Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences

2000 ◽  
Vol 77 (12) ◽  
pp. 1790-1800 ◽  
Author(s):  
Alexandra Riethmüller ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Bootstrap Method ◽  
Large Subunit ◽  
Phytophthora Megasperma ◽  
Parsimony Method ◽  
Natural Group ◽  
Maximum Parsimony Method ◽  
Phylogenetic Studies ◽  
Main Emphasis

To reveal phylogenetic relationships within the Peronosporomycetes (Oomycetes), we sequenced a part of the nuclear rDNA coding for the ribosomal large subunit of 46 Peronosporomycetes species and one representative of the Xanthophyta. The main emphasis of our study was put on the phylogenetic relationships within the Saprolegniomycetidae. We supplemented our data with a sequence of Phytophthora megasperma Drechsler from GenBank. Two sets of sequences were analysed using the neighbor-joining method, statistically supported by the bootstrap method, as well as the maximum parsimony method. Our results are well compatible with the tripartite subclassification of the Peronosporomycetes into Saprolegniomycetidae, Rhipidiomycetidae and Peronosporomycetidae, as well as with the placement of the orders Saprolegniales and Leptomitales in the Saprolegniomycetidae. Pachymetra chaunorhiza Croft & Dick, which has been placed in the Sclerosporales, was grouped within the Saprolegniales. Within the Peronosporomycetidae, the orders Peronosporales and Pythiales could not be separated. There are indications that Phytophthora de Bary and the Peronosporales form a common natural group. The genus Achlya Nees proved to be a heterogeneous group.

scholarly journals Phylogenetic Relationships of Agaric Fungi Based on Nuclear Large Subunit Ribosomal DNA Sequences

2000 ◽  
Vol 49 (2) ◽  
pp. 278-305 ◽  
Author(s):  
Jean-Marc Moncalvo ◽  
François M. Lutzoni ◽  
Stephen A. Rehner ◽  
Jacqui Johnson ◽  
Rytas Vilgalys
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Large Subunit

Molecular phylogenetic studies in the genus Amanita

1998 ◽  
Vol 76 (7) ◽  
pp. 1170-1179 ◽  
Author(s):  
Michael Weiß ◽  
Zhu-Liang Yang ◽  
Franz Oberwinkler
Keyword(s):  
Dna Sequences ◽  
Nuclear Dna ◽  
Large Subunit ◽  
Bootstrap Analysis ◽  
Phylogenetic Studies ◽  
Maximum Likelihood Methods ◽  
Molecular Phylogenetic ◽  
Large Subunit Rdna ◽  
Conditional Clustering ◽  
Natural Groups

A group of 49 Amanita species that had been thoroughly examined morphologically and anatomically was analyzed by DNA sequence comparison to estimate natural groups and phylogenetic relationships within the genus. Nuclear DNA sequences coding for a part of the ribosomal large subunit were determined and evaluated using neighbor-joining with bootstrap analysis, parsimony analysis, conditional clustering, and maximum likelihood methods. Sections Amanita, Caesarea, Vaginatae, Validae, Phalloideae, and Amidella were substantially confirmed as monophyletic groups, while the monophyly of section Lepidella remained unclear. Branching topologies between and within sections could also partially be derived. Subgenera Amanita and Lepidella were not supported. The Mappae group was included in section Validae. Grouping hypotheses obtained by DNA analyses are discussed in relation to the distribution of morphological and anatomical characters in the studied species.Key words: fungi, basidiomycetes phylogeny, Agaricales, Amanita systematics, large subunit rDNA, 28S.

