scholarly journals A Phylogenetic Assessment of Endocalyx (Cainiaceae, Xylariales) With E. Grossus Comb. et Stat. Nov.

2021 ◽  
Author(s):  
Gregorio Delgado ◽  
Andrew N Miller ◽  
Akira Hashimoto ◽  
Toshiya Iida ◽  
Moriya Ohkuma ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Nuclear Ribosomal Dna ◽  
Species Status ◽  
Characteristic Mode ◽  
Dna Sequence Data ◽  
Monophyletic Lineage ◽  
The Family ◽  
Phylogenetic Affinities ◽  
Lsu Nrdna

Abstract The phylogenetic affinities of four representative Endocalyx taxa, including three species and two varieties, are studied based on materials collected on different palm hosts in Japan and the states of Hawaii and Texas, USA. They include specimens and their isolates belonging to E. cinctus, E. indumentum, E. melanoxanthus var. grossus and E. melanoxanthus var. melanoxanthus. Phylogenetic analyses of nuclear ribosomal DNA sequence data (ITS-LSU nrDNA) confirmed that Endocalyx belongs to the order Xylariales (Sordariomycetes) where all species and varieties treated form a strongly supported monophyletic lineage within the family Cainiaceae. They were also phylogenetically well resolved and consistent with their morphological and ecological circumscription. Species status is proposed for E. melanoxanthus var. grossus under the name E. grossus comb. et stat. nov. on the basis of its distinct morphological, molecular, cultural and ecological characteristics. The putative placement of Endocalyx within the family Apiosporaceae (Amphisphaeriales) based on the presence of basauxic conidiophores is rejected considering that all species treated clustered within the distant Cainiaceae (Xylariales). This characteristic mode of conidiophore elongation is determined to have evolved independently within unrelated or distant ascomycetous lineages. Novel morphological and cultural features of Endocalyx taxa based on new isolates are commented. The recently described E. metroxyli is reduced to synonym with E. melanoxanthus.

Marinophialophora garethjonesii gen. et sp. nov.: a new hyphomycete associated with Halocyphina from marine habitats in Thailand

Phytotaxa ◽  
2018 ◽  
Vol 345 (1) ◽  
pp. 1 ◽  
Author(s):  
JUNFU LI ◽  
RAJESH JEEWON ◽  
RUNGTIWA PHOOKAMSAK ◽  
DARBHE J. BHAT ◽  
AUSANA MAPOOK ◽  
...  
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Marine Habitats ◽  
The Family ◽  
Statistical Support ◽  
Branched Chains ◽  
Mangrove Wood ◽  
High Statistical Support ◽  
Basidiomycete Fungus

Marinophialophora garethjonesii sp. nov., representing a novel genus Marinophialophora gen. nov., associated with the basidiomycete fungus, Halocyphina on mangrove wood from Phetchaburi, Thailand, is described and illustrated. Marinophialophora morphologically resembles Phialophora and Junctospora (Herpotrichiellaceae, Chaetothyriales) in having macronematous, unbranched or branched conidiophores, globose to subglobose, solitary, acrogenous, pale to subhyaline, aseptate, conidia in chains and phialidic conidiogenous cells. Marinophialophora mainly differs from other related genera due to its conidia borne in basipetally developing branched chains and septate conidiophores. Phylogenetic analyses of a combined ITS, LSU and SSU sequence data show that Marinophialophora garethjonesii constitutes an independent lineage with high statistical support basal to the genus Exophiala within the family Herpotrichiellaceae (Chaetothyriales). The new marine taxon is described herein with illustrations and relationships inferred from DNA sequence data.

