Rosa Rubicondior: Creationism In Crisis - How Fungi Created The Conditions For Land Plants

Top L. Chicken of the woods (Laetiporus sulphureus)

Top R. Sulphur tufts (Hypholoma fasciculare)

Bottom L. Common mould (Penicillium)

Bottom R. Mucor (microscopic view)

Fungi set the stage for life on land hundreds of millions of years earlier than thought | Okinawa Institute of Science and Technology OIST

In that vast expanse of pre-‘Creation Week’ history, when 99.9975% of Earth’s story had already unfolded, a pivotal event occurred that would set the planet on a path towards the astonishing diversity of life we see today. According to researchers led by scientists at the Okinawa Institute of Science and Technology, Japan, that turning point was the evolution of multicellular fungi.

Unlike animals and plants, in which multicellularity appears to have arisen only once, fungi seem to have achieved it independently on at least five separate occasions, between 1.4 and 0.9 billion years ago.

This innovation allowed fungi to colonise land and begin transforming bare rock and rock debris into soil. That process, in turn, created the conditions that later enabled plants to establish themselves on land.

In addition to shedding light on how multicellularity evolved in fungi — a process that involved horizontal gene transfer — this research significantly extends the known timeline of fungal evolution, pushing it back by hundreds of millions of years.

Of course, the authors of Genesis, unaware of the distinction between plants and fungi and apparently thinking all plants were angiosperms, made no mention of fungi at all. Their myth betrays no understanding that plants are living organisms or that green plants depend on sunlight for photosynthesis, since it describes them as being created the day before the sun (Genesis 1:15-17). It names only angiosperms while ignoring ferns, mosses, and algae (Genesis 1:11-12), and later claims that “every living substance” outside the Ark was destroyed (Genesis 7:4), as though plants, like rocks, would somehow have survived unscathed, to provide food for the animals afterwards, despite no mention of their preservation during the flood genocide.

Science, as ever, tells a very different story — one based not on gap-filling tales but on evidence written in fungal DNA and preserved in the fossil record. It is a story of awe and wonder, not at the supposed magical powers of an imagined creator, but at the relentless processes of evolution: variation, natural selection, and the exploitation of opportunity, producing the extraordinary biodiversity we see today.

Main Divisions of Fungi. Fungi are a diverse kingdom of eukaryotic organisms, divided into several major lineages. Molecular studies have clarified their relationships and evolutionary history.

Chytridiomycota (Chytrids)

The most basal (earliest-branching) fungal group.
Mostly aquatic; produce motile spores with flagella.
Important in decomposition; some species parasitic (e.g., on amphibians).

Blastocladiomycota

Close relatives of chytrids, also producing motile spores.
Distinct life cycle with alternation of generations.

They alternate between a haploid gametophyte phase and a diploid sporophyte phase.
Both phases are multicellular and independent, which is closer to what we see in plants than in most fungi.
By contrast, in most other fungi (e.g., Ascomycota, Basidiomycota), the haploid phase dominates. The diploid stage is fleeting, usually limited to the zygote formed by nuclear fusion, which immediately undergoes meiosis to restore the haploid state.

Zoopagomycota

Includes parasites and pathogens of animals, amoebae, and other fungi.
Related to the older “zygomycete” fungi, now split into separate groups.

Mucoromycota

Another branch formerly lumped into “zygomycetes.”
Includes moulds such as Rhizopus, often found on bread and fruit.
Some form important symbioses with plants (arbuscular mycorrhizae).

Glomeromycota

Obligate symbionts of plant roots (arbuscular mycorrhizae).
Critical in the colonisation of land by plants.
Reproduce asexually, but genetically diverse.

Ascomycota (Sac Fungi)

The largest fungal group.
Includes yeasts, morels, truffles, and many moulds.
Characterised by spore production in sac-like structures (asci).

Basidiomycota (Club Fungi)

Includes mushrooms, puffballs, rusts, and smuts.
Characterised by spores produced on club-shaped cells (basidia).
Important decomposers and plant symbionts.

