Recent Papers

Volume 7 - 2016 - Issue 11 (SI Evolution)

1. Special issue on naming species, ranking and evolution of fungi

Authors: Hongsanan S, Sánchez-Ramírez S, Zhao RL

Recieved: 30 November -0001, Accepted: 30 November -0001, Published: 29 December 2016

Keywords:

2. Taxonomic utility of old names in current fungal classification and nomenclature: Conflicts, confusion & clarifications

Authors: Dayarathne MC, Boonmee S, Braun U, Crous PW, Daranagama DA, Dissanayake AJ, Ekanayaka H, Jayawardena R, Jones EBG, Maharachchikumbura SSN, Perera RH, Phillips AJL, Stadler M, Thambugala KM, Wanasinghe DN, Zhao Q, Hyde KD, Jeewon R

Recieved: 26 October 2016, Accepted: 10 December 2016, Published: 29 December 2016

Fungal taxonomy has a long history and nomenclatural type specimens constitute an integral part of fungal classification and nomenclature. To date, type specimens/old names have served as excellent exemplars and references and have been the pillar for a stable classification and appropriate nomenclature. However, with an increase in the number of species being discovered and the practical problems associated with re-examination and over reliance of old names as exemplars, there is a need to reconsider our traditional taxonomic thinking towards such an approach. It is becoming increasingly clear that loaning specimens, especially of rare and old species, is becoming too tedious, difficult and in some cases, practically impossible. This paper addresses in detail some of the major practical difficulties in referring to old names from a stable nomenclatural system viewpoint, in particular, reluctance of herbaria to loan specimens and poor conditions of specimens. Specific case studies where problems are encountered that hinder references to old names are discussed. Last but not least, mycologists express their opinions and concerns and provide deductive conclusions based on facts and their long experience in mycology. With regards to fungal nomenclature, taxonomists, devoted to bring about rational changes to fungal taxonomy, should be encouraged to use more friendly and practical approaches, with minimum hassle to examine old specimens. We contemplate that this paper will provide potential solutions to facilitate future naming/classification of fungal species.

Keywords: type species – type materials and specimens – species nomenclature –taxonomy – DNA sequence data – phylogeny

3. Perspectives into the value of genera, families and orders in classification

Authors: Liu NG, Ariyawansa HA, Hyde KD, Maharachchikumbura SSN, Zhao RL, Phillips AJL, Jayawardena RS, Thambugala KM, Dissanayake AJ, Wijayawardene NN, Liu JK, Liu ZY, Jeewon R, Jones EBG, Jumpathong J

Recieved: 15 November 2016, Accepted: 05 December 2016, Published: 29 December 2016

This paper briefly discusses the history of fungal taxonomy and contributes to the concepts and the importance of ranking genera, families and orders. We propose recommendations for introducing species into appropriate ranks such as genera, families and orders, as well as the rationale to maintain species in one genus or segregate one genus into several genera. Various ways to rank fungi have commonly been based on morphological and phylogenetic species concepts. More recently, the use of molecular clocks, coupled with estimates of divergence times, has provided insights into how to assign species and support their establishment at different taxonomic hierarchical levels. Case studies are given from the order Botryosphaeriales and Pleosporales, and the genera Camarosporium, Colletotrichum, Diaporthe, Pestalotiopsis, Lophiostoma and Agaricus to demonstrate taxonomic ambiguities and the subjectivity in classification of fungi.

Keywords: Divergence time – Hierarchy – Ranks – Recommendation – Taxonomic Concepts

4. Establishing species boundaries and new taxa among fungi: recommendations to resolve taxonomic ambiguities

Authors: Jeewon R, Hyde KD

Recieved: 11 October 2016, Accepted: 08 November 2016, Published: 29 December 2016

Accurate identification and demarcation of taxa has far reaching implications in mycology, especially when plant pathogens are involved. Yet few publications have seriously proposed recommendations as to how to delineate species boundaries. Morphology, with all its taxonomic disparities, has been the main criterion upon which current fungal species concepts are based and morphologically defined species make up the largest number of named species. Although phylogenomic based studies arguably offer novel insights into classification at higher taxonomic levels, relationships at the species level and recognition of species remain largely controversial and subject to different interpretations. Our recommendations herein will provide a more rational framework based on scientific data on how to delineate species and establish a new taxon.

