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Benjamin D. Hall - One of the best experts on this subject based on the ideXlab platform.
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loss of the flagellum happened only once in the fungal lineage phylogenetic structure of kingdom fungi inferred from rna polymerase ii subunit genes
BMC Evolutionary Biology, 2006Co-Authors: Matthew C Hodson, Benjamin D. HallAbstract:Background At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion.
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loss of the flagellum happened only once in the fungal lineage phylogenetic structure of kingdom fungi inferred from rna polymerase ii subunit genes
BMC Evolutionary Biology, 2006Co-Authors: Yajuan J Liu, Matthew C Hodson, Benjamin D. HallAbstract:At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.
Timothy Y. James - One of the best experts on this subject based on the ideXlab platform.
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Novel soil-inhabiting clades fill gaps in the fungal tree of life
Microbiome, 2017Co-Authors: Leho Tedersoo, Rasmus Puusepp, R. Henrik Nilsson, Mohammad Bahram, Timothy Y. JamesAbstract:BackgroundFungi are a diverse eukaryotic group of degraders, pathogens, and symbionts, with many lineages known only from DNA sequences in soil, sediments, air, and water.ResultsWe provide rough phylogenetic placement and principal niche analysis for >40 previously unrecognized fungal groups at the order and class level from global soil samples based on combined 18S (nSSU) and 28S (nLSU) rRNA gene sequences. Especially, Rozellomycota (Cryptomycota), Zygomycota s.lat , Ascomycota, and Basidiomycota are rich in novel fungal lineages, most of which exhibit distinct preferences for climate and soil pH.ConclusionsThis study uncovers the great phylogenetic richness of previously unrecognized order- to phylum-level fungal lineages. Most of these rare groups are distributed in different ecosystems of the world but exhibit distinct ecological preferences for climate or soil pH. Across the fungal kingdom, tropical and non-tropical habitats are equally likely to harbor novel groups. We advocate that a combination of traditional and high-throughput sequencing methods enable efficient recovery and phylogenetic placement of such unknown taxonomic groups.
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a higher level phylogenetic classification of the fungi
Fungal Biology, 2007Co-Authors: David S Hibbett, Joseph F. Bischoff, Sabine Huhndorf, Meredith Blackwell, Ove E Eriksson, Timothy Y. James, Paul M Kirk, Paul F Cannon, Manfred Binder, Robert LückingAbstract:A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella.
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sex in the rest mysterious mating in the chytridiomycota and Zygomycota
2007Co-Authors: Alexander Idnurm, Timothy Y. JamesAbstract:This chapter discusses mating biology of basal fungi with emphasis on chytridiomycetes and zygomycetes. The chytrids and zygomycetes are ecologically diverse. Many of them are parasites, on hosts such as plants, algae, invertebrates, or other fungi. These nutritional requirements have precluded their isolation into axenic culture. Both chytrids and zygomycetes are capable of causing diseases in humans and other animals. A number of zygomycete fungi cause human diseases that are particularly difficult to treat with current antifungal agents. Most of the knowledge of sex in basal fungi comes from studies of behaviors of axenic cultures or careful observations made using light microscopy on natural substrates for the fungi. Chytridiomycetes have long been recognized to be divisible into several major groups based on life cycles and sexual mechanisms. Blastocladiales are exceptional among Fungi by having a life cycle with alternation of generations in which a diploid sporophyte can undergo extensive vegetative growth including asexual reproduction. The Zygomycota comprise nine orders, eight of which include species that undergo homothallic or heterothallic sex. Among the Zygomycota, the Mucorales are the best studied: it is generally inferred that similar patterns of mating occur in the other zygomycetes, although this may not be the case. Microsporidia are obligate intracellular parasites of animals (often insects) and humans, characterized by the absence or remnants of mitochondria and the presence of a specialized structure, the polar tube, with which they infect cells.