Molecular evolution and diversification of the vestimentiferan tube worms

1993 ◽  
Vol 73 (2) ◽  
pp. 437-452 ◽  
Author(s):  
Nic A. Williams ◽  
David R. Dixon ◽  
Eve C. Southward ◽  
Peter W. H. Holland
Keyword(s):  
Dna Sequences ◽  
Deep Sea ◽  
Marine Invertebrates ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Dna Sequence Data ◽  
Evolutionary Diversification ◽  
Tube Worms ◽  
Eastern Atlantic Ocean ◽  
Phylogenetic Affinities

The Vestimentifera, or deep-sea tube worms, comprise an ecologically and anatomically unusual group of marine invertebrates, with poorly understood biogeography, ecology, phylogenetic affinities and evolutionary radiation. To gain insight into evolutionary diversification within the group, we have used a molecular biological approach. We report the cloning of a region of 28S ribosomal DNA from representatives of five vestimentiferan genera plus, for comparison, a polychaete and a perviate pogonophore. Phylogenetic analyses using these DNA sequences confirm thatRidgeiaandTevniaare closely related genera. The analyses also lead us to propose the hypothesis that the earliest vestimentiferan lineage to diverge gave rise to the genusLamellibrachiaonly. In addition, our comparative DNA sequence data now provide a means to use molecular methods for identification of deep-sea tube worms; we employed this approach to demonstrate that the first vestimentiferan specimen from the eastern Atlantic Ocean belongs to the genusLamellibrachia. DNA-based identification should have wide applications in the study of vestimentiferan biogeography and ecology.

scholarly journals Phylogeny of the family Trogidae (Coleoptera: Scarabaeoidea) inferred from mitochondrial and nuclear ribosomal DNA sequence data

2014 ◽  
Vol 39 (3) ◽  
pp. 548-562 ◽  
Author(s):  
WERNER P. STRÜMPHER ◽  
CATHERINE L. SOLE ◽  
MARTIN H. VILLET ◽  
CLARKE H. SCHOLTZ
Keyword(s):  
Dna Sequence ◽  
Ribosomal Dna ◽  
Sequence Data ◽  
Nuclear Ribosomal Dna ◽  
Dna Sequence Data ◽  
The Family ◽  
Ribosomal Dna Sequence

scholarly journals Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8999
Author(s):  
Sigrid Liede-Schumann ◽  
Guido W. Grimm ◽  
Nicolai M. Nürk ◽  
Alastair J. Potts ◽  
Ulrich Meve ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Rapid Radiation ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities ◽  
African Genus

Background Drosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum, together with the highly succulent and species-rich tribe Ruschieae, constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution. Methods Using chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species of Drosanthemum with multiple accessions for widespread species. A well-curated, geo-referenced occurrence dataset comprising the 134 genetically analysed and 863 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole. Results Phylogenetic inference supports nine clades within Drosanthemum, seven of which group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as cryptic species. In-depth analyses of sequence patterns in each gene region were used to reveal phylogenetic affinities inside the retrieved clades in more detail. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are genetically and morphologically diverse. In contrast, less species-rich, genetically less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest that the main lineages arose from an initial rapid radiation, with subsequent diversification in some clades.

scholarly journals Phylogenetic relationships in the southern African genus Drosanthemum (Ruschioideae, Aizoaceae)

2019 ◽  
Author(s):  
Sigrid Liede-Schumann ◽  
Guido W. Grimm ◽  
Nicolai M. Nürk ◽  
Alastair J. Potts ◽  
Ulrich Meve ◽  
...  
Keyword(s):  
Phylogenetic Relationships ◽  
Nuclear Dna ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Cape Floristic Region ◽  
Rapid Radiation ◽  
Data Set ◽  
Widespread Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

