Lichen systematics
Lichen systematics is the study of how lichens are classified and related to each other, combining the naming of lichen taxa, the reconstruction of their evolutionary history, and the organization of this diversity into a coherent framework. In contrast to an individual fungus or plant, a lichen is not a single organism but a miniature ecosystem—a symbiotic partnership between a fungus and a photosynthetic partner. Because a lichen has no independent evolutionary lineage apart from its partners, classification is based chiefly on the fungus's family tree.
Lichen systematics underpins broader biodiversity research and conservation. Species are the fundamental units in ecology and biogeography, so a stable taxonomy is essential for tracking environmental changes and protecting vulnerable species. Inaccurate taxonomy can mislead science and policy. One audit of conservation data found that database records for a rare lichen had been misidentified or filed under obsolete names, distorting assessments of its geographic range. Modern lichen systematics therefore emphasizes rigorous definition of species boundaries and thorough documentation as the foundation for studying lichens' ecology and evolution.
At its core, lichen systematics rests on four interlinked pillars. These are taxonomy, nomenclature, phylogeny, and classification. These activities are interdependent. For example, naming a new species automatically places it within a genus, implicitly hypothesizing a relationship to other members of that genus. Likewise, classifications are continually revised as phylogenetic studies uncover more natural groupings. A guiding principle in modern systematics is to ensure that each recognized group includes all descendants of one common ancestor. Groupings based only on superficial similarity rather than real ancestry are considered artificial; when studies reveal such cases, the groups are reorganized to reflect true evolutionary lineages. In practice this means many traditional lichen groups defined by convenient field have been dismantled, and their members redistributed, to ensure that each genus or family reflects a single evolutionary lineage.
Lichen systematics has been revolutionized in recent decades by molecular biology and genomics. DNA sequencing now allows researchers to resolve cryptic species and deep evolutionary relationships that were impossible to discern from morphology alone. Entire genomes of lichen-forming fungi can be sequenced, offering a wealth of characters for phylogenetic analysis and revealing genes involved in symbiosis. These advances have led to a surge of new insights—for instance, the discovery of many previously unrecognized species within what were thought to be single, widespread taxa. Yet, traditional morphology and chemistry remain indispensable in the field. A 2018–2020 survey found that fewer than half of newly described lichen species were accompanied by any DNA data, and only about 10% had more than three genetic loci sequenced. Most new species are still identified and circumscribed using features like spores, reproductive structures, and secondary metabolites. Lichenologists thus operate with a blend of old and new methods: high-throughput sequencing might pinpoint lineages of interest, but microscopy, spot tests, and thin-layer chromatography are still routinely used to characterize and confirm the organisms. The field is moving toward an integrative approach in which morphological, chemical, and molecular evidence are all brought to bear on defining species and higher taxa.
Overview of historical development
Pre-dual hypothesis concepts (before 1867)
For centuries, naturalists treated lichens as self-contained, plant-like organisms distinguished only by outward appearance. Theophrastus introduced the word lichen for crusty bark growths, yet offered little insight beyond the name. Until the mid-1700s, taxonomists lumped lichens with algae, mosses, or fungi in broad, pre-evolutionary schemes. A pivotal step came in 1700, when the French botanist Joseph Pitton de Tournefort erected the genus Lichen, acknowledging the group's distinctiveness—even while keeping it beside mosses and liverworts. Robert Morison's 1699 Herbarium, for instance, split lichens into five "Muscofungi" types, a purely morphological scheme that left little mark on later work. The Italian polymath Pier Antonio Micheli published the first recognizable lichen classification in his 1729 Nova plantarum genera. While he kept all species in the catch‑all genus Lichen—echoing Tournefort—Micheli organized them into several "orders" based on thallus texture and fruiting body form. Those informal groupings later became the nuclei of modern genera, and his morphological terminology laid the groundwork for subsequent binomial treatments.In 1753 Carl Linnaeus introduced the first coherent plant-classification scheme in Species Plantarum. He listed roughly 80 lichen species, grouping almost all under the single genus Lichen. Such compression mirrored 18th-century ignorance of lichen diversity: 'lichen' was little more than a catch-all for crusty or leafy growths on bark and stone. Real advancement came in the early 1800s, when Linnaeus's student Erik Acharius—later hailed as the "father of lichenology"—re-examined the group. From 1798 to 1814, Acharius published four influential monographs that divided Lichen into numerous genera and sketched a finer hierarchy: Lichenographiae Suecicae Prodromus, Methodus, Lichenographia Universalis, and Synopsis Methodica Lichenum. Beyond cataloguing hundreds of species, he introduced microscopic —such as the structure of the spore-producing bodies —as classificatory tools. His anatomical focus freed lichenology from its old dependence on thallus form and laid the groundwork for a multi-character "natural" system.