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Phylogeny of the Zygomycota based on nuclear ribosomal sequence data
Mycologia, 2006Co-Authors: Timothy Y. James, Kerry O'donnell, Matías J. Cafaro, Yuuhiko TanabeAbstract:The Zygomycota is an ecologically heter- ogenous assemblage of nonzoosporic fungi compris- ing two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested that the phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpel- lales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogo- nales and Mortierellales, which appear more closely related to the Ascomycota + Basidiomycota + Glomeromycota. The final major group, the insect- associated Entomophthorales, appears to be poly- phyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping mor- phological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota.
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molecular phylogenetics of the chytridiomycota supports the utility of ultrastructural data in chytrid systematics
Botany, 2000Co-Authors: Timothy Y. James, David Porter, Celeste LeanderAbstract:The chytrids (Chytridiomycota) are morphologically simple aquatic fungi that are unified by their possession of zoospores that typically have a single, posteriorly directed flagellum. This study addresses the systematics of the chytrids by generating a phylogeny of ribosomal DNA sequences coding for the small subunit gene of 54 chytrids, with emphasis on sampling the largest order, the Chytridiales. Selected chytrid sequences were also compared with se- quences from Zygomycota, Ascomycota, and Basidiomycota to derive an overall fungal phylogeny. These analyses show that the Chytridiomycota is probably not a monophyletic group; the Blastocladiales cluster with the Zygomycota. Analyses did not resolve relationships among chytrid orders, or among clades within the Chytridiales, which suggests that the divergence times of these groups may be ancient. Four clades were well supported within the Chytridiales, and each of these clades was coincident with a group previously identified by possession of a common subtype of zoospore ultrastructure. In contrast, the analyses revealed homoplasy in several developmental and zoosporangial characters.
Matthew C Hodson - One of the best experts on this subject based on the ideXlab platform.
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loss of the flagellum happened only once in the fungal lineage phylogenetic structure of kingdom fungi inferred from rna polymerase ii subunit genes
BMC Evolutionary Biology, 2006Co-Authors: Matthew C Hodson, Benjamin D. HallAbstract:Background At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion.
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loss of the flagellum happened only once in the fungal lineage phylogenetic structure of kingdom fungi inferred from rna polymerase ii subunit genes
BMC Evolutionary Biology, 2006Co-Authors: Yajuan J Liu, Matthew C Hodson, Benjamin D. HallAbstract:At present, there is not a widely accepted consensus view regarding the phylogenetic structure of kingdom Fungi although two major phyla, Ascomycota and Basidiomycota, are clearly delineated. Regarding the lower fungi, Zygomycota and Chytridiomycota, a variety of proposals have been advanced. Microsporidia may or may not be fungi; the Glomales (vesicular-arbuscular mycorrhizal fungi) may or may not constitute a fifth fungal phylum, and the loss of the flagellum may have occurred either once or multiple times during fungal evolution. All of these issues are capable of being resolved by a molecular phylogenetic analysis which achieves strong statistical support for major branches. To date, no fungal phylogeny based upon molecular characters has satisfied this criterion. Using the translated amino acid sequences of the RPB1 and RPB2 genes, we have inferred a fungal phylogeny that consists largely of well-supported monophyletic phyla. Our major results, each with significant statistical support, are: (1) Microsporidia are sister to kingdom Fungi and are not members of Zygomycota; that is, Microsporidia and fungi originated from a common ancestor. (2) Chytridiomycota, the only fungal phylum having a developmental stage with a flagellum, is paraphyletic and is the basal lineage. (3) Zygomycota is monophyletic based upon sampling of Trichomycetes, Zygomycetes, and Glomales. (4) Zygomycota, Basidiomycota, and Ascomycota form a monophyletic group separate from Chytridiomycota. (5) Basidiomycota and Ascomycota are monophyletic sister groups. In general, this paper highlights the evolutionary position and significance of the lower fungi (Zygomycota and Chytridiomycota). Our results suggest that loss of the flagellum happened only once during early stages of fungal evolution; consequently, the majority of fungi, unlike plants and animals, are nonflagellated. The phylogeny we infer from gene sequences is the first one that is congruent with the widely accepted morphology-based classification of Fungi. We find that, contrary to what has been published elsewhere, the four morphologically defined phyla (Ascomycota, Basidiomycota, Zygomycota and Chytridiomycota) do not overlap with one another. Microsporidia are not included within kingdom Fungi; rather they are a sister-group to the Fungi. Our study demonstrates the applicability of protein sequences from large, slowly-evolving genes to the derivation of well-resolved and highly supported phylogenies across long evolutionary distances.