Phylogeny of the rust fungi: an approach using nuclear large subunit ribosomal DNA sequences

2003 ◽  
Vol 81 (1) ◽  
pp. 12-23 ◽  
Author(s):  
Wolfgang Maier ◽  
Dominik Begerow ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Large Subunit ◽  
Rust Fungi ◽  
Monophyletic Group ◽  
Neighbor Joining ◽  
Natural Group ◽  
Outgroup Species ◽  
Large Subunit Rdna

Sequence data from nuclear large subunit ribosomal DNA was used to infer phylogenetic relationships of selected genera of the Uredinales. We investigated 52 rust fungi representing nine families and three outgroup species. Neighbor joining analysis and a Bayesian method of phylogenetic inference using Monte Carlo Markov chains confirm the rust fungi as a natural group and indicate that Puccinia, Uromyces, Endophyllum, and Cumminsiella have a common origin. The autoecious Rosaceae-rusts Phragmidium, Kuehneola, Triphragmium, and Trachyspora are a monophyletic group. The gasteroid genus Ochropsora is closely related to Tranzschelia. While the Pucciniastreae sensu Dietel (1938) is recognized as a monophyletic group in neighbor joining analysis, the Pucciniaceae s.l. (Dietel 1928) is supported by Bayesian analysis. The following genera appear to be monophyletic: Chrysomyxa, Coleosporium, Cronartium, Gymnosporangium, Melampsora, Phragmidium, and Tranzschelia, whereas the genera Puccinia, Pucciniastrum, Thekopsora, and Uromyces are not.Key words: molecular phylogeny, systematics, nuclear large subunit rDNA, Basidiomycota, Urediniomycetes, Uredinales.

scholarly journals A New Species of Andean Gymnophthalmid Lizard (Squamata: Gymnophthalmidae) from the Peruvian Andes, and Resolution of Some Taxonomic Problems

Diversity ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 361
Author(s):  
Luis Mamani ◽  
Juan C. Chaparro ◽  
Claudio Correa ◽  
Consuelo Alarcón ◽  
Cinthya Y. Salas ◽  
...  
Keyword(s):  
New Species ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Taxonomic Status ◽  
Neotropical Region ◽  
Likelihood Method ◽  
Peruvian Andes ◽  
Phylogenetic Studies ◽  
The Family ◽  
A New Species

The family Gymnophthalmidae is one of the most speciose lineages of lizards in the Neotropical region. Despite recent phylogenetic studies, the species diversity of this family is unknown and thus, its phylogenetic relationships remain unclear and its taxonomy unstable. We analyzed four mitochondrial (12S, 16S, Cytb, ND4) and one nuclear (c-mos) DNA sequences of Pholidobolus anomalus, Cercosaura manicata boliviana and Cercosaura sp., using the maximum likelihood method to give insights into the phylogenetic relationships of these taxa within Cercosaurinae. Our results suggest that Pholidolus anomalus is nested within the clade of Cercosaura spp., that material we collected near Oxapampa belongs to a new species of Cercosaura, and that lizards identified as Cercosaura manicata boliviana belong to a separate lineage, possibly a new genus. We assign Pholidobolus anomalus to Cercosaura, redescribe the species, and designate a neotype to replace the lost holotype. In addition, we describe the new species of Cercosaura, and comment about the taxonomic status of “Cercosaura manicata boliviana”incertae sedis.

A REASSESSMENT OF PHYLOGENETIC RELATIONSHIPS WITHIN THE PHAEOPHYCEAE BASED ON RUBISCO LARGE SUBUNIT AND RIBOSOMAL DNA SEQUENCES

2001 ◽  
Vol 37 (4) ◽  
pp. 586-603 ◽  
Author(s):  
Stefano G. A. Draisma ◽  
Willem F. Prud'Homme van Reine ◽  
Wytze T. Stam ◽  
Jeanine L. Olsen
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Large Subunit

A preliminary phylogenetic analysis of the genus Fulvius Stål (Hemiptera:Miridae: Cylapinae) based on molecular data

2008 ◽  
Vol 39 (4) ◽  
pp. 407-417 ◽  
Author(s):  
Izabela Sadowska-Woda ◽  
Tobias Malm ◽  
Frédéric Chérot
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Sequence Data ◽  
Large Subunit ◽  
Morphological Characters ◽  
Molecular Data ◽  
Dna Sequence Data ◽  
Species Groups ◽  
Coi Sequences ◽  
Preliminary Phylogenetic Analysis