Keywords: DNA sequence data – Fungal species concepts – Interspecific variability – Morphological discrepancies – Phenetics – Phylogenetics – Ribosomal and protein genes – Taxonomic perceptions

5. Divergence and ranking of taxa across the kingdoms Animalia, Fungi and Plantae

Authors: Samarakoon MC, Hyde KD, Promputtha I, Ariyawansa HA, Hongsanan S

Recieved: 04 September 2016, Accepted: 13 December 2016, Published: 29 December 2016

In science, species are grouped and ranked in kingdoms, phyla, classes, orders, families and genera and several other intermediate taxa, in a taxonomic hierarchy. However, the ranking of phyla, classes, orders and families across kingdoms is not linked and there is unlikely to be any correlation between these ranks in animals, fungi or plants. In a few recent studies, divergence times have been used to develop more natural groupings within ranks and it has been suggested that divergence times should be used as a universal criterion in high level ranking. It would therefore be desirable to develop more stable and standardized grouping of taxa in phyla, classes, orders and families across the kingdoms using divergence times. However, is this feasible? The origins of the kingdoms have been well-studied, however a comparison of the earliest divergence of major taxa (phyla, classes, orders, and families) across these kingdoms is lacking. We therefore considered that it would be of interest to look at ranking of groups across three kingdoms, Animalia, Fungi and Plantae. Are the ranking in these kingdoms comparable or has one or more kingdoms been more liberal in splitting taxa at the higher levels (e.g phyla, classes, orders, families)? We used paleobiological information from early diverged groups among the kingdoms Animalia, Fungi and Plantae corresponding to the geological time scale for comparisons. As a general rule, we found that groups of Animalia classified as phyla, classes, orders and families, diverged earlier as compared to those of the kingdoms Fungi and Plantae. This suggests that animal taxonomists have been more liberal when splitting ranks at the phylum, class and order levels, while at the family level the ranking across kingdoms is comparable. The common trend of evolutionary events could therefore be applied for re-ranking of some groups, especially at the generic and perhaps family levels. However, it would appear an impossible task to standardize higher level rankings across the kingdoms, as there would need to be huge, and probably unacceptable changes. Basically, the mycologists and botanists would need to split much more at the phylum, class and order levels, while the zoologists would need to combine many of their phyla, classes and orders. The data however, suggests that fungal and plant taxonomists could be more liberal when considering new families, orders, classes and phyla in the future.

Keywords: eukaryotic kingdoms – re-ranking – species richness – taxonomic classification

6. The evolution of fungal epiphytes

Authors: Hongsanan S, Sánchez-Ramírez S, Crous PW, Ariyawansa HA, Zhao RL, Hyde KD

Recieved: 13 October 2016, Accepted: 11 December 2016, Published: 29 December 2016

Fungal epiphytes are a polyphyletic group found on the surface of plants, particularly on leaves, with a worldwide distribution. They belong in the phylum Ascomycota, which contains the largest known number of fungal genera. There has been little research dating the origins of the common ancestors of fungal epiphytes. This study uses a molecular clock to provide a rough time frame for the origins of fungal epiphytes in the orders Asterinales, Capnodiales, Meliolales, Microthyriales and Zeloasperisporiales. LSU, SSU, RPB1 and RPB2 sequence data from representative strains of the major classes of Ascomycota are used to represent internal calibration points in the phylogenetic tree, to estimate divergence times of fungal epiphyte lineages. The estimated date crowns of fungal epiphytes included in the orders Asterinales, Capnodiales, Meliolales occur in the middle or the end of Jurassic, with Meliolales and Zeloasperisporiales occurring in the Cretaceous. Foliar epiphytes placed in totally unrelated classes evolved as early as the Permian (298.9 to 252.17 Mya) based on sequence data from representative foliar epiphytes and fossil calibrations. The evolution of the most closely related groups of fungi and foliar epiphytes occurred during the Triassic to Jurassic. Phylogenetic relationships, evolution of morphological characters and nutritional mode of foliar epiphytes are discussed.

