No abstract

Agaricus (Basidiomycota) is a genus of saprobic fungi that includes edible cultivated species such as Agaricus bisporus, the button mushroom. There has been considerable ecological, nutritional and medicinal interest in the genus, yet the extent of its diversity remains poorly known, particularly in subtropical and tropical areas. Classification of tropical species has for a large part followed the classification of temperate species. The objective of our study was to examine to what extent this system of classification is appropriate for tropical Agaricus species. Species from temperate sections were therefore compared to the major clades of tropical species using a phylogenetic approach. ITS1+2 sequence data from 128 species were used in the phylogenetic analysis. Specimens included four species of genera closely related to Agaricus, 38 temperate species representing the eight classical sections of the genus, and 86 putative species of Agaricus from tropical areas of Africa, Asia and the Americas. Bayesian and maximum likelihood analyses produced relatively congruent trees and almost identical clades. Our data show that (i) only about one-third of tropical species belong to the classical sections based on temperate species; the systematics of the genus therefore needs to be expanded; (ii) among the remaining two-thirds of tropical species, those from the Americas and those from Africa and/or Asia group in distinct clades, suggesting that secondary diversification occurred in these two areas; (iii) in contrast, several clades of classical sections contain American and African+Asian species along with temperate species. In this study, we used approximately 50 distinct species from a small area of northern Thailand, most probably being novel species. This diversity indicates that Agaricus is a species-rich genus in the tropics as well as in temperate regions. The number of species and the hypothetical paleotropical origin of the genus are discussed.

Within Agaricus subg. Minores, A. sect. Minores remains a little-studied section due generally to its delicate sporocarps often lacking taxonomically relevant morphological characters. To reconstruct the section, using the recent taxonomic system based on divergence times, and to evaluate the species diversity of A. sect. Minores in the Greater Mekong Subregion, 165 specimens were incorporated in phylogenetic analyses. A dated tree based on nuclear ITS, LSU and tef1-α sequence data allowed us to better circumscribe A. subg. Minores and to propose a new subgenus, A. subg. Minoriopsis, which is only known from tropical and subtropical regions of the Americas. A larger tree based on ITS sequences indicated that, with 81 phylogenetic species, the reconstructed section Minores is now one of the largest sections in the genus. Within A. subg. Minores, a new section, A. sect. Leucocarpi, and eleven new species are described from the Greater Mekong Subregion. Thirty-eight species of A. sect. Minores from this region of Asia were distributed in multiple clades that successively diverged over the past 24 million years. In contrast, species reported from Europe mostly grouped in a single non-tropical clade, suggesting a major species diversification following the middle Miocene climatic optimum.

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to amend the International Code of Nomenclature for algae, fungi, and plants (ICN), allowing DNA sequences alone (of any region and extent) to serve as types of taxon names for voucherless fungi (mainly putative taxa from environmental DNA sequences), have been submitted to be voted on at the 11th International Mycological Congress (Puerto Rico, July 2018). We consider various genetic processes affecting the distribution of alleles among taxa and find that alleles may not consistently and uniquely represent the species within which they are contained. Should the proposals be accepted, the meaning of nomenclatural types would change in a fundamental way from physical objects as sources of data to the data themselves. Such changes are conducive to irreproducible science, the potential typification on artefactual data, and massive creation of names with low information content, ultimately causing nomenclatural instability and unnecessary work for future researchers that would stall future explorations of fungal diversity. We conclude that the acceptance of DNA sequences alone as types of names of taxa, under the terms used in the current proposals, is unnecessary and would not solve the problem of naming putative taxa known only from DNA sequences in a scientifically defensible way. As an alternative, we highlight the use of formulas for naming putative taxa (candidate taxa) that do not require any modification of the ICN.

Agaricus is a genus of saprobic basidiomycetes including species of nutritional and medicinal interest. Historically the temperate species have been grouped into eight classical sections. Recent phylogenetic analyses however, revealed that two-thirds of the tropical taxa do not cluster in these sections, but form exclusively tropical clades. Seven (TR I to TR VII) strongly supported tropical clades have been revealed and it was hypothesized that clade TR I might represent Agaricus section Brunneopicti. This section was initially characterized by the presence of punctiform squamules, the remains of the veil, on the pileus and stipe. The present morphological study and phylogenetic ML, MP and Bayesian analyses based on ITS1+2 sequences show that clade TR I corresponds to Agaricus section Brunneopicti and includes 16 taxa grouped in four strongly supported subclades and two isolated branches. The six species with punctiform squamules which initially characterized the section constitute one of these subclades. We propose the new replacement name Agaricus brunneopunctatus for the illegitimate name Agaricus brunneopictus. All 16 species are discussed, full descriptions are provided for five, among them, A. brunneosquamulosus, A. niveogranulatus, A. sordidocarpus and A. toluenolens are described as new species. We also report on certain members of section Brunneopicti traits which generally characterize species belonging to other sections. These shared characters raise the issue of their origin and complicate the systematics and the identification of the tropical Agaricus species. An artificial dichotomous key is presented for species identification. Section Brunneopicti is the first reconstructed section of tropical Agaricus. Its known geographical distribution range is strictly palaeotropical. We predict that the species richness of other somewhat forgotten or new tropical sections will also increase in coming years.

