First collected in 1843, it was not until 14 years later that
J.W. Dawson, a Canadian scientist, studied
Prototaxites fossils, which he described as partially rotten giant
conifers, containing the remains of the fungi which had been decomposing them. Carruthers faulted the name
Prototaxites (loosely translated as "first
yew") and insisted that the name
Nematophycus ("stringy
alga") be adopted, Dawson fought adamantly to defend his original interpretation until studies of the microstructure made it clear that his position was untenable, whence he promptly attempted to rename the genus himself, calling it
Nematophyton ("stringy plant"), and denying with great vehemence that he had ever considered it to be a tree. Carruthers' interpretation that it was a giant marine alga was challenged just once, in 1919, when
A.H. Church suggested that Carruthers had been too quick to rule out the possibility that it was a fungus. The lack of any characters diagnostic of any extant group made the presentation of a firm hypothesis difficult; This idea was received with disbelief, denial, and strong skepticism, but further evidence has emerged to support it. In 2007,
isotopic analyses by a team including Hueber and
K.C. Boyce of the
University of Chicago concluded that
Prototaxites was a giant fungus. They detected a highly variable range of values of
carbon isotope ratios in a range of
Prototaxites specimens. Autotrophs (organisms such as plants and algae that sustain themselves via
photosynthesis) living at the same time draw on the same (i.e.,
atmospheric) source of
carbon; as organisms of the same type share the same chemical machinery, they reflect this atmospheric composition with a constant carbon
isotope trace. The inconsistent ratio observed in
Prototaxites appears to show that the organism did not survive by photosynthesis, and Boyce's team deduced that the organism fed on a range of
substrates, such as the remains of whichever other organisms were nearby. Other research has suggested that
Prototaxites represents a rolled-up bundle of
liverworts, A similar genus,
Nematasketum, also consists of banded and branching tubes in axial bundles; this seems to be a fungus. In 2019,
Gregory Retallack described the new species
Prototaxites honeggeri from the
Darriwilian stage of the Middle
Ordovician Douglas Lake Member of the
Lenoir Limestone, at
Douglas Dam,
Tennessee, which marks the earliest known appearance of the genus
Prototaxites. While an Ordovician origin of the genus is mentioned by some studies, , referring to Retallack's study, maintained that the first appearance of the genus was in the Late Silurian. A 2026 paper found that the chemical composition of
Prototaxites fossils from the
Rhynie chert assemblage in Scotland are distinct from other organisms in the same environment, including fungi due to lacking chitin, a key structural element in extant fungi. The paper additionally found that the medullary spots of
Prototaxites taiti are composed of highly dense fine branching, and identified that some tubes have internal banding. The authors suggest that both of these features are distinct from anything found in extant fungi, and may be involved in physiological functions like gas exchange and water transport that extant fungi do not have. The authors propose that
Prototaxites represents a completely new extinct lineage, separate from plants, fungi and other eukaryotes. ==Ecological context==