Relationships

Chytrids and Blastocladiomycota: early-diverging fungi, retaining motile spores.
Zoopagomycota + Mucoromycota + Glomeromycota: once grouped as “Zygomycota,” now known to form separate but related lineages.
Ascomycota + Basidiomycota: together form the Dikarya, the most recently evolved and most diverse group, containing the majority of known fungi.

The Okinawa-led team’s findings are reported, open access, in the journal, Nature Ecology & Evolution, and summarised in a news release from the Okinawa Institute of Science and Technology.

Fungi set the stage for life on land hundreds of millions of years earlier than thought
From fossils and rare genetic ‘gene-swap’ clues, researchers reconstruct fungi’s deep timeline and reveal how they helped shape early Earth ecosystems.
New research published in Nature Ecology & Evolution sheds light on the timelines and pathways of evolution of fungi, finding evidence of their influence on ancient terrestrial ecosystems. The study, led by researchers from the Okinawa Institute of Science and Technology (OIST) and collaborators, indicates the diversification of fungi hundreds of millions of years before the emergence of land plants.

The five paths to a complex world

Associate Professor Gergely János Szöllősi, author on this study and head of the Model-Based Evolutionary Genomics Unit explains the foundations of this research.

Complex multicellular life — organisms made of many cooperating cells with specialized jobs — evolved independently in five major groups: animals, land plants, fungi, red algae, and brown algae. On a planet once dominated by single-celled organisms, a revolutionary change occurred not once, but at least five separate times: the evolution of complex multicellular life. Understanding when these groups emerged is fundamental to piecing together the history of life on Earth.

Associate Professor Gergely János Szöllősi, co-corresponding author.
Model-Based Evolutionary Genomics Unit
Okinawa Institute of Science and Technology Graduate University
Okinawa, Japan.

Emergence here was not simply a matter of cells clumping together; it was the dawn of organisms, where cells took on specialized jobs and were organized into distinct tissues and organs, much like in our own bodies. This evolutionary leap required sophisticated new tools, including highly developed mechanisms for cells to adhere to one another and intricate systems for them to communicate across the organism, and arose independently in each of the five major groups.

The difficulties of dating evolutionary divergence

For most of these groups, the fossil record acts as a geological calendar, providing anchor points in deep time. For example, red algae show up possibly as early as about 1.6 billion years ago (in candidate seaweed-like fossils from India); animals appear by around 600 million years ago (Ediacaran fossils such as the quilted pancake like Dickinsonia); land plants take root roughly 470 million years ago (tiny fossil spores); and brown algae (kelp-like forms) diversified tens to hundreds of millions of years later still. Based on this evidence, a chronological picture of life’s complexity emerges.

A Dickinsonia fossil observed at Nilpena Ediacara National Park, with negative relief.

Clear fossil evidence can be found most of the five major groups – here we see a Dickinsonia fossil, providing evidence of ancient animal life.

Citronnel/Wikimedia Commons, (CC-BY-SA-4.0)

There is, however, a notable exception to this fossil-based timeline: fungi. The fungal kingdom has long been an enigma for paleontologists. Their typically soft, filamentous bodies mean they rarely fossilize well. Furthermore, unlike animals or plants, which appear to have a single origin of complex multicellularity, fungi evolved this trait multiple times from diverse unicellular ancestors, making it difficult to pinpoint a single origin event in the sparse fossil record.

Reading the genetic clock

To overcome the gaps in the fungal fossil record, scientists use a "molecular clock." The concept is that genetic mutations accumulate in an organism's DNA at a relatively steady rate over generations, like the ticking of a clock. By comparing the number of genetic differences between two species, researchers can estimate how long ago they diverged from a common ancestor.

However, a molecular clock is uncalibrated; it can reveal relative time but not absolute years. To set the clock, scientists need to calibrate it with "anchor points" from the fossil record. Given the scarcity of fungal fossils, this has always been a major challenge. The OIST-led team addressed this by incorporating a novel source of information: rare gene "swaps" between different fungal lineages, a process known as horizontal gene transfer (HGT).
While genes are normally passed down "vertically" from parent to child, HGT is like a gene jumping "sideways" from one species to another. These events provide powerful temporal clues,” he says. “If a gene from lineage A is found to have jumped into lineage B, it establishes a clear rule: the ancestors of lineage A must be older than the descendants of lineage B.