Keywords: BEAST – Fossil fungi – MrBayes – Phylogeny – Sooty molds – Taxonomy

7. The evolution of Massarineae with Longipedicellataceae fam. nov.

Authors: Phukhamsakda C, Hongsanan S, Ryberg M, Ariyawansa HA, Chomnunti P, Bahkali AH, Hyde KD

Recieved: 08 November 2016, Accepted: 11 December 2016, Published: 29 December 2016

Massarineae is a suborder of Pleosporales, the latter being the largest order in Dothideomycetes. Massarineae comprises 14 families and six taxa of uncertain placement. In this study, we introduce an additional new family, Longipedicellataceae in Massarineae, which accommodates the genera Longipedicellata and Pseudoxylomyces. The family inhabits submerged culms of plants in freshwater habitats. The family can be distinguished by its very long pedicellate asci and chlamydospore-like structures, which are produced in culture. A LSU, SSU, and RPB2 dataset from representative strains used in our phylogenetic analyses shows the separation of Longipedicellataceae from the other families of Massarineae. In addition, divergence times of families in Massarineae were estimated using a molecular clock methodology. We used an Eocene fossil of Margaretbarromyces dictyosporus to estimate dates in Pleosporales with emphasis on Massarineae. In this study, the crown of Pleosporales is dated to the late Triassic (211 Mya), while the suborder Massarineae is dated to the Cretaceous (130 Mya) and family Longipedicellataceae is dated to Eocene (56 Mya).

Keywords: BEAST – Chlamydospores – Fossil fungi – freshwater fungi – Margaretbarromyces dictyosporus – Pleosporales

8. Palawaniaceae fam. nov., a new family (Dothideomycetes, Ascomycota) to accommodate Palawania species and their evolutionary time estimates

Authors: Mapook A, Hyde KD, Hongsanan S, Phukhamsakda C, Li JF, Boonmee S

Recieved: 02 November 2016, Accepted: 03 December 2016, Published: 29 December 2016

Palawania species are common on palms, occurring on dried fronds and spines, rarely on leaves, at first appearing as solitary, circular, black spots and then being confluent and lacking superficial hyphae. The taxonomy of the genus has been problematic because of lack of some important morphological characters as well as molecular data. Two collections made in Thailand are characterized based on analyses of combined LSU, SSU and RPB2 sequence datasets. Phylogenetic analyses indicate that Palawania species form a sister clade with Pleurotremataceae (= Dyfrolomycetaceae) and have a close relationship with Muyocopronales and Acrospermales. Thus, we introduce a new family Palawaniaceae (Dothideomycetes family, incertae sedis). A new Palawania species is also introduced from northern Thailand based on its distinct phylogeny and comparison of morphological characteristics. The present study clarifies the phylogenetic placement of Palawania and divergence time estimates are provided for the new family.

Keywords: Ascomycota – Dothideomycetes – evolution – new species – phylogeny – taxonomy

9. Evolution of Xylariomycetidae (Ascomycota: Sordariomycetes)

Authors: Samarakoon MC, Hyde KD, Promputtha I, Hongsanan S, Ariyawansa HA, Maharachchikumbura SSN, Daranagama DA, Stadler M, Mapook A

Recieved: 03 December 2016, Accepted: 26 December 2016, Published: 29 December 2016

The class Sordariomycetes, which is the second largest class in the phylum Ascomycota, comprises highly diversified fungal groups, with relatively high substitution and evolutionary rates. In this preliminary study, divergence estimates of taxa of Xylariomycetidae are calculated using Ophiocordyceps fossil evidence and secondary data. The combination of fossil and secondary calibration can affect the divergence time estimates by pushing the ages towards the roots. The estimated divergence of Hypocreomycetidae, Lulworthiomycetidae and Xylariomycetidae occurred during the Early Mesozoic (201-252 Mya) and Diaporthomycetidae and Sordariomycetidae occurred later during the Late Mesozoic (145-252 Mya). Two characteristic divergence groups have evolved 168 and 147 Mya and probably provide additional evidence for continuation and species richness of the orders Amphisphaeriales and Xylariales. The early diversifications of the families in Xylariomycetidae have occurred during the Early Cretaceous (100-145 Mya).

Keywords: divergence time–fossil–paleobiology–secondary data