AbstractBackgroundDrosanthemum, the only genus of the tribe Drosanthemeae, is widespread over the Greater Cape Floristic Region in southern Africa. With 114 recognized species, Drosanthemum together with the highly succulent and species-rich tribe Ruschieae constitute the ‘core ruschioids’ in Aizoaceae. Within Drosanthemum, nine subgenera have been described based on flower and fruit morphology. Their phylogenetic relationships, however, have not yet been investigated, hampering understanding of monophyletic entities and patterns of geographic distribution.MethodsUsing chloroplast and nuclear DNA sequence data, we performed network- and tree-based phylogenetic analyses of 73 species represented by multiple accessions of Drosanthemum. A well-curated, geo-referenced occurrence data set comprising the phylogenetically studied and 867 further accessions was used to describe the distributional ranges of intrageneric lineages and the genus as a whole.ResultsPhylogenetic inference supports nine clades within Drosanthemum, seven of them group in two major clades, while the remaining two show ambiguous affinities. The nine clades are generally congruent to previously described subgenera within Drosanthemum, with exceptions such as (pseudo-) cryptic species. In-depth analyses of sequence patterns in each gene region revealed phylogenetic affinities not obvious in the phylogenetic tree. We observe a complex distribution pattern including widespread, species-rich clades expanding into arid habitats of the interior (subgenera Drosanthemum p.p., Vespertina, Xamera) that are molecular and morphologically diverse. In contrast, less species-rich, molecularly less divergent, and morphologically unique lineages are restricted to the central Cape region and more mesic conditions (Decidua, Necopina, Ossicula, Quastea, Quadrata, Speciosa). Our results suggest initial rapid radiation generating the main lineages, with some clades showing subsequent diversification.

scholarly journals Phylogenetic Relationships of the Red-Bellied Grackle (Icteridae: Hypopyrrhus Pyrohypogaster) Inferred From Mitochondrial DNA Sequence Data

The Condor ◽  
2004 ◽  
Vol 106 (3) ◽  
pp. 664-670 ◽  
Author(s):  
Carlos Daniel Cadena ◽  
Andrés M. Cuervo ◽  
Scott M. Lanyon
Keyword(s):  
New World ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Mitochondrial Genes ◽  
Morphological Data ◽  
South American ◽  
South American Species ◽  
Dna Sequence Data ◽  
Phylogenetic Affinities

Abstract The phylogenetic affinities of the Red-bellied Grackle (Hypopyrrhus pyrohypogaster), a Colombian endemic and the only member of this genus, are enigmatic. Based on phylogenetic analyses of sequences from the cytochrome b and ND2 mitochondrial genes, we present a first hypothesis on the systematic position of Hypopyrrhus. In so doing, we complete the sampling at the genus level for a published phylogeny of New World blackbirds (Johnson and Lanyon 1999). Hypopyrrhus belongs in a clade composed of mostly South American species within the grackles and allies assemblage, one of the five main lineages in the Icteridae. Within this lineage, Hypopyrrhus is consistently placed in a clade with Gymnomystax mexicanus and Lampropsar tanagrinus, but parsimony and maximum-likelihood reconstructions do not agree on which of these species is its sister taxon. Vocal and morphological data suggest that Hypopyrrhus and Gymnomystax are likely sister taxa. The addition of Hypopyrrhus does not cause major topological changes to Johnson and Lanyon's (1999) phylogeny of the grackles and allies; thus, the conclusions of evolutionary studies that used this phylogeny as a baseline remain largely unaltered. Relaciones Filogenéticas de Hypopyrrhus pyrohypogaster (Icteridae) Inferidas a Partir de Secuencias de ADN Mitocondrial Resumen. Las afinidades filogenéticas de Hypopyrrhus pyrohypogaster, el único miembro de este género endémico de Colombia, son enigmáticas. En este estudio establecemos la posición sistemática de Hypopyrrhus con base en análisis filogenéticos de secuencias de los genes mitocondriales citocromo b y ND2. Además, completamos el muestreo a nivel genérico para una filogenia del grupo publicada por Johnson y Lanyon (1999). Hypopyrrhus pertenece a un clado compuesto principalmente por especies suramericanas dentro del grupo de los changos y chamones, uno de los cinco clados principales de los Icteridae. Dentro de este grupo, Hypopyrrhus se ubica consistentemente en un clado junto con Gymnomystax mexicanus y Lampropsar tanagrinus, pero las reconstrucciones de parsimonia y máxima verosimilitud se contradicen en cuanto a cuál de estas especies es su taxón hermano. Datos de vocalizaciones y morfología sugieren que Hypopyrrhus y Gymnomystax son probablemente géneros hermanos. La incorporación de Hypopyrrhus a la filogenia de Johnson y Lanyon (1989) no causó cambios topoló gicos importantes, por lo que las conclusiones de los estudios evolutivos que usaron esta filogenia como base no fueron alteradas.

