomy, including the application of transformer-based language models for sequence analysis. The review also explores ecological perspectives, highlighting the interplay between fungi and their environments, as well as genomic insights into fungal evolution and dispersal. Despite these advancements, we identify research gaps and propose a future agenda that includes the need for in-depth sampling, enhanced phylogenetic resolution, the development of specialized molecular databases, and a deeper exploration of fungal ecology and genetics. Our synthesis underscores the critical importance and challenges of integrating molecular data with traditional taxonomy for a holistic understanding of fungal systematics.