Crust Fungi Clock: Ancient White-Rot Genus Phanerochaete Traced Back 100 Million Years

Hidden beneath the bark of fallen branches across the world’s forests lies a group of fungi that most hikers never notice and few could name. These crust fungi, pressed flat against dead wood like dried paint, belong to the genus Phanerochaete, one of the most ecologically important lineages of wood-decaying organisms on Earth. Now, an integrative study published in IMA Fungus has delivered the most complete evolutionary portrait of the genus to date, combining a five-gene phylogeny, molecular clock dating and historical biogeographic reconstruction. The headline finding is striking: Phanerochaete originated roughly 100 million years ago, during the Early Cretaceous, meaning these unassuming white-rot fungi were dismantling wood while dinosaurs still dominated the planet.

The research team, led by Minwoo Cho and Jae-Jin Kim, analysed 72 specimens collected throughout the Republic of Korea between 2010 and 2024, alongside a global sampling of reference sequences including type-derived material. Among the Korean collections, the multi-locus analysis revealed 14 phylogenetically distinct species, two of which proved to be entirely new to science. The first, Phanerochaete koreana, is characterised by a leathery, coriaceous basidiome and, unusually for the genus, the complete absence of leptocystidia, the sterile cells that most of its relatives produce. The second, Phanerochaete membranacea, presents ochraceous, membranous fruiting bodies and leptocystidia heavily encrusted with crystals. Both species were found growing on dead angiosperm branches, including Mongolian oak, in Korean forests from southern lowlands to northern mountains.

What makes the study methodologically significant is its departure from the standard two-marker approach. Most recent work on Phanerochaete has relied on the nuclear ribosomal internal transcribed spacer (ITS) and the nuclear large subunit ribosomal DNA (nLSU), the workhorse barcodes of fungal taxonomy. The new study added three protein-coding loci: translation elongation factor 1-alpha (tef1) and the two largest subunits of RNA polymerase II, rpb1 and rpb2. The resulting five-gene dataset spanned 111 taxa and 4,810 aligned characters, of which 1,547 were parsimony-informative, providing substantially greater resolving power than ITS and nLSU alone. Maximum likelihood and Bayesian analyses of this concatenated dataset recovered three well-supported clades within the genus, and the authors note that protein-coding markers such as tef1 are essential for delimiting closely related species complexes where ITS variation is limited or polymorphic.

The taxonomic context matters here. Phanerochaete was established by Karsten in 1889 and typified by P. alnea, but the twentieth century saw a sprawling, ill-defined genus that became a dumping ground for crust-like corticioid fungi. DNA-based analyses later revealed that Phanerochaete as broadly construed was polyphyletic, with species scattered across three different families within the phlebioid clade of the order Polyporales: Irpicaceae, Meruliaceae and Phanerochaetaceae. Subsequent revisions have re-assigned many former members to other genera, including Ceriporia, Efibula, Hydnophanerochaete, Hydnophlebia, Luteochaete, Phaeophlebiopsis, Phanericium, Phanerochaetella, Phaneroites, Phlebiopsis, Rhizochaete and Scopuloides. Today, databases list 212 species names under Phanerochaete, of which 127 are currently accepted, yet sequence data exist for only 87 of those accepted species, leaving 40 known solely from morphology.

That gap in molecular coverage is precisely why the new phylogeny is valuable. The combined ITS and nLSU dataset comprised 151 taxa and 1,882 aligned characters, and the analyses confirmed that all 72 Korean specimens belonged to core Phanerochaete. Previously described species shared 99.11 to 100.00 percent ITS sequence identity with authoritative reference sequences, while the two novel species showed markedly lower similarity to their closest relatives, 95.77 to 97.58 percent for ITS and 98.89 to 99.22 percent for nLSU, supporting their recognition as distinct taxa. For species described before the era of DNA sequencing, such as P. australis, P. laevis and P. sordida, the team used sequences from well-documented specimens in earlier phylogenetic studies as reference points, a pragmatic solution to the persistent problem of unsequenced type material.

The divergence time estimates place the story in deep geological time. Using BEAST with an uncorrelated lognormal relaxed clock and a Yule speciation prior, the researchers calibrated their tree with two Cretaceous fossils: Archaeomarasmius leggetti, an agaric preserved in amber that constrains the minimum age of Agaricales, and Quatsinoporites cranhamii, a poroid hymenochaetoid fossil constraining the minimum age of Hymenochaetales. The analysis suggested that the class Agaricomycetes extends back to the Early Permian, around 294.30 million years ago, while the family Phanerochaetaceae reached a mean crown age of 163.38 million years in the Late Jurassic. The genus Phanerochaete itself emerged in the Early Cretaceous, with a mean stem age of 111.66 million years and a mean crown age of 101.66 million years, bounded by a 95 percent highest posterior density interval of 98.38 to 104.86 million years.