scholarly journals A Study on the Phylogeny of the Dyer's Woad Rust Fungus and Other Species of Puccinia from Crucifers

1997 ◽  
Vol 87 (5) ◽  
pp. 565-571 ◽  
Author(s):  
Bradley R. Kropp ◽  
Dane R. Hansen ◽  
Paul G. Wolf ◽  
Karen M. Flint ◽  
Sherman V. Thomson
Keyword(s):  
North America ◽  
Sequence Data ◽  
Biological Control Agent ◽  
Rust Fungus ◽  
Control Agent ◽  
Nuclear Ribosomal Dna ◽  
Indigenous Plants ◽  
Dna Sequence Data ◽  
The North ◽  
The Family

The identity of a Puccinia species occurring on the introduced weed dyer's woad (Isatis tinctoria) was studied using sequences from the internal transcribed spacer of the nuclear ribosomal DNA. The relationship of this fungus to other Puccinia species occurring on the family Brassicaceae in Europe and North America was examined, and we tested the hypothesis that P. thlaspeos and P. monoica are correlated species. The data suggest that the Puccinia species from dyer's woad is closely related to the North American species P. consimilis and may be derived from an indigenous strain of P. consimilis that switched hosts. Thus, the Puccinia species from dyer's woad is probably native to North America and is unlikely to cause disease epidemics on indigenous plants if used as a biological control agent against dyer's woad. P. thlaspeos appears to be polyphyletic and, therefore, P. thlaspeos and P. monoica do not appear to be correlated species. Additional DNA sequence data will be needed to clarify further the phylogeny of Puccinia species on the family Brassicaceae.

scholarly journals Taxonomic Re-Examination of Nine Rosellinia Types (Ascomycota, Xylariales) Stored in the Saccardo Mycological Collection

2021 ◽  
Vol 9 (3) ◽  
pp. 666
Author(s):  
Niccolò Forin ◽  
Alfredo Vizzini ◽  
Federico Fainelli ◽  
Enrico Ercole ◽  
Barbara Baldan
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Illumina Miseq ◽  
Botanical Garden ◽  
Molecular Study ◽  
Its2 Sequence ◽  
Type Specimens ◽  
Its1 Sequence ◽  
Dna Sequence Data ◽  
Nomen Novum

In a recent monograph on the genus Rosellinia, type specimens worldwide were revised and re-classified using a morphological approach. Among them, some came from Pier Andrea Saccardo’s fungarium stored in the Herbarium of the Padova Botanical Garden. In this work, we taxonomically re-examine via a morphological and molecular approach nine different Roselliniasensu Saccardo types. ITS1 and/or ITS2 sequences were successfully obtained applying Illumina MiSeq technology and phylogenetic analyses were carried out in order to elucidate their current taxonomic position. Only the ITS1 sequence was recovered for Rosellinia areolata, while for R. geophila, only the ITS2 sequence was recovered. We proposed here new combinations for Rosellinia chordicola, R. geophila and R. horridula, while for R. ambigua, R. areolata, R. australis, R. romana and R. somala, we did not suggest taxonomic changes compared to the current ones. The name Rosellinia subsimilis Sacc. is invalid, as it is a later homonym of R. subsimilis P. Karst. & Starbäck. Therefore, we introduced Coniochaeta dakotensis as a nomen novum for R. subsimilis Sacc. This is the first time that these types have been subjected to a molecular study. Our results demonstrate that old types are an important source of DNA sequence data for taxonomic re-examinations.

scholarly journals Sequence data from isolated lichen-associated melanized fungi enhance delimitation of two new lineages within Chaetothyriomycetidae

