Phacopsis

''Phacopsis'' is a genus of lichenicolous (lichen. They are parasites of members of the large lichen family Parmeliaceae, of which they are also a member. Originally proposed by Edmond Tulasne in 1852 to contain 3 species, ''Phacopsis'' now contains 10 species, although historically, 33 taxa have been described in the genus. Many of the species are poorly known, some of them having been documented only from the type specimen.

''Phacopsis'' species appear as partially immersed, shiny brown to black apothecia that cause gall-like deformations on the thallus of the host lichen. Features of ''Phacopsis'' used to distinguish species from each other include the shape of their spores, and the colour and reaction of the hypothecium (a tissue layer under the spore-bearing hymenium) when stained using an iodine–starch test. Since ''Phacopsis'' fungi are usually restricted to living on hosts belonging to a single phylogenetic clade, the identity of the host lichen is another diagnostic character used to identify species.

Systematics

''Phacopsis'' was circumscribed by French mycologist Edmond Tulasne in 1852 with multiple species originally classified in genus ''Abrothallus''. Tulasne included three species: ''P. clemens'', ''P. varia'', and ''P. vulpina''. The last-mentioned species was later selected as the type species by Frederic Clements and Cornelius Shear (1931), and by John Axel Nannfeldt (1932). Of the other two species originally included in ''Phacopsis'' by Tulasne, ''P. clemens'' has since been referred to the genus '' Arthonia'', while ''P. varia'' is now known as '' Opegrapha physciaria''.

In 1988, Dagmar Triebel and Gerhard Rambold proposed that ''Phacopsis'' should be considered synonymous with '' Nesolechia'' (another genus of lichenicolous fungi in the Parmeliaceae), owing to similarities both in the structure of their apothecia and the characteristics of their hymenia. This proposed synonymy, however, was not accepted by several authors in the years following, until 1995 when Triebel, Rambold, and John Elix showed that the supposed differences that separated the two genera were not consistent. Following this, Ove Eriksson and David L. Hawksworth used an expanded generic concept of ''Phacopsis'' (''sensu lato'') in the next update of their regular publication on ascomycete systematics, ''Systema Ascomycetum''.

Molecular phylogenetic analysis published in 2015 demonstrated that the group of species then considered to be members of ''Phacopsis'' actually comprised three distinct lineages, representing three genera: ''Phacopsis'', ''Nesolechia'', and the newly circumscribed '' Raesaenenia''. In 2017, Divakar and colleagues used a then-recently developed "temporal phylogenetic" approach in an attempt to make family- and genus-level classification more consistent with evolutionary history. They proposed to synonymize genus ''Nesolechia'' with ''Punctelia'', and ''Raesaenenia'' with ''Protousnea'', because the lichenicolous genera originated relatively recently and fell under the timeframe threshold for genus level. This proposed synonymy was not accepted in a later critical analysis of the temporal phylogenetic approach for fungal classification. In a 2018 review of taxonomic developments in the family Parmeliaceae, the authors recommended not synonymizing ''Nesolechia'' and ''Phacopsis'', suggesting that the separation between these two genera has not yet been sufficiently established.

The higher-level classification of ''Phacopsis'' has changed several times in its taxonomic history. It has been placed in the order Arthoniales, in the families Graphidaceae, and the Acarosporaceae. Using electron microscopy, Josef Hafellner examined the asci (spore-bearing cells) of the type species ''P. vulpina'', showing them to be similar to those commonly found in members of the Lecanoraceae, and so he considered the genus most appropriately classified in this family. This familial placement, however, was not corroborated in Triebel and colleagues' 1995 review and revision of the genus. Molecular phylogenetic analysis eventually revealed its true phylogenetic placement in the family Parmeliaceae. This relationship is an example of adelpho-parasitism, in which the host species is closely related to the parasite; this type of relationship is fairly common in the Lecanorales. The genus ''Protousnea'' has a sister taxon relationship with ''Phacopsis''. It has been estimated that the lichenicolous ''Phacopsis'' diverged evolutionarily from the lichen-forming ''Protousnea'' during the Miocene (23.03 to 5.333 mya).

Description

All species are endokapylic, meaning they possess a thallus in which no morphologically distinct lichenized structure is formed. Their apothecia are circular to irregular in shape, and may be dispersed or aggregated. The excipulum (the outer margin of the apothecium) range from colourless to blackish-brown, and often comprises "a few rows of cells which may be difficult to recognize". The hypothecium (a layer of dense hyphal tissue just below the hymenium) is colourless to blackish-brown. In some species, the hyphae in the hypothecium have a violet staining reaction with an iodine–starch test; this characteristic can be used to distinguish between some species. The hymenium is colourless, pale brownish, or pale olivaceous. Asci are more or less club-shaped, and contain eight spores. They are surrounded by a thin outer amyloid wall layer and a thicker, non-amyloid inner wall layer; a non-amyloid zone rests above the axial body of the ascus.

The ascospores are colourless, lack septa, and have smooth walls with occasional thickening at either end. The spores have a range of shapes; depending on the species, the following shapes have been recorded: ellipsoid, ovoid (egg-shaped), fusiform (spindle-shaped), lemon-shaped, falciform (sickle-shaped), fabiform (bean-shaped), and partly curved. The pycnidia of ''Phacopsis'' are immersed in the thallus of the host. Pycnospore