Associate Professor Gergely János Szöllősi.

By identifying 17 such transfers, the team established a series of "older than/younger than" relationships that, alongside fossil records, helped to tighten and constrain the fungal timeline.

A new history for an ancient kingdom

The analysis suggests a common ancestor of living fungi dating to roughly 1.4–0.9 billion years ago—well before land plants. That timing supports a long prelude of fungi–algae interactions that helped set the stage for life on land.

Fungi run ecosystems—recycling nutrients, partnering with other organisms, and sometimes causing disease. Pinning down their timeline shows fungi were diversifying long before plants, consistent with early partnerships with algae that likely helped pave the way for terrestrial ecosystems.

Dr. Lénárd L. Szánthó, Co-first author.
Model-Based Evolutionary Genomics Unit
Okinawa Institute of Science and Technology Graduate University
Okinawa, Japan.

This revised timeline fundamentally reframes the story of life's colonization of land. It suggests that for hundreds of millions of years before the first true plants took root, fungi were already present, likely interacting with algae in microbial communities. This long, preparatory phase may have been essential for making Earth's continents habitable. By breaking down rock and cycling nutrients, these ancient fungi could have been the first true ecosystem engineers, creating the first primitive soils and fundamentally altering the terrestrial environment. In this new view, plants did not colonize a barren wasteland, but rather a world that had been prepared for them over eons by the ancient and persistent activity of the fungal kingdom.

Publication:
Szánthó, L.L., Merényi, Z., Donoghue, P. et al.
A timetree of Fungi dated with fossils and horizontal gene transfers. Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02851-z

A timetree of Fungi dated with fossils and horizontal gene transfers.
Lénárd L. Szánthó, Zsolt Merényi, Philip Donoghue, Toni Gabaldón, László G. Nagy, Gergely J. Szöllősi & Eduard Ocaña-Pallarès
Nature Ecology & Evolution (2025)

Abstract
Dating the tree of Fungi has been challenging due to a paucity of fossil calibrations and high taxonomic diversity of the group. Here we reconstructed and dated a comprehensive phylogeny comprising 110 fungal species, utilizing 225 phylogenetic markers and accounting for across-site compositional heterogeneity in amino acid sequences. To address uncertainties in fungal dating, we sampled chronograms from four relaxed molecular clock analyses, each integrating distinct sets of calibrations and relative time-order constraints. The first analysis used a core set of 27 calibrations alongside 17 relative constraints derived from fungi-to-fungi horizontal gene transfer events. Three further analyses extended this core set with additional timing information identified in our reevaluation of the evolution of pectin-specific enzymes in Fungi. Our timetree, integrating analytic uncertainties, suggests older ages for crown Fungi (1,401–896 Ma) than recently reported, providing a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma). This supports a protracted gap between the onset of these interactions and the rise of modern land plants. Altogether, our study provides a refined timescale for fungal diversification and a temporal framework for future investigations into early interactions involving fungi and the algal ancestors of embryophytes.

Main
The fungal kingdom is composed of an extensive diversity of organisms that evolved to inhabit nearly all of Earth’s ecosystems¹. Fungi are involved in key ecological interactions that were probably important during the early evolution of complex life². Among other hypotheses, it has been proposed that fungi and plants colonized land as mutualistic partners, paving the way for the radiation of macroscopic life in terrestrial habitats^3,4.

Fungi exhibit diverse morphologies⁵, lifestyles⁶ and complexity levels⁷, the best known of which are filamentous and mushroom-forming fungi and yeasts, most of which belong to the subkingdom Dikarya. Fungi, however, also contain several ‘early-diverging’ non-Dikarya phyla, including Zoopagomycota, Mucoromycota, Olpidiomycota, Blastocladiomycota and Chytridiomycota1. While less studied than Dikarya, these phyla and their ancestors experienced some of the most important events in fungal evolution, including the origin of multicellular hyphae⁸, terrestrialization(s) and the loss(es) of a flagellum^9,10, and the transition from a phagotrophic feeding strategy to osmotrophy¹¹. Osmotrophy unites Dikarya with the early-diverging non-Dikarya phyla¹², and we use it as a defining feature of Fungi that leaves Aphelida, Rozellida, Microsporidia and Nucleariidea as the closest relatives of Fungi in the tree of life^12,13,14 (Fig. 1).