Yuuhiko Tanabe - One of the best experts on this subject based on the ideXlab platform.
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Phylogeny of the Zygomycota based on nuclear ribosomal sequence data
Mycologia, 2006Co-Authors: Timothy Y. James, Kerry O'donnell, Matías J. Cafaro, Yuuhiko TanabeAbstract:The Zygomycota is an ecologically heter- ogenous assemblage of nonzoosporic fungi compris- ing two classes, Zygomycetes and Trichomycetes. Phylogenetic analyses have suggested that the phylum is polyphyletic; two of four orders of Trichomycetes are related to the Mesomycetozoa (protists) that diverged near the fungal/animal split. Current circumscription of the Zygomycota includes only orders with representatives that produce zygospores. We present a molecular-based phylogeny including recognized representatives of the Zygomycetes and Trichomycetes with a combined dataset for nuclear rRNA 18S (SSU), 5.8S and 28S (LSU) genes. Tree reconstruction by Bayesian analyses suggests the Zygomycota is paraphyletic. Although 12 clades were identified only some of these correspond to the nine orders of Zygomycota currently recognized. A large superordinal clade, comprising the Dimargaritales, Harpellales, Kickxellales and Zoopagales, grouping together many symbiotic fungi, also is identified in part by a unique septal structure. Although Harpel- lales and Kickxellales are not monophyletic, these lineages are distinct from the Mucorales, Endogo- nales and Mortierellales, which appear more closely related to the Ascomycota + Basidiomycota + Glomeromycota. The final major group, the insect- associated Entomophthorales, appears to be poly- phyletic. In the present analyses Basidiobolus and Neozygites group within Zygomycota but not with the Entomophthorales. Clades are discussed with special reference to traditional classifications, mapping mor- phological characters and ecology, where possible, as a snapshot of our current phylogenetic perspective of the Zygomycota.
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evolutionary relationships among basal fungi chytridiomycota and Zygomycota insights from molecular phylogenetics
Journal of General and Applied Microbiology, 2005Co-Authors: Yuuhiko Tanabe, Makoto M WatanabeAbstract:Evolutionary relationships of the two basal fungal phyla Chytridiomycota and Zygomycota are reviewed in light of recent molecular phylogenetic investigation based on rDNA (nSSU, nLSU rDNA), entire mitochondrial genomes, and nuclear protein coding gene sequences (e.g., EF-1α, RPB1). Accumulated molecular evidence strongly suggests that the two basal fungal phyla are not monophyletic. For example, the chytridiomycete order Blastocladiales appears to be closely related to the zygomycete order Entomophthorales. Within the Zygomycota, a monophyletic clade, consisting of the Dimargaritales, Harpellales, and Kickxellales, which is characterized by a shared unique septal ultrastructure, was identified. Moreover, evidence for the exclusion of zygomycete orders Amoebidiales and Eccrinales from the Fungi, and their placement at the Animal-Fungi boundary has been clearly documented. Microsporidia, a group of amitochondriate organisms currently under intensive study, is not supported as derived within the Fungi, but a fungal affinity cannot be ruled out. Taking these molecular phylogenetic studies into account, we proposed a hypothetical evolutionary framework of basal fungi.