AbstractThe systematics and phylogeny of the genus Fulvius Stål remains unclear. We present herein the first analysis of the phylogenetic relationships within the genus Fulvius based on DNA sequences. The phylogenetic interrelationships in the genus Fulvius are investigated using partial DNA sequence data from two mitochondrial genes, the 16S ribosomal large subunit and the cytochrome oxidase I (COI). DNA sequences for Fulvius species representing three different subgroups distinguished previously on the base of morphological characters alone are compared to sequences from the closely related genera Rhinocylapidius and Cylapus. The data are analyzed using parsimony and Bayesian inference. The results confirm that on the basis of molecular data we can distinguish the same congruent groups of Fulvius species as using morphological characters, however with inclusion of the specimens of the genus Rhinocylapidius in the bifenestratus-group. Additional studies are needed to clarify the phylogenetic relationships within the tribe Fulviini, as well as within the genus Fulvius and its relation to Rhinocylapidius. However, the results of this study suggest that 16S and COI sequences will be very useful as molecular markers for such studies among these species-groups.

Phylogenetic studies of Saprolegniomycetidae and related groups based on nuclear large subunit ribosomal DNA sequences

1999 ◽  
Vol 77 (12) ◽  
pp. 1790-1800 ◽  
Author(s):  
Ale×andra Riethmüller ◽  
Michael Weiß ◽  
Franz Oberwinkler
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Large Subunit ◽  
Phylogenetic Studies

Phylogenetic Relationships of the Downy Mildews (Peronosporales) and Related Groups Based on Nuclear Large Subunit Ribosomal DNA Sequences

Mycologia ◽  
2002 ◽  
Vol 94 (5) ◽  
pp. 834 ◽  
Author(s):  
A. Riethmuller ◽  
H. Voglmayr ◽  
M. Goker ◽  
M. Weiss ◽  
F. Oberwinkler
Keyword(s):  
Ribosomal Dna ◽  
Dna Sequences ◽  
Phylogenetic Relationships ◽  
Large Subunit ◽  
Downy Mildews

Phylogenetic relationships among species of Contracaecum Railliet & Henry, 1912 and Phocascaris Høst, 1932 (Nematoda[ratio ]Ascaridoidea) based on nuclear rDNA sequence data

Parasitology ◽  
2000 ◽  
Vol 121 (4) ◽  
pp. 455-463 ◽  
Author(s):  
S. A. NADLER ◽  
S. D'AMELIO ◽  
H.-P. FAGERHOLM ◽  
B. BERLAND ◽  
L. PAGGI
Keyword(s):  
Dna Sequences ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Large Subunit ◽  
Strong Support ◽  
Structural Features ◽  
Nominal Species ◽  
Phylogenetic Hypothesis ◽  
Natural Group ◽  
Phocid Seals

Nuclear-encoded large-subunit ribosomal DNA sequences were used to infer a phylogenetic hypothesis for 17 taxa (16 nominal species) of the genera Contracaecum and Phocascaris. Phylogenetic trees based on these data have been used to assess the validity of the taxonomic distinction between these genera, which was based on the presence or absence of certain structural features, rather than on explicit hypotheses of evolutionary history. Phylogenetic hypotheses based on parsimony, likelihood, and neighbor-joining analyses of these sequence data strongly support the hypothesis that species of Phocascaris are nested within the clade of Contracaecum species hosted by phocid seals, and are more closely related to species of the Contracaecum osculatum complex than to other Contracaecum species. Alternative tree topologies representing Phocascaris as not nested within the C. osculatum complex were significantly worse interpretations of these sequence data. Phylogenetic analysis also provides strong support for the monophyly of all taxa (Contracaecum and Phocascaris) from phocid seals, which is consistent with Berland's (1964) proposal that such species form a natural group; however, his proposal to recognize all species in phocid seals as Phocascaris, with all species from birds as Contracaecum would result in a paraphyletic Contracaecum, according to the molecular phylogenetic hypothesis.

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