Within the genus, the three major clades all originated during the Late Cretaceous, with mean crown ages of 85.80, 77.48 and 79.97 million years respectively, and Phanerochaete chrysosporium, the famous model white-rot fungus, was inferred as the first species to diverge. Species-level diversification then unfolded mainly from the Palaeogene to the Neogene, with some lineages remarkably young: P. argillacea, P. canolutea and P. robusta date only to the Pleistocene, while others, such as P. cacao at 58.66 million years, are Palaeocene survivors. The timing is evolutionarily suggestive. Angiosperms emerged in the Late Jurassic and expanded dramatically after the Late Cretaceous mass extinction, replacing gymnosperm-dominated forests. Because the overwhelming majority of Phanerochaete species, 90 of the accepted species including both new Korean taxa, occur exclusively on angiosperm hosts, the authors propose that the genus’s post-Cretaceous diversification may be linked to the rise of flowering trees and the wood they shed.

The biogeographic reconstruction adds a continental dimension to the story. Using the Bayesian Binary MCMC method in RASP, with the world divided into six regions, the analysis identified Asia as the most probable centre of origin for Phanerochaete, with high probabilities of Asian ancestry at most internal nodes. From this Asian cradle, the genus repeatedly dispersed outward, particularly to North America and Europe, while dispersal to Africa, Oceania and South America remained rare. The three clades, however, tell different stories. Clade III, containing widespread species such as P. chrysosporium, P. concrescens and P. magnoliae, showed frequent intercontinental movement, whereas Clades I and II were largely restricted to Asia, with only limited long-distance dispersal in a handful of species. Several species in the Asian clades, including P. alnea, P. burtii and P. subceracea, carry Asian ancestral signatures but are now confined to Europe or North America, a pattern consistent with long-distance dispersal followed by independent diversification on each continent, alongside vicariance events between Asia and North America.

Beyond the evolutionary narrative, the study carries practical weight. Phanerochaete chrysosporium and P. carnosa are among the most intensively studied wood-decaying fungi on the planet, their genomes sequenced because they produce industrially significant ligninolytic and cellulolytic enzymes, including lignin peroxidases, manganese peroxidases and glyoxal oxidases, that can break down lignin, the polymer that makes wood resistant to decay. Understanding how the genus diversified, which hosts it prefers and where its lineages originated therefore informs both biotechnology and forest ecology. The authors also compiled a taxonomic key to the 13 Phanerochaete species now known from Korea, and their morphological survey showed that cystidia, the encrusted or smooth sterile cells that vary widely across species, along with hymenial surface texture, remain useful characters for distinguishing species, even though hymenial features appear to reflect phylogenetic tendencies rather than absolute diagnostic rules.

The study is candid about its limitations. Forty of the 127 accepted species still lack any sequence data, and the concentration of sequenced type localities in Asia could introduce geographic sampling bias, although the distribution of type localities proved similar between sequenced and unsequenced species, lending support to the Asian origin hypothesis. The authors also flag several species currently placed in Phanerochaete, including P. daliensis, P. hiulca, P. tamariciphila and P. tongbiguanensis, whose phylogenetic positions suggest they may belong elsewhere, indicating that the generic concept still requires refinement. What the work ultimately delivers is a template for how mycology is changing: rather than describing a new species from a single specimen and a barcode, the field is moving toward integrative studies that weave morphology, multi-locus phylogenetics, molecular clocks and biogeography into a single evolutionary framework. For Phanerochaete, that framework now stretches back 100 million years, from Cretaceous forests to the oak branches of Korean national parks, with two new species joining the lineage along the way.

Subject of Research: Evolutionary history, divergence times and biogeography of the white-rot fungus genus Phanerochaete, with two new Korean species

Article Title: Phylogeny, divergence time and historical biogeography of Phanerochaete ( Basidiomycota , Polyporales ), with a description of two new species in Korea

Article References: Cho, M., Kwon, S. L., Yoo, Y., Lee, S. H., Kim, C., Lim, Y. W., & Kim, J.-J. (2026). Phylogeny, divergence time and historical biogeography of Phanerochaete (Basidiomycota, Polyporales), with a description of two new species in Korea. IMA Fungus, 17, Article e204198. https://doi.org/10.3897/imafungus.17.204198

Image Credits: AI Generated

DOI: 10.3897/imafungus.17.204198

Keywords: Phanerochaete, Polyporales, white-rot fungi, corticioid fungi, molecular clock, phylogenetics, biogeography, new species, Korea, ITS barcode, tef1, Cretaceous