Fig. 1: Features of main fungal groups (coloured) and of the sister relatives of fungi.

We defined Fungi as the clade including the coloured groups, as they are characterized by an absorptive/filamentous specialized osmotrophic lifestyle that distinguishes them from their closest relatives in the tree of life (non-coloured groups). Silhouettes are from PhyloPic (see Supplementary Information section 6 for credit and license details).

The evolution of non-Dikarya phyla has been the subject of intense study. As a result, their phylogenetic relationships are relatively well known^{9,12,13,14,15,16}, with the exception of a few hard-to-resolve relationships, which seem to be sensitive to methodological choices¹⁷. Aside from the phylogenetic relationships, establishing a dated phylogeny of Fungi is crucial to understand when major clades originated or how interactions between fungi and other lineages shaped the biosphere.

Main challenges in dating the ToF
The reconstruction of a dated tree of Fungi (ToF) is confronted by four major challenges (Challenges A–D; Fig. 2a). From a taxonomic standpoint, the availability of genomic data has historically been skewed towards Dikarya¹⁸, leaving some early-diverging phyla underrepresented in genomic databases (Challenge A, although substantial progress has been achieved thanks to initiatives such as the ‘1000 Fungal Genomes Project’¹⁹). In addition, dating a broad and diverse phylogeny constitutes a difficult computational endeavour. While researchers have developed tools to accelerate molecular dating analyses for large phylogenetic datasets²⁰, these often use simplified models that cannot account for complex protein sequence properties, such as amino acid site compositional heterogeneity^21,22 (Challenge B). Furthermore, deep phylogenetic relationships are not yet fully resolved¹⁷, including: (1) whether Chytridiomycota¹² or Blastocladiomycota¹⁵ is the sister group to the rest of the fungi; (2) the position of the flagellated group Olpidiomycota⁹, which is critical to understanding whether terrestrial fungal groups originated from one or multiple terrestrialization events; and (3) the placement of the genus Basidiobolus, which has been variably positioned near Mucoromycota¹⁶ or Zoopagomycota¹⁵ (Challenge C). Finally, fungal fossils are scarce, especially for unicellular groups that diverged before Dikarya. This issue is compounded by previous studies largely relying on a narrow set of calibration points, such as Paleopyrenomycites, with limited exploration of additional fossils^23,24 (Challenge D). Aiming to address these challenges, we implemented a comprehensive methodological workflow that integrates cutting-edge phylogenetic and molecular dating techniques (Fig. 2b).
Fig. 2: Reconstructing a dated ToF.

a, Main challenges. b, A summary of the methodological workflow executed to deal with these challenges and produce the ‘Default’ set of chronograms. See the main text and Methods for further details.

Szánthó, L.L., Merényi, Z., Donoghue, P. et al.
A timetree of Fungi dated with fossils and horizontal gene transfers. Nat Ecol Evol (2025). https://doi.org/10.1038/s41559-025-02851-z

Copyright: © 2025 The authors.
Published by Springer Nature Ltd. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)

What makes this research especially significant is that it identifies horizontal gene transfer (HGT) as a key factor in the evolution of fungal multicellularity. In other words, fungi did not just shuffle their existing genetic material, but actually incorporated new genetic information from other organisms into their genomes, enabling the development of novel traits.

This is important because creationists often insist that evolution cannot produce “new information.” Yet here is a clear example of exactly that happening, written into the genomes of fungi hundreds of millions of years before the first humans began to invent myths to explain the world. Far from being impossible, the acquisition of genetic information through HGT is now recognised as a common and powerful mechanism of evolutionary innovation across all domains of life.

So once again, real science delivers what creationist dogma cannot: an evidence-based account of how complexity arises, how life adapts to new environments, and how key evolutionary transitions occurred. Instead of clinging to ancient fables, science reads the record encoded in DNA and the fossil archive, revealing a history far richer, stranger, and more awe-inspiring than any human invention.

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