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Group I Introns from Zygomycota: Evolutionary Implications for the Fungal IC1 Intron Subgroup
Journal of Molecular Evolution, 2002Co-Authors: Yuuhiko Tanabe, Akira YokotaAbstract:The origins of fungal group I introns within nuclear small-subunit (nSSU) rDNA are enigmatic. This is partly because they have never been reported in basal fungal phyla (Zygomycota and Chytridiomycota), which are hypothesized to be ancestral to derived phyla (Ascomycota and Basidiomycota). Here we report group I introns from the nSSU rDNA of two zygomycete fungi, Zoophagus insidians (Zoopagales) and Coemansia mojavensis (Kickxellales). Secondary structure analyses predicted that both introns belong to the IC1 subgroup and that they are distantly related to each other, which is also suggested by different insertion sites. Molecular phylogenetic analyses indicated that the IC1 intron of Z. insidians is closely related to the IC1 intron inserted in the LSU rDNA of the basidiomycete fungus Clavicorona taxophila , which strongly suggests interphylum horizontal transfer. The IC1 intron of C. mojavensis has a low phylogenetic affinity to other fungal IC1 introns inserted into site 943 of nSSU rDNA (relative to E. coli 16S rDNA). It is noteworthy that this intron contains a putative ORF containing a His–Cys box motif in the antisense strand, a hallmark for nuclear-encoded homing endonucleases. Overall, molecular phylogenetic analyses do not support the placement of these two introns in basal fungal IC1 intron lineages. This result leads to the suggestion that fungal IC1 introns might have invaded or been transferred laterally after the divergence of the four major fungal phyla.
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Molecular Phylogeny of Parasitic Zygomycota (Dimargaritales, Zoopagales) Based on Nuclear Small Subunit Ribosomal DNA Sequences
Molecular phylogenetics and evolution, 2000Co-Authors: Yuuhiko Tanabe, Kerry O'donnell, Masatoshi SaikawaAbstract:We analyzed sequence data of the 18S rDNA gene from representatives of nine mycoparasitic or zooparasitic genera to infer the phylogenetic relationships of these fungi within the Zygomycota. Phylogenetic analyses identified a novel monophyletic clade consisting of the Zoopagales, Kickxellales, Spiromyces, and Harpellales. Analyses also identified a monophyletic mycoparasitic–zooparasitic Zoopagales clade in which Syncephalis, Thamnocephalis, and Rhopalomyces form a sister group to a Piptocephalis–Kuzuhaea clade. Although monophyly of the mycoparasitic Dimargaritales received strong bootstrap and decay index support, phylogenetic relationships of this order could not be resolved because of the unusually high rate of base substitutions within the 18S rDNA gene. Overall, the 18S gene tree topology is weak, as reflected by low bootstrap and decay index support for virtually all internal nodes uniting ordinal and superordinal taxa. Nevertheless, the 18S rDNA phylogeny is mostly consistent with traditional phenotypic-based classification schemes of the Fungi.
Jonathan M. Adams - One of the best experts on this subject based on the ideXlab platform.
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Fungal Elevational Rapoport pattern from a High Mountain in Japan
Scientific Reports, 2019Co-Authors: Matthew Chidozie Ogwu, Itumeleng Moroenyane, Bruce Waldman, Ho-kyung Song, Ke Dong, Koichi Takahashi, Jonathan M. AdamsAbstract:Little is known of how fungal distribution ranges vary with elevation. We studied fungal diversity and community composition from 740 to 2940 m above sea level on Mt. Norikura, Japan, sequencing the ITS2 region. There was a clear trend, repeated across each of the fungal phyla (Basidiomycota, Ascomycota, Zygomycota, Chytridomycota and Glomeromycota), and across the whole fungal community combined, towards an increased elevational range of higher elevation OTUs, conforming to the elevational Rapoport pattern. It appears that fungi from higher elevation environments are more generalized ecologically, at least in terms of climate-related gradients. These findings add to the picture from latitudinal studies of fungal ranges, which also suggest that the classic Rapoport Rule (broader ranges at higher latitudes) applies on a geographical scale. However, there was no mid-elevation maximum in diversity in any of the phyla studied, and different diversity trends for the different phyla, when different diversity indices were used. In terms of functional guilds, on Norikura there were trends towards increased saprotrophism (Zygomycota), symbiotrophism (Basidiomycota), symbiotrophism and saprotrophism (Ascomycota) and pathotrophism (Chytridiomycota) with elevation. The causes of each of these trends require further investigation from an ecological and evolutionary viewpoint.