PREMISE OF THE STUDY:Fossils show that fly-speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ~250 million years. We analyze morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa. METHODS:We placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature.We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny. KEY RESULTS: Thyriothecia evolved convergently in multiple lineages of superficial, leafinhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae (order incertae sedis). Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales-Zeloasperisporiales clade within Dothideomycetes. CONCLUSIONS: This is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa

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In this commentary, we discuss evidence for the phylogenetic affiliations of Tortotubus protuberans, the subject of Martin Smith's 2016 paper in the Botanical Journal of the Linnean Society entitled, ‘Cord‐forming Palaeozoic fungi in terrestrial assemblages’. We agree that the fossilized, branching, somatic filaments probably represent fungal hyphae. We were not convinced by Smith's proposal that T. protuberans represents Dikarya, the clade of fungi that includes most modern moulds, yeasts and mushrooms. To justify classification, Smith relied on structures that are analogous between T. protuberans and modern fungi, and argued ‘that Dikarya can produce the range of morphologies expressed by T. protuberans’. We review available information about homologies of the characteristics of T. protuberans, including mycelial cords, retrograde growth, septal pores and ornamented hyphae. Retrograde growth in T. protuberans is intriguing from an evolutionary developmental point of view, but it differs sufficiently in fine detail when compared with growth patterns in croziers or clamp connections of Dikarya, so that homologies are unclear. Tortotubus protuberans is an important fossil form, but we suggest taking a step back and relating it to the distribution of character evolution through the fungal phylogeny rather than to derived characters of modern taxa.

25PREMISE OF THE STUDY: Fossils show that fly-speck fungi have been reproducing with 26 small, black thyriothecia on leaf surfaces for ~250 million years. We analyze morphological 27 characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting 28 fossil taxa. 29 METHODS:We placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using 30 nuclear ribosomal large and small subunit sequences, including newly determined sequences 31 from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum 32 likelihood after coding 11 morphological characters based on original observations and literature. 33We analyzed the relationships of three previously published Mesozoic fossils using parsimony 34 and our morphological character matrix, constrained by the molecular phylogeny. 35 KEY RESULTS: Thyriothecia evolved convergently in multiple lineages of superficial, leaf-36 inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to 37 Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes 38 Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent 39 hyphae characterizes Aulographaceae (order incertae sedis). Scutella in Microthyriales are 40 initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute 41 to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is 42 further resolved as a member of a Microthyriales-Zeloasperisporiales clade within 43 Dothideomycetes. 44 CONCLUSIONS: This is the most comprehensive systematic study of thyriothecial fungi and 45 their relatives to date. Parsimony analysis of the matrix of character states of modern taxa 46 p. 3 provides an objective basis for interpreting fossils, leading to insights into morphological 47 evolution and geological ages of Dothideomycetes clades. 48

An important compendium of fossil fungi is now publicly available through a searchable online database. The original compendium was the work of Kalgutkar and Jansonius, who combed through 238 references and collated and annotated published descriptions for 1783 taxa of fungal fossils. By translating these data to a FileMaker Pro database and to the Web, we increase options for searching, sorting, annotating and updating this information. Database search results provide lists of names, ages and thumbnail images of palynomorphs. An individual record from the results list can be expanded in a new browser window to show a complete description for a taxon. The database is timely because developments in molecular systematics are helping to place spore characters in a phylogenetic framework. Some of the previously ambiguous fossil fungi can now be placed into phylogenetic lineages. We anticipate that the Web version of the data will serve as a convenient entry point into the fungal fossil record, leading to integration of more information from fossils into fungal phylogenies.