During the early–mid 1800s, lichen taxonomists steadily wove fresh microscopic insights into their work. With compound microscopes common by the 1830s, researchers saw that lichens contain distinct internal layers and reproductive organs. A cadre of European "microscope taxonomists"—Antoine Fée, Giuseppe De Notaris, Vittore Trevisan, Camille Montagne, Ernst Stizenberger and Edward Tuckerman—used those details to delimit genera on ascospore shape, septation and anatomy, giving lichenology its first genuinely anatomical classification.
Meanwhile, William Nylander drew on micro‑anatomy to craft a far richer hierarchical scheme, describing hundreds of new taxa yet largely ignoring spore data. In his 1858 synopsis he even arranged lichens along an "algal‑to‑fungal continuum"—a speculative evolutionary ladder that cast the thallus as a transitional stage between algae and true fungi. Although soon eclipsed by Schwendener's dual‑symbiosis hypothesis, the idea shows that lichenologists were already grappling with gradations between the symbionts well before the composite nature of the organism was proved.
Other botanists emphasised spores and propagules as diagnostic features. Britons William Lauder Lindsay and Henry Mudd proposed splitting genera by spore number, size and septation, while continental workers such as Abramo Bartolommeo Massalongo and Gustav Wilhelm Körber built whole generic frameworks around ascospore traits, sparking debate yet adding critical descriptors. By 1867 lichenology had grown from Linnaeus's single‑genus sketch into a specialized field, complete with dozens of experts, thousands of named species and a nascent multi-character taxonomy linking thallus form, anatomy and reproduction—just in time for the coming revolution that would redefine lichens as symbiotic fungi.
The dual hypothesis and its controversy (1867–1900)
In 1867 the Swiss botanist Simon Schwendener upended orthodox lichen theory with a daring new hypothesis. In a lecture in September he argued that a lichen is a duo—a fungus that houses an alga—rather than a lone organism. His "dual hypothesis" cast the thallus as fungal tissue farming algal cells for photosynthate. Microscopy revealed algal embedded in the fungal matrix, but many colleagues dismissed his reading. William Nylander repudiated the "composite" idea, viewing it as an affront to his life's work. The British lichenologist James Crombie derided the notion as a "master-and-slave" model—an enslaving parasitic fungus and its algal captive—and rebutted it in Encyclopædia Britannica. The dispute turned bitter, exposing both paradigm shock and the insularity of 19th-century lichenology.Despite the early backlash, proof for the dual hypothesis piled up during the 1870s–1880s. In 1872 Heinrich Anton de Bary—later to codify "symbiosis"—published work backing the fungal–algal alliance. Albert Frank coined "symbiose" in 1877, recasting the partnership as mutualistic, not parasitic. Significantly, botanists started lab resynthesis—laboratory recreation of lichens from separated components. In 1873 Édouard Bornet matched lichen gonidia to free-living algae from 60-plus genera, proving the algae could live alone. Soon after, Hermann Reess grew fresh Collema thalli from fungal spores and algal cells; by 1886 Jules Bonnier had done the same with Xanthoria'' and other genera. These resynthesis experiments provided strong evidence: lichens are a product of symbiosis. The dual hypothesis gained influential supporters; in 1878, Royal Society president Joseph Hooker publicly endorsed Schwendener's theory in his annual address, and by 1880 leading British and American textbooks presented lichens as dual organisms.
By 1900 the consensus had shifted. Most botanists now viewed lichens as fungi partnered with algae or cyanobacteria and reclassified them accordingly. Dissent lingered. In a 1909 poll of 42 botanists, Bruce Fink found 18 calling lichens dual organisms, 14 insisting they were fungi, and the rest undecided. Yet even holdouts were beginning to adopt the dual view. The Finnish lichenologist Edvard Vainio folded lichens into a fungal scheme—labelling them fungi that happen to form symbioses—a move said to have cost him a professorship. The next puzzle was how to classify lichens now that their dual nature was clear. Taxonomists questioned whether to base classification on fungal traits, algal traits, or both. In practice, they chose the fungus. Since the fungus governs reproduction and form, its fruiting bodies and spores carried the most taxonomic weight. By the late 1800s, taxonomists grouped lichens by fungal traits—spore colour, septation, fruiting-body type—rather than thallus shape or algal partner. The shift broke with thallus-based schemes and aligned lichen study with modern fungal taxonomy. Yet the symbiosis raised a century-long puzzle: if multiple fungi adopted algal partners independently, the "lichen condition" might be polyphyletic. This question of how many times lichenization evolved remained speculative until the advent of molecular phylogenetics. Early lichenologists such as Walter Watson warned that symbiosis can so remodel a fungus that its ancestry becomes hard to trace. Modern molecular studies confirm the problem: convergent thallus forms have evolved repeatedly and even been lost again, making ancestry hard to infer.