The genus Agaricus is known for its medicinal and edible species but also includes toxic species that belong to section Xanthodermatei. Previous phylogenetic reconstruction for temperate species, based on sequence data of nuc rRNA gene (rDNA) internal transcribed spacers (ITS), has revealed two major groups in this section and a possible third lineage for A. pseudopratensis. Recent research in Agaricus has shown that classifications need improving with the addition of tropical taxa. In this study we add new tropical collections to section Xanthodermatei. We describe three species from collections made in Pakistan and Thailand and include them in a larger analysis using all available ITS data for section Xanthodermatei. Agaricus bisporiticus sp. nov. and A. fuscopunctatus sp. nov. are introduced based on molecular and morphological studies, whereas A. microvolvatulus is recorded for the first time in Asia. Specimens from Thailand however have a much larger pileus than the type specimens from Congo. In maximum likelihood (ML) and maximum parsimony (MP) phylogenetic analyses these three species cluster with A. pseudopratensis from the Mediterranean area and A. murinocephalus recently described from Thailand. In Agaricus section Xanthodermatei this new group is monophyletic and receives low bootstrap support whereas the two previously known groups receive strong support. Within the new group, the most closely related species share some traits, but we did not find any unifying morphological character; however the five species of the group share a unique short nucleotide sequence. Two putatively toxic species of section Xanthodermatei are now recognized in Pakistan and six in Thailand.

Field collections of Agaricus were collected in the Dominican Republic from 2009–2016 with the intent to evaluate the diversity in this genus, which was quasi-unknown in this country. In the same period, studies on tropical Agaricus revealed tropical clades that remained unclassified. A new taxonomic system of classification was developed, with the aim, inter alia, to integrate such tropical clades. A recent phylogenetic study, which included some samples from the Dominican Republic, revealed they belonged to three putative new sections. Our objective in this paper is to describe the species of Agaricus collected in this country and to classify them whitin the new taxonomic system, including formal descriptions of the three new sections to which they belong. A preliminary study indicated that the collections of the Dominican Republic belong either to a group of three related subgenera (Flavoagaricus, Minores, and Minoriopsis) or to the unrelated A. subg. Pseudochitonia. For the species of the three related subgenera, a phylogenetic analysis based on ITS sequences data reliably confirmed the classification of the species into five sections including the three new sections, which were well supported. For the collections of A. subg. Pseudochitonia, preliminary studies indicated that they all belonged to species of A. sect. Xanthodermatei without any doubt except for one species. This species was included in a multi-gene (ITS, LSU and tef-1α) phylogenetic analysis which confirmed placement in this section. Consequently, all the samples were included in a phylogenetic analysis based on ITS sequences and focusing on A. sect. Xanthodermatei. We noted an unusually high intraspecific variability in the ITS sequences of five of the 12 studied species. Fifteen taxa are described, among which three sections and six species are new for science: Agaricus sect. Kerrigania, Agaricus sect. Minoriopsis, Agaricus sect. Pantropicales, A. argenteopurpureus, A. candussoi, A. flavidodiscus, A. lodgeae, A. porphyropos and A. tephrolepidus. We report all these taxa from the Dominican Republic but the latter three species are also recorded from Puerto Rico, United States Virgin Islands, and Mexico, respectively.

Agaricus section Xanthodermatei comprises a group of species allied to A. xanthodermus and generally characterized by basidiomata having phenolic odors, transiently yellowing discolorations in some parts of the basidiome, Schaeffer's reaction negative, and mild to substantial toxicity. The section has a global distribution, while most included species have distributions restricted to regions of single continents. Using specimens and cultures from Europe, North America, and Hawaii, we analyzed DNA sequences from the ITS1+2 region of the nuclear rDNA to identify and characterize phylogenetically distinct entities and to construct a hypothesis of relationships, both among members of the section and with representative taxa from other sections of the genus. 61 sequences from affiliated taxa, plus 20 from six (or seven) other sections of Agaricus, and one Micropsalliota sequence, were evaluated under distance, maximum parsimony and maximum likelihood methods. We recognized 21 discrete entities in Xanthodermatei, including 14 established species and 7 new ones, three of which are described elsewhere. Four species from California, New Mexico, and France deserve further study before they are described. Type studies of American taxa are particularly emphasized, and a lectotype is designated for A. californicus. Section Xanthodermatei formed a single clade in most analyses, indicating that the traditional sectional characters noted above are good unifying characters that appear to have arisen only once within Agaricus. Deep divisions within the sequence-derived structure of the section could be interpreted as subsections in Xanthodermatei; however, various considerations led us to refrain from proposing new supraspecific taxa. The nearest neighbors of section Xanthodermatei are putatively in section Duploannulati.