2021 ◽  
Vol 20 (7) ◽  
pp. 911-927
Author(s):  
Lucia Muggia ◽  
Yu Quan ◽  
Cécile Gueidan ◽  
Abdullah M. S. Al-Hatmi ◽  
Martin Grube ◽  
...  
Keyword(s):  
Sequence Data ◽  
Single Species ◽  
Sister Group ◽  
Asexual Propagation ◽  
Dna Sequence Data ◽  
Wide Range ◽  
The Family ◽  
Rock Inhabiting Fungi ◽  
Stable Habitat

AbstractLichen thalli provide a long-lived and stable habitat for colonization by a wide range of microorganisms. Increased interest in these lichen-associated microbial communities has revealed an impressive diversity of fungi, including several novel lineages which still await formal taxonomic recognition. Among these, members of the Eurotiomycetes and Dothideomycetes usually occur asymptomatically in the lichen thalli, even if they share ancestry with fungi that may be parasitic on their host. Mycelia of the isolates are characterized by melanized cell walls and the fungi display exclusively asexual propagation. Their taxonomic placement requires, therefore, the use of DNA sequence data. Here, we consider recently published sequence data from lichen-associated fungi and characterize and formally describe two new, individually monophyletic lineages at family, genus, and species levels. The Pleostigmataceae fam. nov. and Melanina gen. nov. both comprise rock-inhabiting fungi that associate with epilithic, crust-forming lichens in subalpine habitats. The phylogenetic placement and the monophyly of Pleostigmataceae lack statistical support, but the family was resolved as sister to the order Verrucariales. This family comprises the species Pleostigma alpinum sp. nov., P. frigidum sp. nov., P. jungermannicola, and P. lichenophilum sp. nov. The placement of the genus Melanina is supported as a lineage within the Chaetothyriales. To date, this genus comprises the single species M. gunde-cimermaniae sp. nov. and forms a sister group to a large lineage including Herpotrichiellaceae, Chaetothyriaceae, Cyphellophoraceae, and Trichomeriaceae. The new phylogenetic analysis of the subclass Chaetothyiomycetidae provides new insight into genus and family level delimitation and classification of this ecologically diverse group of fungi.

scholarly journals Biological and Phylogenetic Analyses Suggest that Two Cryphonectria spp. Cause Cankers of Eucalyptus in Africa

Plant Disease ◽  
2003 ◽  
Vol 87 (11) ◽  
pp. 1329-1332 ◽  
Author(s):  
J. Roux ◽  
H. Myburg ◽  
B. D. Wingfield ◽  
M. J. Wingfield
Keyword(s):  
South Africa ◽  
South America ◽  
South African ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Eucalyptus Grandis ◽  
Its Region ◽  
South African Isolate ◽  
Dna Sequence Data ◽  
The Republic

Cryphonectria cubensis is an economically important pathogen of commercial Eucalyptus spp. Differences have been reported for disease symptoms associated with Cryphonectria canker in South Africa and other parts of the world, and recent DNA-based comparisons have confirmed that the fungus in South Africa is different from that in South America and Australasia. During a disease survey in the Republic of Congo, Cryphonectria canker was identified as an important disease on Eucalyptus grandis and E. urophylla. In this study, we compared Congolese and South African isolates of C. cubensis using DNA sequence data and pathogenicity under greenhouse conditions. The β-tubulin and internal transcribed spacer (ITS) region sequences show that C. cubensis in Congo is different from the fungus in South Africa and that Congolese isolates group most closely with South American isolates. Furthermore, pathogenicity tests showed that a South African isolate was more aggressive than two Congolese isolates. We conclude that two distinct Cryphonectria spp. occur in Africa and hypothesize that the fungus in the Congo probably was introduced into Africa from South America. Both fungi are important pathogens causing disease and death of economically important plantation trees. However, they apparently have different origins and must be treated separately in terms of disease management and quarantine considerations.

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