Phylogenetic Analysis and Species Delimitation of Lichenized Fungi

Phylogenetic analysis and species delimitation form the cornerstone of modern systematics in lichenized fungi, integrating molecular, morphological and ecological evidence to elucidate evolutionary relationships and define species boundaries. Multi-locus sequence data, often encompassing ribosomal and protein-coding markers, are analysed through both concatenation and coalescent frameworks to resolve lineage coherence and divergence. Such approaches have revealed extensive cryptic diversity, challenging traditional morphology-based taxonomy and uncovering novel lineages across major clades. Integrative methods combine statistical coalescent-based models with phenotype and geography to establish robust species hypotheses, while genomic techniques such as target enrichment and restriction-site associated DNA sequencing (RADseq) enable fine-scale resolution of rapid radiations and reticulate evolution. This body of work has global implications, informing conservation priorities, biogeographical inference and the use of lichens as bioindicators in changing environments.

Research from Nature Portfolio

Recent studies have applied phylogenomic approaches to two of the largest families of lichenized fungi, revealing contrasting diversification dynamics. In one analysis, time-calibrated phylogenies demonstrated that one family underwent a pronounced increase in speciation rate coincident with palaeoclimatic aridification, indicative of adaptive radiation into novel habitats, whereas its sister lineage exhibited a more constant, lower rate of lineage accumulation. In a second study, target enrichment of hundreds of single-copy nuclear genes exposed pervasive gene-tree discordance in a third family, attributable to rapid diversification and reticulate evolution near major geological transitions. These findings underscore the need for complementary analytical methods and highlight the complex historical processes shaping lichen evolution.

Phylogenetic Analysis and Species Delimitation of Lichenized Fungi publication trend

The graph below shows the total number of articles in phylogenetic analysis and species delimitation of lichenized fungi across all publications each year (not limited to Nature Index journals).

Technical terms

Phylogenetic analysis: The reconstruction of evolutionary relationships among taxa using molecular or morphological data.

Species delimitation: The process of defining biological species boundaries through genetic, morphological and ecological evidence.

Cryptic species: Distinct evolutionary lineages that exhibit little or no morphological differentiation.

Coalescent-based methods: Statistical models that trace gene genealogies back to common ancestors to infer species boundaries and demographic history.

Target enrichment: A genomic technique that isolates and sequences selected loci across the genome for high-resolution phylogenomic studies.

References

1. Species in lichen-forming fungi: balancing between conceptual and practical considerations, and between phenotype and phylogenomics. Fungal Diversity (2021).
2. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science. Persoonia (2023).
3. Global phylogeny of the family Gomphillaceae (Ascomycota, Graphidales) sheds light on the origin, diversification and endemism in foliicolous lineages. IMA Fungus (2025).
4. An Integrative Approach for Understanding Diversity in the Punctelia rudecta Species Complex (Parmeliaceae, Ascomycota). PLOS ONE (2016).
5. A Tale of Two Hyper-diversities: Diversification dynamics of the two largest families of lichenized fungi. Scientific Reports (2015).
6. Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group (Lobariaceae, Ascomycota). Scientific Reports (2019).